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Abstract Background RNA interference is a gene regulatory mechanism that employs small RNA molecules such as microRNA. Previous work has shown that HIV-1 produces TAR viral microRNA. Here we describe the effects of the HIV-1 TAR derived microRNA on cellular gene expression. Results Using a variation of standard techniques we have cloned and sequenced both the 5' and 3' arms of the TAR miRNA. We show that expression of the TAR microRNA protects infected cells from apoptosis and acts by down-regulating cellular genes involved in apoptosis. Specifically, the microRNA down-regulates ERCC1 and IER3, protecting the cell from apoptosis. Comparison to our cloned sequence reveals possible target sites for the TAR miRNA as well. Conclusion The TAR microRNA is expressed in all stages of the viral life cycle, can be detected in latently infected cells, and represents a mechanism wherein the virus extends the life of the infected cell for the purpose of increasing viral replication.

Abstract Background Hodgkin's lymphoma (HL) survivors who undergo radiotherapy experience increased risks of second cancers (SC) and cardiac sequelae. To reduce such risks, extended-field radiotherapy (RT) for HL has largely been replaced by involved field radiotherapy (IFRT). While it has generally been assumed that IFRT will reduce SC risks, there are few data that quantify the reduction in dose to normal tissues associated with modern RT practice for patients with mediastinal HL, and no estimates of the expected reduction in SC risk. Methods Organ-specific dose-volume histograms (DVH) were generated for 41 patients receiving 35 Gy mantle RT, 35 Gy IFRT, or 20 Gy IFRT, and integrated organ mean doses were compared for the three protocols. Organ-specific SC risk estimates were estimated using a dosimetric risk-modeling approach, analyzing DVH data with quantitative, mechanistic models of radiation-induced cancer. Results Dose reductions resulted in corresponding reductions in predicted excess relative risks (ERR) for SC induction. Moving from 35 Gy mantle RT to 35 Gy IFRT reduces predicted ERR for female breast and lung cancer by approximately 65%, and for male lung cancer by approximately 35%; moving from 35 Gy IFRT to 20 Gy IFRT reduces predicted ERRs approximately 40% more. The median reduction in integral dose to the whole heart with the transition to 35 Gy IFRT was 35%, with a smaller (2%) reduction in dose to proximal coronary arteries. There was no significant reduction in thyroid dose. Conclusion The significant decreases estimated for radiation-induced SC risks associated with modern IFRT provide strong support for the use of IFRT to reduce the late effects of treatment. The approach employed here can provide new insight into the risks associated with contemporary IFRT for HL, and may facilitate the counseling of patients regarding the risks associated with this treatment.

Purpose/Objective(s): The purpose of this study was to retrospectively evaluate the dosimetric coverage of I-125 plaque brachytherapy (IBT) specific to juxtapapillary choroidal melanoma (JCM) using the Plaque Simulator treatment planning system. Materials and Methods: Thirty patients with medium-sized JCM treated using COMS IBT and loaded non-uniformly but with circular symmetry, were identified from a prospective database. The distance from the tumor edge to the optic disk ranged from 0.75-2.5 mm, the median tumour thickness and longest diameter was 4.3 mm and 9.9 mm, respectively. The proximity of the tumor to the optic nerve did not allow the round plaque to be centered over the tumor, so the tumor edge closest to the optic nerve did not receive the dose specified as per the COMS study. Initially these cases were planned with an in-house treatment planning system, and each case was replanned with the Plaque Simulator treatment planning system (BEBIG, Germany) for accurate dosimetric evaluations. Results: With all corrections for dose calculation "ON" in the Plaque Simulator, mean dose to the tumor edge nearestthe optic nerve was significantly lowerthan COMS recommendations (61 Gy vs. 69Gy, p<0.02). However, the tumour control rate was 90%, eye preservation rate was 90%, and rate of developing systemic metastases was 7%. Complications included cataract in 53%, neovascular glaucoma in 10%, retinopathy in 53%, and papillopathy in 33% of patients which was comparable to previously reported COMS outcomes. Conclusion Despite relative underdosing secondary to the physical impediment of the optic nerve for JCM, our results imply that the tumor edge may not need as high a dose as compared to the tumor apex. Disclosure: No significant relationships. [ABSTRACT FROM AUTHOR]

Proteogenomics is a growing "multi-omics" research area that combines mass spectrometry-based proteomics and high-throughput nucleotide sequencing technologies. Proteogenomics has helped in genomic annotation for organisms whose complete genome sequences became available by using high-throughput DNA sequencing technologies. Apart from genome annotation, this multi-omics approach has also helped researchers confirm expression of variant proteins belonging to unique proteoforms that could have resulted from single-nucleotide polymorphism (SNP), insertion and deletions (Indels), splice isoforms, or other genome or transcriptome variations.A proteogenomic study depends on a multistep informatics workflow, requiring different software at each step. These integrated steps include creating an appropriate protein sequence database, matching spectral data against these sequences, and finally identifying peptide sequences corresponding to novel proteoforms followed by variant classification and functional analysis. The disparate software required for a proteogenomic study is difficult for most researchers to access and use, especially those lacking computational expertise. Furthermore, using them disjointedly can be error-prone as it requires setting up individual parameters for each software. Consequently, reproducibility suffers. Managing output files from each software is an additional challenge. One solution for these challenges in proteogenomics is the open-source Web-based computational platform Galaxy. Its capability to create and manage workflows comprised of disparate software while recording and saving all important parameters promotes both usability and reproducibility. Here, we describe a workflow that can perform proteogenomic analysis on a Galaxy-based platform. This Galaxy workflow facilitates matching of spectral data with a customized protein sequence database, identifying novel protein variants, assessing quality of results, and classifying variants along with visualization against the genome., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Background: Fatigue leads to an acute decline in muscle strength, altered patterns of lower extremity muscle activation, changes in hip and knee kinematics. In terms of the effects of fatigue on knee joint kinematics during plyometric training, there is still a lack of knowledge regarding kinematic differences between athletes who passed the ACL reconstructions rehabilitation period and healthy athletes. Therefore, this study aimed to compare lower limb joint kinematic parameters between reconstructed cruciate ligament and healthy control soccer players during jump landing in a fatigued setting., Methods: Lower limb kinematic parameters were recorded in 20 professional soccer players (age, 24.95 ± 2.92 years; body mass, 77.20 ± 12.88 kg; height, 1.77 ± 3.19 m) during jump landing task before and after the fatigue protocol. The control group consisted of healthy subjects and the experimental group consisted of subjects with ACL reconstruction by thigh transplantation. Kinematic data was recorded with 4 cameras to measure lower limb angles at first foot contact and maximum range of motion., Results: The results showed that before fatigue, there was only a significant difference between the two groups in the maximum range of motion of the non-involved hip joint (P = 0.022) and angle of the involved hip at first contact (P = 0.049). In other data on joint range of motion or initial contact angle, no significant difference was observed between the two groups (P > 0.05). After fatigue protocol, there was a significant difference in initial foot contact in non-involved (P = 0.030), and involved (P = 0.020) hip joint angles between the two groups. However, no significant difference in initial contact angle or range of motion of other joints was observed between the groups., Conclusions: This study shows that plyometric fatigue does not contribute to numerous changes in contact angles and range of motion in lower extremity joints in healthy soccer players and those with a history of cruciate ligament repairs., (© 2024. The Author(s).)

