9,583 results on '"Varghese P"'
Search Results
2. Atypical low-frequency cortical encoding of speech identifies children with developmental dyslexia
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João Araújo, Benjamin D. Simons, Varghese Peter, Kanad Mandke, Marina Kalashnikova, Annabel Macfarlane, Fiona Gabrielczyk, Angela Wilson, Giovanni M. Di Liberto, Denis Burnham, and Usha Goswami
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speech ,developmental dyslexia ,oscillations ,unsupervised learning ,supervised learning ,classification ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Slow cortical oscillations play a crucial role in processing the speech amplitude envelope, which is perceived atypically by children with developmental dyslexia. Here we use electroencephalography (EEG) recorded during natural speech listening to identify neural processing patterns involving slow oscillations that may characterize children with dyslexia. In a story listening paradigm, we find that atypical power dynamics and phase-amplitude coupling between delta and theta oscillations characterize dyslexic versus other child control groups (typically-developing controls, other language disorder controls). We further isolate EEG common spatial patterns (CSP) during speech listening across delta and theta oscillations that identify dyslexic children. A linear classifier using four delta-band CSP variables predicted dyslexia status (0.77 AUC). Crucially, these spatial patterns also identified children with dyslexia when applied to EEG measured during a rhythmic syllable processing task. This transfer effect (i.e., the ability to use neural features derived from a story listening task as input features to a classifier based on a rhythmic syllable task) is consistent with a core developmental deficit in neural processing of speech rhythm. The findings are suggestive of distinct atypical neurocognitive speech encoding mechanisms underlying dyslexia, which could be targeted by novel interventions.
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- 2024
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3. Spiritual-Religious Coping in Patients with Schizophrenia: A Qualitative Analysis
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Soumitra Das, Barikar Chandrappa Malathesh, Seshadri Sekhar Chatterjee, Sayantanava Mitra, and Varghese P. Punnoose
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coping ,religiousness ,schizophrenia ,spirituality ,Psychiatry ,RC435-571 - Abstract
Background: Spiritual and religious ways of coping are adaptive for individuals battling schizophrenia in the face of various illness-related factors. Related research is mainly focused on those with acute symptoms. Schizophrenia and a qualitative analysis of the connotation of spirituality-religiosity (SR) in processing illness-related difficulties in Indian context is sparse. This study analyzed how the SR helps people with schizophrenia to handle various day-to-day challenges in life. Methods: A qualitative approach was adopted, and consenting patients were asked open-ended questions. Data collected from these in-depth interviews with 15 individuals with schizophrenia and currently in remission were analyzed according to a predetermined model. Data were collected and analyzed based on grounded theory principles. Results: Twelve out of 15 of the individuals regarded SR as an inherent part of their well-being. At a personal level, the descriptions reflected a tendency toward achieving inner peace, meaning, and purpose in life; whereas at social/interpersonal levels, it was more about acceptance and seeking other’s support. These individuals regarded SR as a way of sharing love, care, and support, which would further help them in handling difficulties and accepting responsibilities. Conclusion: A well-formed SR belief system helps the patients with schizophrenia to navigate better through the day-to-day life stressors by changing the ways of coping.
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- 2023
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4. Factors predicting difficulty in insertion of real-time-three-dimensional transesophageal echocardiography probe in adult patients undergoing cardiac surgery
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Molli Kiran, Shrinivas Gadhinglajkar, Rupa Sreedhar, Subin Sukesan, Vivek Pillai, and Varghese Panicker
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cardiac surgery ,difficult airway ,obesity ,probe ,three-dimensional echocardiography ,Anesthesiology ,RD78.3-87.3 ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Background: Transesophageal echocardiography (TEE) probe insertion may be associated with many complications. Demographic factors and airway conditions such as high Mallampati scores (MMC) and Cormack-Lehane grades (MCLG) are likely to have an impact on its ease of insertion. The primary aim of this study was to identify the predictive factors for difficult real-time-three-dimensional TEE probe insertion. Methods: A total of 153 adult patients undergoing cardiac surgery were prospectively evaluated. The upper airway manipulations required for TEE probe placement were jaw thrust, reverse Sellick's maneuver, and laryngoscopy. All the patients who required airway manipulations were grouped under difficult TEE probe placement group. We evaluated the patients' predictive factors such as demographic characteristics and factors related to difficult intubation. Results: Out of 153 patients, 123 were males and 30 were females. Overall, 27.5% (n = 42) patients had difficulty in probe placement. About 31.7% (n = 39) males had difficulty in TEE probe placement against 13% (n = 4) females (P-value 0.045). Difficulty in TEE probe placement was found in 72.7% (n = 16) of obese patients (body mass index [BMI] > 30), compared to 18.6% (n = 17) in the patients with BMI less than 25 (P-value < 0.001). Probe insertion was significantly more difficult in the presence of MMC III and IV (50%, n = 18) compared to class I (19.2%, n = 10) (P-value 0.001) and MCLG III (73.3%, n = 22) compared to grade I (11.1%, n = 7) (P-value 0.001). Conclusion: Male gender, obesity, higher grades of MMC and MCLG were found to be the risk factors for difficult TEE probe placement in anesthetized patients.
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- 2023
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5. CAR-cell therapy in the era of solid tumor treatment: current challenges and emerging therapeutic advances
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Karama Makni Maalej, Maysaloun Merhi, Varghese P. Inchakalody, Sarra Mestiri, Majid Alam, Cristina Maccalli, Honar Cherif, Shahab Uddin, Martin Steinhoff, Francesco M. Marincola, and Said Dermime
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CAR-T ,CAR-NK ,CAR-M ,Cellular immunotherapy ,Solid tumors ,Combined therapies ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract In the last decade, Chimeric Antigen Receptor (CAR)-T cell therapy has emerged as a promising immunotherapeutic approach to fight cancers. This approach consists of genetically engineered immune cells expressing a surface receptor, called CAR, that specifically targets antigens expressed on the surface of tumor cells. In hematological malignancies like leukemias, myeloma, and non-Hodgkin B-cell lymphomas, adoptive CAR-T cell therapy has shown efficacy in treating chemotherapy refractory patients. However, the value of this therapy remains inconclusive in the context of solid tumors and is restrained by several obstacles including limited tumor trafficking and infiltration, the presence of an immunosuppressive tumor microenvironment, as well as adverse events associated with such therapy. Recently, CAR-Natural Killer (CAR-NK) and CAR-macrophages (CAR-M) were introduced as a complement/alternative to CAR-T cell therapy for solid tumors. CAR-NK cells could be a favorable substitute for CAR-T cells since they do not require HLA compatibility and have limited toxicity. Additionally, CAR-NK cells might be generated in large scale from several sources which would suggest them as promising off-the-shelf product. CAR-M immunotherapy with its capabilities of phagocytosis, tumor-antigen presentation, and broad tumor infiltration, is currently being investigated. Here, we discuss the emerging role of CAR-T, CAR-NK, and CAR-M cells in solid tumors. We also highlight the advantages and drawbacks of CAR-NK and CAR-M cells compared to CAR-T cells. Finally, we suggest prospective solutions such as potential combination therapies to enhance the efficacy of CAR-cells immunotherapy.
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- 2023
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6. Emerging COVID-19 variants and their impact on SARS-CoV-2 diagnosis, therapeutics and vaccines
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Queenie Fernandes, Varghese Philipose Inchakalody, Maysaloun Merhi, Sarra Mestiri, Nassiba Taib, Dina Moustafa Abo El-Ella, Takwa Bedhiafi, Afsheen Raza, Lobna Al-Zaidan, Mona O. Mohsen, Mariam Ali Yousuf Al-Nesf, Ali Ait Hssain, Hadi Mohamad Yassine, Martin F. Bachmann, Shahab Uddin, and Said Dermime
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covid-19 ,sars-cov-2 ,omicron ,coronaviruses ,diagnostic testing ,vaccine ,immunological responses ,viral epidemic ,Medicine - Abstract
The emergence of novel and evolving variants of SARS-CoV-2 has fostered the need for change in the form of newer and more adaptive diagnostic methods for the detection of SARS-CoV-2 infections. On the other hand, developing rapid and sensitive diagnostic technologies is now more challenging due to emerging variants and varying symptoms exhibited among the infected individuals. In addition to this, vaccines remain the major mainstay of prevention and protection against infection. Novel vaccines and drugs are constantly being developed to unleash an immune response for the robust targeting of SARS-CoV-2 and its associated variants. In this review, we provide an updated perspective on the current challenges posed by the emergence of novel SARS-CoV-2 mutants/variants and the evolution of diagnostic techniques to enable their detection. In addition, we also discuss the development, formulation, working mechanisms, advantages, and drawbacks of some of the most used vaccines/therapeutic drugs and their subsequent immunological impact.Key message The emergence of novel variants of the SARS-CoV-2 in the past couple of months, highlights one of the primary challenges in the diagnostics, treatment, as well as vaccine development against the virus. Advancements in SARS-CoV-2 detection include nucleic acid based, antigen and immuno- assay-based and antibody-based detection methodologies for efficient, robust, and quick testing; while advancements in COVID-19 preventive and therapeutic strategies include novel antiviral and immunomodulatory drugs and SARS-CoV-2 targeted vaccines. The varied COVID-19 vaccine platforms and the immune responses induced by each one of them as well as their ability to battle post-vaccination infections have all been discussed in this review.
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- 2022
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7. Transformative Pedagogies: A Bibliometric Journey through Adaptive Learning Systems
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Jobin Jose, Alice Joselph, Pratheesh Abraham, Roshna Varghese, Beenamole T., Sony Mary Varghese, and Suby Elizabeth Oommen
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As a major shift in education technologies, Adaptive Learning Systems (ALS) use artificial intelligence and similar technologies, adapting the lessons to the needs of individual students. Emphasizing transformative pedagogy and teaching strategies that transform the learners' cognitive and interactive patterns, this study presents a comprehensive bibliometric analysis of ASL. Contrary to conventional teaching methods, ALS alters dramatically the way students think and interact with their environment. This research has utilized an all-inclusive bibliometric analysis to analyze the evolution, trends, and themes in ALS by using an extensive set of data from the Web of Science (WoS) and Scopus. The primary objective of Bibliometric analysis is to map the development of ALS in teaching and learning while marking the important trends, models, and thematic priorities. The relevance of this research lies in its comprehensive analysis of the Adaptive Learning Systems (ALS) field through bibliometric methods, offering critical insights into the trends, key contributors, and thematic developments over time. The systematic evaluation enables the appraisal of the impact created by major contributors like authors, organizations, journals, etc. The study also examines, using the advanced data collection technique, influential articles, and publications that enormously contributed to shaping ALS. Similarly, it does the rating effectively upon evaluating the mutual relationships among important terms, concepts, and factors through co-references and co-occurrences. It highlights the increasing scholarly output and identifies key contributors and influential works, underscoring the growing recognition of ALS's importance due to technological advancements. The study's findings on global research contributions, thematic analyses, and collaboration networks offer new insights into the field's dynamics, setting a foundation for future research directions. To visually represent bibliometric data, web analytic tools are used, explaining intricate relationships and thematic clusters. Identifying the unexplored areas and discussing the practical implications of ASL development, research, and analysis of combined data taken from WoS and Scopus provides a unique perspective. Consequently, researchers, educators, policymakers, etc., get valuable insights that enable advancing and understanding the area. This bibliometric analysis will undoubtedly guide future research in the area of transformative pedagogy as it is the most sought-after method in understanding the scholarly landscape of ALS.
