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Abstract Programmed death-ligand 1 (PD-L1) expression is currently used in the clinic to assess eligibility for immune-checkpoint inhibitors via the tumor proportion score (TPS), but its efficacy is limited by high interobserver variability. Multiple papers have presented systems for the automatic quantification of TPS, but none report on the task of determining cell-level PD-L1 expression and often reserve their evaluation to a single PD-L1 monoclonal antibody or clinical center. In this paper, we report on a deep learning algorithm for detecting PD-L1 negative and positive tumor cells at a cellular level and evaluate it on a cell-level reference standard established by six readers on a multi-centric, multi PD-L1 assay dataset. This reference standard also provides for the first time a benchmark for computer vision algorithms. In addition, in line with other papers, we also evaluate our algorithm at slide-level by measuring the agreement between the algorithm and six pathologists on TPS quantification. We find a moderately low interobserver agreement at cell-level level (mean reader-reader F1 score = 0.68) which our algorithm sits slightly under (mean reader-AI F1 score = 0.55), especially for cases from the clinical center not included in the training set. Despite this, we find good AI-pathologist agreement on quantifying TPS compared to the interobserver agreement (mean reader-reader Cohen’s kappa = 0.54, 95% CI 0.26–0.81, mean reader-AI kappa = 0.49, 95% CI 0.27—0.72). In conclusion, our deep learning algorithm demonstrates promise in detecting PD-L1 expression at a cellular level and exhibits favorable agreement with pathologists in quantifying the tumor proportion score (TPS). We publicly release our models for use via the Grand-Challenge platform.

Abstract The congruency sequence effect (CSE) is one of the most investigated effects in the cognitive control literature. The conflict monitoring theory suggests that the CSE is the result of adjustments in cognitive control based on perceived conflict. A recent paper by Zhang and colleagues, has investigated whether the manipulation of conflict level by changing distractor incompatibility in a flanker task affects the amount of adjustments in cognitive control. Their study produced mixed findings, somewhat supporting the original conflict monitoring theory, but also suggesting other explanations, such as the repetition expectancy account. We replicated the experimental design in a multisite online study (N = 347), with Hungarian, Italian, and Singaporean participants. Our results supported the prediction that changes in the level of conflict trigger conflict adaptation, revealing that increasing conflict levels induced stronger adaptive control. Bayesian hypothesis testing indicated a monotonic reduction in congruency effects as a function of previous conflict strength. This finding is in line with the extension of the traditional conflict monitoring theory, as well as other theories like affective signaling and expected value of control, implying that the relationship between conflict and interference effects is gradual, rather than a binary function.

Summary: Background: Bivalent SARS-CoV-2 vaccines were developed to counter increasing susceptibility to emerging SARS-CoV-2 variants. We evaluated the durability of immunity and protection following first bivalent vaccination among nursing home residents. Methods: We evaluated anti-spike and neutralization titers from blood in 653 community nursing home residents before and after each monovalent booster, and a bivalent vaccine. Concurrent clinical outcomes were evaluated using electronic health record data from a separate cohort of 3783 residents of Veterans Affairs (VA) nursing homes who had received at least the primary series monovalent vaccination. Using target trial emulation, we compared VA residents who did and did not receive the bivalent vaccine to measure vaccine effectiveness against infection, hospitalization, and death. Findings: In the community cohort, Omicron BA.5 neutralization activity rose after each monovalent and bivalent booster vaccination regardless of prior infection history. Titers declined over time but six months post-bivalent vaccination, BA.5 neutralization persisted at detectable levels in 75% of infection-naive and 98% of prior-infected individuals. In the VA nursing home cohort, bivalent vaccine added effectiveness to monovalent booster vaccination by 18.5% for infection (95% confidence interval (CI) −5.6, 34.0%), and 29.2% for hospitalization or death (95% CI −14.2, 56.2%) over five months. Interpretation: The level of protection declined after bivalent vaccination over a 6 month period and may open a window of added vulnerability before the next updated vaccine becomes available, suggesting a subset of nursing home residents may benefit from an additional vaccination booster. Funding: CDC, NIH, VHA.

Abstract The aim of this study was to evaluate qualitative and quantitative differences in vascular density analysis of an established and a novel alternative for post-processing on optical coherence tomography angiography (OCTA) images in healthy individuals. OCTA examinations of 38 subjects were performed. After extracting the images, two semi-manual post-processing techniques, the already established Mexican hat filtering (MHF) and an alternative, the Shanbhag thresholding (ST) were applied. We assessed Vessel Density (VD), Skeleton Density (SkD) and Vessel Diameter Index (VDI). We analyzed the results in order to establish similarities or potentially relevant differences. Regarding SkD and VD, MHF generally gave higher values than ST. Simultaneously, mean values were also predominantly higher by MHF; however, standard deviations (SD) were higher by ST (range [mean ± SD]: 0.054 ± 0.038 to 0.134 ± 0.01 and 0.134 ± 0.095 to 0.362 ± 0.028 vs 0.012 ± 0.014 to 0.087 ± 0.03 and 0.039 ± 0.047 to 0.4 ± 0.095 for SkD and VD with MHF vs SkD and VD with ST, respectively). Values of VDI were considerably higher with ST than with MHF, while standard deviation was still significantly higher with ST (range [mean ± SD]: 2.459 ± 0.144 to 2.71 ± 0.084 and 2.983 ± 0.929 to 5.19 ± 1.064 for VDI with MHF and ST, respectively). The noise level reduction of the two methods were almost identical (noise levels: 65.8% with MHT and 65.24% with ST). Using MHF, the vascular network gets more fragmented by an average of 40% compared to ST. Both methods allow the segmentation of the vascular network and the examination of vascular density parameters, but they produce largely inconsistent results. To determine if these inconsistent results are clinically meaningful, and which method is more suitable for clinical use, our results provide further evidence that detailed understanding of the image analysis method is essential for reliable decision making for patients with retinal pathology. For longitudinal monitoring, use of the same image processing method is recommended.

Background: Tenofovir alafenamide (TAF) is a novel prodrug of tenofovir for the treatment of chronic hepatitis B (CHB) that has shown a favourable renal safety profile while offering suppression of HBV DNA similar to tenofovir disoproxil fumarate (TDF). We aimed to study changes in markers of HBV replication and renal function in a real-world setting in European patients. Methods: In our prospective single-arm, non-interventional observational study, HBeAg-positive and HBeAg-negative patients with chronic HBV mono-infection receiving TAF as their first or following line treatment were enrolled. HBV DNA, HBsAg, markers of bone metabolism, and renal function were determined at baseline and every consecutive 3 months. Results: A total of 50 patients (70% male) were included. The mean duration of TAF treatment was 18 (3–36) months. In 20 patients with detectable HBV DNA at baseline, median serum levels of HBV DNA log10 changed from 2.33 (0.766–6.47) to 1.04 IU/mL at the end of observation and became undetectable in 11 patients. Median HBsAg log10 decreased from 3.37 (0.88–5.10) to 2.39 (1.52–4.19) IU/mL. During the entire observation period, the renal function parameters remained stable in patients with normal renal function and even in those with renal dysfunction. Mild adverse events were reported by 14 patients (28%). Conclusions: TAF was a safe and effective treatment, also in patients with decreased renal function.