Blastocystis is the most common gastrointestinal protozoan parasite of humans and many vertebrates. This study was carried out to investigate the prevalence and determination subtype (ST) of Blastocystis in domestic ruminants of Shahrekord County, southwestern Iran. In this descriptive cross-sectional study, 330 ruminant fecal samples (107 cows, 115 sheep, and 108 goats) were evaluated by parasitological methods (direct wet mount microscopic examination and formalin-ether concentration), Giemsa staining, In vitro xenic culture (The modified Dobell and Laidlaw culture method), polymerase chain reaction, and sequencing from 2018 to 2019, then data were analyzed using SPSS software version 21. The overall Blastocystis positive in ruminants was 14.2% and the frequency of Blastocystis sp. in cattle, sheep, and goats were 0.93%, 17.4%, and 24.1% respectively. Molecular diagnosis techniques revealed that ruminants were infected with four STs (genotypes) of Blastocystis including ST5(21.3%), ST7(2.1%), ST10(17.1%) and ST14(57.4%). Also, the STs identified in cows were ST10, and the observed STs in sheep were ST5 (40%), ST7 (3%), ST10 (5%), ST14 (45%), and one unknown subspecies. Goats were infected by ST5 (7.7%), ST10 (23.1%), and ST14 (69.2%). In this study, ST14 was identified as the most common subtype of Blastocystis sp. that was not common between humans and livestock, meanwhile, ST5 and ST7 are common between humans and animals accounted 21.3% and 2.1% of the positive cases, respectively, and reinforces the hypothesis that ruminants are reservoirs of blastocystosis in humans., (© 2024. The Author(s).)

Introduction: Environmental pollutants injure the mucociliary elevator, thereby provoking disease progression in chronic obstructive pulmonary disease (COPD). Epithelial resilience mechanisms to environmental nanoparticles in health and disease are poorly characterised., Methods: We delineated the impact of prevalent pollutants such as carbon and zinc oxide nanoparticles, on cellular function and progeny in primary human bronchial epithelial cells (pHBECs) from end-stage COPD (COPD-IV, n=4), early disease (COPD-II, n=3) and pulmonary healthy individuals (n=4). After nanoparticle exposure of pHBECs at air-liquid interface, cell cultures were characterised by functional assays, transcriptome and protein analysis, complemented by single-cell analysis in serial samples of pHBEC cultures focusing on basal cell differentiation., Results: COPD-IV was characterised by a prosecretory phenotype (twofold increase in MUC5AC + ) at the expense of the multiciliated epithelium (threefold reduction in Ac-Tub + ), resulting in an increased resilience towards particle-induced cell damage (fivefold reduction in transepithelial electrical resistance), as exemplified by environmentally abundant doses of zinc oxide nanoparticles. Exposure of COPD-II cultures to cigarette smoke extract provoked the COPD-IV characteristic, prosecretory phenotype. Time-resolved single-cell transcriptomics revealed an underlying COPD-IV unique basal cell state characterised by a twofold increase in KRT5 + ( P =0.018) and LAMB3 + ( P =0.050) expression, as well as a significant activation of Wnt-specific ( P =0.014) and Notch-specific ( P =0.021) genes, especially in precursors of suprabasal and secretory cells., Conclusion: We identified COPD stage-specific gene alterations in basal cells that affect the cellular composition of the bronchial elevator and may control disease-specific epithelial resilience mechanisms in response to environmental nanoparticles. The identified phenomena likely inform treatment and prevention strategies., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Pulmonary vascular disease (PVD) affects the majority of preterm neonates with bronchopulmonary dysplasia (BPD) and significantly determines long-term mortality through undetected progression into pulmonary hypertension. Our objectives were to associate characteristics of pulmonary artery (PA) flow and cardiac function with BPD-associated PVD near term using advanced magnetic resonance imaging (MRI) for improved risk stratification., Methods: Preterms <32 weeks postmenstrual age (PMA) with/without BPD were clinically monitored including standard echocardiography and prospectively enrolled for 3 T MRI in spontaneous sleep near term (AIRR (Attention to Infants at Respiratory Risks) study). Semi-manual PA flow quantification (phase-contrast MRI; no BPD n=28, mild BPD n=35 and moderate/severe BPD n=25) was complemented by cardiac function assessment (cine MRI)., Results: We identified abnormalities in PA flow and cardiac function, i.e. increased net forward volume right/left ratio, decreased mean relative area change and pathological right end-diastolic volume, to sensitively detect BPD-associated PVD while correcting for PMA (leave-one-out area under the curve 0.88, sensitivity 0.80 and specificity 0.81). We linked these changes to increased right ventricular (RV) afterload (RV-arterial coupling (p=0.02), PA mid-systolic notching (t2; p=0.015) and cardiac index (p=1.67×10 -8 )) and correlated echocardiographic findings. Identified in moderate/severe BPD, we successfully applied the PA flow model in heterogeneous mild BPD cases, demonstrating strong correlation of PVD probability with indicators of BPD severity, i.e. duration of mechanical ventilation (r s =0.63, p=2.20×10 -4 ) and oxygen supplementation (r s =0.60, p=6.00×10 -4 )., Conclusions: Abnormalities in MRI PA flow and cardiac function exhibit significant, synergistic potential to detect BPD-associated PVD, advancing the possibilities of risk-adapted monitoring., Competing Interests: Conflict of interest: No authors have any potential conflicts of interest to disclose., (Copyright ©The authors 2023.)

The efficiency of perovskite/silicon tandem solar cells has exceeded the previous record for III-V-based dual-junction solar cells. This shows the high potential of perovskite solar cells in multi-junction applications. Perovskite/perovskite/silicon triple-junction solar cells are now the next step to achieve efficient and low-cost multi-junction solar cells with an efficiency potential even higher than that for dual-junction solar cells. Here we present a perovskite/perovskite/silicon triple-junction solar cell with an open circuit voltage of >2.8 V, which is the record value reported for this structure so far. This is achieved through employing a gas quenching method for deposition of the top perovskite layer as well as optimization of interlayers between perovskite subcells. Moreover, for the measurement of our triple-junction solar cells, precise measurement procedures are implemented to ensure the reliability and accuracy of the reported values., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

The development of chronic lung disease in the neonate, also known as bronchopulmonary dysplasia (BPD), is the most common long-term complication in prematurely born infants. In BPD, the disease-characteristic inflammatory response culminates in nonreversible remodeling of the developing gas exchange area, provoked by the impact of postnatal treatments such as mechanical ventilation (MV) and oxygen treatment. To evaluate the potential of prenatal treatment regimens to modulate this inflammatory response and thereby impact the vulnerability of the lung toward postnatal injury, we designed a multilayered preclinical mouse model. After administration of either prenatal vitamin D-enriched (VitD+; 1,500 IU/g food) or -deprived (VitD-; <10 IU/kg) food during gestation in C57B6 mice (the onset of mating until birth), neonatal mice were exposed to hyperoxia (Fi O 2 = 0.4) with or without MV for 8 h at days 5-7 of life, whereas controls spontaneously breathed room air. Prenatal vitamin D supplementation resulted in a decreased number of monocytes/macrophages in the neonatal lung undergoing postnatal injury together with reduced TGF-β pathway activation. In consequence, neonatal mice that received a VitD+ diet during gestation demonstrated less extracellular matrix (ECM) remodeling upon lung injury, reflected by the reduction of pulmonary α-smooth muscle actin-positive fibroblasts, decreased collagen and elastin deposition, and lower amounts of interstitial tissue in the lung periphery. In conclusion, our findings support strategies that attempt to prevent vitamin D insufficiency during pregnancy as they could impact lung health in the offspring by mitigating inflammatory changes in neonatal lung injury and ameliorating subsequent remodeling of the developing gas exchange area. NEW & NOTEWORTHY Vitamin D-enriched diet during gestation resulted in reduced lung inflammation and matrix remodeling in neonatal mice exposed to clinically relevant, postnatal injury. The results underscore the need to monitor the subclinical effects of vitamin D insufficiency that impact health in the offspring when other risk factors come into play.