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- 2024
8. Language specificity in cortical tracking of speech rhythm at the mora, syllable, and foot levels
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Varghese Peter, Sandrien van Ommen, Marina Kalashnikova, Reiko Mazuka, Thierry Nazzi, and Denis Burnham
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Medicine ,Science - Abstract
Abstract Recent research shows that adults’ neural oscillations track the rhythm of the speech signal. However, the extent to which this tracking is driven by the acoustics of the signal, or by language-specific processing remains unknown. Here adult native listeners of three rhythmically different languages (English, French, Japanese) were compared on their cortical tracking of speech envelopes synthesized in their three native languages, which allowed for coding at each of the three language’s dominant rhythmic unit, respectively the foot (2.5 Hz), syllable (5 Hz), or mora (10 Hz) level. The three language groups were also tested with a sequence in a non-native language, Polish, and a non-speech vocoded equivalent, to investigate possible differential speech/nonspeech processing. The results first showed that cortical tracking was most prominent at 5 Hz (syllable rate) for all three groups, but the French listeners showed enhanced tracking at 5 Hz compared to the English and the Japanese groups. Second, across groups, there were no differences in responses for speech versus non-speech at 5 Hz (syllable rate), but there was better tracking for speech than for non-speech at 10 Hz (not the syllable rate). Together these results provide evidence for both language-general and language-specific influences on cortical tracking.
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- 2022
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9. Association between Sociodemographic Factors and Severity of Psychiatric Symptoms with Duration of Untreated Psychosis in Patients with First Episode Psychosis: A Cross-sectional Study
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Veena A Harshan, PG Saji, Jaimon Plathottathil Michael, Ganga Gangadhara Kaimal, and Varghese P Punnoose
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mental illness ,social determinants ,symptom severity ,Medicine - Abstract
Introduction: The Duration of Untreated Psychosis (DUP) is the time interval between the manifestation of the first psychotic symptom in a patient and the starting of proper treatment. Though, considered as a modifiable factor in the outcome of mental illness, many confounding variables such as sociodemographic factors and illness related factors can affect the DUP. Aim: To identify the association between sociodemographic factors and the severity of psychiatric symptoms with the DUP in patients with the first episode of psychosis. Materials and Methods: A descriptive cross-sectional study conducted in the Department of Psychiatry, Government Medical College, Kottayam, Kerala, India, from March 2018 to February 2019. The first 50 consecutive patients reporting for treatment for the first time, who were diagnosed with psychotic disorders were recruited into the study. Details of the onset of psychosis were collected from the relative based on a clear, unequivocal description of symptoms by the relative. A specially designed proforma was used to gather the sociodemographic details and Brief Psychiatric Rating Scale (BPRS) was used to assess the severity of psychotic symptoms. Statistical analysis was done using independent Student’s t-test, one-way Analysis of Variance (ANOVA) and Pearson’s correlation and p-value
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- 2023
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10. Serum immune mediators as novel predictors of response to anti-PD-1/PD-L1 therapy in non-small cell lung cancer patients with high tissue-PD-L1 expression
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Afsheen Raza, Reyad Mohsen, Aladdin Kanbour, Abdul Rehman Zar Gul, Anite Philip, Suma Vijayakumar, Shereena Hydrose, Kirti S. Prabhu, Aisha Khamis Al-Suwaidi, Varghese Philipose Inchakalody, Maysaloun Merhi, Dina M. Abo El-Ella, Melissa Annrose Tauro, Shayista Akbar, Issam Al-Bozom, Wafa Abualainin, Rajaa Al-Abdulla, Shaza Abu Sirriya, Suparna Hassnad, Shahab Uddin, Mohamed Izham Mohamed Ibrahim, Ussama Al Homsi, and Said Demime
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non-small cell lung cancer ,anti-PD-1 ,anti-PD-L1 ,tissue PD-L1 ,predictive soluble biomarkers ,CEA ,Immunologic diseases. Allergy ,RC581-607 - Abstract
BackgroundNon-small cell lung cancer (NSCLC) is the leading cause of cancer-related morbidity and mortality worldwide. Immune checkpoint inhibitors (ICIs) including anti-PD-1 and anti-PD-L1 antibodies, have significantly changed the treatment outcomes with better overall survival, but only 15-40% of the patients respond to ICIs therapy. The search for predictive biomarkers of responses is warranted for better clinical outcomes. We aim here to identify pre-treatment soluble immune molecules as surrogate biomarkers for tissue PD-L1 (TPD-L1) status and as predictors of response to anti-PD-1/PD-L1 therapy in NSCLC patients. Sera from 31 metastatic NSCLC patients, eligible for anti-PD-1/PD-L1 or combined chemoimmunotherapy, were collected prior to treatment. Analysis of soluble biomarkers with TPD-L1 status showed significant up/down regulation of the immune inhibitory checkpoint markers (sSiglec7, sSiglec9, sULBP4 and sPD-L2) in patients with higher TPD-L1 (TPD-L1 >50%) expression. Moreover, correlation analysis showed significant positive linear correlation of soluble PD-L1 (sPD-L1) with higher TPD-L1 expression. Interestingly, only responders in the TPD-L1 >50% group showed significant down regulation of the immune inhibitory markers (sPD-L2, sTIMD4, sNectin2 and CEA). When responders vs. non-responders were compared, significant down regulation of other immune inhibitory biomarkers (sCD80, sTIMD4 and CEA) was recorded only in responding patients. In this, the optimal cut-off values of CD80
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- 2023
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11. A novel system architecture for secure authentication and data sharing in cloud enabled Big Data Environment
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Uma Narayanan, Varghese Paul, and Shelbi Joseph
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Big data outsourcing ,Big data sharing ,Big data management ,SALSA encryption with MapReduce ,Fractal index tree ,SHA-3 ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
With the rapid growth of data sources, Big data security in Cloud is a big challenge. Different issues have ascended in the area of Big data security such as infrastructure security, data privacy, data management and data integrity. Currently, Big data processing, analytics and storage is secured using cryptography algorithms, which are not appropriate for Big data protection over Cloud. In this paper, we present a solution for addressing the main issues in Big data security over Cloud. We propose a novel system architecture called the Secure Authentication and Data Sharing in Cloud (SADS-Cloud). There are three processes involved in this paper including (i). Big Data Outsourcing, (ii). Big Data Sharing and (iii). Big Data Management. In Big data outsourcing, the data owners are registered to a Trust Center using SHA-3 hashing algorithm. The MapReduce model is used to split the input file into fixed-size of blocks of data and SALSA20 encryption algorithm is applied over each block. In Big data sharing, data users participate in a secure file retrieval. For this purpose, user's credentials (ID, password, secure ID, and current timestamp, email id) are hashed and compared with that stored in a database. In Big data management, there are three important processes implemented to organize data. They are as follows: Compression using Lemperl Ziv Markow Algorithm (LZMA), Clustering using Density-based Clustering of Applications with Noise (DBSCAN), and Indexing using Fractal Index Tree. The proposed scheme for these processes are implemented using Java Programming and performance tested for the following metrics: Information Loss, Compression Ratio, Throughput, Encryption Time and Decryption Time.
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- 2022
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12. A prime-masked ERP investigation on phonology in visual word processing among bilingual speakers of alphasyllabic and alphabetic orthographies
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Adhvika Shetty, Sanjana P. Hebbar, Rajath Shenoy, Varghese Peter, and Gopee Krishnan
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Medicine ,Science - Abstract
Abstract In this study, we experimentally manipulated the phonology of the cross-script prime-target dyads in an ERP-coupled masked priming paradigm to explore the role phonology plays in visual word processing. The written characters of certain bilingual dyads seldom show any visual/orthographic similarity, yet have the same phonological representation. While the Bilingual Interactive Activation (BIA) model relies on the orthographic similarity between the languages in a bilingual dyad, its revised version (BIA + model) additionally banks on the phonological (and semantic) similarity between the words in such dyads. Thus, there exists the need to investigate the role of phonological (and semantic) similarity between the words of a bilingual dyad, especially in the absence of orthographic similarity. Borrowed words from one language to another provide a suitable avenue to explore this question. Cross-orthographic (or cross-script) bilingual participants of this study performed the semantic judgment of visually presented words in a masked priming paradigm in each of their languages while we simultaneously collected the event-related potentials (ERPs). The primes were either translations (different phonology & orthography: P–O–; phonologically incongruent) or transliterations (same phonology & different orthography: P + O–; phonologically congruent) of the target. Overall, the results showed no difference between the two prime conditions. We discuss our findings in light of the BIA and BIA + models of bilingual visual word processing and discuss the relevance of the former model in orthographically distinct bilingual language dyads.