All major ear rots (F. graminearum, F. verticillioides, and Aspergillus flavus) and their toxins are present in maize of preharvest origin in Hungary. Resistance can be an important tool in reducing the infection and toxin contamination from these rots in maize. Previous results identified resistance differences in maize hybrids that were suitable for use in evaluating their risk from toxigenic fungi and their toxins. During the tests, two methodical improvements were achieved: the use of three isolates of the fungus secured and a more precise estimation of resistance to ear rots and their resistance to toxin accumulation or overproduction. The improvement in sampling and the tests of subsamples made the evaluation for the statistics much more exact. This way, we were able to reduce the Within value, providing a statistically more reliable method of evaluation. Earlier data had confirmed that toxin contamination could not be predicted well from visual ear rot severity data. Contradictory results for hybrid ranking were often identified between isolates. The resistance to disease and toxin contamination is not generally valid. The new suggested methodology compares the performance of hybrids in a large number of epidemic situations to identify adaptable hybrids that can respond to diverse conditions; therefore, the stability of resistance and toxin response is decisive information to evaluate risk analyses. The increased number of disease toxin data allowed for lower LSD 5% values for toxins, a much finer analysis of toxin overproduction and underproduction, and a wider database for stability analyses. This way, we obtained important additional separated information about resistance to accumulation of toxins and about maize resistance to these pathogens that is suitable to provide much more reliable testing than was possible until now. Globally, about 50–100 million metric tons can be saved by excluding susceptible hybrids from commercial production.

Robust prognostic and predictive factors for hepatocellular carcinoma, a leading cause of cancer-related deaths worldwide, have not yet been identified. Previous studies have identified potential HCC determinants such as genetic mutations, epigenetic alterations, and pathway dysregulation. However, the clinical significance of these molecular alterations remains elusive. MicroRNAs are major regulators of protein expression. MiRNA functions are frequently altered in cancer. In this study, we aimed to explore the prognostic value of differentially expressed miRNAs in HCC, to elucidate their associated pathways and their impact on treatment response. To this aim, bioinformatics techniques and clinical dataset analyses were employed to identify differentially expressed miRNAs in HCC compared to normal hepatic tissue. We validated known associations and identified a novel miRNA signature with potential prognostic significance. Our comprehensive analysis identified new miRNA-targeted pathways and showed that some of these protein coding genes predict HCC patients' response to the tyrosine kinase inhibitor sorafenib.

Abstract Background The incidence of obesity, a known risk factor for several metabolic and chronic diseases, including numerous malignancies, has risen sharply in the world. Various clinical studies demonstrate that excessive Body Mass Index (BMI) may worsen the incidence, prognosis, and mortality rates of breast cancer. Thus, understanding the link tying up obesity and breast cancer onset and progression is critically important, as it can impact patients’ survival and quality of life. Recently, circulating extracellular vesicle (EV) derived miRNAs have attracted much attention for their diagnostic, prognostic and therapeutic potential in oncology research. Although the potential role of EV-derived miRNAs in the early detection of breast cancer has been repeatedly mentioned, screening of miRNAs packaged within serum EVs has not yet been reported in patients with obesity. Methods Circulating EVs were isolated from normal weight (NW), and overweight/obese (OW/Ob) breast cancer patients and characterized by Transmission Electron Microscopy (TEM), Nanoparticle Tracking Analysis (NTA), and protein marker expression. Evaluation of EV-associated miRNAs was conducted in a screening (RNA-seq) and a validation (qRT-PCR) cohort. Bioinformatic analysis was performed to uncover significantly enriched biological processes, molecular functions and pathways. ROC and Kaplain-Meier survival analyses were used for clinical significance. Results Comparison of serum EV-derived miRNAs from NW and OW/Ob patients detected seven differentially expressed miRNAs (let-7a-5p, miR-122-5p, miR-30d-5p, miR-126-3p, miR-27b-3p, miR-4772-3p, and miR-10a-5p) in the screening cohort. GO analysis revealed the enrichment of protein phosphorylation, intracellular signal transduction, signal transduction, and vesicle-mediated transport among the top biological processes. In addition, the target genes were significantly enriched in pathways related to PI3K/Akt, growth hormones, and insulin signalings, which are all involved in obesity-related diseases and/or breast cancer progression. In the validation cohort, qRT-PCR confirmed a significant down-regulation of EV-derived let-7a in the serum of OW/Ob breast cancer patients compared to NW patients. Let-7a levels also exhibited a negative correlation with BMI values. Importantly, decreased let-7a miRNA expression was associated with higher tumor grade and poor survival in patients with breast cancer. Conclusion These results suggest that serum-EV derived miRNAs may reflect a differential profile in relation to a patient’s BMI, which, once validated in larger cohorts of patients, could provide insights into novel specific biomarkers and innovative targets to prevent the progression of obesity-mediated breast cancer.

Any large dataset can be analyzed in a number of ways, and it is possible that the use of different analysis strategies will lead to different results and conclusions. One way to assess whether the results obtained depend on the analysis strategy chosen is to employ multiple analysts and leave each of them free to follow their own approach. Here, we present consensus-based guidance for conducting and reporting such multi-analyst studies, and we discuss how broader adoption of the multi-analyst approach has the potential to strengthen the robustness of results and conclusions obtained from analyses of datasets in basic and applied research.

Creatine transporter deficiency (CTD) is an X-linked disease caused by mutations in the SLC6A8 gene. The impaired creatine uptake in the brain results in intellectual disability, behavioral disorders, language delay, and seizures. In this work, we generated human brain organoids from induced pluripotent stem cells of healthy subjects and CTD patients. Brain organoids from CTD donors had reduced creatine uptake compared with those from healthy donors. The expression of neural progenitor cell markers SOX2 and PAX6 was reduced in CTD-derived organoids, while GSK3β, a key regulator of neurogenesis, was up-regulated. Shotgun proteomics combined with integrative bioinformatic and statistical analysis identified changes in the abundance of proteins associated with intellectual disability, epilepsy, and autism. Re-establishment of the expression of a functional SLC6A8 in CTD-derived organoids restored creatine uptake and normalized the expression of SOX2, GSK3β, and other key proteins associated with clinical features of CTD patients. Our brain organoid model opens new avenues for further characterizing the CTD pathophysiology and supports the concept that reinstating creatine levels in patients with CTD could result in therapeutic efficacy.

Abstract Inertial Measurement Units (IMUs) are a potential way to monitor the mobility of people outside clinical or laboratory settings at an acceptable cost. To increase accuracy, multiple IMUs can be used. By embedding multiple sensors into everyday clothing, it is possible to simplify having to put on individual sensors, ensuring sensors are correctly located and oriented. This research demonstrates how clothing-mounted IMU readings can be used to identify 4 common postures: standing, sitting, lying down and sitting on the floor. Data were collected from 5 healthy adults, with each providing 1–4 days of data with approximately 5 h each day. Each day, participants performed a fixed set of activities that were video-recorded to provide a ground truth. This is an analysis of accelerometry data from 3 sensors incorporated into right trouser-leg at the waist, thigh and ankle. Data were classified as static/ dynamic activities using a K-nearest neighbour (KNN) algorithm. For static activities, the inclination angles of the three sensors were estimated and used to train a second KNN classifier. For this highly-selected dataset (60000–70000 data points/posture), the static postures were classified with 100% accuracy, illustrating the potential for clothing-mounted sensors to be used in posture classification.

Abstract Mild cognitive impairment (MCI) is the prodromal phase of dementia, and it is highly underdiagnosed in the community. We aimed to develop an automated, rapid ( 0.05). Our study draws attention to the utility of hand movement analysis, especially to the estimation of entropy in the early recognition of MCI. It also suggests that our system might provide a promising tool for the cognitive screening of large populations.

