bluuebunny/crossref_metadata_2025 huggingface dataset:
Knowledge, attitude and practice among Ophthalmic Health Care Personnel (HCP) towards COVID-19 pandemic in Nepal: A web-based cross-sectional study
Authors: Ansari Dr Zahir , Chaurasiya Dr Babu Dhanendra , Adhikari Dr Sirjana , Prakash Dr Uday Chandra , Adhikari Bikram , Khatoon Dr Sahana
Published: August 2020

Background:
Being an added high-risk group, ophthalmic HCP are actively providing emergency eye care services, also enthusiastically participating in prevention and control of the COVID-19 pandemic. Hence, this study aimed to assess the level of knowledge, attitude, and practice (KAP) among ophthalmic HCP towards COVID-19 pandemic.
Methods:
A web-based cross-sectional study was conducted during the period of lockdown among ophthalmic HCP including consultant ophthalmologist, resident, optometrist, ophthalmic assistant, nursing staff, and other paramedics of eye care centers in Nepal. The KAP questionnaire was designed and distributed online. Data were analyzed using the Chi-square test, Pearson correlation, and binary logistic regression. All tests were performed at 95% Confidence Interval (CI) and p-value <0.05 was considered statistically significant.
Results:
Of 694 participants, the majority were male (59.1%) from the age group 31-40 years (41.5%) and tertiary eye center (68.9%). Among ophthalmic HCP, there were 29.8% consultants ophthalmologist, 22.6% residents, 23.3% optometrist, 15% ophthalmic assistant, and 9.2% other ophthalmic paramedics, 11.7% working as front-liners in COVID-19 centers. Findings showed, 98.1% had good knowledge, 59.4% had a positive attitude and only 13.3% had good practice regarding COVID-19. Binary logistic regression analysis demonstrated the age of HCP to be a significant determinant of good knowledge (Crude Odds Ratio (COR)=0.72, 95%CI=0.62-0.82), positive attitude (COR=0.92, 95%CI=0.90-0.94) and good practice (COR=1.16, 95%CI=1.10-1.21). Lower odds of poor practice was seen among junior resident (COR=0.26, 95% CI=0.14-0.47) and higher odds of poor practice was seen among HCP with job experience of 5-10 years (COR=2.38, 95% CI=1.23-4.60) towards COVID-19 pandemic.
Conclusion:
The majority of ophthalmic HCP have good knowledge, insufficient positive attitude, and inadequate evidence-based practice towards the COVID-19 pandemic in Nepal. Hence, this study conclusively recommends to modify existing guidelines and formulate new policies to improve KAP among ophthalmic HCP to effectively control the spread of COVID-19.
Assessing the efficacy and safety of angiotensinogen inhibition using human genetics
Authors: Bovijn Jonas , Censin Jenny C , Lindgren Cecilia M , Holmes Michael V
Published: August 2020

Background

Novel angiotensinogen (AGT) inhibitors are in early clinical development for treatment of hypertension. Evidence that this therapeutic approach will safely reduce risk of cardiovascular outcomes in humans is limited. We leveraged genetic data from more than one million individuals to characterise the effects of AGT inhibition.

Methods

We identified a genetic instrument for AGT inhibition from systolic blood pressure (SBP) genome-wide association study data, and investigated its relationship withAGTgene expression and circulating AGT protein concentration. We examined the instrument’s association with cardiovascular and renal outcomes, and compared the effect of the instrument with that of genetic instruments for other renin-angiotensin system (RAS) components and the causal effect of SBP overall. We performed phenome-wide association analyses to identify unanticipated effects of AGT inhibition.

Results

The AGT instrument (rs2478539; 0.49 mmHg lower SBP per G-allele) was strongly associated with hypertension, and showed evidence of colocalisation withAGTmRNA expression across various tissues. Scaled to a 10 mmHg lower SBP, the AGT instrument was associated with a 41% lower risk of major cardiovascular events, a composite of myocardial infarction, coronary revascularisation and stroke (111,549 cases; odds ratio 0.59, 95% confidence interval, 0.47 – 0.74;P= 3.1 × 10-6). There was little evidence of heterogeneity between the AGT vascular estimates when compared to equivalent estimates from other RAS targets and the effect of SBP lowering more broadly, and no strong evidence of potential target-mediated adverse effects.