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- 2022
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13. Persistence of spike-specific immune responses in BNT162b2-vaccinated donors and generation of rapid ex-vivo T cells expansion protocol for adoptive immunotherapy: A pilot study
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Sarra Mestiri, Maysaloun Merhi, Varghese P. Inchakalody, Nassiba Taib, Maria K. Smatti, Fareed Ahmad, Afsheen Raza, Fatma H. Ali, Shereena Hydrose, Queenie Fernandes, Abdul W. Ansari, Fairooz Sahir, Lobna Al-Zaidan, Munir Jalis, Mokhtar Ghoul, Niloofar Allahverdi, Mohammed U. Al Homsi, Shahab Uddin, Andrew Martin Jeremijenko, Mai Nimir, Laith J. Abu-Raddad, Fatma Ben Abid, Ahmed Zaqout, Sameer R. Alfheid, Hassan Mohamed Hassan Saqr, Ali S. Omrani, Ali Ait Hssain, Muna Al Maslamani, Hadi M. Yassine, and Said Dermime
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SARS-CoV-2 ,COVID-19 vaccine ,spike-specific immune responses ,surrogate neutralization ,spike-specific T cells expansion ,Immunologic diseases. Allergy ,RC581-607 - Abstract
IntroductionThe BNT162b2 mRNA-based vaccine has shown high efficacy in preventing COVID-19 infection but there are limited data on the types and persistence of the humoral and T cell responses to such a vaccine.MethodsHere, we dissect the vaccine-induced humoral and cellular responses in a cohort of six healthy recipients of two doses of this vaccine.Results and discussionOverall, there was heterogeneity in the spike-specific humoral and cellular responses among vaccinated individuals. Interestingly, we demonstrated that anti-spike antibody levels detected by a novel simple automated assay (Jess) were strongly correlated (r=0.863, P
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- 2023
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14. Frequency and Severity of Exacerbations of COPD Associated with Future Risk of Exacerbations and Mortality: A UK Routine Health Care Data Study
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Whittaker H, Rubino A, Müllerová H, Morris T, Varghese P, Xu Y, De Nigris E, and Quint JK
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copd ,exacerbations of copd ,Diseases of the respiratory system ,RC705-779 - Abstract
Hannah Whittaker,1 Annalisa Rubino,2 Hana Müllerová,2 Tamsin Morris,3 Precil Varghese,4 Yang Xu,3 Enrico De Nigris,5 Jennifer K Quint1 1National Heart and Lung Institute, Imperial College London, London, UK; 2Epidemiology, AstraZeneca, Cambridge, UK; 3Medical and Scientific Affairs, AstraZeneca, Luton, UK; 4Biopharmaceuticals Medical, Respiratory and Immunology, AstraZeneca, Gaithersburg, MD, USA; 5Health Economics, AstraZeneca, Cambridge, UKCorrespondence: Hannah Whittaker, Email h.whittaker@imperial.ac.ukBackground: Studies have shown that chronic obstructive pulmonary disease (COPD) exacerbation events are related to future events; however, previous literature typically reports frequent vs infrequent exacerbations per patient-year and no studies have investigated increasing number of severe exacerbations in relation to COPD outcomes.Objective: To investigate the association between baseline frequency and severity of exacerbations and subsequent mortality and exacerbation risk in a COPD cohort.Methods: Clinical Practice Research Datalink (CPRD) Aurum and Hospital Episode Statistics data were used to identify patients registered at general practices in the UK, who had a diagnosis of COPD, were over the age of 40 years, were smokers or ex-smokers and had data recorded from 2004 onwards. Frequency and severity of exacerbations in the baseline year were identified as moderate exacerbations (general practice events) and severe exacerbations (hospitalised events). Patients were categorised as having: none, 1 moderate only, 2 moderate only, 3+ moderate only, 1 severe (and any moderate), 2 severe (and any moderate), and 3+ severe (and any moderate exacerbations). Poisson regression was used to investigate the association between baseline exacerbation frequency/severity and exacerbation events and mortality over follow-up.Results: Overall, 340,515 COPD patients were included. Patients had higher rates of future exacerbations with increasing frequency and severity of baseline exacerbations compared to no baseline exacerbations. Adjusted incidence rate ratios (IRR) for patients with 1, 2, and 3+ moderate exacerbations compared to 0 exacerbations were 1.70 (95% CI 1.66– 1.74), 2.31 (95% CI 2.24– 2.37), and 3.52 (95% CI 3.43– 3.62), respectively. Patients with increased frequency of baseline exacerbations were more likely to die from all-cause, COPD-related, and cardiovascular-related mortality in a graduated fashion.Conclusion: Increasing number and severity of exacerbations were associated with increasing risk of subsequent exacerbations, all-cause mortality and COPD-related mortality. Even a single moderate event increases the risk of future events, illustrating that every exacerbation counts.Keywords: COPD, exacerbations of COPD
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- 2022
15. Dynamic liquid biopsy components as predictive and prognostic biomarkers in colorectal cancer
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Afsheen Raza, Abdul Q. Khan, Varghese Philipose Inchakalody, Sarra Mestiri, Zeenath Safira K. M. Yoosuf, Takwa Bedhiafi, Dina Moustafa Abo El-Ella, Nassiba Taib, Shereena Hydrose, Shayista Akbar, Queenie Fernandes, Lobna Al-Zaidan, Roopesh Krishnankutty, Maysaloun Merhi, Shahab Uddin, and Said Dermime
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Liquid biopsy ,Colorectal cancer ,Microbiome ,Exosomes ,Circulating tumor DNA ,Circulating noncoding RNAs ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Colorectal cancer (CRC) is one of the most common cancers worldwide. The diagnosis, prognosis and therapeutic monitoring of CRC depends largely on tissue biopsy. However, due to tumor heterogeneity and limitations such as invasiveness, high cost and limited applicability in longitudinal monitoring, liquid biopsy has gathered immense attention in CRC. Liquid biopsy has several advantages over tissue biopsy including ease of sampling, effective monitoring, and longitudinal assessment of treatment dynamics. Furthermore, the importance of liquid biopsy is signified by approval of several liquid biopsy assays by regulatory bodies indicating the powerful approach of liquid biopsy for comprehensive CRC screening, diagnostic and prognostics. Several liquid biopsy biomarkers such as novel components of the microbiome, non-coding RNAs, extracellular vesicles and circulating tumor DNA are extensively being researched for their role in CRC management. Majority of these components have shown promising results on their clinical application in CRC including early detection, observe tumor heterogeneity for treatment and response, prediction of metastases and relapse and detection of minimal residual disease. Therefore, in this review, we aim to provide updated information on various novel liquid biopsy markers such as a) oral microbiota related bacterial network b) gut microbiome-associated serum metabolites c) PIWI-interacting RNAs (piRNAs), microRNA(miRNAs), Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and d) circulating tumor DNAs (ctDNA) and circulating tumor cells (CTC) for their role in disease diagnosis, prognosis, treatment monitoring and their applicability for personalized management of CRC.
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- 2022
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16. Circulating exosomal immuno-oncological checkpoints and cytokines are potential biomarkers to monitor tumor response to anti-PD-1/PD-L1 therapy in non-small cell lung cancer patients
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Shayista Akbar, Afsheen Raza, Reyad Mohsin, Aladdin Kanbour, Shahnaz Qadri, Aijaz Parray, Abdul Rehman Zar Gul, Anite Philip, Suma Vijayakumar, Maysaloun Merhi, Shereena Hydrose, Varghese Philipose Inchakalody, Rajaa Al-Abdulla, Wafa Abualainin, Shaza Abu Sirriya, Issam Al-Bozom, Shahab Uddin, Omar Muhammad Khan, Mohamed Izham Mohamed Ibrahim, Ussama Al Homsi, and Said Dermime
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exosomes ,NSCLC ,biomarkers ,immune-checkpoint inhibitors ,immune-oncological-checkpoints ,cytokines ,Immunologic diseases. Allergy ,RC581-607 - Abstract
Immune checkpoint inhibitors (ICIs) including anti-PD-1 and anti-PD-L1 antibodies, have significantly changed the treatment outcomes of NSCLC patients with better overall survival. However, 15-40% of the patients still fail to respond to ICIs therapy. Identification of biomarkers associated with responses are mandated in order to increase the efficacy of such therapy. In this study we evaluated 27 serum-derived exosomal immuno-oncological proteins and 44 cytokines/chemokines before and after ICIs therapy in 17 NSCLC patients to identify surrogate biomarkers for treatment/monitoring patient stratification for maximum therapeutic benefit. We first confirmed the identity of the isolated exosomes to have their specific markers (CD63, CD81, HSP70 and CD91). We have demonstrated that baseline concentration of exosomal-PD-L1 (p
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- 2023
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17. The Use of Hydroxyurea in the Treatment of COVID-19
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Foster Melissa Robin Bowman, Hijazi Ali Atef, Opoku Rebecca, Varghese Priya, and Li Chun
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covid-19 ,treatment ,hydroxyurea ,critical respiratory care ,Medical emergencies. Critical care. Intensive care. First aid ,RC86-88.9 - Abstract
The rapid worldwide spread of COVID-19 motivated medical professionals to pursue and authenticate appropriate remedies and treatment protocols. This article aims to analyze the potential benefits of one treatment protocol developed by a group of care providers caring for severe COVID-19 patients.
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- 2021
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18. Searching for GEMS: TOI-6383Ab, a giant planet transiting an M3-dwarf star in a binary system
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Bernabò, Lia Marta, Kanodia, Shubham, Canas, Caleb I., Cochran, William D., Csizmadia, Szilárd, Mahadevan, Suvrath, Stefánsson, Gudhmundur, Gupta, Arvind F., Monson, Andrew, Kobulnicky, Henry A., Larsen, Alexander K., Cotter, Ethan G., Birkholz, Alexina, Swaby, Tera N., Zeimann, Gregory, Bender, Chad F., Diddams, Scott A., Libby-Roberts, Jessica E., Lin, Andrea S. J., Ninan, Joe P., Rauer, Heike, Reji, Varghese, Robertson, Paul, Roy, Arpita, and Schwab, Christian
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Astrophysics - Earth and Planetary Astrophysics - Abstract
We report on the discovery of a transiting giant planet around the 3500 K M3-dwarf star TOI-6383A located 172 pc from Earth. It was detected by the Transiting Exoplanet Survey Satellite (TESS) and confirmed by a combination of ground-based follow-up photometry and precise radial velocity measurements. This planet has an orbital period of $\sim$1.791 days, mass of 1.040$\pm$0.094 $M_J$ and a radius of 1d.008$^{+0.036}_{-0.033} ~R_J$, resulting in a mean bulk density of 1.26$^{+0.18}_{-0.17}$ g cm$^{-3}$. TOI-6383A has an M-dwarf companion star, TOI-6383B, which has a stellar effective temperature $T_{eff}$ $\sim$ 3100 K and a projected orbital separation of 3100 AU. TOI-6383A is a low-mass dwarf star hosting a giant planet and is an intriguing object for planetary evolution studies due to its high planet-to-star mass ratio. This discovery is part of the \textit{Searching for Giant Exoplanets around M-dwarf Stars (GEMS)} Survey, intending to provide robust and accurate estimates of the occurrence of GEMS and the statistics on their physical and orbital parameters. This paper presents an interesting addition to the small number of confirmed GEMS, particularly notable since its formation necessitates massive, ust-rich protoplanetary discs and high accretion efficiency ($>$ 10\%)., Comment: 20 pages, 8 figures
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- 2024
19. Highly polarized single photon emitter from intrinsic localized excitons in a WSe2/CrSBr heterostructure
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Alapatt, Varghese, Marques-Moros, Francisco, Boix-Constant, Carla, Manas-Valero, Samuel, Bolotin, Kirill, Canet-Ferrer, Josep, and Coronado, Eugenio
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Condensed Matter - Materials Science ,Physics - Applied Physics - Abstract
Single photons emitters (SPEs) are key components in quantum information applications and are commonly generated in 2D materials by inhomogeneous strain engineering. Here, we report an alternative approach that involves a 2D semiconductor/2D magnet heterostructure. The optical study of the WSe2/CrSBr heterostructures reveals several new emission lines at lower energies compared to characteristic WSe2 emissions, that are assigned to localized excitons. Further investigation demonstrates that one of these emergent lines is an SPE with a strong valley polarization response and large energy shift with the field-induced metamagnetic transition in CrSBr, linking it to the magnetic proximity effect of the adjacent CrSBr layer. In contrast to previous reports on WSe2 that only allow tuning of the SPEs by out-of-plane magnetic field, our emitter is sensitive to both in- and out-of-plane fields. Our findings demonstrate the potential of this approach for improved control and polarization of SPEs in 2D materials., Comment: 17 pages, 4 figures, plus suporting information
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- 2024
20. Performance of PIP-II High-beta 650 Cryomodule After Transatlantic Shipping
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Ozelis, J., Barba, M., Bernardini, J., Contreras-Martinez, C., Crawford, D., Dong, J., Grzelak, V., Hanlet, P., Holzbauer, J., Jia, Y., Kazakov, S., Khabiboulline, T., Makara, J., Patel, N., Patel, V., Pei, L., Peterson, D., Pischalnikov, Y., Porwisiak, D., Ranpariya, S., Steimel, J., Solyak, N., Subedi, J., Sukhanov, A., Varghese, P., Wallace, T., White, M., Wijethunga, S., Xie, Y., and Yoon, S.