Abstract Lung cancer has been the most common cancer worldwide for several decades. The outcomes of patients with locally advanced lung cancer remain dismal, and only a minority of patients survive more than 5 years. However, tumor therapeutic resistance mechanisms are poorly studied. Identification of therapeutic resistance pathways in lung cancer in order to increase the sensitivity of lung tumor cells to therapeutic agents is a crucial but challenging need. To identify novel genes that modulate the response to platinum-based therapy, we performed a genome-wide high-throughput ribonucleic acid interference (RNAi) screen via transfection of human lung cancer (PC9) cells with a viral short hairpin RNA (shRNA) library. We further validated a potential target via 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and clonogenic survival assays on PC9 and A549 lung tumor cells transfected with small interfering RNAs (siRNAs) to successfully downregulate protein expression and then treated with increasing doses of cisplatin or X-ray radiation. We determined protein expression by immunohistochemistry (IHC) after chemoradiotherapy and analyzed gene expression-based survival outcomes in two cohorts of human non-small-cell lung cancer (NSCLC) patients. The screen identified several targets involved in epithelial-to-mesenchymal transition (EMT), including Smurf1, Smurf2, YAP1, and CEBPZ, and glycolytic pathway proteins, including PFKFB3. Furthermore, we found that the small molecule proteasome inhibitor bortezomib significantly downregulated Smurf2 in lung cancer cells. The addition of bortezomib in combination with cisplatin and radiation therapy in PC9 and A549 cells led to an increase in deoxyribonucleic acid (DNA) double-strand breaks with increased numbers of γ-H2AX-positive cells and upregulation of apoptosis. Finally, we found that Smurf2 protein expression was upregulated in situ after treatment with cisplatin and radiation therapy in a relevant cohort of patients with stage III NSCLC. Additionally, Smurf2 gene expression was the strongest predictor of survival in patients with squamous NSCLC after chemotherapy or chemoradiotherapy. We successfully identified and validated Smurf2 as both a common modulator of resistance and an actionable target in lung cancer. These results suggest the urgent need to investigate clinical Smurf2 inhibition via bortezomib in combination with cisplatin and radiation for patients with locally advanced NSCLC.

Background: Cancer patients show increased morbidity with COVID-19 and need effective immunization strategies. Many healthcare regulatory agencies recommend administering ‘booster’ doses of COVID-19 vaccines beyond the standard two-dose series, for this group of patients. Therefore, studying the efficacy of these additional vaccine doses against SARS-CoV-2 and variants of concern is of utmost importance in this immunocompromised patient population Methods: We conducted a prospective single arm clinical trial enrolling patients with cancer that had received two doses of mRNA or one dose of AD26.CoV2.S vaccine and administered a third dose of mRNA vaccine. We further enrolled patients that had no or low responses to three mRNA COVID vaccines and assessed the efficacy of a fourth dose of mRNA vaccine. Efficacy was assessed by changes in anti-spike antibody, T-cell activity, and neutralization activity, which were again assessed at baseline and 4 weeks. Results: We demonstrate that a third dose of COVID-19 vaccine leads to seroconversion in 57% of patients that were seronegative after primary vaccination series. The immune response is durable as assessed by anti-SARS-CoV-2 (anti-S) antibody titers, T-cell activity, and neutralization activity against wild-type (WT) SARS-CoV2 and BA1.1.529 at 6 months of follow-up. A subset of severely immunocompromised hematologic malignancy patients that were unable to mount an adequate immune response (titer

Abstract The evolution of forearc and backarc domains is usually treated separately, as they are separated by a volcanic arc. We analyse their spatial and temporal relationships in the Tyrrhenian subduction system, using seismic profiles and numerical modelling. A volcanic arc, which included the Marsili volcano, was involved in arc-rifting during the Pliocene. This process led to the formation of an oceanic backarc basin (~ 1.8 Ma) to the west of the Marsili volcano. The eastern region corresponded to the forearc domain, floored by serpentinised mantle. Here, a new volcanic arc formed at ~ 1 Ma, marking the onset of the forearc-rifting. This work highlights that fluids and melts induce weakening of the volcanic arc region and drive the arc-rifting that led to the backarc basin formation. Later, the slab rollback causes the trench-ward migration of volcanism that led to the forearc- rifting under the control of fluids released from the downgoing plate.

Abstract Knowing who to target with certain messages is the prerequisite of efficient public health campaigns during pandemics. Using the COVID-19 pandemic situation, we explored which facets of the society—defined by age, gender, income, and education levels—are the most likely to visit social gatherings and aggravate the spread of a disease. Analyzing the reported behavior of 87,169 individuals from 41 countries, we found that in the majority of the countries, the proportion of social gathering-goers was higher in male than female, younger than older, lower-educated than higher educated, and low-income than high-income subgroups of the populations. However, the data showed noteworthy heterogeneity between the countries warranting against generalizing from one country to another. The analysis also revealed that relative to other demographic factors, income was the strongest predictor of avoidance of social gatherings followed by age, education, and gender. Although the observed strength of these associations was relatively small, we argue that incorporating demographic-based segmentation into public health campaigns can increase the efficiency of campaigns with an important caveat: the exploration of these associations needs to be done on a country level before using the information to target populations in behavior change interventions.

ObjectivesRecording and reproducing mandibular movements have been of key importance in the practice of dentistry for over a century. Recently, it has become possible to use digital technologies for these tasks. This study presents a preliminary method to try to identify the mandibular instantaneous centres of rotation based solely on intraoral scanners.MethodsThe dentitions of four participants were scanned, multiple inter-occlusal registrations and buccal scans were performed in closed and opened positions. Blender software was used to align the meshes during the post-scan digital workflow. Bite alignment accuracy was assessed and then improved with a strict exclusion protocol. An automated algorithm was used to find rotations between closed stage and open stage meshes.ResultsOur exclusion protocol reduced the bite alignment error significantly (p = 0.001) and the root-mean-square error value of the meshes decreased from 0.09 mm (SD = 0.15) to 0.03 mm (SD = 0.017). However, the remaining translational error caused an unexpectedly large shift in the axis of rotation (mean = 1.35 mm, SD = 0.77) with a 41.83: 1 ratio. As found in other studies, our results showed even a small amount of error during registration can shift the axis of rotation a large amount. This phenomenon will compromise the results of common pantographic methods which assume a rotation axis of the condyle. It also adds valuable information to the concept of instantaneous centers of rotation by revealing their true characteristics.

BackgroundInflammation has been associated with progression and complications of chronic heart failure (HF) but no effective therapy has yet been identified to treat this dysregulated immunologic state. The selective cytopheretic device (SCD) provides extracorporeal autologous cell processing to lessen the burden of inflammatory activity of circulating leukocytes of the innate immunologic system.AimThe objective of this study was to evaluate the effects of the SCD as an extracorporeal immunomodulatory device on the immune dysregulated state of HF. HF.Methods and resultsSCD treatment in a canine model of systolic HF or HF with reduced ejection fraction (HFrEF) diminished leukocyte inflammatory activity and enhanced cardiac performance as measured by left ventricular (LV) ejection fraction and stroke volume (SV) up to 4 weeks after treatment initiation. Translation of these observations in first in human, proof of concept clinical study was evaluated in a patient with severe HFrEFHFrEF ineligible for cardiac transplantation or LV LV assist device (LVAD) due to renal insufficiency and right ventricular dysfunction. Six hour SCD treatments over 6 consecutive days resulted in selective removal of inflammatory neutrophils and monocytes and reduction in key plasma cytokines, including tumor necrosis factor-alpha (TNF-α),), interleukin (IL)-6, IL-8, and monocyte chemoattractant protein (MCP)-1. These immunologic changes were associated with significant improvements in cardiac power output, right ventricular stroke work index, cardiac index and LVSV index…. Stabilization of renal function with progressive volume removal permitted successful LVAD implantation.ConclusionThis translational research study demonstrates a promising immunomodulatory approach to improve cardiac performance in HFrEFHFrEF and supports the important role of inflammation in the progression of HFHF.