Conclusion

Our findings suggest that inhibition of AGT safely reduces risk of major vascular events. These results support ongoing clinical development programmes for AGT inhibitors.
Bilirubin is not associated with urinary bladder cancer risk and prognosis: A Mendelian Randomization Study in the UK Biobank
Authors: Lipunova Nadezda , Bryan Richard T , Zeegers Maurice
Published: August 2020

Background

Mutations in UGT1A gene have been associated with the development and prognosis of urinary bladder cancer (UBC). UGT1A proteins are involved in a spectrum of detoxification processes, hence the biological mechanism between UGT1A and UBC is difficult to elucidate. Concurrently, mild hyperbilirubinemia, caused by alterations in UGT1A, has been associated with multiple health outcomes. We have investigated the potential effect of mild hyperbilirubinemia on UBC risk and prognosis, using a Mendelian Randomization (MR) approach in the UK Biobank.

Methods

Data on 1,281 UBC patients and 4,071 controls was available for a two-stage least squares MR estimation with rs6742078 as an instrumental variable. First, linear regression was fitted to establish the relationship between the rs6742078 and bilirubin levels (total and unconjugated). Secondly, bilirubin values were used to predict tested outcomes under a logistic model. Both stages were adjusted for participant sex, smoking status, and age.

Results

MR analysis showed no significant effects of bilirubin levels on UBC risk (total bilirubin: OR=1.02, 95% CI: 0.99-1.04; unconjugated bilirubin: OR=1.02, 95% CI: 0.99-1.05). No effects were observed for events of UBC recurrence, progression, or survival.

Conclusion

Our study suggests mild hyperbilirubinemia is not associated with urinary bladder cancer risk and prognosis.
Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region
Authors: Thielen Peter M. , Wohl Shirlee , Mehoke Thomas , Ramakrishnan Srividya , Kirsche Melanie , Falade-Nwulia Oluwaseun , Trovão Nídia S. , Ernlund Amanda , Howser Craig , Sadowski Norah , Morris Paul , Hopkins Mark , Schwartz Matthew , Fan Yunfan , Gniazdowski Victoria , Lessler Justin , Sauer Lauren , Schatz Michael C. , Evans Jared D. , Ray Stuart C. , Timp Winston , Mostafa Heba H.
Published: August 2020

Background

The early COVID-19 pandemic has been characterized by rapid global spread. In the United States National Capital Region, over 2,000 cases were reported within three weeks of its first detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2, the virus that causes COVID-19, in the region. By correlating genetic information to disease phenotype, we also aimed to gain insight into any correlation between viral genotype and case severity or transmissibility.

Methods

We performed whole genome sequencing of clinical SARS-CoV-2 samples collected in March 2020 by the Johns Hopkins Health System. We analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and the global phylogeny to understand early establishment of the virus within the region.

Results

We analyzed 620 samples from the Johns Hopkins Health System collected between March 11–31, 2020, comprising 37.3% of the total cases in Maryland during this period. We selected 143 of these samples for sequencing, generating 114 complete viral genomes. These genomes belong to all five major Nextstrain-defined clades, suggesting multiple introductions into the region and underscoring the diversity of the regional epidemic. We also found that clinically severe cases had genomes belonging to all of these clades.

Conclusions

We established a pipeline for SARS-CoV-2 sequencing within the Johns Hopkins Health system, which enabled us to capture the significant viral diversity present in the region as early as March 2020. Efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and interconnectedness of the region as a whole.
Efficacy of Corticosteroids in COVID-19 Patients: A Systematic Review and Meta-Analysis
Authors: Tlayjeh Haytham , Mhish Olaa H. , Enani Mushira A. , Alruwaili Alya , Tleyjeh Rana , Thalib Lukman , Hassett Leslie , Arabi Yaseen M. , Kashour Tarek , Tleyjeh Imad M.
Published: August 2020

Background

To systematically review the literature about the effect of systemic corticosteroid therapy (CST) on outcomes of COVID-19 patients.

Methods

We searched Medline, Embase, EBM Reviews, Scopus, Web of Science, and preprints up to July 20, 2020. We included observational studies and randomized controlled trials (RCT) that assessed COVID-19 patients treated with CST. We pooled adjusted effect estimates of mortality and other outcomes using a random effect model, among studies at low or moderate risk for bias. We assessed the certainty of evidence for each outcome using the GRADE approach.