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Physics - Accelerator Physics - Abstract
After shipment to the Daresbury Lab and return to Fermilab, the prototype HB650 cryomodule underwent another phase of 2K RF testing to ascertain any performance issues that may have arisen from the transport of the cryomodule. While measurements taken at room temperature after the conclusion of shipment indicated that there were no negative impacts on cavity alignment, beamline vacuum, or cavity frequency, testing at 2K was required to validate other aspects such as tuner operation, cavity coupling, cryogenic system integrity, and cavity performance. Results of this latest round of limited 2K testing will be presented., Comment: 32nd Linear Accelerator Conference (LINAC 2024)
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- 2024
21. Searching for GEMS: TOI-5688 A b, a low-density giant orbiting a high-metallicity early M-dwarf
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Reji, Varghese, Kanodia, Shubham, Ninan, Joe, Cañas, Caleb I., Libby-Roberts, Jessica, Lin, Andrea S. J., Gupta, Arvind F, Sewaby, Tera N., Larsen, Alexander, Kobulnicky, Henry A., Choi, Philip I., Evans, Nez, Santomenna, Sage, Winnick, Isabelle, Yu, Larry, Alvarado-Montes, Jaime A., Bender, Chad, Bernabò, Lia Marta, Blake, Cullen H., Cochran, William D., Diddams, Scott A., Halverson, Samuel, Han, Te, Hearty, Fred, Logsdon, Sarah E., Mahadevan, Suvrath, Monson, Andrew, McElwain, Michael, Robertson, Paul, Ojha, Devendra, Roy, Arpita, Schwab, Christian, Stefansson, Gudmundur, and Wright, Jason
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Astrophysics - Earth and Planetary Astrophysics - Abstract
We present the discovery of a low-density planet transiting TOI-5688 A b, a high-metallicity M2V star. This planet was discovered as part of the search for transiting giant planets ($R \gtrsim8$ M$_\oplus$) through the Searching for GEMS (Giant Exoplanets around M-dwarf Stars) survey. The planet TOI-5688 A b was discovered with the Transiting Exoplanet Survey Satellite (TESS), and characterized with ground-based transits from Red Buttes Observatory (RBO), the Table Mountain Observatory of Pomona College, and radial velocity (RV) measurements with the Habitable-Zone Planet Finder (HPF) on the 10 m Hobby Eberly Telescope (HET) and NEID on the WIYN 3.5 m telescope. From the joint fit of transit and RV data, the mass of the planet is $124\pm24$ M$_\oplus$ and the radius is $10.4\pm0.7$ R$_\oplus$. This planet has a density of $0.61^{+0.20}_{-0.15}$ g/cm${}^3$, and is on a $\sim2.95$ day orbit around its host star. The spectroscopic and photometric analysis of the host star TOI-5688 A shows that it is a high metallicity ([Fe/H] $ = 0.47\pm0.16$ dex) M2V star, favoring the core-accretion formation pathway as the likely formation scenario for this planet. In this paper, we analyze potential mechanisms of planet formation in the context of the formation of TOI-5688 A b. Additionally, observations with Gaia suggest the presence of a wide-separation binary companion, TOI-5688 B, which has a projected separation of $\sim5"$ (1110 AU) and is an M4V. This makes TOI-5688 A b part of a growing number of GEMS in wide-separation binary systems., Comment: 20 pages, 7 figures, Submitted to AJ, Comments are welcome
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- 2024
22. Diffusion based multi-domain neuroimaging harmonization method with preservation of anatomical details
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Lan, Haoyu, Varghese, Bino A., Sheikh-Bahaei, Nasim, Sepehrband, Farshid, Toga, Arthur W, and Choupan, Jeiran
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence ,Electrical Engineering and Systems Science - Image and Video Processing - Abstract
Multi-center neuroimaging studies face technical variability due to batch differences across sites, which potentially hinders data aggregation and impacts study reliability.Recent efforts in neuroimaging harmonization have aimed to minimize these technical gaps and reduce technical variability across batches. While Generative Adversarial Networks (GAN) has been a prominent method for addressing image harmonization tasks, GAN-harmonized images suffer from artifacts or anatomical distortions. Given the advancements of denoising diffusion probabilistic model which produces high-fidelity images, we have assessed the efficacy of the diffusion model for neuroimaging harmonization. we have demonstrated the diffusion model's superior capability in harmonizing images from multiple domains, while GAN-based methods are limited to harmonizing images between two domains per model. Our experiments highlight that the learned domain invariant anatomical condition reinforces the model to accurately preserve the anatomical details while differentiating batch differences at each diffusion step. Our proposed method has been tested on two public neuroimaging dataset ADNI1 and ABIDE II, yielding harmonization results with consistent anatomy preservation and superior FID score compared to the GAN-based methods. We have conducted multiple analysis including extensive quantitative and qualitative evaluations against the baseline models, ablation study showcasing the benefits of the learned conditions, and improvements in the consistency of perivascular spaces (PVS) segmentation through harmonization.
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- 2024
23. A fast solver for the spatially homogeneous electron Boltzmann equation
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Fernando, Milinda, Bochkov, Daniil, Almgren-Bell, James, Oliver, Todd, Moser, Robert, Varghese, Philip, Raja, Laxminarayan, and Biros, George
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Physics - Plasma Physics ,Computer Science - Computational Engineering, Finance, and Science ,Mathematics - Numerical Analysis ,Physics - Computational Physics - Abstract
We present a numerical method for the velocity-space, spatially homogeneous, collisional Boltzmann equation for electron transport in low-temperature plasma (LTP) conditions. Modeling LTP plasmas is useful in many applications, including advanced manufacturing, material processing, semiconductor processing, and hypersonics, to name a few. Most state-of-the-art methods for electron kinetics are based on Monte-Carlo sampling for collisions combined with Lagrangian particle-in-cell methods. We discuss an Eulerian solver that approximates the electron velocity distribution function using spherical harmonics (angular components) and B-splines (energy component). Our solver supports electron-heavy elastic and inelastic binary collisions, electron-electron Coulomb interactions, steady-state and transient dynamics, and an arbitrary nmber of angular terms in the electron distribution function. We report convergence results and compare our solver to two other codes: an in-house particle Monte-Carlo ethod; and Bolsig+, a state-of-the-art Eulerian solver for electron transport in LTPs. Furthermore, we use our solver to study the relaxation time scales of the higher-order anisotropic correction terms. Our code is open-source and provides an interface that allows coupling to multiphysics simulations of low-temperature plasmas.
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- 2024
24. SympGNNs: Symplectic Graph Neural Networks for identifiying high-dimensional Hamiltonian systems and node classification
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Varghese, Alan John, Zhang, Zhen, and Karniadakis, George Em
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Computer Science - Machine Learning ,Physics - Computational Physics - Abstract
Existing neural network models to learn Hamiltonian systems, such as SympNets, although accurate in low-dimensions, struggle to learn the correct dynamics for high-dimensional many-body systems. Herein, we introduce Symplectic Graph Neural Networks (SympGNNs) that can effectively handle system identification in high-dimensional Hamiltonian systems, as well as node classification. SympGNNs combines symplectic maps with permutation equivariance, a property of graph neural networks. Specifically, we propose two variants of SympGNNs: i) G-SympGNN and ii) LA-SympGNN, arising from different parameterizations of the kinetic and potential energy. We demonstrate the capabilities of SympGNN on two physical examples: a 40-particle coupled Harmonic oscillator, and a 2000-particle molecular dynamics simulation in a two-dimensional Lennard-Jones potential. Furthermore, we demonstrate the performance of SympGNN in the node classification task, achieving accuracy comparable to the state-of-the-art. We also empirically show that SympGNN can overcome the oversmoothing and heterophily problems, two key challenges in the field of graph neural networks., Comment: 17 pages, 10 figures
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- 2024
25. Electron FLASH platform for pre-clinical research: LINAC modification, simplification of pulse control and dosimetry
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Zhou, Banghao, Guo, Lixiang, Lu, Weiguo, Rahman, Mahbubur, Zhang, Rongxiao, Chirayath, Varghese Anto, Park, Yang Kyun, Stojadinovic, Strahinja, Garza, Marvin, and Wang, Ken Kang-Hsin
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Physics - Medical Physics - Abstract
Background: FLASH radiotherapy is a treatment regime that delivers therapeutic dose to tumors at an ultra-high dose rate while maintaining adequate normal tissue sparing. However, a comprehensive understanding of the underlying mechanisms, potential late toxicities, and optimal fractionation schemes is important for successful clinical translation. This has necessitated extensive pre-clinical investigations, leading several research institutions to initiate dedicated FLASH research programs. Purpose: This work describes a workflow for establishing an easily accessible electron FLASH (eFLASH) platform. The platform incorporates simplified pulse control, optimized dose rate delivery, and validated Monte Carlo (MC) dose engine for accurate in vivo dosimetry dedicated to FLASH pre-clinical studies. Methods: Adjustment of the automatic frequency control (AFC) module allowed us to optimize the LINAC pulse form to achieve a uniform dose rate. A MC model for the 6 MeV FLASH beam was commissioned to ensure accurate dose calculation necessary for reproducible in vivo studies. Results: Optimizing the AFC module enabled the generation of a uniform pulse form, ensuring consistent dose per pulse and a uniform dose rate throughout FLASH irradiation. The MC model closely agreed with film measurements. MC dose calculations indicated that 6 MeV FLASH is adequate to achieve a uniform dose distribution for mouse whole brain irradiation but may not be optimal for the spinal cord study. Conclusions: We present a novel workflow for establishing a LINAC-based eFLASH research platform, incorporating techniques for optimized dose rate delivery, a simplified pulse control system, and validated MC engine. This work provides researchers with valuable new approaches to facilitate the development of robust and accessible LINAC-based system for FLASH studies., Comment: 29 pages, 6 figures
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- 2024
26. Searching for GEMS: Characterizing Six Giant Planets around Cool Dwarfs
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Kanodia, Shubham, Gupta, Arvind F., Canas, Caleb I., Bernabo, Lia Marta, Reji, Varghese, Han, Te, Brady, Madison, Seifahrt, Andreas, Cochran, William D., Morrell, Nidia, Basant, Ritvik, Bean, Jacob, Bender, Chad F., de Beurs, Zoe L., Bieryla, Allyson, Birkholz, Alexina, Brown, Nina, Chapman, Franklin, Ciardi, David R., Clark, Catherine A., Cotter, Ethan G., Diddams, Scott A., Halverson, Samuel, Hawley, Suzanne, Hebb, Leslie, Holcomb, Rae, Howell, Steve B., Kobulnicky, Henry A., Kowalski, Adam F., Larsen, Alexander, Libby-Roberts, Jessica, Lin, Andrea S. J., Lund, Michael B., Luque, Rafael, Monson, Andrew, Ninan, Joe P., Parker, Brock A., Patel, Nishka, Rodruck, Michael, Ross, Gabrielle, Roy, Arpita, Schwab, Christian, Stefánsson, Guðmundur, Thoms, Aubrie, and Vanderburg, Andrew
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Astrophysics - Earth and Planetary Astrophysics - Abstract
Transiting giant exoplanets around M-dwarf stars (GEMS) are rare, owing to the low-mass host stars. However, the all-sky coverage of TESS has enabled the detection of an increasingly large number of them to enable statistical surveys like the \textit{Searching for GEMS} survey. As part of this endeavour, we describe the observations of six transiting giant planets, which includes precise mass measurements for two GEMS (K2-419Ab, TOI-6034b) and statistical validation for four systems, which includes validation and mass upper limits for three of them (TOI-5218b, TOI-5616b, TOI-5634Ab), while the fourth one -- TOI-5414b is classified as a `likely planet'. Our observations include radial velocities from the Habitable-zone Planet Finder on the Hobby-Eberly Telescope, and MAROON-X on Gemini-North, along with photometry and high-contrast imaging from multiple ground-based facilities. In addition to TESS photometry, K2-419Ab was also observed and statistically validated as part of the K2 mission in Campaigns 5 and 18, which provides precise orbital and planetary constraints despite the faint host star and long orbital period of $\sim 20.4$ days. With an equilibrium temperature of only 380 K, K2-419Ab is one of the coolest known well-characterized transiting planets. TOI-6034 has a late F-type companion about 40\arcsec~away, making it the first GEMS host star to have an earlier main-sequence binary companion. These confirmations add to the existing small sample of confirmed transiting GEMS., Comment: Accepted in AJ
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- 2024
27. Physics-Informed Neural Network for Concrete Manufacturing Process Optimization
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Varghese, Sam, Anand, Rahul, and Paliwal, Gaurav
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Computer Science - Machine Learning - Abstract
Concrete manufacturing projects are one of the most common ones for consulting agencies. Because of the highly non-linear dependency of input materials like ash, water, cement, superplastic, etc; with the resultant strength of concrete, it gets difficult for machine learning models to successfully capture this relation and perform cost optimizations. This paper highlights how PINNs (Physics Informed Neural Networks) can be useful in the given situation. This state-of-the-art model shall also get compared with traditional models like Linear Regression, Random Forest, Gradient Boosting, and Deep Neural Network. Results of the research highlights how well PINNs performed even with reduced dataset, thus resolving one of the biggest issues of limited data availability for ML models. On an average, PINN got the loss value reduced by 26.3% even with 40% lesser data compared to the Deep Neural Network. In addition to predicting strength of the concrete given the quantity of raw materials, the paper also highlights the use of heuristic optimization method like Particle Swarm Optimization (PSO) in predicting quantity of raw materials required to manufacture concrete of given strength with least cost.