In the era of Big Data, data collection underpins biological research more than ever before. In many cases, this can be as time-consuming as the analysis itself. It requires downloading multiple public databases with various data structures, and in general, spending days preparing the data before answering any biological questions. Here, we introduce Sherlock, an open-source, cloud-based big data platform (https://earlham-sherlock.github.io/) to solve this problem. Sherlock provides a gap-filling way for computational biologists to store, convert, query, share and generate biology data while ultimately streamlining bioinformatics data management. The Sherlock platform offers a simple interface to leverage big data technologies, such as Docker and PrestoDB. Sherlock is designed to enable users to analyze, process, query and extract information from extremely complex and large data sets. Furthermore, Sherlock can handle different structured data (interaction, localization, or genomic sequence) from several sources and convert them to a common optimized storage format, for example, the Optimized Row Columnar (ORC). This format facilitates Sherlock’s ability to quickly and efficiently execute distributed analytical queries on extremely large data files and share datasets between teams. The Sherlock platform is freely available on GitHub, and contains specific loader scripts for structured data sources of genomics, interaction and expression databases. With these loader scripts, users can easily and quickly create and work with specific file formats, such as JavaScript Object Notation (JSON) or ORC. For computational biology and large-scale bioinformatics projects, Sherlock provides an open-source platform empowering data management, analytics, integration and collaboration through modern big data technologies.

BackgroundRotator cuff tears are a common shoulder injury, but they sometimes remain undiagnosed, as symptoms can be limited. Altered shoulder biomechanics can lead to secondary damage and degeneration. In biomechanical analyses, the shoulder (ie, the glenohumeral joint) is normally idealized as a ball-and-socket joint, even though a translation is often observed clinically. To date, no conclusive changes in glenohumeral translation have been reported in patients with rotator cuff tears, and it is unknown how an additional handheld weight that is comparable to those used during daily activities will affect glenohumeral translations in patients with rotator cuff tears. ObjectiveThis study aims to assess the load-induced glenohumeral translation (liTr) in patients with rotator cuff tears and its association with the load-induced changes in muscle activation (liMA). MethodsPatients and asymptomatic controls will be recruited. Participants will fill out health questionnaires and perform 30° arm abduction and adduction trials, during which they will hold different handheld weights of a maximum of 4 kg while motion capture and electromyographic data are collected. In addition, fluoroscopic images of the shoulders will be taken for the same movements. Isometric shoulder muscle strength for abduction and rotation will be assessed with a dynamometer. Finally, shoulder magnetic resonance images will be acquired to assess muscle status and injury presence. The dose-response relationship between additional weight, liTr, and liMA will be evaluated. ResultsRecruitment and data collection began in May 2021, and they will last until the recruitment target is achieved. Data collection is expected to be completed by the end of 2022. As of November 2022, data processing and analysis are in progress, and the first results are expected to be submitted for publication in 2023. ConclusionsThis study will aid our understanding of biological variations in liTr, the influence of disease pathology on liTr, the potential compensation of rotator cuff tears by muscle activation and size, and the association between liTr and patient outcomes. The outcomes will be relevant for diagnosis, treatment, and rehabilitation planning in patients with rotator cuff tears. Trial RegistrationClinicalTrials.gov NCT04819724; https://clinicaltrials.gov/ct2/show/NCT04819724 International Registered Report Identifier (IRRID)DERR1-10.2196/43769

Efficient planning in complex environments requires that uncertainty associated with current inferences and possible consequences of forthcoming actions is represented. Representation of uncertainty has been established in sensory systems during simple perceptual decision making tasks but it remains unclear if complex cognitive computations such as planning and navigation are also supported by probabilistic neural representations. Here, we capitalized on gradually changing uncertainty along planned motion trajectories during hippocampal theta sequences to capture signatures of uncertainty representation in population responses. In contrast with prominent theories, we found no evidence of encoding parameters of probability distributions in the momentary population activity recorded in an open-field navigation task in rats. Instead, uncertainty was encoded sequentially by sampling motion trajectories randomly and efficiently in subsequent theta cycles from the distribution of potential trajectories. Our analysis is the first to demonstrate that the hippocampus is well equipped to contribute to optimal planning by representing uncertainty.

In the era of Big Data, data collection underpins biological research more than ever before. In many cases, this can be as time-consuming as the analysis itself. It requires downloading multiple public databases with various data structures, and in general, spending days preparing the data before answering any biological questions. Here, we introduce Sherlock, an open-source, cloud-based big data platform (https://earlham-sherlock.github.io/) to solve this problem. Sherlock provides a gap-filling way for computational biologists to store, convert, query, share and generate biology data while ultimately streamlining bioinformatics data management. The Sherlock platform offers a simple interface to leverage big data technologies, such as Docker and PrestoDB. Sherlock is designed to enable users to analyze, process, query and extract information from extremely complex and large data sets. Furthermore, Sherlock can handle different structured data (interaction, localization, or genomic sequence) from several sources and convert them to a common optimized storage format, for example, the Optimized Row Columnar (ORC). This format facilitates Sherlock’s ability to quickly and efficiently execute distributed analytical queries on extremely large data files and share datasets between teams. The Sherlock platform is freely available on GitHub, and contains specific loader scripts for structured data sources of genomics, interaction and expression databases. With these loader scripts, users can easily and quickly create and work with specific file formats, such as JavaScript Object Notation (JSON) or ORC. For computational biology and large-scale bioinformatics projects, Sherlock provides an open-source platform empowering data management, analytics, integration and collaboration through modern big data technologies.

Summary: Background: The prognostic value of tumor-infiltrating lymphocytes (TILs) assessed by machine learning algorithms in melanoma patients has been previously demonstrated but has not been widely adopted in the clinic. We evaluated the prognostic value of objective automated electronic TILs (eTILs) quantification to define a subset of melanoma patients with a low risk of relapse after surgical treatment. Methods: We analyzed data for 785 patients from 5 independent cohorts from multiple institutions to validate our previous finding that automated TIL score is prognostic in clinically-localized primary melanoma patients. Using serial tissue sections of the Yale TMA-76 melanoma cohort, both immunofluorescence and Hematoxylin-and-Eosin (H&E) staining were performed to understand the molecular characteristics of each TIL phenotype and their associations with survival outcomes. Findings: Five previously-described TIL variables were each significantly associated with overall survival (p

Abstract Background Bilayer collagen membranes are routinely used in guided bone/tissue regeneration to serve as osteoconductive scaffolds and prevent the invasion of soft tissues. It is recommended to place the membranes with their dense layer towards the soft tissue and their porous layer towards the bony defect area. However, evidence supporting this recommendation is lacking. This study aimed to determine whether the alignment of bilayer collagen membranes has an effect on bone regeneration. Methods In two groups of ten male Sprague-Dawley rats each, a 5-mm calvarial defect was created. Thereafter, the defect was randomly covered with a bilayer, resorbable, pure type I and III collagen membrane placed either regularly or upside-down (i.e., dense layer towards bone defect). After 4 weeks of healing, micro-computed tomography (μCT), histology, and histomorphometry of the inner cylindrical region of interest (4.5 mm in diameter) were performed to assess new bone formation and the consolidation of the collagen membrane in the defect area. Results Quantitative μCT showed similar bone volume (median 8.0 mm3, interquartile range 7.0–10.0 vs. 6.2 mm3, 4.3–9.4, p = 0.06) and trabecular thickness (0.21 mm, 0.19–0.23 vs. 0.18 mm, 0.17–0.20, p = 0.03) between upside-down and regular placement, both leading to an almost complete bony coverage. Histomorphometry showed comparable new bone areas between the upside-down and regularly placed membranes, 3.9 mm2 (2.7–5.4) vs. 3.8 mm2 (2.2–4.0, p = 0.31), respectively. Both treatment groups revealed the same regeneration patterns and spatial distribution of bone with and without collagen fibers, as well as residual collagen fibers. Conclusions Our data support the osteoconductive properties of collagen membranes and suggest that bone regeneration is facilitated regardless of membrane layer alignment.