Introduction: Inflammation is a key driver of morbidity in the vulnerable preterm infant exposed to pre- and postnatal hazards and significantly contributes to chronic lung disease, i.e. bronchopulmonary dysplasia (BPD). However, the early changes in innate immunity associated with BPD development are incompletely understood., Methods: In very immature preterm infants below 32 weeks gestational age (GA; n=30 infants), monocyte subtypes were identified by Flow Cytometry at birth and throughout the postnatal course including intracellular TNF expression upon LPS stimulation. Complementing these measurements, cytokine end growth factor expression profiles (Luminex ® xMAP ® ; n=110 infants) as well as gene expression profiles (CodeLink TM Human I Bioarray; n=22) were characterized at birth., Results: The abundance of monocyte subtypes differed between preterm and term neonates at birth. Specifically, CD14 ++ CD16 + (intermediate) monocytes demonstrated a dependency on PMA and elevated levels of nonclassical (CD14 + CD16 ++ ) monocytes characterized preterm infants with developing BPD. Postnatally, lung injury was associated with an increase in intermediate monocytes, while high levels of nonclassical monocytes persisted. Both subtypes were revealed as the main source of intracellular TNF-α expression in the preterm infant. We identified a cytokine and growth factor expression profile in cord blood specimen of preterm infants with developing BPD that corresponded to the disease-dependent regulation of monocyte abundances. Multivariate modeling of protein profiles revealed FGF2, sIL-2 Rα, MCP-1, MIP1a, and TNF-α as predictors of BPD when considering GA. Transcriptome analysis demonstrated genes predicting BPD to be overrepresented in inflammatory pathways with increased disease severity characterized by the regulation of immune and defense response pathways and upstream regulator analysis confirmed TNF-α, interleukin (IL) -6, and interferon α as the highest activated cytokines in more severe disease. Whereas all BPD cases showed downstream activation of chemotaxis and activation of inflammatory response pathways , more severe cases were characterized by an additional activation of reactive oxygen species (ROS) synthesis., Discussion: In the present study, we identified the early postnatal presence of nonclassical (CD14 + CD16 ++ ) and intermediate (CD14 ++ CD16 + ) monocytes as a critical characteristic of BPD development including a specific response pattern of monocyte subtypes to lung injury. Pathophysiological insight was provided by the protein and transcriptome signature identified at birth, centered around monocyte and corresponding granulocyte activation and highlighting TNFα as a critical regulator in infants with developing BPD. The disease severity-dependent expression patterns could inform future diagnostic and treatment strategies targeting the monocytic cell and its progeny., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Windhorst, Heydarian, Schwarz, Oak, Förster, Frankenberger, Gonzalez Rodriguez, Zhang, Ehrhardt, Hübener, Flemmer, Hossain, Stoeger, Schulz and Hilgendorff.)

High mobility group A1 (HMGA1) chromatin regulators are upregulated in diverse tumors where they portend adverse outcomes, although how they function in cancer remains unclear. Pancreatic ductal adenocarcinomas (PDACs) are highly lethal tumors characterized by dense desmoplastic stroma composed predominantly of cancer-associated fibroblasts and fibrotic tissue. Here, we uncover an epigenetic program whereby HMGA1 upregulates FGF19 during tumor progression and stroma formation. HMGA1 deficiency disrupts oncogenic properties in vitro while impairing tumor inception and progression in KPC mice and subcutaneous or orthotopic models of PDAC. RNA sequencing revealed HMGA1 transcriptional networks governing proliferation and tumor-stroma interactions, including the FGF19 gene. HMGA1 directly induces FGF19 expression and increases its protein secretion by recruiting active histone marks (H3K4me3, H3K27Ac). Surprisingly, disrupting FGF19 via gene silencing or the FGFR4 inhibitor BLU9931 recapitulates most phenotypes observed with HMGA1 deficiency, decreasing tumor growth and formation of a desmoplastic stroma in mouse models of PDAC. In human PDAC, overexpression of HMGA1 and FGF19 defines a subset of tumors with extremely poor outcomes. Our results reveal what we believe is a new paradigm whereby HMGA1 and FGF19 drive tumor progression and stroma formation, thus illuminating FGF19 as a rational therapeutic target for a molecularly defined PDAC subtype.

SARS-CoV-2 remains an acute threat to human health, endangering hospital capacities worldwide. Previous studies have aimed at informing pathophysiologic understanding and identification of disease indicators for risk assessment, monitoring, and therapeutic guidance. While findings start to emerge in the general population, observations in high-risk patients with complex pre-existing conditions are limited. We addressed the gap of existing knowledge with regard to a differentiated understanding of disease dynamics in SARS-CoV-2 infection while specifically considering disease stage and severity. We biomedically characterized quantitative proteomics in a hospitalized cohort of COVID-19 patients with mild to severe symptoms suffering from different (co)-morbidities in comparison to both healthy individuals and patients with non-COVID related inflammation. Deep clinical phenotyping enabled the identification of individual disease trajectories in COVID-19 patients. By the use of the individualized disease phase assignment, proteome analysis revealed a severity dependent general type-2-centered host response side-by-side with a disease specific antiviral immune reaction in early disease. The identification of phenomena such as neutrophil extracellular trap (NET) formation and a pro-coagulatory response characterizing severe disease was successfully validated in a second cohort. Together with the regulation of proteins related to SARS-CoV-2-specific symptoms identified by proteome screening, we not only confirmed results from previous studies but provide novel information for biomarker and therapy development., Competing Interests: Declaration of competing interest The authors declare no conflict of interest apart from Clemens Scherer, who received speaker honoraria from AstraZeneca, outside the submitted work. All authors were involved in the decision to publish and reviewed the article before submission. The authors declare no conflict of interest apart from Clemens Scherer, who received speaker honoraria from AstraZeneca, outside the submitted work., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Introduction: Chronic lung disease, that is, bronchopulmonary dysplasia (BPD) is the most common complication in preterm infants and develops as a consequence of the misguided formation of the gas-exchange area undergoing prenatal and postnatal injury. Subsequent vascular disease and its progression into pulmonary arterial hypertension critically determines long-term outcome in the BPD infant but lacks identification of early, disease-defining changes., Methods: We link impaired bone morphogenetic protein (BMP) signalling to the earliest onset of vascular pathology in the human preterm lung and delineate the specific effects of the most prevalent prenatal and postnatal clinical risk factors for lung injury mimicking clinically relevant conditions in a multilayered animal model using wild-type and transgenic neonatal mice., Results: We demonstrate (1) the significant reduction in BMP receptor 2 (BMPR2) expression at the onset of vascular pathology in the lung of preterm infants, later mirrored by reduced plasma BMP protein levels in infants with developing BPD, (2) the rapid impairment (and persistent change) of BMPR2 signalling on postnatal exposure to hyperoxia and mechanical ventilation, aggravated by prenatal cigarette smoke in a preclinical mouse model and (3) a link to defective alveolar septation and matrix remodelling through platelet derived growth factor-receptor alpha deficiency. In a treatment approach, we partially reversed vascular pathology by BMPR2-targeted treatment with FK506 in vitro and in vivo., Conclusion: We identified impaired BMP signalling as a hallmark of early vascular disease in the injured neonatal lung while outlining its promising potential as a future biomarker or therapeutic target in this growing, high-risk patient population., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

In the neonatal lung, exposure to both prenatal and early postnatal risk factors converge into the development of injury and ultimately chronic disease, also known as bronchopulmonary dysplasia (BPD). The focus of many studies has been the characteristic inflammatory responses provoked by these exposures. Here, we review the relationship between immaturity and prenatal conditions, as well as postnatal exposure to mechanical ventilation and oxygen toxicity, with the imbalance of pro- and anti-inflammatory regulatory networks. In these conditions, cytokine release, protease activity, and sustained presence of innate immune cells in the lung result in pathologic processes contributing to lung injury. We highlight the recruitment and function of myeloid innate immune cells, in particular, neutrophils and monocyte/macrophages in the BPD lung in human patients and animal models. We also discuss dissimilarities between the infant and adult immune system as a basis for the development of novel therapeutic strategies., (© 2022. The Author(s).)