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- 2024
28. Generative Blockchain: Transforming Blockchain from Transaction Recording to Transaction Generation through Proof-of-Merit
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Zhang, Haozhao, Zhang, Zhe, Zheng, Zhiqiang, and Jacob, Varghese
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Computer Science - Cryptography and Security ,Computer Science - Emerging Technologies - Abstract
This paper proposes a new paradigm: generative blockchain, which aims to transform conventional blockchain technology by combining transaction generation and recording, rather than focusing solely on transaction recording. Central to our design is a novel consensus mechanism, Proof-of-Merit (PoM), specifically crafted for environments where businesses must solve complex problems before transactions can be recorded. PoM integrates the generation and recording of transactions within a unified blockchain system, fundamentally differing from prevailing consensus mechanisms that primarily record existing transactions. We demonstrate PoM on a ride service on-demand platform, where the task of solving complex transaction-generating problems is delegated to a pool of independent problem solvers. These solvers generate transactions, and their solutions are selected based on merit. The winning solvers then register these transactions onto the blockchain and are rewarded accordingly. We introduce a Decentralized Control Parameter (DCP) to balance two key performance metrics: efficiency and equity. The applicability of our generative blockchain is illustrated through a ridesharing context, where matchers (solvers) are tasked with matching riders to drivers. We demonstrate PoM's performance and nuanced properties using agent-based simulation, exploring how to find the optimal DCP value to achieve a desirable balance of efficiency and equity in a generative blockchain.
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- 2024
29. QEDCartographer: Automating Formal Verification Using Reward-Free Reinforcement Learning
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Sanchez-Stern, Alex, Varghese, Abhishek, Kaufman, Zhanna, Zhang, Dylan, Ringer, Talia, and Brun, Yuriy
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Computer Science - Software Engineering ,Computer Science - Machine Learning ,Computer Science - Programming Languages - Abstract
Formal verification is a promising method for producing reliable software, but the difficulty of manually writing verification proofs severely limits its utility in practice. Recent methods have automated some proof synthesis by guiding a search through the proof space using a theorem prover. Unfortunately, the theorem prover provides only the crudest estimate of progress, resulting in effectively undirected search. To address this problem, we create QEDCartographer, an automated proof-synthesis tool that combines supervised and reinforcement learning to more effectively explore the proof space. QEDCartographer incorporates the proofs' branching structure, enabling reward-free search and overcoming the sparse reward problem inherent to formal verification. We evaluate QEDCartographer using the CoqGym benchmark of 68.5K theorems from 124 open-source Coq projects. QEDCartographer fully automatically proves 21.4% of the test-set theorems. Previous search-based proof-synthesis tools Tok, Tac, ASTactic, Passport, and Proverbot9001, which rely only on supervised learning, prove 9.6%, 9.8%, 10.9%, 12.5%, and 19.8%, respectively. Diva, which combines 62 tools, proves 19.2%. Comparing to the most effective prior tool, Proverbot9001, QEDCartographer produces 34% shorter proofs 29% faster, on average over the theorems both tools prove. Together, QEDCartographer and non-learning-based CoqHammer prove 30.3% of the theorems, while CoqHammer alone proves 26.6%. Our work demonstrates that reinforcement learning is a fruitful research direction for improving proof-synthesis tools' search mechanisms., Comment: Published in the International Conference on Software Engineering (ICSE) 2025: Alex Sanchez-Stern, Abhishek Varghese, Zhanna Kaufman, Dylan Zhang, Talia Ringer, and Yuriy Brun, QEDCartographer: Automating Formal Verification Using Reward-Free Reinforcement Learning, in Proceedings of the 47th International Conference on Software Engineering (ICSE), 2025
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- 2024
30. Radiative Cooling and Thermoregulation of Vertical Facades with Micropatterned Directional Emitters
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Degeorges, Mathis, Anand, Jyothis, Varghese, Nithin Jo, and Mandal, Jyotirmoy
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Physics - Applied Physics - Abstract
We demonstrate a micropatterned directional emitter ({\mu}DE) with an ultrabroadband, azimuthally selective and tailorable emittance across the thermal wavelengths and over wide angles. The {\mu}DE can enable a novel and passive seasonal thermoregulation of buildings by reducing summertime terrestrial radiative heat gain, and wintertime loss. We show several types of {\mu}DE, such as metallic and white variants, made using low-cost materials and scalable manufacturing techniques that are already in large-scale use. Furthermore, we show that its directional emittance can be geometrically tailored to sky-view factors in different urban scenarios. Outdoor experiments show that {\mu}DEs stay up to 1.53{\deg}C cooler than traditional building envelopes when exposed to direct sunlight on summer days and up to 0.46{\deg}C warmer during winter nights. Additionally, {\mu}DEs demonstrate significant cooling powers of up to 40 Wm-2 in warm conditions and heating powers of up to 30 Wm-2 in cool conditions, relative to typical building envelopes. Building energy models show that {\mu}DEs can achieve all-season energy savings similar to or higher than those of cool roofs. Collectively, our findings show {\mu}DEs as highly promising for thermoregulating buildings.
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- 2024
31. A Systematic Study on Impact of Binder Formulation on Green Body Strength of Vat-Photopolymerisation 3D Printed Silica Ceramics Used in Investment Casting
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Ozkan Basar, Varghese Paul Veliyath, Fatih Tarak, and Ehsan Sabet
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vat photopolymerisation ,ceramics ,ceramic core ,investment casting ,3D printing ceramics ,Organic chemistry ,QD241-441 - Abstract
Additive ceramics manufacturing with vat-photopolymerisation (VP) is a developing field, and the need for suitable printing materials hinders its fast growth. Binder mixtures significantly influence the mechanical properties of printed ceramic bodies by VP, considering their rheological properties, curing performances and green body characteristics. Improving mechanical characteristics and reducing cracks during printing and post-processes is mainly related to binder formulations. The study aims to develop a binder formulation to provide the printed ceramic specimens with additional green strength. The impact on mechanical properties (ultimate tensile strength, flexural strength, Young’s and strain at breakpoint), viscosity and cure performance of Urethane Acrylate (UA) and thermoplastic Polyether Acrylate (PEA) oligomers to monofunctional N-Vinylpyrrolidone (NVP), 1,6-Hexanediol Diacrylate (HDDA) and Tri-functional Photocentric 34 (PC34) monomers were investigated under varying concentrations. The best mechanical characteristic was showcased when the PC34 was replaced with 20–30 wt.% of UA in the organic medium. The Thermogravimetric Analysis (TGA) and sintering test outcomes revealed that increasing the content of NVP in the organic medium (above 15 wt.%) leads to uncontrolled thermal degradation during debinding and defects on ceramic parts after sintering. The negative effect of UA on the viscosity of ceramic-loaded mixtures was controlled by eliminating the PC34 compound with NVP and HDDA, and optimum mechanical properties were achieved at 15 wt.% of NVP and 65 wt.% of HDDA. PEA is added to provide additional flexibility to the ceramic parts. It was found that strain and other mechanical parameters peaked at 15 wt.% of PEA. The study formulated the most suitable binder formulation on the green body strength of printing silica ceramics as 50 wt.% HDDA, 20 wt.% Urethane Acrylate, 15 wt.% NVP and 15 wt.% PEA.
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- 2023
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32. A Systematic Literature Review of the Humanistic Burden of COPD
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Hurst JR, Siddiqui MK, Singh B, Varghese P, Holmgren U, and de Nigris E
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chronic obstructive pulmonary disease ,quality of life ,humanistic burden ,patient-reported outcomes. ,Diseases of the respiratory system ,RC705-779 - Abstract
John R Hurst,1 Mohd Kashif Siddiqui,2 Barinder Singh,3 Precil Varghese,4 Ulf Holmgren,5 Enrico de Nigris6 1UCL Respiratory, University College London, London, UK; 2HEOR and RWE Analytics, Regulatory Access, Parexel International Ltd, Mohali, India; 3HEOR Evidence Evaluation, Parexel International Ltd, Mohali, India; 4Biopharmaceuticals Medical, Respiratory and Immunology, AstraZeneca, Gothenburg, MD, USA; 5Real World Science and Digital, Biopharmaceutical Medical, AstraZeneca, Gothenburg, Sweden; 6Global Product and Portfolio Strategy, AstraZeneca, Cambridge, UKCorrespondence: John R HurstUCL Respiratory, Royal Free Campus, London, NW3 2QG, UKTel +44 203 108 7761Email j.hurst@ucl.ac.ukBackground: Chronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality worldwide, causing substantial economic and social burden.Objective: This review assessed the patient-reported humanistic burden associated with moderate to very severe COPD, specifically the impact on health-related quality of life (HRQoL), symptoms, limitations in daily life, and emotional implications, through the use of HRQoL instruments.Methods: A systematic review was conducted to retrieve relevant clinical data from published literature using a representative sample of countries where healthcare systems provide wide availability of COPD medications and/or universal coverage includes respiratory medicines (Australia, Canada, China, France, Germany, Italy, Spain, the UK, and the USA). The primary inclusion criteria were patients with moderate to very severe COPD. HRQoL was quantified with non-disease-specific and disease-specific questionnaires.Results: In total, 82 studies from 95 publications presented HRQoL data from patients with moderate to very severe COPD. Patient-reported HRQoL declined with worsening airflow limitation, advancing GOLD group, and increasing exacerbation frequency. Both increasing frequency of hospitalization for COPD exacerbations and recurrent hospitalization adversely impacted HRQoL. Comorbidity incidence was higher in patients with increased airflow limitation. It was associated with a further decline in HRQoL and increased depression and anxiety, particularly as disease-associated pain worsened. Physical activity improved HRQoL over time.Conclusion: This review highlighted the impact of exacerbations and associated hospitalizations on the humanistic burden of COPD. These findings underline the importance of managing COPD actively, including prompt and appropriate use of pharmacological and non-pharmacological therapies that can improve symptoms and reduce the risk of exacerbations, thereby lessening the humanistic burden. Future reviews could consider a broader range of countries and publications to further assess the humanistic impact of COPD in low- and middle-income economies.Keywords: chronic obstructive pulmonary disease, quality of life, humanistic burden, patient-reported outcomes
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- 2021
33. Educational Utility of Social Media for Laparoscopic Surgery in India: A Cross-Sectional Survey of Popular Indian Communities on Facebook
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Rajan D, Pillai VG, and Varghese P
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online learning ,distance learning ,surgical education ,laparoscopic gynecology ,covid pandemic ,social media ,Special aspects of education ,LC8-6691 ,Medicine (General) ,R5-920 - Abstract
Deepa Rajan,1 Vinod G Pillai,2 Patsy Varghese1 1Department of Obstetrics and Gynecology, Believers Church Medical College Hospital, Thiruvalla, Kerala, India; 2Department of Surgery, Believers Church Medical College Hospital, Thiruvalla, Kerala, IndiaCorrespondence: Vinod G PillaiDepartment of Surgery, Believers Church Medical College Hospital, Thiruvalla, Kerala, 689103, IndiaTel/Fax +91 469 3503100Email drvinodpillai@gmail.comIntroduction: The Covid pandemic and social distancing has adversely impacted the conventional apprenticeship method of postgraduate training in laparoscopic surgery. Social media may be a useful adjunct for laparoscopic training, but its utility in developing countries like India has not been studied carefully. This paper describes an observational, cross-sectional study on the educational utility of Facebook groups based in India and which focus on laparoscopic gynecologic surgery.Methods: The most popular Facebook groups involving Indians and focusing on laparoscopic gynecology were identified using appropriate search terms as well as inclusion and exclusion criteria. Demographic data related to the groups, the authors of posts as well as descriptive statistics of all the posts during the study period were collected and appropriate statistical analysis was performed.Results: All the groups in this study were large and growing steadily. Posts related to laparoscopy were more likely to be videos, dealing with operative techniques and having educational value for postgraduate residents (p value < 0.001) compared to posts unrelated to laparoscopic surgery. The majority of posts (88.2%) presented original content created by group members rather than material shared from other sources. Members preferred to share laparoscopic content using links to their personal YouTube channels rather than using institutional YouTube channels, dedicated websites for laparoscopic surgery or direct posts on Facebook. Group members liked educational content and laparoscopic surgery-related content significantly more than other content. Only 16.7% of the laparoscopic surgeons could be identified to be working in academic institutes.Conclusion: Social media for medical education has inherent advantages and disadvantages. This article provides objective data regarding its utilisation in a developing country in the midst of the Covid pandemic, and provides a guide for further research and development of innovative teaching methods.Keywords: online learning, distance learning, surgical education, laparoscopic gynecology, Covid pandemic, social media