Summary: Background: Nursing home (NH) residents have borne a disproportionate share of SARS-CoV-2 morbidity and mortality. Vaccines have limited hospitalisation and death from earlier variants in this vulnerable population. With the rise of Omicron and future variants, it is vital to sustain and broaden vaccine-induced protection. We examined the effect of boosting with BNT162b2 mRNA vaccine on humoral immunity and Omicron-specific neutralising activity among NH residents and healthcare workers (HCWs). Methods: We longitudinally enrolled 85 NH residents (median age 77) and 48 HCWs (median age 51), and sampled them after the initial vaccination series; and just before and 2 weeks after booster vaccination. Anti-spike, anti-receptor binding domain (RBD) and neutralisation titres to the original Wuhan strain and neutralisation to the Omicron strain were obtained. Findings: Booster vaccination significantly increased vaccine-specific anti-spike, anti-RBD, and neutralisation levels above the pre-booster levels in NH residents and HCWs, both in those with and without prior SARS-CoV-2 infection. Omicron-specific neutralisation activity was low after the initial 2 dose series with only 28% of NH residents’ and 28% HCWs’ titres above the assay's lower limit of detection. Omicron neutralising activity following the booster lifted 86% of NH residents and 93% of HCWs to the detectable range. Interpretation: With boosting, the vast majority of HCWs and NH residents developed detectable Omicron-specific neutralising activity. These data provide immunologic evidence that strongly supports booster vaccination to broaden neutralising activity and counter waning immunity in the hope it will better protect this vulnerable, high-risk population against the Omicron variant. Funding: NIH AI129709-03S1, U01 CA260539-01, CDC 200-2016-91773, and VA BX005507-01.

Abstract This study primarily focuses on the assessment of dentistry students’ improvement of manual skills resulting from their participation in courses. We aimed to prove that systematic manual skills development significantly improves dexterity. We hypothesized that the dexterity training regimen improves manual dexterity demonstrated by the HAM-Man (Hamburg Assessment Test for Medicine-Manual Dexterity) test scores and CGM (cerebellar grey matter) growth. Thirty volunteers were randomly divided into two equal groups (study and control). Firstly, volunteers were examined by the HAM-Man test and baseline MRI scans. Afterwards, a manual skills development course was launched for the “study group”. Secondly, all the manual skills of the students were evaluated longitudinally, by the HAM-Man test. Simultaneously, the follow-up MRI scans were taken to observe morphologic changes in the cerebellum. The Wilcoxon signed-rank test and Student Paired t-test were used for statistical analyses. Value p

Abstract Accurate prognostic biomarkers in early-stage melanoma are urgently needed to stratify patients for clinical trials of adjuvant therapy. We applied a previously developed open source deep learning algorithm to detect tumor-infiltrating lymphocytes (TILs) in hematoxylin and eosin (H&E) images of early-stage melanomas. We tested whether automated digital (TIL) analysis (ADTA) improved accuracy of prediction of disease specific survival (DSS) based on current pathology standards. ADTA was applied to a training cohort (n = 80) and a cutoff value was defined based on a Receiver Operating Curve. ADTA was then applied to a validation cohort (n = 145) and the previously determined cutoff value was used to stratify high and low risk patients, as demonstrated by Kaplan–Meier analysis (p ≤ 0.001). Multivariable Cox proportional hazards analysis was performed using ADTA, depth, and ulceration as co-variables and showed that ADTA contributed to DSS prediction (HR: 4.18, CI 1.51–11.58, p = 0.006). ADTA provides an effective and attainable assessment of TILs and should be further evaluated in larger studies for inclusion in staging algorithms.

Abstract Alveolar macrophages (AMs) are critical for defense against airborne pathogens and AM dysfunction is thought to contribute to the increased burden of pulmonary infections observed in individuals living with HIV-1 (HIV). While HIV nucleic acids have been detected in AMs early in infection, circulating HIV during acute and chronic infection is usually CCR5 T cell-tropic (T-tropic) and enters macrophages inefficiently in vitro. The mechanism by which T-tropic viruses infect AMs remains unknown. We collected AMs by bronchoscopy performed in HIV-infected, antiretroviral therapy (ART)-naive and uninfected subjects. We found that viral constructs made with primary HIV envelope sequences isolated from both AMs and plasma were T-tropic and inefficiently infected macrophages. However, these isolates productively infected macrophages when co-cultured with HIV-infected CD4+ T cells. In addition, we provide evidence that T-tropic HIV is transmitted from infected CD4+ T cells to the AM cytosol. We conclude that AM-derived HIV isolates are T-tropic and can enter macrophages through contact with an infected CD4+ T cell, which results in productive infection of AMs. CD4+ T cell-dependent entry of HIV into AMs helps explain the presence of HIV in AMs despite inefficient cell-free infection, and may contribute to AM dysfunction in people living with HIV.

Multi-target drug candidate BGP-15 has shown cardioprotective and antiarrhythmic actions in diseased models. Here, we investigated the effects of BGP-15 on ECG and echocardiographic parameters, heart rate variability (HRV), and arrhythmia incidence in telemetry-implanted rats, under beta-adrenergic stimulation by isoproterenol (ISO). In total, 40 rats were implanted with radiotelemetry transmitters. First, dose escalation studies (40–160 mg/kg BGP-15), ECG parameters, and 24 h HRV parameters were assessed. After, rats were divided into Control, Control+BGP-15, ISO, and ISO+BGP-15 subgroups for 2 weeks. ECG recordings were obtained from conscious rats, arrhythmias and HRV parameters were assessed, and echocardiography was carried out. ISO-BGP-15 interaction was also evaluated on an isolated canine cardiomyocyte model. BGP-15 had no observable effects on the ECG waveforms; however, it decreased heart rate. HRV monitoring showed that BGP-15 increased RMSSD, SD1, and HF% parameters. BGP-15 failed to counteract 1 mg/kg ISO-induced tachycardia, but diminished the ECG of ischemia and suppressed ventricular arrhythmia incidence. Under echocardiography, after low-dose ISO injection, BGP-15 administration lowered HR and atrial velocities, and increased end-diastolic volume and ventricle relaxation, but did not counteract the positive inotropic effects of ISO. Two weeks of BGP-15 treatment also improved diastolic function in ISO-treated rats. In isolated cardiomyocytes, BGP-15 prevented 100 nM ISO-induced aftercontractions. Here, we show that BGP-15 increases vagally mediated HRV, reduces arrhythmogenesis, enhances left ventricle relaxation, and suppresses the aftercontractions of cardiomyocytes. As the drug is well tolerated, it may have a clinical value in preventing fatal arrhythmias.