Results

Out of 1067 citations screened for eligibility, one RCT and 19 cohort studies were included (16,977 hospitalized patients). Ten studies (1 RCT and 9 cohorts) with 10,278 patients examined the effect of CST on short term mortality. The pooled adjusted RR was 0.92 (95% CI 0.69-1.22, I2=81.94 %). This effect was observed across all stages of disease severity. Four cohort studies examined the effect of CST on composite outcome of death, ICU admission and mechanical ventilation need. The pooled adjusted RR was 0.41(0.23-0.73, I2=78.69%). Six cohort studies examined the effect of CST on delayed viral clearance. The pooled adjusted RR was 1.47(95% CI 1.11-1.93, I2=43.38%).

Conclusion

Heterogeneous and low certainty cumulative evidence suggests that CST lacks efficacy in reducing short-term mortality while possibly delaying viral clearance in patients hospitalized with COVID-19. Because of the discordant results between the single RCT and observational studies, more research should continue to identify the clinical and biochemical characteristics of patients’ population that could benefit from CST.
Long-Term Exposure to Outdoor Air Pollution and COVID-19 Mortality: an ecological analysis in England
Authors: Feng Zhiqiang , Cherrie Mark , Dibben Chris
Published: August 2020

There is an urgent need to examine what individual and environmental risk factors are associated with COVID-19 mortality. This objective of this study is to investigate the association between long term exposure to air pollution and COVID-19 mortality. We conducted a nationwide, ecological study using zero-inflated negative binomial models to estimate the association between long term (2014-2018) small area level exposure to NOx, PM2.5, PM10 and SO2 and COVID-19 mortality rates in England adjusting for socioeconomic factors and infection exposure. We found that all four pollutant concentrations were positively associated with COVID-19 mortality. The increase in mortality risk ratio per inter quarter range increase was for PM2.5:11%, 95%CIs 6%-17%), PM10 (5%; 95%CIs 1%-11%), NOx (11%, 95%CIs 6%-15%) and SO2 (7%, 95%CIs 3%-11%) were respectively in adjusted models. Public health intervention may need to protect people who are in highly polluted areas from COVID-19 infections.
Timing HIV infection with nonlinear viral dynamics
Authors: Reeves Daniel , Rolland Morgane , Dearlove Bethany L , Li Yifan , Robb Merlin , Schiffer Joshua T , Gilbert Peter , Cardozo-Ojeda E Fabian , Mayer Bryan
Published: August 2020

In HIV prevention trials, precise identification of infection time is critical to quantify drug efficacy but difficult to estimate as trials may have relatively sparse visit schedules. The last negative visit does not guarantee a boundary on infection time because viral nucleic acid is not present in the blood during early infection. Here, we developed a framework that combines stochastic and deterministic within-host mathematical modeling of viral dynamics accounting for the early unobservable viral load phase until it reaches a high chronic set point. The infection time estimation is based on a population non-linear mixed effects (pNLME) framework that includes the with-in host modeling. We applied this framework to viral load data from the RV217 trial and found a parsimonious model capable of recapitulating the viral loads. When adding the stochastic and deterministic portion of the best model, the estimated infection time for the RV217 data had an average of 2 weeks between infecting exposure and first positive. We assessed the sensitivity of the infection time estimation by conducting in silico studies with varying viral load sampling schemes before and after infection. pNLME accurately estimates infection times for a daily sampling scheme and is fairly robust to sparser schemes. For a monthly sampling scheme before and after first positive bias increases to -7 days. For pragmatic trial design, we found sampling weekly before and monthly after first positive allows accurate pNLME estimation. Our estimates can be used in parallel with other approaches that rely on viral sequencing, and because the model is mechanistic, it is primed for future application to infection timing for specific interventions.
Bio-Inspired Attentive Segmentation of Retinal OCT imaging
Authors: Lazaridis Georgios , Xu Moucheng , Afgeh Saman Sadeghi , Montesano Giovanni , Garway-Heath David
Published: August 2020