Background: The "Coronavirus Disease 2019" (COVID-19) pandemic has become a major challenge for all healthcare systems worldwide, and besides generating a high toll of deaths, it has caused economic losses. Hospitals have played a key role in providing services to patients and the volume of hospital activities has been refocused on COVID-19 patients. Other activities have been limited/repurposed or even suspended and hospitals have been operating with reduced capacity. With the decrease in non-COVID-19 activities, their financial system and sustainability have been threatened, with hospitals facing shortage of financial resources. The aim of this study was to investigate the effects of COVID-19 on the revenues of public hospitals in Lorestan province in western Iran, as a case study., Method: In this quasi-experimental study, we conducted the interrupted time series analysis to evaluate COVID-19 induced changes in monthly revenues of 18 public hospitals, from April 2018 to August 2021, in Lorestan, Iran. In doing so, public hospitals report their earnings to the University of Medical Sciences monthly; then, we collected this data through the finance office., Results: Due to COVID-19, the revenues of public hospitals experienced an average monthly decrease of $172,636 thousand (P-value = 0.01232). For about 13 months, the trend of declining hospital revenues continued. However, after February 2021, a relatively stable increase could be observed, with patient admission and elective surgeries restrictions being lifted. The average monthly income of hospitals increased by $83,574 thousand., Conclusion: COVID-19 has reduced the revenues of public hospitals, which have faced many problems due to the high costs they have incurred. During the crisis, lack of adequate fundings can damage healthcare service delivery, and policymakers should allocate resources to prevent potential shocks., Competing Interests: All authors declare that there are no conflicts of interest.

Ovarian cancer is the second most common gynecological malignancy in women. More than 70% of the cases are diagnosed at the advanced stage, presenting as primary peritoneal metastasis, which results in a poor 5-year survival rate of around 40%. Mechanisms of peritoneal metastasis, including adhesion, migration, and invasion, are still not completely understood and therapeutic options are extremely limited. Therefore, there is a strong requirement for a 3D model mimicking the in vivo situation. In this study, we describe the establishment of a 3D tissue model of the human peritoneum based on decellularized porcine small intestinal submucosa (SIS) scaffold. The SIS scaffold was populated with human dermal fibroblasts, with LP-9 cells on the apical side representing the peritoneal mesothelium, while HUVEC cells on the basal side of the scaffold served to mimic the endothelial cell layer. Functional analyses of the transepithelial electrical resistance (TEER) and the FITC-dextran assay indicated the high barrier integrity of our model. The histological, immunohistochemical, and ultrastructural analyses showed the main characteristics of the site of adhesion. Initial experiments using the SKOV-3 cell line as representative for ovarian carcinoma demonstrated the usefulness of our models for studying tumor cell adhesion, as well as the effect of tumor cells on endothelial cell-to-cell contacts. Taken together, our data show that the novel peritoneal 3D tissue model is a promising tool for studying the peritoneal dissemination of ovarian cancer., Competing Interests: Declaration of conflicting interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2022.)

Neisseria gonorrhoeae is a human-specific pathogen that causes gonorrhea, the second most common sexually transmitted infection worldwide. Disease progression, drug discovery, and basic host-pathogen interactions are studied using different approaches, which rely on models ranging from 2D cell culture to complex 3D tissues and animals. In this review, we discuss the models used in N. gonorrhoeae research. We address both in vivo (animal) and in vitro cell culture models, discussing the pros and cons of each and outlining the recent advancements in the field of three-dimensional tissue models. From simple 2D monoculture to complex advanced 3D tissue models, we provide an overview of the relevant methodology and its application. Finally, we discuss future directions in the exciting field of 3D tissue models and how they can be applied for studying the interaction of N. gonorrhoeae with host cells under conditions closely resembling those found at the native sites of infection., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Heydarian, Rühl, Rawal and Kozjak-Pavlovic.)

Objective: Severe acute respiratory syndrome coronavirus 2 (SARS-COV2) was first detected in Wuhan, China in December, 2019. The emerging virus causes a respiratory illness, that can trigger a cytokine storm in the body., Method: Cytokine storm in patient's body is associated with severe forms of disease. It is one of the main complications of coronavirus disease-2019 (COVID-19), in which immune cells play a major role. Studies have shown immune cells in the tumor environment can be effective to induce resistance to chemotherapy in cancer patients., Result: Therefore, considering the role of immune cells to induce cytokine storm in COVID-19 patients, and their role to cause resistance to chemotherapy, they are effective on disease progression and creation of severe form of disease., Conclusion: By examining the signaling pathways and inducing resistance to chemotherapy in tumor cells and the cells affect them, it is possible to prevent the occurrence of severe forms of the disease in cancer patients with COVID-19; it is applicable using target therapy and other subsequent treatment strategies., (© 2021. The Author(s), under exclusive licence to Springer Nature B.V.)

Background: In February 2020, the Ministry of Health and Medical Education in Iran announced the first case of COVID-19. The aim of this study was to investigate the impact of COVID-19 on the number of CT-Scans and MRI services in public hospitals in western Iran., Methods: We collected CT-scans and MRI services data from 18 public hospitals via Vice-Chancellor Office, Lorestan University of Medical Sciences from January 2017 to February 2021. Interrupted time series analysis (ITSA) was conducted to assess the impact of COVID-19 on CT-Scans and MRI services. More specifically, ITSA was conducted using ordinary least squares regression with the number of CT-Scans and MRI services per 1,000 registered persons per month as dependent variable., Results: At the beginning of the observation period, the monthly rate of CT-Scans was constant (p for trend = 0.267) at 291.9 (from 95%CI 240.5 to 343.4) per 1,000 registered patients. The first case of COVID-19 coincided with an abrupt increase by 211.8 (from 95%CI 102.9 to 320.7) per 1,000 patients. Thereafter, the trend of CT-Scans did not change (p=0.576) compared to the pre-pandemic period. The rate of MRI services was 363.5 per 1,000 per registered patients per month (P = <0.0001) with a slightly decreasing trend (coefficient=-5; 95%CI, -6.9 to -3.1)., Conclusion: The findings of this study showed that crises such as COVID-19 can affect the service delivery process. Health policymakers and decision makers should work to prevent potential reductions in health care during events such as COVID-19., (© 2021 Mohammad H. et al.)

Gonorrhea, a sexually transmitted disease caused by the bacteria Neisseria gonorrhoeae , is characterized by a large number of neutrophils recruited to the site of infection. Therefore, proper modeling of the N. gonorrhoeae interaction with neutrophils is very important for investigating and understanding the mechanisms that gonococci use to evade the immune response. We have used a combination of a unique human 3D tissue model together with a dynamic culture system to study neutrophil transmigration to the site of N. gonorrhoeae infection. The triple co-culture model consisted of epithelial cells (T84 human colorectal carcinoma cells), human primary dermal fibroblasts, and human umbilical vein endothelial cells on a biological scaffold (SIS). After the infection of the tissue model with N. gonorrhoeae , we introduced primary human neutrophils to the endothelial side of the model using a perfusion-based bioreactor system. By this approach, we were able to demonstrate the activation and transmigration of neutrophils across the 3D tissue model and their recruitment to the site of infection. In summary, the triple co-culture model supplemented by neutrophils represents a promising tool for investigating N. gonorrhoeae and other bacterial infections and interactions with the innate immunity cells under conditions closely resembling the native tissue environment., Competing Interests: Declaration of conflicting interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2021.)

Background: The vast ecosystem of single-cell RNA-sequencing tools has until recently been plagued by an excess of diverging analysis strategies, inconsistent file formats, and compatibility issues between different software suites. The uptake of 10x Genomics datasets has begun to calm this diversity, and the bioinformatics community leans once more towards the large computing requirements and the statistically driven methods needed to process and understand these ever-growing datasets., Results: Here we outline several Galaxy workflows and learning resources for single-cell RNA-sequencing, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The Galaxy reproducible bioinformatics framework provides tools, workflows, and trainings that not only enable users to perform 1-click 10x preprocessing but also empower them to demultiplex raw sequencing from custom tagged and full-length sequencing protocols. The downstream analysis supports a range of high-quality interoperable suites separated into common stages of analysis: inspection, filtering, normalization, confounder removal, and clustering. The teaching resources cover concepts from computer science to cell biology. Access to all resources is provided at the singlecell.usegalaxy.eu portal., Conclusions: The reproducible and training-oriented Galaxy framework provides a sustainable high-performance computing environment for users to run flexible analyses on both 10x and alternative platforms. The tutorials from the Galaxy Training Network along with the frequent training workshops hosted by the Galaxy community provide a means for users to learn, publish, and teach single-cell RNA-sequencing analysis., (© The Author(s) 2020. Published by Oxford University Press GigaScience.)