Abstract Pituitary adenylate cyclase activating polypeptide (PACAP) is a regulatory and cytoprotective neuropeptide, its deficiency implies accelerated aging in mice. It is present in the auditory system having antiapoptotic effects. Expression of Ca2+-binding proteins and its PAC1 receptor differs in the inner ear of PACAP-deficient (KO) and wild-type (WT) mice. Our aim was to elucidate the functional role of PACAP in the auditory system. Auditory brainstem response (ABR) tests found higher hearing thresholds in KO mice at click and low frequency burst stimuli. Hearing impairment at higher frequencies showed as reduced ABR wave amplitudes and latencies in KO animals. Increase in neuronal activity, demonstrated by c-Fos immunolabeling, was lower in KO mice after noise exposure in the ventral and dorsal cochlear nuclei. Noise induced neuronal activation was similar in further relay nuclei of the auditory pathway of WT and KO mice. Based on the similar inflammatory and angiogenic protein profile data from cochlear duct lysates, neither inflammation nor disturbed angiogenesis, as potential pathological components in sensorineural hearing losses, seem to be involved in the pathomechanism of the presented functional and morphological changes in PACAP KO mice. The hearing impairment is probably concomitant with the markedly accelerated aging processes in these animals.

Voluntary isolation is one of the most effective methods for individuals to help prevent the transmission of diseases such as COVID-19. Understanding why people leave their homes when advised not to do so and identifying what contextual factors predict this non-compliant behavior is essential for policymakers and public health officials. To provide insight on these factors, we collected data from 42,169 individuals across 16 countries. Participants responded to items inquiring about their socio-cultural environment, such as the adherence of fellow citizens, as well as their mental states, such as their level of loneliness and boredom. We trained random forest models to predict whether someone had left their home during a one week period during which they were asked to voluntarily isolate themselves. The analyses indicated that overall, an increase in the feeling of being caged leads to an increased probability of leaving home. In addition, an increased feeling of responsibility and an increased fear of getting infected decreased the probability of leaving home. The models predicted compliance behavior with between 54% and 91% accuracy within each country's sample. In addition, we modeled factors leading to risky behavior in the pandemic context. We observed an increased probability of visiting risky places as both the anticipated number of people and the importance of the activity increased. Conversely, the probability of visiting risky places increased as the perceived putative effectiveness of social distancing decreased. The variance explained in our models predicting risk ranged from < .01 to .54 by country. Together, our findings can inform behavioral interventions to increase adherence to lockdown recommendations in pandemic conditions.

Sit-to-stand transitions are an important part of activities of daily living and play a key role in functional mobility in humans. The sit-to-stand movement is often affected in older adults due to frailty and in patients with motor impairments such as Parkinson’s disease leading to falls. Studying kinematics of sit-to-stand transitions can provide insight in assessment, monitoring and developing rehabilitation strategies for the affected populations. We propose a three-segment body model for estimating sit-to-stand kinematics using only two wearable inertial sensors, placed on the shank and back. Reducing the number of sensors to two instead of one per body segment facilitates monitoring and classifying movements over extended periods, making it more comfortable to wear while reducing the power requirements of sensors. We applied this model on 10 younger healthy adults (YH), 12 older healthy adults (OH) and 12 people with Parkinson’s disease (PwP). We have achieved this by incorporating unique sit-to-stand classification technique using unsupervised learning in the model based reconstruction of angular kinematics using extended Kalman filter. Our proposed model showed that it was possible to successfully estimate thigh kinematics despite not measuring the thigh motion with inertial sensor. We classified sit-to-stand transitions, sitting and standing states with the accuracies of 98.67%, 94.20% and 91.41% for YH, OH and PwP respectively. We have proposed a novel integrated approach of modelling and classification for estimating the body kinematics during sit-to-stand motion and successfully applied it on YH, OH and PwP groups.

Mortality from triple negative breast cancer (TNBC) is significantly higher in African American (AA) women compared to White American (WA) women emphasizing ethnicity as a major risk factor; however, the molecular determinants that drive aggressive progression of AA-TNBC remain elusive. Here, we demonstrate for the first time that AA-TNBC cells are inherently aggressive, exhibiting elevated growth, migration, and cancer stem-like phenotype compared to WA-TNBC cells. Meta-analysis of RNA-sequencing data of multiple AA- and WA-TNBC cell lines shows enrichment of GLI1 and Notch1 pathways in AA-TNBC cells. Enrichment of GLI1 and Notch1 pathway genes was observed in AA-TNBC. In line with this observation, analysis of TCGA dataset reveals a positive correlation between GLI1 and Notch1 in AA-TNBC and a negative correlation in WA-TNBC. Increased nuclear localization and interaction between GLI1 and Notch1 is observed in AA-TNBC cells. Of importance, inhibition of GLI1 and Notch1 synergistically improves the efficacy of chemotherapy in AA-TNBC cells. Combined treatment of AA-TNBC-derived tumors with GANT61, DAPT, and doxorubicin/carboplatin results in significant tumor regression, and tumor-dissociated cells show mitigated migration, invasion, mammosphere formation, and CD44+/CD24- population. Indeed, secondary tumors derived from triple-therapy-treated AA-TNBC tumors show diminished stem-like phenotype. Finally, we show that TNBC tumors from AA women express significantly higher level of GLI1 and Notch1 expression in comparison to TNBC tumors from WA women. This work sheds light on the racial disparity in TNBC, implicates the GLI1 and Notch1 axis as its functional mediators, and proposes a triple-combination therapy that can prove beneficial for AA-TNBC.

Any large dataset can be analyzed in a number of ways, and it is possible that the use of different analysis strategies will lead to different results and conclusions. One way to assess whether the results obtained depend on the analysis strategy chosen is to employ multiple analysts and leave each of them free to follow their own approach. Here, we present consensus-based guidance for conducting and reporting such multi-analyst studies, and we discuss how broader adoption of the multi-analyst approach has the potential to strengthen the robustness of results and conclusions obtained from analyses of datasets in basic and applied research.

Interleukin-1 beta (IL-1β) promotes liver disease progression and hepatocarcinogenesis in chronic hepatitis B (CHB). Single nucleotide polymorphisms (SNPs) within the promotor region of the IL-1β gene can affect the progression towards liver cirrhosis and hepatocellular carcinoma (HCC). Aims: We aimed to investigate the association of three common IL-1β SNPs with hepatitis B virus (HBV)-related HCC in Caucasian patients. Method: A Caucasian cohort of 99 patients with HBe antigen (Ag)-positive CHB, 255 patients with HBeAg-negative CHB and 278 inactive carriers (IC) were enrolled. 105 patients were diagnosed with liver cirrhosis, and 64 with HCC and cirrhosis. Genotyping of the IL-1β rs1143623, rs1143627 and rs16944 was performed. Results: The rs1143627 TT and rs16944 CC genotypes were more frequent in patients with HCC compared to patients without liver tumours (48% vs. 33%, p = 0.018 and 47% vs. 31%, p = 0.001, respectively). In multivariate analysis, the rs16944 CC genotype was independently associated with HCC (OR = 6.44 [95% CI 1.50–27.59] p = 0.012). The haplotype, including rs1143623 TT and rs16944 CC, was a risk factor for HCC development (OR = 1.55 [95% CI 1.04–2.32] p = 0.031). Conclusions: We identified an association of common IL-1β SNPs with HBV-related HCC in a Caucasian population. The effect was independent of the phases of chronic HBV infection, which are currently regarded as important HCC risk factors.