- Published
- 2021
34. Depression, Perceived Stress and Socio-demographic Correlates among General Population during COVID-19 Pandemic: A Cross-sectional Survey from Southern India
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Aparna Sasikumar, Aravind Karunakaran, Jaico Paulose, Chitra Venkateswaran, Jaimon Plathottathil Michael, and Varghese P Punnoose
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anxiety ,coronavirus disease 2019 ,epidemiology ,mental health ,psychological distress ,Medicine - Abstract
Introduction: The Coronavirus Disease 2019 (COVID-19) pandemic and its socio-economic consequences have had a significant impact on mental health. A quantifiable data regarding increase of mental health problems as a result of the pandemic is required to take necessary steps in tackling the issue. Aim: To estimate the prevalence of depression, perceived stress and its socio-demographic correlates among general population of South India during COVID-19. Materials and Methods: This cross-sectional survey conducted from 25th August 2021 to 25th October 2021 among the general population of South India during COVID-19. A total of 600 subjects were enrolled into the study. Study subjects included people of either sex between 20-50 years of age who were able to read and understand English and with access to internet. Subjects responded to a questionnaire packet of Patient Health Questionnaire-9 (PHQ-9), Perceived Stress Scale 10 (PSS-10) and a proforma for socio-demographic data. Data was analysed using GNU PSPP version 1. One-way Analysis of Variance (ANOVA) and independent t-test were used to assess associations. A value of p-value
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- 2022
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35. Prescribing Pathways to Triple Therapy: A Retrospective Observational Study of Adults with Chronic Obstructive Pulmonary Disease in the UK
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Quint JK, Venerus A, O'Leary C, Myland M, Holmgren U, Varghese P, and Cabrera C
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chronic obstructive pulmonary disease ,patient pathways ,real-world ,retrospective study ,treatment initiation ,triple therapy ,Diseases of the respiratory system ,RC705-779 - Abstract
Jennifer K Quint,1 Alessandra Venerus,2 Caroline O’Leary,2 Melissa Myland,2 Ulf Holmgren,3 Precil Varghese,4 Claudia Cabrera3,5 1Imperial College London, London, UK; 2IQVIA, London, UK; 3Real World Science and Digital, BioPharmaceuticals Medical, AstraZeneca, Gothenburg, Sweden; 4Global Medical Affairs, AstraZeneca, Gaithersburg, MD, USA; 5Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, SwedenCorrespondence: Claudia CabreraBioPharmaceuticals Medical, AstraZeneca, Pepparedsleden 1, SE-431 83 Mölndal, Gothenburg, SwedenTel +46 (0)31 776 2890Email claudia.s.cabrera@astrazeneca.comPurpose: Treatment guidance for chronic obstructive pulmonary disease (COPD) recommends inhaled corticosteroid (ICS)+long-acting muscarinic antagonist+long-acting β2-agonist (LABA) triple therapy for patients who experience recurrent exacerbations, persistent breathlessness, or exercise limitation on dual therapy. However, information is limited on pathways to triple therapy in the UK.Patients and Methods: A retrospective cohort study was conducted using de-identified patient-level data from UK primary care electronic medical records from January 1, 2005 to May 1, 2016. Data were included from patients who had their first triple therapy regimen (index date) recorded during the study period and a minimum of 12 months’ pre-index data. Treatment pathways to triple therapy were recorded, and the proportion of patients on triple therapy before their COPD diagnosis was determined. Adherence to triple therapy was estimated using the proportion of days covered (PDC).Results: After applying eligibility criteria, 82,300 patients were included, with a mean age at COPD diagnosis of 64.7 years. The major treatment pathway (27.9%) was the first initiation of ICS+LABA prior to triple therapy. Following COPD diagnosis, the median time to triple therapy was approximately 3.5 years. The estimated mean adherence to triple therapy was 81.8% PDC. Multivariate analysis showed that the following groups were more likely to have received previous therapy prior to triple therapy: females (versus males), patients with asthma (versus those without asthma), severe COPD (versus those with non-severe COPD), or fewer exacerbations (versus those with more exacerbations).Conclusion: Treatment pathways to triple therapy in the UK are diverse, highlighting the need to better understand factors involved in clinical decision-making.Keywords: chronic obstructive pulmonary disease, patient pathways, real-world, retrospective study, treatment initiation, triple therapy
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- 2020
36. The potential role of vitamin C in empowering cancer immunotherapy
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Takwa Bedhiafi, Varghese Philipose Inchakalody, Queenie Fernandes, Sarra Mestiri, Nashiru Billa, Shahab Uddin, Maysaloun Merhi, and Said Dermime
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Vitamin C ,Immune checkpoint blockade ,Immunotherapy ,Cancer therapy ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Vitamin C also known as L-ascorbic acid is a nutrient naturally occurring in many fruits and vegetables and widely known for its potent antioxidant activity. Several studies have highlighted the importance of using high dose vitamin C as an adjuvant anti-cancer therapy. Interestingly, it has been shown that vitamin C is able to modulate the anti-cancer immune response and to help to overcome the resistance to immune checkpoints blockade (ICB) drugs such as cytotoxic T-lymphocyte antigen 4 (CLTA-4) and programmed cell death ligand 1 (PD-L1/PD-1) inhibitors. Indeed, it was reported that vitamin C regulates several mechanisms developed by cancer cells to escape T cells immune response and resist ICB. Understanding the role of vitamin C in the anti-tumor immune response will pave the way to the development of novel combination therapies that would enhance the response of cancer patients to ICB immunotherapy. In this review, we discuss the effect of vitamin C on the immune system and its potential role in empowering cancer immunotherapy through its pro-oxidant potential, its ability to modulate epigenetic factors and its capacity to regulate the expression of different cytokines involved in the immune response.
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- 2022
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37. Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota.
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Oliver, Tiffany, Varghese, Neha, Roux, Simon, Schulz, Frederik, Huntemann, Marcel, Clum, Alicia, Foster, Brian, Foster, Bryce, Riley, Robert, LaButti, Kurt, Egan, Robert, Hajek, Patrick, Mukherjee, Supratim, Ovchinnikova, Galina, Reddy, TBK, Calhoun, Sara, Hayes, Richard, Rohwer, Robin, Zhou, Zhichao, Daum, Christopher, Copeland, Alex, Chen, I-Min, Ivanova, Natalia, Kyrpides, Nikos, Mouncey, Nigel, Del Rio, Tijana, Grigoriev, Igor, Hofmeyr, Steven, Oliker, Leonid, Yelick, Katherine, Anantharaman, Karthik, McMahon, Katherine, Woyke, Tanja, and Eloe-Fadrosh, Emiley
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Bacteria ,Lakes ,Metagenome ,Metagenomics ,Phylogeny - Abstract
The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.
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- 2024
38. A therapeutic small molecule enhances γ-oscillations and improves cognition/memory in Alzheimers disease model mice.
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Wei, Xiaofei, Campagna, Jesus, Jagodzinska, Barbara, Wi, Dongwook, Cohn, Whitaker, Lee, Jessica, Zhu, Chunni, Huang, Christine, Molnár, László, Houser, Carolyn, John, Varghese, and Mody, Istvan
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Alzheimer’s disease ,GABA-A receptors ,gamma oscillations ,interneurons ,parvalbumin ,Animals ,Alzheimer Disease ,Mice ,Disease Models ,Animal ,Cognition ,Gamma Rhythm ,Memory ,Receptors ,GABA-A ,Mice ,Transgenic ,Humans ,Male ,Memory ,Short-Term ,Brain ,Alanine ,Azepines - Abstract
Brain rhythms provide the timing for recruitment of brain activity required for linking together neuronal ensembles engaged in specific tasks. The γ-oscillations (30 to 120 Hz) orchestrate neuronal circuits underlying cognitive processes and working memory. These oscillations are reduced in numerous neurological and psychiatric disorders, including early cognitive decline in Alzheimers disease (AD). Here, we report on a potent brain-permeable small molecule, DDL-920 that increases γ-oscillations and improves cognition/memory in a mouse model of AD, thus showing promise as a class of therapeutics for AD. We employed anatomical, in vitro and in vivo electrophysiological, and behavioral methods to examine the effects of our lead therapeutic candidate small molecule. As a novel in central nervous system pharmacotherapy, our lead molecule acts as a potent, efficacious, and selective negative allosteric modulator of the γ-aminobutyric acid type A receptors most likely assembled from α1β2δ subunits. These receptors, identified through anatomical and pharmacological means, underlie the tonic inhibition of parvalbumin (PV) expressing interneurons (PV+INs) critically involved in the generation of γ-oscillations. When orally administered twice daily for 2 wk, DDL-920 restored the cognitive/memory impairments of 3- to 4-mo-old AD model mice as measured by their performance in the Barnes maze. Our approach is unique as it is meant to enhance cognitive performance and working memory in a state-dependent manner by engaging and amplifying the brains endogenous γ-oscillations through enhancing the function of PV+INs.
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- 2024
39. Estimating the Seroincidence of Scrub Typhus using Antibody Dynamics after Infection
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Aiemjoy, Kristen, Katuwal, Nishan, Vaidya, Krista, Shrestha, Sony, Thapa, Melina, Teunis, Peter, Bogoch, Isaac I, Trowbridge, Paul, Blacksell, Stuart D, Paris, Daniel H, Wangrangsimakul, Tri, Varghese, George M, Maude, Richard J, Tamrakar, Dipesh, and Andrews, Jason R
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Biomedical and Clinical Sciences ,Clinical Sciences ,Vector-Borne Diseases ,Infectious Diseases ,Clinical Research ,Prevention ,Infection ,Good Health and Well Being ,Scrub Typhus ,Humans ,India ,Seroepidemiologic Studies ,Nepal ,Immunoglobulin G ,Antibodies ,Bacterial ,Orientia tsutsugamushi ,Immunoglobulin M ,Incidence ,Adult ,Male ,Female ,Thailand ,Adolescent ,Young Adult ,Bayes Theorem ,Middle Aged ,Medical and Health Sciences ,Tropical Medicine ,Biomedical and clinical sciences ,Health sciences - Abstract
Scrub typhus, a vector-borne bacterial infection, is an important but neglected disease globally. Accurately characterizing the burden is challenging because of nonspecific symptoms and limited diagnostics. Prior seroepidemiology studies have struggled to find consensus cutoffs that permit comparisons of estimates across contexts and time. In this study, we present a novel approach that does not require a cutoff and instead uses information about antibody kinetics after infection to estimate seroincidence. We use data from three cohorts of scrub typhus patients in Chiang Rai, Thailand, and Vellore, India, to characterize antibody kinetics after infection and two population serosurveys in the Kathmandu Valley, Nepal, and Tamil Nadu, India, to estimate seroincidence. The samples were tested for IgM and IgG responses to Orientia tsutsugamushi-derived recombinant 56-kDa antigen using commercial enzyme-linked immunosorbent assay kits. We used Bayesian hierarchical models to characterize antibody responses after scrub typhus infection and used the joint distributions of the peak antibody titers and decay rates to estimate population-level incidence rates in the cross-sectional serosurveys. Median responses persisted above an optical density (OD) of 1.8 for 23.6 months for IgG and an OD of 1 for 4.5 months for IgM. Among 18- to 29-year-olds, the seroincidence was 10 per 1,000 person-years (95% CI, 5-19) in Tamil Nadu, India, and 14 per 1,000 person-years (95% CI: 10-20) in the Kathmandu Valley, Nepal. When seroincidence was calculated with antibody decay ignored, the disease burden was underestimated by more than 50%. The approach can be deployed prospectively, coupled with existing serosurveys, or leverage banked samples to efficiently generate scrub typhus seroincidence estimates.