Background: Change in the lower extremity alignments in the frontal plane and muscle activation patterns have been associated with lower extremity injuries. Therefore, to prevent injuries, many therapeutic protocols focus on find ways to correct dynamic knee valgus (DKV)., Methods: Thirty-one recreational male cyclists with DKV (26.4 ± 4.5 years, 176.63 ± 7.51 cm, 75.81 ± 9.29 kg, 23.20 ± 4.15 kg/m2) volunteered to participate in this study. Simultaneous recordings of kinematic and electromyography data were performed on ten consecutive pedal cycles which began during the last 30 seconds of each four test condition: with band at 0.5 kg workload, with band at 2 kg workload, without band at 0.5 kg workload, and without band at 2 kg workload. The paired t-test was used for statistical analysis (p < 0.05)., Results: The results indicated significant differences in VM (band = 0.029, no band = 0.031) and VL (band = 0.015, no band = 0.035) activation between workloads in each condition. Also there were significant differences in Gmed activation (0.5kg = 0.001, 2kg = 0.037), onset of Gmed (0.5kg = 0.048, 2kg = 0.012), offset of Gmed (0.5kg = 0.048, 2kg = 0.015), TFL activation (0.5kg = 0.001, 2kg = 0.041) and offset of TFL (0.5kg = 0.078, 2kg = 0.005) between the band and no band conditions. There was no different significant in VM/VL ratio between in each of four testing conditions (p > 0.05). The Gmed/TFL ratio was significantly greater in band condition than no band at both 0.5 (p = 0.045) and 2 kg (p = 0.001) workload. Knee abduction angle was affected by the band loop during the pedaling at two different workloads (0.5 kg: p = 0.047, 2 kg: p = 0.021) but mean (p = 0.027) and peak (p = 0.033) knee abduction angle significantly increased with increasing workload during the pedaling with band loop., Conclusions: pedaling with the band loop can be considered as an effective method to increase the Gmed, Gmed/TFL ratio and control of DKV but increasing the workload during pedaling must be done with caution to prevent DKV., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Neisseria gonorrhoeae , a Gram-negative obligate human pathogenic bacterium, infects human epithelial cells and causes sexually transmitted diseases. Emerging multi-antibiotic resistant gonococci and increasing numbers of infections complicate the treatment of infected patients. Here, we used an shRNA library screen and next-generation sequencing to identify factors involved in epithelial cell infection. Folliculin (FLCN), a 64 kDa protein with a tumor repressor function was identified as a novel host factor important for N. gonorrhoeae survival after uptake. We further determined that FLCN did not affect N. gonorrhoeae adherence and invasion but was essential for its survival in the cells by modulating autophagy. In addition, FLCN was also required to maintain cell to cell contacts in the epithelial layer. In an infection model with polarized cells, FLCN inhibited the polarized localization of E-cadherin and the transcytosis of gonococci across polarized epithelial cells. In conclusion, we demonstrate here the connection between FLCN and bacterial infection and in particular the role of FLCN in the intracellular survival and transcytosis of gonococci across polarized epithelial cell layers., (Copyright © 2020 Yang, Heydarian, Kozjak-Pavlovic, Urban, Harbottle and Rudel.)

Gonorrhea is the second most common sexually transmitted infection in the world and is caused by Gram-negative diplococcus Neisseria gonorrhoeae . Since N. gonorrhoeae is a human-specific pathogen, animal infection models are only of limited use. Therefore, a suitable in vitro cell culture model for studying the complete infection including adhesion, transmigration and transport to deeper tissue layers is required. In the present study, we generated three independent 3D tissue models based on porcine small intestinal submucosa (SIS) scaffold by co-culturing human dermal fibroblasts with human colorectal carcinoma, endometrial epithelial, and male uroepithelial cells. Functional analyses such as transepithelial electrical resistance (TEER) and FITC-dextran assay indicated the high barrier integrity of the created monolayer. The histological, immunohistochemical, and ultra-structural analyses showed that the 3D SIS scaffold-based models closely mimic the main characteristics of the site of gonococcal infection in human host including the epithelial monolayer, the underlying connective tissue, mucus production, tight junction, and microvilli formation. We infected the established 3D tissue models with different N. gonorrhoeae strains and derivatives presenting various phenotypes regarding adhesion and invasion. The results indicated that the disruption of tight junctions and increase in interleukin production in response to the infection is strain and cell type-dependent. In addition, the models supported bacterial survival and proved to be better suitable for studying infection over the course of several days in comparison to commonly used Transwell® models. This was primarily due to increased resilience of the SIS scaffold models to infection in terms of changes in permeability, cell destruction and bacterial transmigration. In summary, the SIS scaffold-based 3D tissue models of human mucosal tissues represent promising tools for investigating N. gonorrhoeae infections under close-to-natural conditions.

Next-generation sequencing technologies, coupled to advances in mass-spectrometry-based proteomics, have facilitated system-wide quantitative profiling of expressed mRNA transcripts and proteins. Proteo-transcriptomic analysis compares the relative abundance levels of transcripts and their corresponding proteins, illuminating discordant gene product responses to perturbations. These results reveal potential post-transcriptional regulation, providing researchers with important new insights into underlying biological and pathological disease mechanisms. To carry out proteo-transcriptomic analysis, researchers require software that statistically determines transcript-protein abundance correlation levels and provides results visualization and interpretation functionality, ideally within a flexible, user-friendly platform. As a solution, we have developed the QuanTP software within the Galaxy platform. The software offers a suite of tools and functionalities critical for proteo-transcriptomics, including statistical algorithms for assessing the correlation between single transcript-protein pairs as well as across two cohorts, outlier identification and clustering, along with a diverse set of results visualizations. It is compatible with analyses of results from single experiment data or from a two-cohort comparison of aggregated replicate experiments. The tool is available in the Galaxy Tool Shed through a cloud-based instance and a Docker container. In all, QuanTP provides an accessible and effective software resource, which should enable new multiomic discoveries from quantitative proteo-transcriptomic data sets.

In this study, the extracting parameters of crude polysaccharides (CPSs) from the Hypericum perforatum (HP) including extraction time (ETi, 60-180min), extraction temperature (ETe, 60-90°C), and the water/solid ratio (W/S, 10-30 was optimized by using three-variable-three-level Box-Behnken design-response surface methodology (BBD-RSM) based on the single-factor experiments. The optimal extraction conditions were as follow: ETi 117.5min, ETe 74.28°C, and W/S 20.3:1. Under these conditions, the experimental yield was 6.69%. Fourier transform-infrared spectroscopy (FT-IR) was used to identify structure of polysaccharide extracted at the optimal operating point. HP-CPSs was proved to possess antioxidant activities including 2, 2-diphenyl-1-picrylhydrazyl (DPPH) and OH free-radicals scavenging activates in vitro. The antibacterial activities of HP-CPSs against Escherichia coli, Shigella dysenteriae and Salmonella typhi, Bacillus cereus and Staphylococcus aureus were evaluated by determining clear growth inhibition zone diameters and by essays in liquid media. Overall, the results indicated that those polysaccharides could offer promising sources of polysaccharides for future application as antioxidant ingredients in the food industry., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Proteogenomics has emerged as a valuable approach in cancer research, which integrates genomic and transcriptomic data with mass spectrometry-based proteomics data to directly identify expressed, variant protein sequences that may have functional roles in cancer. This approach is computationally intensive, requiring integration of disparate software tools into sophisticated workflows, challenging its adoption by nonexpert, bench scientists. To address this need, we have developed an extensible, Galaxy-based resource aimed at providing more researchers access to, and training in, proteogenomic informatics. Our resource brings together software from several leading research groups to address two foundational aspects of proteogenomics: (i) generation of customized, annotated protein sequence databases from RNA-Seq data; and (ii) accurate matching of tandem mass spectrometry data to putative variants, followed by filtering to confirm their novelty. Directions for accessing software tools and workflows, along with instructional documentation, can be found at z.umn.edu/canresgithub. Cancer Res; 77(21); e43-46. ©2017 AACR ., (©2017 American Association for Cancer Research.)