Background: Complicating the COVID-19 pandemic are the healthcare disparities experienced by ethnic minorities, especially those with comorbidities including cancer. The introduction of COVID-19 vaccines has been instrumental in blunting the morbidity and mortality from the pandemic; however, vaccine hesitancy, particularly among ethnic minorities, has been a major concern. Thus, we sought to evaluate the knowledge and perspectives of COVID-19 and vaccines among our ethnic minority cancer patient population. Methods: Following an IRB approved protocol, questionnaires were completed by patients in a predominantly ethnic minority population at a single institution between 1 February and 30 June 2021. Included were any adult cancer patients with either a solid or hematologic malignancy. Results: Among the 84 patients that were offered the questionnaires, 52 patients responded, with a median age of 63.5 years. Overall, 36% were non-Hispanic Blacks and 30% were Hispanics; 65% were receiving active treatment for their cancer. Seventy-nine percent believed COVID-19 to be dangerous or harmful to them, 61% were concerned about the side effects, yet 65% considered COVID-19 vaccines as safe. Among the seven patients that refused the vaccine, (71%, n = 5) cited side effects and/or (57%, n = 4) believed that the vaccine was not needed. Overall, there was a significantly higher chance of being vaccinated if patients were receiving active cancer treatment, believed COVID-19 was harmful, or that the vaccine was safe, and knew COVID-19 was a virus. Conclusions: This exploratory study demonstrates that most ethnic minority cancer patients are receptive to vaccines, with a majority being vaccinated. However, we also discovered various reasons why this group of patients may not want be vaccinated, including concerns about side effects and perception that COVID-19 is not harmful. These findings can help us further understand the complex nature of vaccine hesitancy in ethnic minority cancer patients, and aid in developing future vaccine awareness strategies as the COVID-19 pandemic continues to evolve.

Background: There is a lack of information as to which molecular processes, present at diagnosis, favor tumour escape from standard-of-care treatments in cervical cancer (CC). RAIDs consortium (www.raids-fp7.eu), conducted a prospectively monitored trial, [BioRAIDs (NCT02428842)] with the objectives to generate high quality samples and molecular assessments to stratify patient populations and to identify molecular patterns associated with poor outcome. Methods: Between 2013 and 2017, RAIDs collected a prospective CC sample and clinical dataset involving 419 participant patients from 18 centers in seven EU countries. Next Generation Sequencing has so far been carried out on a total of 182 samples from 377 evaluable (48%) patients, allowing to define dominant genetic alterations. Reverse phase protein expression arrays (RPPA) was applied to group patients into clusters. Activation of key genetic pathways and protein expression signatures were tested for associations with outcome. Findings: At a median follow up (FU) of 22 months, progression-free survival rates of this FIGO stage IB1-IV population, treated predominantly (87%) by chemoradiation, were65•4% [CI95%: 60•2-71.1]. Dominant oncogenic alterations were seen in PIK3CA (40%), while dominant suppressor gene alterations were seen in KMT2D (15%) and KMT2C (16%). Cumulative frequency of loss-of-function (LOF) mutations in any epigenetic modulator gene alteration was 47% and it was associated with PIK3CA gene alterations in 32%. Patients with tumours harboring alterations in both pathways had a significantly poorer PFS. A new finding was the detection of a high frequency of gains of TLR4 gene amplifications (10%), as well as amplifications, mutations, and non-frame-shift deletions of Androgen receptor (AR) gene in 7% of patients. Finally, RPPA protein expression analysis defined three expression clusters. Interpretation: Our data suggests that patient population may be stratified into four different treatment strategies based on molecular markers at the outset. Fund: European Union's Seventh Program grant agreement No 304810. Keywords: Bioraids study, Prospective database, Cervical cancers, Whole exome sequencing, Reverse phase protein array, Epigenetics pathways, PI3KCA, Patient stratification

Background: Aristotle’s tripartite concept of man—body, soul and spirit—formed the basis of the Galenic system that distinguished nurturing, vitalizing and animating tributary domains, governed by the liver, heart and brain, respectively. The Gothic cathedral structures into similar tripartite arrangements of nave, choir and sanctuary. We studied whether consistent parallels can be found between the Galenic concept of man, the Galenic heart itself and the structuring of the Gothic cathedral. Methods: Galenic literature along with scholastic texts were reviewed. Examples of Gothic cathedrals were visited and studied in locations. We used medieval analytical tools to compare characteristics of cathedral architecture and contemporary concepts on man and the heart. Results: Consistent parallels were found between the Galenic system and the structural parts of the Gothic cathedral. The principle of homology, intrinsic to both the Galenic system and Gothic architecture, identified the same tripartite organization in the Galenic heart itself and the segments could be projected onto the cathedral structure. Thus, the physical/nurturing domain was identified with the right ventricle inlet and the nave; the psychological/vitalizing domain corresponded with the right ventricle outlet/interventricular septum and the cathedral’s choir; the animating/spiritual domain paralleled with the left ventricle/aortic valve and the sanctuary in the cathedral. Conclusions: The Aristotelian/Galenic tripartite concept appears consistent with Gothic architecture and both provided a comprehensive view of the world; their relationship stems in a common philosophical and symbolic foundation. The tripartite interpretation was so coherent that it effectively delayed recognition of circulation and the heart’s role in it.

CIS43 is a potent neutralizing human mAb that targets a highly conserved “junctional” epitope in the Plasmodium falciparum (Pf) circumsporozoite protein (PfCSP). Enhancing the durability of CIS43 in vivo will be important for clinical translation. Here, 2 approaches were used to improve the durability of CIS43 in vivo while maintaining potent neutralization. First, the Fc domain was modified with the LS mutations (CIS43LS) to increase CIS43 binding affinity for the neonatal Fc receptor (FcRn). CIS43LS and CIS43 showed comparable in vivo protective efficacy. CIS43LS had 9- to 13-fold increased binding affinity for human (6.2 nM versus 54.2 nM) and rhesus (25.1 nM versus 325.8 nM) FcRn at endosomal pH 6.0 compared with CIS43. Importantly, the half-life of CIS43LS in rhesus macaques increased from 22 days to 39 days compared with CIS43. The second approach for sustaining antibody levels of CIS43 in vivo is through adeno-associated virus (AAV) expression. Mice administered once with AAV-expressing CIS43 had sustained antibody levels of approximately 300 μg/mL and mediated protection against sequential malaria challenges up to 36 weeks. Based on these data, CIS43LS has advanced to phase I clinical trials, and AAV delivery provides a potential next-generation approach for malaria prevention.

Water affordability is central to water access but remains a challenge to measure. California enshrined the human right to safe and affordable water in 2012 but the question remains: how should water affordability be measured across the state? This paper contributes to this question in three steps. First, we identify key dimensions of water affordability measures (including scale, volume of water needed to meet 'basic' needs, and affordability criteria) and a cross-cutting theme (social equity). Second, using these dimensions, we develop three affordability ratios measured at the water system scale for households with median, poverty level, and deep poverty (i.e., half the poverty level) incomes and estimate the corresponding percentage of households at these income levels. Using multiple measures conveys a fuller picture of affordability given the known limitations of specific affordability measures. Third, we analyze our results disaggregated by a key characteristic of water system vulnerability-water system size. We find that water is relatively affordable for median income households. However, we identify high unaffordability for households in poverty in a large fraction of water systems. We identify several scenarios with different policy implications for the human right to water, such as very small systems with high water bills and low-income households within large water systems. We also characterize how data gaps complicate theoretical ideals and present barriers in human right to water monitoring efforts. This paper presents a systematic approach to measuring affordability and represents the first statewide assessment of water affordability within California's community water systems.

Both the intake of beneficial olive oil and of harmful trans-fatty acids (TFAs) in consumed foods are of great significance in tumor biology. In our present study we examined the effects they exert on the expression patterns of miR-134, miR-132, miR-124-1, miR-9-3 and mTOR in the liver, spleen and kidney of mice treated with 7,12-dimethylbenz [a] anthracene (DMBA). Feeding of TFA-containing diet significantly increased the expression of all studied miRs and mTORC1 in all organs examined, except the expression of mTORC1 in the spleen and kidney. Diet containing olive oil significantly reduced the expression of miR-124-1, miR-9-3 and mTORC1 in the liver and spleen. In the kidney, apart from the mTORC1 gene, the expression of all miRs examined significantly decreased compared to the DMBA control. According to our results, the cell membrane protective, antioxidant, and anti-inflammatory effects of olive oil and the cell membrane damaging, inflammatory, and carcinogenic properties of TFA suggest negative feedback regulatory mechanisms. In contrast to our expectations, mTORC1 gene expression in the kidney has not been shown to be an appropriate biomarker-presumably, because the many complex effects that regulate mTOR expression may quench each other.