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- 2024
40. The Rlign Algorithm for Enhanced Electrocardiogram Analysis through R-Peak Alignment for Explainable Classification and Clustering
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Plagwitz, Lucas, Bickmann, Lucas, Fujarski, Michael, Brenner, Alexander, Gobalakrishnan, Warnes, Eckardt, Lars, Büscher, Antonius, and Varghese, Julian
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Electrical Engineering and Systems Science - Signal Processing ,Computer Science - Machine Learning - Abstract
Electrocardiogram (ECG) recordings have long been vital in diagnosing different cardiac conditions. Recently, research in the field of automatic ECG processing using machine learning methods has gained importance, mainly by utilizing deep learning methods on raw ECG signals. A major advantage of models like convolutional neural networks (CNNs) is their ability to effectively process biomedical imaging or signal data. However, this strength is tempered by challenges related to their lack of explainability, the need for a large amount of training data, and the complexities involved in adapting them for unsupervised clustering tasks. In addressing these tasks, we aim to reintroduce shallow learning techniques, including support vector machines and principal components analysis, into ECG signal processing by leveraging their semi-structured, cyclic form. To this end, we developed and evaluated a transformation that effectively restructures ECG signals into a fully structured format, facilitating their subsequent analysis using shallow learning algorithms. In this study, we present this adaptive transformative approach that aligns R-peaks across all signals in a dataset and resamples the segments between R-peaks, both with and without heart rate dependencies. We illustrate the substantial benefit of this transformation for traditional analysis techniques in the areas of classification, clustering, and explainability, outperforming commercial software for median beat transformation and CNN approaches. Our approach demonstrates a significant advantage for shallow machine learning methods over CNNs, especially when dealing with limited training data. Additionally, we release a fully tested and publicly accessible code framework, providing a robust alignment pipeline to support future research, available at https://github.com/imi-ms/rlign.
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- 2024
41. Existence of a maximum flow rate in electro-osmotic systems
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Varghese, Sleeba, Todd, Billy D., and Hansen, Jesper S.
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Condensed Matter - Soft Condensed Matter - Abstract
In this work, we investigate the effect of the hydrodynamic wall-fluid friction in electro-osmotic flows. First, we present the solution to the electro-hydrodynamic equation for the electro-osmotic velocity profile, which is derived for an ionic system composed of cations immersed in uncharged solvent particles. The system (solution and walls) is kept electrically neutral using negatively charged walls and will here be referred to as a "counterion-only" system. The theory predicts the existence of a counterion concentration that results in a maximum electro-osmotic flow rate, but only if the wall-fluid friction, or equivalently the slip length, is correlated with the system electrostatic screening length. Through equilibrium molecular dynamics simulations we precisely determine the hydrodynamic slip from the wall-fluid friction, and this is then used as input to the theoretical predictions. Comparison between the theory and independent non-equilibrium molecular dynamics simulation data confirms the existence of the maximum. Also, we find that standard hydrodynamic theory quantitatively agrees with simulation results for charged nanoscale systems for sufficiently small charge densities and ion charges, if the correct slip boundaries are applied., Comment: Main manuscript: 21 pages, 8 figures. Supporting information: 6 pages, 2 figures
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- 2024
42. View-Invariant Pixelwise Anomaly Detection in Multi-object Scenes with Adaptive View Synthesis
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Varghese, Subin and Hoskere, Vedhus
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence - Abstract
The inspection and monitoring of infrastructure assets typically requires identifying visual anomalies in scenes periodically photographed over time. Images collected manually or with robots such as unmanned aerial vehicles from the same scene at different instances in time are typically not perfectly aligned. Supervised segmentation methods can be applied to identify known problems, but unsupervised anomaly detection approaches are required when unknown anomalies occur. Current unsupervised pixel-level anomaly detection methods have mainly been developed for industrial settings where the camera position is known and constant. However, we find that these methods fail to generalize to the case when images are not perfectly aligned. We term the problem of unsupervised anomaly detection between two such imperfectly aligned sets of images as Scene Anomaly Detection (Scene AD). We present a novel network termed OmniAD to address the Scene AD problem posed. Specifically, we refine the anomaly detection method reverse distillation to achieve a 40% increase in pixel-level anomaly detection performance. The network's performance is further demonstrated to improve with two new data augmentation strategies proposed that leverage novel view synthesis and camera localization to improve generalization. We validate our approach with qualitative and quantitative results on a new dataset, ToyCity, the first Scene AD dataset with multiple objects, as well as on the established single object-centric dataset, MAD. https://drags99.github.io/OmniAD/
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- 2024
43. A tutorial on fairness in machine learning in healthcare
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Gao, Jianhui, Chou, Benson, McCaw, Zachary R., Thurston, Hilary, Varghese, Paul, Hong, Chuan, and Gronsbell, Jessica
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Computer Science - Machine Learning ,Computer Science - Computers and Society ,Statistics - Machine Learning - Abstract
$\textbf{OBJECTIVE}$: Ensuring that machine learning (ML) algorithms are safe and effective within all patient groups, and do not disadvantage particular patients, is essential to clinical decision making and preventing the reinforcement of existing healthcare inequities. The objective of this tutorial is to introduce the medical informatics community to the common notions of fairness within ML, focusing on clinical applications and implementation in practice. $\textbf{TARGET AUDIENCE}$: As gaps in fairness arise in a variety of healthcare applications, this tutorial is designed to provide an understanding of fairness, without assuming prior knowledge, to researchers and clinicians who make use of modern clinical data. $\textbf{SCOPE}$: We describe the fundamental concepts and methods used to define fairness in ML, including an overview of why models in healthcare may be unfair, a summary and comparison of the metrics used to quantify fairness, and a discussion of some ongoing research. We illustrate some of the fairness methods introduced through a case study of mortality prediction in a publicly available electronic health record dataset. Finally, we provide a user-friendly R package for comprehensive group fairness evaluation, enabling researchers and clinicians to assess fairness in their own ML work.
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- 2024
44. SETC: A Vulnerability Telemetry Collection Framework
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Holeman, Ryan, Hastings, John, and Vaidyan, Varghese Mathew
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Computer Science - Cryptography and Security ,D.4.6 - Abstract
As emerging software vulnerabilities continuously threaten enterprises and Internet services, there is a critical need for improved security research capabilities. This paper introduces the Security Exploit Telemetry Collection (SETC) framework - an automated framework to generate reproducible vulnerability exploit data at scale for robust defensive security research. SETC deploys configurable environments to execute and record rich telemetry of vulnerability exploits within isolated containers. Exploits, vulnerable services, monitoring tools, and logging pipelines are defined via modular JSON configurations and deployed on demand. Compared to current manual processes, SETC enables automated, customizable, and repeatable vulnerability testing to produce diverse security telemetry. This research enables scalable exploit data generation to drive innovations in threat modeling, detection methods, analysis techniques, and remediation strategies. The capabilities of the framework are demonstrated through an example scenario. By addressing key barriers in security data generation, SETC represents a valuable platform to support impactful vulnerability and defensive security research., Comment: 7 pages, 2 figures
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- 2024
45. Effect of Rotation on Wave Mixing in Intermediate Mass Stars
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Varghese, A., Ratnasingam, R. P., Vanon, R., Edelmann, P. V. F., Mathis, S., and Rogers, T. M.
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
Internal gravity waves (IGWs) are likely to cause mixing in stellar interiors. Studies show that the mixing by these waves changes drastically across age and mass (Varghese et al. 2023, arXiv:2211.06432). Here, we study the effect of rotation on this wave mixing by considering a 7 M$_{\odot}$ model at ZAMS and midMS. We compare the mixing profiles at a range of rotation rates ($1\times 10^{-5}$, $2\times 10^{-5}$, $3\times 10^{-5}$, $4\times 10^{-5}$ and $1\times 10^{-4}$ rad.s$^{-1}$) and observe that the mixing decreases with decreasing Rossby number. This can be attributed to the effect of rotation on convection which influences the amplitude with which the waves are excited near the convective-radiative interface., Comment: 13 pages, 8 figures, accepted at ApJ
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- 2024
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46. Synthetic Programming Elicitation and Repair for Text-to-Code in Very Low-Resource Programming Languages
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Mora, Federico, Wong, Justin, Lepe, Haley, Bhatia, Sahil, Elmaaroufi, Karim, Varghese, George, Gonzalez, Joseph E., Polgreen, Elizabeth, and Seshia, Sanjit A.