Objectives: Although uterine cancer is the fourth most common cause for cancer death in women worldwide, the molecular underpinnings of tumor progression remain poorly understood. The High Mobility Group A1 (HMGA1) gene is overexpressed in aggressive cancers and high levels portend adverse outcomes in diverse tumors. We previously reported that Hmga1a transgenic mice develop uterine tumors with complete penetrance. Because HMGA1 drives tumor progression by inducing MatrixMetalloproteinase (MMP) and other genes involved in invasion, we explored the HMGA1-MMP-2 pathway in uterine cancer., Methods: To investigate MMP-2 in uterine tumors driven by HMGA1, we used a genetic approach with mouse models. Next, we assessed HMGA1 and MMP-2 expression in primary human uterine tumors, including low-grade carcinomas (endometrial endometrioid) and more aggressive tumors (endometrial serous carcinomas, uterine carcinosarcomas/malignant mesodermal mixed tumors)., Results: Here, we report for the first time that uterine tumor growth is impaired in Hmga1a transgenic mice crossed on to an Mmp-2 deficient background. In human tumors, we discovered that HMGA1 is highest in aggressive carcinosarcomas and serous carcinomas, with lower levels in the more indolent endometrioid carcinomas. Moreover, HMGA1 and MMP-2 were positively correlated, but only in a subset of carcinosarcomas. HMGA1 also occupies the MMP-2 promoter in human carcinosarcoma cells., Conclusions: Together, our studies define a novel HMGA1-MMP-2 pathway involved in a subset of human carcinosarcomas and tumor progression in murine models. Our work also suggests that targeting HMGA1 could be effective adjuvant therapy for more aggressive uterine cancers and provides compelling data for further preclinical studies., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Objective: To test fumigant and repellent properties of sesquiterpene-rich essential oil from Teucrium polium subsp. capitatum (L.)., Methods: The fumigant toxicity test was performed at (27±1)°C, (65±5)% relative humidity, and under darkness condition and 24 h exposure time. The chemical composition of the isolated oils was examined by gas chromatography-mass spectrometry., Results: The major compounds were α-cadinol (46.2%), caryophyllene oxide (25.9%), α muurolol epi (8.1%), cadalene (3.7%) and longiverbenone (2.9%). In all cases, considerable differences in mortality of insect to essential oil vapor were observed in different concentrations and exposure times. Callosobruchus maculatus (C. maculates) (LC50=148.9 μL/L air) was more susceptible to the tested plant product than Teucrium castaneum (T. castaneum) (LC50=360.2 μL/L air) based on LC50 values. In the present investigation, the concentration of 3 μL /mL acetone showed 60% and 52% repellency against T. casteneum and C. maculatus adults, respectively., Conclusions: The results suggests that sesquiterpene-rich essential oils from the tested plant could be used as a potential control agent for stored-product insects., (Copyright © 2014 Hainan Medical College. Published by Elsevier B.V. All rights reserved.)

An increasingly common method for predicting gene activity is genome-wide chromatin immuno-precipitation of 'active' chromatin modifications followed by massively parallel sequencing (ChIP-seq). In order to understand better the relationship between developmentally regulated chromatin landscapes and regulation of early B cell development, we determined how differentially active promoter regions were able to predict relative RNA and protein levels at the pre-pro-B and pro-B stages. Herein, we describe a novel ChIP-seq quantification method (cRPKM) to identify active promoters and a multi-omics approach that compares promoter chromatin status with ongoing active transcription (GRO-seq), steady state mRNA (RNA-seq), inferred mRNA stability, and relative proteome abundance measurements (iTRAQ). We demonstrate that active chromatin modifications at promoters are good indicators of transcription and steady state mRNA levels. Moreover, we found that promoters with active chromatin modifications exclusively in one of these cell states frequently predicted the differential abundance of proteins. However, we found that many genes whose promoters have non-differential but active chromatin modifications also displayed changes in abundance of their cognate proteins. As expected, this large class of developmentally and differentially regulated proteins that was uncoupled from chromatin status used mostly post-transcriptional mechanisms. Strikingly, the most differentially abundant protein in our B-cell development system, 2410004B18Rik, was regulated by a post-transcriptional mechanism, which further analyses indicated was mediated by a micro-RNA. These data highlight how this integrated multi-omics data set can be a useful resource in uncovering regulatory mechanisms. This data can be accessed at: https://usegalaxy.org/u/thereddylab/p/prediction-of-gene-activity-based-on-an-integrative-multi-omics-analysis.

Accurate measurements of airway diameter and wall thickness are important parameters in understanding numerous pulmonary diseases. Here, we describe an automated method of measuring small airway luminal diameter and wall thickness over numerous contiguous computed tomography (CT) images. Using CT lung images from 22 patients and an airway phantom, a seeded region-growing algorithm was first applied to identify the lumen of the airway. The result was applied as an initial region for boundary determination using the level set method. Once found, subsequent algorithmic expansion of the luminal border was used to calculate airway wall thickness. This algorithm automatically evaluates neighboring slices of the airway and measures the airway luminal diameter and wall thickness. This approach also detects airway bifurcations. Our new procedure provides rapid, automated, accurate, and clinically important lung airway measurements that would be useful to radiologists who use CT images for pulmonary disease assessment.

Accurate measurement of human airway lumen bifurcation angle in the bronchial tree may be an important parameter for evidence of pulmonary diseases. Here, we describe a new method for recognizing and following airway bifurcation over numerous contiguous CT images. Based on morphological properties of airways and specific changes to airway properties while digitally navigating through the bifurcation, our method is able to track airways through several levels of bifurcation. Then, based on the center of the lumen area, determined by the level set segmentation algorithm, we estimate the centerline of each branch and calculate the angle between two bifurcating branches. By applying this method to an airway imaging phantom, we obtained accurate results in a short computational time. This new approach provides a rapid, automated, and accurate lung airway angle measurement and may prove useful to radiologists who use CT images for pulmonary disease assessment.

Purpose: To compare the dose distributions and late radiation toxicities for (125)I brachytherapy (IBT) and stereotactic radiation therapy (SRT) in the treatment of juxtapapillary choroidal melanoma., Methods: Ninety-four consecutive patients with juxtapapillary melanoma were reviewed: 30 have been treated with IBT and 64 with SRT. Iodine-125 brachytherapy cases were modeled with plaque simulator software for dosimetric analysis. The SRT dosimetric data were obtained from the Radionics XKnife RT3 software. Mean doses at predetermined intraocular points were calculated. Kaplan-Meier estimates determined the actuarial rates of late toxicities, and the log-rank test compared the estimates., Results: The median follow-up was 46 months in both cohorts. The 2 cohorts were balanced with respect to pretreatment clinical and tumor characteristics. Comparisons of radiation toxicity rates between the IBT and SRT cohorts yielded actuarial rates at 50 months for cataracts of 62% and 75% (P=.1), for neovascular glaucoma 8% and 47% (P=.002), for radiation retinopathy 59% and 89% (P=.0001), and for radiation papillopathy 39% and 74% (P=.003), respectively. Dosimetric comparisons between the IBT and SRT cohorts yielded mean doses of 12.8 and 14.1 Gy (P=.56) for the lens center, 17.6 and 19.7 Gy (P=.44) for the lens posterior pole, 13.9 and 10.8 Gy (P=.30) for the ciliary body, 61.9 and 69.7 Gy (P=.03) for optic disc center, and 48.9 and 60.1 Gy (P<.0001) for retina at 5-mm distance from tumor margin, respectively., Conclusions: Late radiation-induced toxicities were greater with SRT, which is secondary to the high-dose exposure inherent to the technique as compared with IBT. When technically feasible, IBT is preferred to treat juxtapapillary choroidal melanoma., (Copyright © 2013 Elsevier Inc. All rights reserved.)