The intake of carcinogenic and chemopreventive compounds are important nutritional factors related to the development of malignant tumorous diseases. Repetitive long interspersed element-1 (LINE-1) DNA methylation pattern plays a key role in both carcinogenesis and chemoprevention. In our present in vivo animal model, we examined LINE-1 DNA methylation pattern as potential biomarker in the liver, spleen and kidney of mice consuming green tea (Camellia sinensis) extract (catechins 80%), a chinese bayberry (Morella rubra) extract (myricetin 80%), a flavonoid extract (with added resveratrol) and coffee (Coffee arabica) extract. In the organs examined, carcinogen 7,12-dimethylbenz(a)anthracene (DMBA)-induced hypomethylation was prevented by all test materials except chinese bayberry extract in the kidneys. Moreover, the flavonoid extract caused significant hypermethylation in the liver compared to untreated controls and to other test materials. The tested chemopreventive substances have antioxidant, anti-inflammatory properties and regulate molecular biological signaling pathways. They increase glutathione levels, induce antioxidant enzymes, which decrease free radical damage caused by DMBA, and ultimately, they are able to increase the activity of DNA methyltransferase enzymes. Furthermore, flavonoids in the liver may inhibit the procarcinogen to carcinogen activation of DMBA through the inhibition of CYP1A1 enzyme. At the same time, paradoxically, myricetin can act as a prooxidant as a result of free radical damage, which can explain that it did not prevent hypomethylation in the kidneys. Our results demonstrated that LINE-1 DNA methylation pattern is a useful potential biomarker for detecting and monitoring carcinogenic and chemopreventive effects of dietary compounds.

The flexibility allowed by the mobilization of technology disintegrated the traditional work-life boundary for most professionals. Whether working from home is the key or impediment to academics' efficiency and work-life balance became a daunting question for both scientists and their employers. The recent pandemic brought into focus the merits and challenges of working from home on a level of personal experience. Using a convenient sampling, we surveyed 704 academics while working from home and found that the pandemic lockdown decreased the work efficiency for almost half of the researchers but around a quarter of them were more efficient during this time compared to the time before. Based on the gathered personal experience, 70% of the researchers think that in the future they would be similarly or more efficient than before if they could spend more of their work-time at home. They indicated that in the office they are better at sharing thoughts with colleagues, keeping in touch with their team, and collecting data, whereas at home they are better at working on their manuscript, reading the literature, and analyzing their data. Taking well-being also into account, 66% of them would find it ideal to work more from home in the future than they did before the lockdown. These results draw attention to how working from home is becoming a major element of researchers' life and that we have to learn more about its influencer factors and coping tactics in order to optimize its arrangements.

Impaired exercise tolerance and lung function is a marker for increased mortality in lung cancer patients undergoing lung resection surgery. Recent data suggest that the gut-lung axis regulates systemic metabolic and immune functions, and microbiota might alter exercise tolerance. Here, we aimed to evaluate the associations between gut microbiota and outcomes in lung cancer patients who underwent lung resection surgery. We analysed stool samples, from 15 early-stage lung cancer patients, collected before and after surgical resection using shotgun metagenomic and Internal Transcribed Spacer (ITS) sequencing. We analysed microbiome and mycobiome associations with post-surgery lung function and cardiopulmonary exercise testing (CPET) to assess the maximum level of work achieved. There was a significant difference, between pre- and post-surgical resection samples, in microbial community functional profiles and several species from Alistipes and Bacteroides genus, associated with the production of SCFAs, increased significantly in abundance. Interestingly, an increase in VO2 coincides with an increase in certain species and the "GABA shunt" pathway, suggesting that treatment outcome might improve by enriching butyrate-producing species. Here, we revealed associations between specific gut bacteria, fungi, and their metabolic pathways with the recovery of lung function and exercise capacity.

BackgroundTorque teno virus (TTV) is a ubiquitous non-pathogenic virus, which is suppressed in immunological healthy individuals but replicates in immune compromised patients. Thus, TTV load is a suitable biomarker for monitoring the immunosuppression also in lung transplant recipients. Since little is known about the changes of TTV load in lung cancer patients, we analyzed TTV plasma DNA levels in lung cancer patients and its perioperative changes after lung cancer surgery.Material and methodsPatients with lung cancer and non-malignant nodules as control group were included prospectively. TTV DNA levels were measured by quantiative PCR using DNA isolated from patients plasma and correlated with routine circulating biomarkers and clinicopathological variables.Results47 patients (early stage lung cancer n = 30, stage IV lung cancer n = 10, non-malignant nodules n = 7) were included. TTV DNA levels were not detected in seven patients (15%). There was no significant difference between the stage IV cases and the preoperative TTV plasma DNA levels in patients with early stage lung cancer or non-malignant nodules (p = 0.627). While gender, tumor stage and tumor histology showed no correlation with TTV load patients below 65 years of age had a significantly lower TTV load then older patients (p = 0.022). Regarding routine blood based biomarkers, LDH activity was significantly higher in patients with stage IV lung cancer (p = 0.043), however, TTV load showed no correlation with LDH activity, albumin, hemoglobin, CRP or WBC. Comparing the preoperative, postoperative and discharge day TTV load, no unequivocal pattern in the kinetics were.ConclusionOur study suggest that lung cancer has no stage dependent impact on TTV plasma DNA levels and confirms that elderly patients have a significantly higher TTV load. Furthermore, we found no uniform perioperative changes during early stage lung cancer resection on plasma TTV DNA levels.

ABSTRACT: BACKGROUND: Cervical cancer (CC) remains a leading cause of gynaecological cancer-related mortality world wide and constitutes the third most common malignancy in women. The RAIDs consortium (http://www.raids-fp7.eu/) conducted a prospective European study [BioRAIDs (NCT02428842)] with the objective to stratify CC patients for innovative treatments. A “metagene” of genomic markers in the PI3K pathway and epigenetic regulators had been previously associated with poor outcome [2]. METHODS: To detect new, more specific, targets for treatment of patients who resist standard chemo-radiation, a high-dimensional Cox model was applied to define dominant molecular variants, copy number variations, and reverse phase protein arrays (RPPA). FINDINGS: Survival analysis on 89 patients with all omics data available, suggested loss-of-function (LOF) or activating molecular alterations in nine genes to be candidate biomarkers for worse prognosis in patients treated by chemo-radiation while LOF of ATRX, MED13 as well as CASP8 were associated with better prognosis. When protein expression data by RPPA were factored in, the supposedly low molecular weight and nuclear form, of beta-catenin, phosphorylated in Ser552 (pβ-Cat552), ranked highest for good prognosis, while pβ-Cat675 was associated with worse prognosis. INTERPRETATION: These findings call for molecularly targeted treatments involving p53, Wnt pathway, PI3K pathway, and epigenetic regulator genes. Pβ-Cat552 and pβ-Cat675 may be useful biomarkers to predict outcome to chemo-radiation, which targets the DNA repair axis. FUNDING: European Union's Seventh Program for research, technological development and demonstration (agreement N°304,810), the Fondation ARC pour la recherche contre le cancer.