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Computer Science - Programming Languages ,Computer Science - Machine Learning - Abstract
Recent advances in large language models (LLMs) for code applications have demonstrated remarkable zero-shot fluency and instruction following on challenging code related tasks ranging from test case generation to self-repair. Unsurprisingly, however, models struggle to compose syntactically valid programs in programming languages unrepresented in pre-training, referred to as very low-resource Programming Languages (VLPLs). VLPLs appear in crucial settings, including domain-specific languages for internal tools and tool-chains for legacy languages. Inspired by an HCI technique called natural program elicitation, we propose designing an intermediate language that LLMs ``naturally'' know how to use and which can be automatically compiled to a target VLPL. When LLMs generate code that lies outside of this intermediate language, we use compiler techniques to repair the code into programs in the intermediate language. Overall, we introduce \emph{synthetic programming elicitation and compilation} (SPEAC), an approach that enables LLMs to generate syntactically valid code even for VLPLs. We empirically evaluate the performance of SPEAC in a case study and find that, compared to existing retrieval and fine-tuning baselines, SPEAC produces syntactically correct programs significantly more frequently without sacrificing semantic correctness., Comment: 15 pages, 6 figures, 1 table
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- 2024
47. First joint oscillation analysis of Super-Kamiokande atmospheric and T2K accelerator neutrino data
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Super-Kamiokande, collaborations, T2K, Abe, S., Abe, K., Akhlaq, N., Akutsu, R., Alarakia-Charles, H., Ali, A., Hakim, Y. I. Alj, Monsalve, S. Alonso, Amanai, S., Andreopoulos, C., Anthony, L. H. V., Antonova, M., Aoki, S., Apte, K. A., Arai, T., Arihara, T., Arimoto, S., Asada, Y., Asaka, R., Ashida, Y., Atkin, E. T., Babu, N., Barbi, M., Barker, G. J., Barr, G., Barrow, D., Bates, P., Batkiewicz-Kwasniak, M., Beauchêne, A., Berardi, V., Berns, L., Bhadra, S., Bhuiyan, N., Bian, J., Blanchet, A., Blondel, A., Bodur, B., Bolognesi, S., Bordoni, S., Boyd, S. B., Bravar, A., Bronner, C., Bubak, A., Avanzini, M. Buizza, Burton, G. T., Caballero, J. A., Calabria, N. F., Cao, S., Carabadjac, D., Carter, A. J., Cartwright, S. L., Casado, M. P., Catanesi, M. G., Cervera, A., Chakrani, J., Chalumeau, A., Chen, S., Cherdack, D., Choi, K., Chong, P. S., Chvirova, A., Cicerchia, M., Coleman, J., Collazuol, G., Cook, L., Cormier, F., Cudd, A., Dalmazzone, C., Daret, T., Dasgupta, P., Davis, C., Davydov, Yu. I., De Roeck, A., De Rosa, G., Dealtry, T., Delogu, C. C., Densham, C., Dergacheva, A., Dharmapal, R., Di Lodovico, F., Lopez, G. Diaz, Dolan, S., Douqa, D., Doyle, T. A., Drapier, O., Duffy, K. E., Dumarchez, J., Dunne, P., Dygnarowicz, K., D'ago, D., Edwards, R., Eguchi, A., Elias, J., Emery-Schrenk, S., Erofeev, G., Ershova, A., Eurin, G., Fannon, J. E. P., Fedorova, D., Fedotov, S., Feltre, M., Feng, J., Feng, L., Ferlewicz, D., Fernandez, P., Finch, A. J., Aguirre, G. A. Fiorentini, Fiorillo, G., Fitton, M. D., Patiño, J. M. Franco, Friend, M., Fujii, Y., Fujisawa, C., Fujita, S., Fukuda, Y., Furui, Y., Gao, J., Gaur, R., Giampaolo, A., Giannessi, L., Giganti, C., Glagolev, V., Goldsack, A., Gonin, M., Rosa, J. González, Goodman, E. A. G., Gorin, A., Gorshanov, K., Gousy-Leblanc, V., Grassi, M., Griskevich, N. J., Guigue, M., Hadley, D., Haigh, J. T., Han, S., Harada, M., Harris, D. A., Hartz, M., Hasegawa, T., Hassani, S., Hastings, N. C., Hayato, Y., Heitkamp, I., Henaff, D., Hill, J., Hino, Y., Hiraide, K., Hogan, M., Holeczek, J., Holin, A., Holvey, T., Van, N. T. Hong, Honjo, T., Horiuchi, S., Hosokawa, K., Hu, Z., Hu, J., Iacob, F., Ichikawa, A. K., Ieki, K., Ikeda, M., Iovine, N., Ishida, T., Ishino, H., Ishitsuka, M., Ishizuka, T., Ito, H., Itow, Y., Izmaylov, A., Izumiyama, S., Jakkapu, M., Jamieson, B., Jang, M. C., Jang, J. S., Jenkins, S. J., Jesús-Valls, C., Ji, J. Y., Jia, M., Jiang, J., Jonsson, P., Joshi, S., Jung, C. K., Jung, S., Kabirnezhad, M., Kaboth, A. C., Kajita, T., Kakuno, H., Kameda, J., Kanemura, Y., Kaneshima, R., Karpova, S., Kasetti, S. P., Kashiwagi, Y., Kasturi, V. S., Kataoka, Y., Katori, T., Kawamura, Y., Kawaue, M., Kearns, E., Khabibullin, M., Khotjantsev, A., Kikawa, T., Kim, S. B., King, S., Kiseeva, V., Kisiel, J., Kneale, L., Kobayashi, H., Kobayashi, T., Kobayashi, M., Koch, L., Kodama, S., Kolupanova, M., Konaka, A., Kormos, L. L., Koshio, Y., Koto, T., Kowalik, K., Kudenko, Y., Kudo, Y., Kuribayashi, S., Kurjata, R., Kurochka, V., Kutter, T., Kuze, M., Kwon, E., La Commara, M., Labarga, L., Lachat, M., Lachner, K., Lagoda, J., Lakshmi, S. M., LamersJames, M., Langella, A., Laporte, J. -F., Last, D., Latham, N., Laveder, M., Lavitola, L., Lawe, M., Learned, J. G., Lee, Y., Lee, S. H., Silverio, D. Leon, Levorato, S., Lewis, S., Li, X., Li, W., Lin, C., Litchfield, R. P., Liu, S. L., Liu, Y. M., Long, K. R., Longhin, A., Moreno, A. Lopez, Lu, X., Ludovici, L., Lux, T., Machado, L. N., Maekawa, Y., Magaletti, L., Mahn, K., Mahtani, K. K., Malek, M., Mandal, M., Manly, S., Marino, A. D., Martens, K., Marti, Ll., Martin, D. G. R., Martin, J. F., Martin, D., Martini, M., Maruyama, T., Matsubara, T., Matsumoto, R., Mattiazzi, M., Matveev, V., Mauger, C., Mavrokoridis, K., Mazzucato, E., McCauley, N., McElwee, J. M., McFarland, K. S., McGrew, C., McKean, J., Mefodiev, A., Megias, G. D., Mehta, P., Mellet, L., Menjo, H., Metelko, C., Mezzetto, M., Migenda, J., Mijakowski, P., Miki, S., Miller, E., Minamino, A., Mine, S., Mineev, O., Mirabito, J., Miura, M., Bueno, L. Molina, Moon, D. H., Mori, M., Moriyama, S., Morrison, P., Muñoz, A., Mueller, Th. A., Munford, D., Munteanu, L., Nagai, Y., Nagai, K., Nakadaira, T., Nakagiri, K., Nakahata, M., Nakajima, Y., Nakamura, A., Nakamura, K., Nakamura, K. D., Nakamura, T., Nakanishi, F., Nakano, Y., Nakaya, T., Nakayama, S., Nakayoshi, K., Naseby, C. E. R., Ngoc, T. V., Nguyen, V. Q., Nguyen, D. T., Nicholson, M., Niewczas, K., Ninomiya, K., Nishijima, K., Nishimori, S., Nishimura, Y., Noguchi, Y., Nosek, T., Nova, F., Novella, P., Nugent, J. C., Odagawa, T., Okazaki, R., Okazawa, H., Okinaga, W., Okumura, K., Okusawa, T., Ommura, Y., Onda, N., Ospina, N., Osu, L., Oyama, Y., O'Flaherty, M., O'Keeffe, H. M., O'Sullivan, L., Périssé, L., Paganini, P., Palladino, V., Paolone, V., Pari, M., Park, R. G., Parlone, J., Pasternak, J., Payne, D., Penn, G. C., de Perio, P., Pershey, D., Pfaff, M., Pickering, L., Pintaudi, G., Pistillo, C., Pointon, B. W., Popov, B., Yrey, A. Portocarrero, Porwit, K., Posiadala-Zezula, M., Prabhu, Y. S., Prasad, H., Pronost, G., Prouse, N. W., Pupilli, F., Quilain, B., Quyen, P. T., Raaf, J. L., Radermacher, T., Radicioni, E., Radics, B., Ramirez, M. A., Ramsden, R. M., Ratoff, P. N., Reh, M., Riccio, C., Richards, B., Rogly, R., Rondio, E., Roth, S., Roy, N., Rubbia, A., Russo, L., Rychter, A., Saenz, W., Sakai, S., Sakashita, K., Samani, S., Santos, A. D., Sato, Y., Sato, K., Schefke, T., Schloesser, C. M., Scholberg, K., Scott, M., Seiya, Y., Sekiguchi, T., Sekiya, H., Seo, J. 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High Energy Physics - Experiment - Abstract
The Super-Kamiokande and T2K collaborations present a joint measurement of neutrino oscillation parameters from their atmospheric and beam neutrino data. It uses a common interaction model for events overlapping in neutrino energy and correlated detector systematic uncertainties between the two datasets, which are found to be compatible. Using 3244.4 days of atmospheric data and a beam exposure of $19.7(16.3) \times 10^{20}$ protons on target in (anti)neutrino mode, the analysis finds a 1.9$\sigma$ exclusion of CP-conservation (defined as $J_{CP}=0$) and a preference for the normal mass ordering., Comment: 10 pages, 3 figures
- Published
- 2024
48. Uncertainty-Aware PPG-2-ECG for Enhanced Cardiovascular Diagnosis using Diffusion Models
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Belhasin, Omer, Kligvasser, Idan, Leifman, George, Cohen, Regev, Rainaldi, Erin, Cheng, Li-Fang, Verma, Nishant, Varghese, Paul, Rivlin, Ehud, and Elad, Michael
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Computer Science - Machine Learning - Abstract
Analyzing the cardiovascular system condition via Electrocardiography (ECG) is a common and highly effective approach, and it has been practiced and perfected over many decades. ECG sensing is non-invasive and relatively easy to acquire, and yet it is still cumbersome for holter monitoring tests that may span over hours and even days. A possible alternative in this context is Photoplethysmography (PPG): An optically-based signal that measures blood volume fluctuations, as typically sensed by conventional ``wearable devices''. While PPG presents clear advantages in acquisition, convenience, and cost-effectiveness, ECG provides more comprehensive information, allowing for a more precise detection of heart conditions. This implies that a conversion from PPG to ECG, as recently discussed in the literature, inherently involves an unavoidable level of uncertainty. In this paper we introduce a novel methodology for addressing the PPG-2-ECG conversion, and offer an enhanced classification of cardiovascular conditions using the given PPG, all while taking into account the uncertainties arising from the conversion process. We provide a mathematical justification for our proposed computational approach, and present empirical studies demonstrating its superior performance compared to state-of-the-art baseline methods.
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- 2024
49. Unleashing the immune response to NY-ESO-1 cancer testis antigen as a potential target for cancer immunotherapy
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Afsheen Raza, Maysaloun Merhi, Varghese Philipose Inchakalody, Roopesh Krishnankutty, Allan Relecom, Shahab Uddin, and Said Dermime
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Cancer immunotherapy ,Cancer testis antigen ,Cancer vaccine ,Immune checkpoint inhibitors ,NY-ESO-1 ,Tumor microenvironment ,Medicine - Abstract
Abstract Introduction Cancer Immunotherapy has recently emerged as a promising and effective modality to treat different malignancies. Antigenic profiling of cancer tissues and determination of any pre-existing immune responses to cancer antigens may help predict responses to immune intervention in cancer. NY-ESO-1, a cancer testis antigen is the most immunogenic antigen to date. The promise of NY-ESO-1 as a candidate for specific immune recognition of cancer comes from its restricted expression in normal adult tissue but frequent occurrence in multiple tumors including melanoma and carcinomas of lung, esophageal, liver, gastric, prostrate, ovarian, and bladder. Main body This review summarizes current knowledge of NY-ESO-1 as efficient biomarker and target of immunotherapy. It also addresses limitations and challenges preventing a robust immune response to NY-ESO-1 expressing cancers, and describes pre-clinical and clinical observations relevant to NY-ESO-1 immunity, holding potential therapeutic relevance for cancer treatment. Conclusion NY-ESO-1 induces strong immune responses in cancer patients but has limited objective clinical responses to NY-ESO-1 expressing tumors due to effect of competitive negative signaling from immune-checkpoints and immune-suppressive tumor microenvironment. We propose that combination therapy to increase the efficacy of NY-ESO-1 specific immunotherapeutic interventions should be explored to unleash the immune response against NY-ESO-1 expressing tumors.
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- 2020
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50. Bedside formulation of a personalized multi-neoantigen vaccine against mammary carcinoma
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Martin F Bachmann, Said Dermime, Daniel E Speiser, Monique Vogel, Georges Coukos, Varghese Philipose Inchakalody, Mona O Mohsen, Justine Michaux, HuiSong Pak, Brian J Stevenson, Simone de Brot, and Michal Bassani-Sternberg
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Published
- 2022
- Full Text
- View/download PDF
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