In this work dosimetric parameters of two multi-leaf collimator (MLC) systems, namely the beam modulator (BM), which is the MLC commercial name for Elekta "Synergy S" linear accelerator and Radionics micro-MLC (MMLC), are compared using measurements and Monte Carlo simulations. Dosimetric parameters, such as percentage depth doses (PDDs), in-plane and cross-plane dose profiles, and penumbras for different depths and field sizes of the 6 MV photon beams were measured using ionization chamber and a water tank. The collimator leakages were measured using radiographic films. MMLC and BM were modeled using the EGSnrc-based BEAMnrc Monte Carlo code and above dosimetric parameters were calculated. The energy fluence spectra for the two MLCs were also determined using the BEAMnrc and BEAMDP. Dosimetric parameters of the two MLCs were similar, except for penumbras. Leaf-side and leaf-end 80-20% dose penumbras at 10 cm depth for a 10×10 cm(2) field size were 4.8 and 5.1mm for MMLC and 5.3 mm and 6.3 mm for BM, respectively. Both Radionics MMLC and Elekta BM can be used effectively based on their dosimetric characteristics for stereotactic radiosurgery and radiotherapy, although the former showed slightly sharper dose penumbra especially in the leaf-end direction., (Copyright © 2012 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.)

Aims: To compare the treatment efficacy and radiation complications between (125)Iodine brachytherapy and stereotactic radiotherapy in the management of juxtapapillary choroidal melanoma., Methods: Consecutive juxtapapillary melanoma patients treated with radiotherapy were included. Patients were divided into two cohorts: patients treated with (125)Iodine brachytherapy and patients with stereotactic radiotherapy. Comparison included the rates postradiotherapy local recurrence, secondary enucleation, metastasis and radiotherapy complications. Kaplan-Meier estimates were used to determine the actuarial rates, and logrank test to compare between the estimates., Results: We included 94 patients with juxtapapillary melanoma treated with radiotherapy. The brachytherapy cohort included 30 patients and stereotactic radiotherapy was 64. The median follow-up was 46 months in both cohorts. No statistically significant differences existed between the two cohorts on comparing pretreatment clinical data and tumour characteristics. On comparing treatment efficacy, the actuarial rates at 50 months for tumour recurrence were 11% and 7% (p=0.61), secondary enucleation was 11% and 21% (p=0.30) and for metastasis were 4% and 16% (p=0.11), respectively. On comparing treatment complications, the actuarial rates at 50 months for cataracts were 62% and 75% (p=0.1), for neovascular glaucoma 8% and 47% (p=0.002), for radiation retinopathy 59% and 89% (p=0.0001), and for radiation papillopathy 39% and 74% (p=0.003), respectively., Conclusions: Both (125)Iodine brachytherapy and stereotactic radiotherapy demonstrate comparable efficacy in the management of juxtapapillary choroidal melanoma. However, stereotactic radiotherapy shows statistically significant higher radiation-induced ocular morbidities at 4 years postradiotherapy.

The HuR protein regulates the expression of thousands of cellular transcripts by modulating mRNA splicing, trafficking, translation, and stability. Although it serves as a model of RNA-protein interactions, many features of HuR's interactions with RNAs remain unknown. In this report, we deployed the cryogenic RNA immunoprecipitation technique to analyze HuR-interacting RNAs with the Affymetrix all-exon microarray platform. We revealed several thousand novel HuR-interacting RNAs, including hundreds of non-coding RNAs such as natural antisense transcripts from stress responsive loci. To gain insight into the mechanisms of specificity and sensitivity of HuR's interaction with its target RNAs, we searched HuR-interacting RNAs for composite patterns of primary sequence and secondary structure. We provide evidence that secondary structures of 66-75 nucleotides enhance HuR's recognition of its specific RNA targets composed of short primary sequence patterns. We validated thousands of these RNAs by analysis of overlap with recently published findings, including HuR's interaction with RNAs in the pathways of RNA splicing and stability. Finally, we observed a striking enrichment for members of ubiquitin ligase pathways among the HuR-interacting mRNAs, suggesting a new role for HuR in the regulation of protein degradation to mirror its known function in protein translation.

Purpose: To define clinical and dosimetric predictors of nonauditory adverse radiation effects after radiosurgery for vestibular schwannoma treated with a 12 Gy prescription dose., Methods: We retrospectively reviewed our experience of vestibular schwannoma patients treated between September 2005 and December 2009. Two hundred patients were treated at a 12 Gy prescription dose; 80 had complete clinical and radiological follow-up for at least 24 months (median, 28.5 months). All treatment plans were reviewed for target volume and dosimetry characteristics; gradient index; homogeneity index, defined as the maximum dose in the treatment volume divided by the prescription dose; conformity index; brainstem; and trigeminal nerve dose. All adverse radiation effects (ARE) were recorded. Because the intent of our study was to focus on the nonauditory adverse effects, hearing outcome was not evaluated in this study., Results: Twenty-seven (33.8%) patients developed ARE, 5 (6%) developed hydrocephalus, 10 (12.5%) reported new ataxia, 17 (21%) developed trigeminal dysfunction, 3 (3.75%) had facial weakness, and 1 patient developed hemifacial spasm. The development of edema within the pons was significantly associated with ARE (p = 0.001). On multivariate analysis, only target volume is a significant predictor of ARE (p = 0.001). There is a target volume threshold of 5 cm3, above which ARE are more likely. The treatment plan dosimetric characteristics are not associated with ARE, although the maximum dose to the 5th nerve is a significant predictor of trigeminal dysfunction, with a threshold of 9 Gy. The overall 2-year tumor control rate was 96%., Conclusions: Target volume is the most important predictor of adverse radiation effects, and we identified the significant treatment volume threshold to be 5 cm3. We also established through our series that the maximum tolerable dose to the 5th nerve is 9 Gy., (Crown Copyright © 2012. Published by Elsevier Inc. All rights reserved.)

The objective of this study was to evaluate the regional effects of bronchodilator administration in chronic obstructive pulmonary disease (COPD) using hyperpolarized helium-3 ((3)He) MRI apparent diffusion coefficient (ADC). Ten COPD ex-smokers provided written, informed consent and underwent diffusion-weighted, hyperpolarized (3)He MRI, spirometry, and plethysmography before and 25 ± 2 min after bronchodilator administration. Pre- and postsalbutamol whole-lung (WL) ADC maps were generated and registered together to identify the lung regions containing the (3)He signal at both time points, and mean ADC within those regions of interest (ROI) was determined for a measurement of previously ventilated ROI ADC (ADC(P)). Lung ROI with (3)He signal at both time points was used as a binary mask on postsalbutamol WL ADC maps to obtain an ADC measurement for newly ventilated ROI (ADC(N)). Postsalbutamol, no significant differences were detected in WL ADC (P = 0.516). There were no significant differences between ADC(N) and ADC(P) postsalbutamol (P = 1.00), suggesting that the ADC(N) lung regions were not more emphysematous than the lung ROI participating in ventilation before bronchodilator administration. Postsalbutamol, a statistically significant decrease in ADC(P) (P = 0.01) was detected, and there were significant differences between ADC(P) in the most anterior and most posterior image slices (P = 0.02), suggesting a reduction in regional gas trapping following bronchodilator administration. Regional evaluation of tissue microstructure using hyperpolarized (3)He MRI ADC provides insights into lung alterations that accompany improvements in regional (3)He gas distribution after bronchodilator administration.

Purpose: To evaluate short-acting bronchodilator effects in chronic obstructive pulmonary disease (COPD) by using hyperpolarized helium 3 (³He) magnetic resonance (MR) imaging, spirometry, and plethysmography., Materials and Methods: Fourteen ex-smokers with COPD provided written informed consent to a local ethics board-approved and Health Insurance and Portability Accountability Act-compliant protocol and underwent hyperpolarized ³He and hydrogen 1 MR imaging, spirometry, and plethysmography before and a mean of 25 minutes ± 2 (standard deviation) after administration of 400 μg salbutamol. Distribution of ³He gas was evaluated by using semiautomated segmentation of ³He voxel intensities, where cluster 1 represented regions of signal void or ventilation defect volume (VDV), and clusters 2-5 (C2-C5) represented gradations of signal intensity from hypointensity (C2) to hyperintensity (C5). ³He ventilation defect percentage (VDP) was calculated as VDV normalized to the thoracic cavity volume. Comparisons of pre- and post-salbutamol means were performed by using a two-way mixed-design repeated measures analysis of variance, and comparisons of the magnitude of the treatment effect between pulmonary function and ³He MR imaging measurements were performed by using effect size (ES) calculations. The relationships between pulmonary function and ³He MR imaging findings were determined by using Spearman correlation coefficients., Results: After salbutamol administration, there were significant changes in forced expiratory volume in 1 second (FEV₁) (P = .001), total lung capacity (P = .04), and functional residual capacity (P = .03), as well as VDP (P < .0001) and ³He gas distribution (C2, P = .01; C3, P = .03; C4, P < .0001; and C5, P = .02). Treatment ES was greater for ³He VDP than for FEV(1) (0.50 vs 0.22). There was a significant correlation between baseline VDP and post-salbutamol FEV₁ change (r = -0.77, P = .001). Although five patients were classified as bronchodilator responders and nine patients were classified as bronchodilator nonresponders according to American Thoracic Society and European Respiratory Society criteria, there was no significant difference in the magnitude of the ³He MR imaging changes after salbutamol administration between responder groups., Conclusion: ³He MR imaging depicted significant improvements in the distribution of ³He gas after bronchodilator therapy in ex-smokers with COPD with and those without clinically important changes in FEV₁., (© RSNA, 2011.)

Purpose: Enucleation after stereotactic radiotherapy (SRT) for juxtapapillary choroidal melanoma may be required because of tumor progression (TP) or the development of intractable radiation-induced neovascular glaucoma (NVG). We compare pathologic changes and dosimetric findings in those eyes enucleated secondary to NVG as opposed to TP to better understand potential mechanisms., Methods and Materials: Patients with juxtapapillary choroidal melanoma treated with SRT (70 Gy in 5 fractions, alternate days over a total of 10 days) at the Princess Margaret Hospital, Toronto, Ontario, Canada, who underwent enucleation between 1998 and 2006 were selected. We correlated dosimetric data based on the patient's original SRT treatment plan with histopathologic findings in the retina, optic nerve head, and anterior chamber. A dedicated ocular pathologist reviewed each case in a blinded fashion., Results: Ten eyes in ten patients were enucleated after SRT. Six were enucleated secondary to NVG and four secondary to because of TP. Aggressive tumor features such as invasion of the sclera and epithelioid cell type were observed predominantly in the TP group. Retinal damage was more predominant in the NVG group, as were findings of radiation-related retinal vascular changes of fibrinoid necrosis and hyalinization. No conclusive radiation-related effects were found in the anterior chamber. The maximum point dose and dose to 0.1 cc were lower for the anterior chamber as compared with the dose to the tumor, retina, and optic nerve head. The mean 0.1-cc doses to the retina were 69.4 Gy and 73.5 Gy and to the anterior chamber were 4.9 Gy and 17.3 Gy for the NVG group and tumor progression group, respectively., Conclusions: Our findings suggest that NVG is due to radiation damage to the posterior chamber of the eye rather than primary radiation damage to the anterior segment., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Stereotactic radiosurgery (SRS) refers to a single radiation treatment delivering a high dose to an intra-cranial target localized in three-dimensions by CT and/or MRI imaging. Traditionally, immobilization of the patient's head has been achieved using a rigid stereotactic head frame as the key step in allowing for accurate dose delivery. SRS has been delivered by both Cobalt-60 (Gamma Knife) and linear accelerator (linac) technologies for many decades. The focus of this review is to highlight recent advances and major innovations in SRS technologies relevant to clinical practice and developments allowing for non-invasive frame SRS.

Objective: To evaluate the efficacy and complications of stereotactic radiotherapy in the management of patients with juxtapapillary choroidal melanoma., Design: Retrospective review., Participants: 64 patients with juxtapapillary choroidal melanoma., Methods: Consecutive patients with juxtapapillary choroidal melanomas located within 2 mm of the optic nerve, treated with stereotactic radiotherapy at Princess Margaret Hospital from October 1998 to January 2006, were reviewed for treatment effect and complication rates., Results: Median age was 63 years. Median tumor height was 4.2 mm, and median maximum tumor diameter was 9.8 mm. The prescribed radiation dose was 70 Gy in 5 fractions over 10 days, and the median follow-up was 26 months. After treatment, there was local tumor recurrence in 3 patients, and in 8 patients there was systemic progression. Actuarial rates of local tumor control, metastases, and survival at 26 months were 94%, 12%, and 94%, respectively. Rates of radiation-induced neovascular glaucoma, cataract, retinopathy, and optic neuropathy at 26 months were 28%, 45%, 80%, and 52%, respectively. Enucleation was necessary for 7 patients., Conclusions: Stereotactic radiotherapy offers a noninvasive alternative with acceptable ocular toxicity rates to enucleation and brachytherapy in the management of juxtapapillary choroidal melanoma.

Overall changes in the host cellular proteome upon retroviral infection intensify from the initial entry of the virus to the incorporation of viral DNA into the host genome, and finally to the consistent latent state of infection. The host cell reacts to both the entry of viral elements and the manipulation of host cellular machinery, resulting in a cascade of signaling events and pathway activation. Cell type- and tissue-specific responses are also characteristic of infection and can be classified based on the differential expression of genes and proteins between normal and disease states. The characterization of differentially expressed proteins upon infection is also critical in identifying potential biomarkers within infected bodily fluids. Biomarkers can be used to monitor the progression of infection, track the effectiveness of specific treatments and characterize the mechanisms of disease pathogenesis. Standard proteomic approaches have been applied to monitor the changes in global protein expression and localization in infected cells, tissues and fluids. Here we report on recent investigations into the characterization of proteomes in response to retroviral infection.

Background: Estimates of radiation-related second cancer risk among Hodgkin lymphoma survivors are largely based on radiation therapy (RT) fields and doses no longer in use, and these estimates do not account for differences in normal tissue dose among individual patients. This study gives individualized estimates for the risks of lung and female breast cancer expected with contemporary involved-field RT and low-dose (20 Gy) RT for mediastinal Hodgkin lymphoma., Methods: Three RT plans were constructed for 37 consecutive patients with mediastinal Hodgkin lymphoma: 35 Gy mantle RT, 35 Gy involved-field RT (IFRT), and 20 Gy IFRT. For each of the 111 RT plans, individual-level dosimetry data were incorporated into a cell initiation/inactivation/proliferation model to estimate the excess relative risk (ERR) and cumulative incidence of radiation-induced second cancer., Results: ERR estimates were compatible with results of epidemiological studies. Compared with 35 Gy mantle radiation therapy, 35 Gy IFRT was predicted to reduce the 20-year ERRs of breast and lung cancer by 63% and 21%, respectively, primarily because of lower normal tissue doses with the omission of axillary RT. Low-dose (20 Gy) IFRT was associated with a 77% and 57% decrease in these ERRs. Patient-specific differences in normal tissue dose with IFRT led to 11-fold and 3.6-fold variations among individual's estimates of breast and lung cancer ERR, respectively., Conclusions: Contemporary IFRT is predicted to substantially reduce risk of secondary breast and lung cancer compared with mantle RT, with considerable variation in risk among individuals. Individualized prospective risk estimates could facilitate patient-specific counseling and the development of more effective RT techniques., (Copyright (c) 2007 American Cancer Society.)