Albeit optical coherence imaging (OCT) is widely used to assess ophthalmic pathologies, localization of intra-retinal boundaries suffers from erroneous segmentations due to image artifacts or topological abnormalities. Although deep learning-based methods have been effectively applied in OCT imaging, accurate automated layer segmentation remains a challenging task, with the flexibility and precision of most methods being highly constrained. In this paper, we propose a novel method to segment all retinal layers, tailored to the bio-topological OCT geometry. In addition to traditional learning of shift-invariant features, our method learns in selected pixels horizontally and vertically, exploiting the orientation of the extracted features. In this way, the most discriminative retinal features are generated in a robust manner, while long-range pixel dependencies across spatial locations are efficiently captured. To validate the effectiveness and generalisation of our method, we implement three sets of networks based on different backbone models. Results on three independent studies show that our methodology consistently produces more accurate segmentations than state-of-the-art networks, and shows better precision and agreement with ground truth. Thus, our method not only improves segmentation, but also enhances the statistical power of clinical trials with layer thickness change outcomes.
Wide-based Foveal Pit: A Predisposition to Idiopathic Epiretinal Membrane
Authors: Ma I-Hsin , Yang Chung-May , Hsieh Yi-Ting
Published: August 2020

Aims

To report the anatomical characteristics of wide-based foveal pit and its associations with macular diseases.

Methods

Wide-based foveal pit was defined as a foveal base width (FBW) larger than the mean value plus one standard deviation of normal population. Eyes with a wide-based foveal pit were retrospectively collected as the study group, and age- and sex-matched subjects with a normal FBW were recruited as the control group. FBW, area of foveal avascular zone (FAZ) and retinal artery trajectory (RAT) were compared between two groups. The characteristics of the fellow eyes in the study group were also described.

Results

Fifty two eyes from 52 patients were identified as having a wide-based foveal pit; 43 (82.7%) were female. Both their FBW (474.7 ± 84.6μm) and area of FAZ (0.50 ± 0.11mm2) were significantly larger than in the control group (297.6 ± 42.3 μm and 0.29 ± 0.10 mm2, respectively; p < 0.001 for both), and they also had a wider RAT than the control group (p < 0.001). During follow-up, three eyes had developed idiopathic epiretinal membrane. As for their fellow eyes, they either also had a wide-based foveal pit (11 eyes) or had various macular diseases including idiopathic epiretinal membrane (27 eyes), macular hole (5 eyes) and others (16 eyes).

Conclusions

Eyes with a wide-based foveal pit also had a large FAZ and a wide RAT, and they might have a predisposition to idiopathic epiretinal membrane formation. Their fellow eyes also had a predisposition to epiretinal membrane and macular hole.

Synopsis

Eyes with a wide-based foveal pit had a predisposition to idiopathic epiretinal membrane formation. Their fellow eyes might also have a wide-based foveal pit and had a predisposition to epiretinal membrane and macular hole.
Influence of adherence to social distancing due to the COVID-19 pandemic on physical activity level in post-bariatric patients
Authors: Rezende Diego Augusto Nunes , Pinto Ana Jéssica , Goessler Karla Fabiana , Nicoletti Carolina Ferreira , Sieczkowska Sofia Mendes , Meireles Kamila , Esteves Gabriel Perri , Genario Rafael , de Oliveira Gersiel Nascimento , Santo Marco Aurélio , de Cleva Roberto , Roschel Hamilton , Gualano Bruno
Published: August 2020

Objectives

To assess physical activity levels in post-bariatric patients who adhered or not to social distancing measures due to the Covid-19 pandemic. Our secondary aim was to compare physical activity estimates between objectively measured and self-reported physical activity level.

Methods

In this descriptive, cross-sectional study, we assessed physical activity level using accelerometers and a validated questionnaire in 33 post-bariatric patients who reported to be adherent (n=15) or not (n=18) to social distancing measures.

Results

Patients adherent to social distancing measures spent more time in sedentary behavior (1.1 hours/day [95%CI: 0.1, 2.2]; p=0.045) and less time in moderate-to-vigorous physical activity (−12.2 min/day [95%CI: −23.8, −0.6]; p=0.040) compared to non-adherent ones. No difference was observed for light-intensity physical activity. Bland-Altman analysis comparing objective and subjective physical activity estimates showed a bias for time spent in sedentary behavior and moderate-to-vigorous physical activity of 2.8 hours/day and 8.5 min/day, respectively.

Conclusion

Post-bariatric patients who were adherent to social distancing measures due to the Covid-19 outbreak were more inactive and sedentary than non-adherent ones. Additionally, questionnaire data widely underestimated sedentary behavior. Strategies to increase or at least sustain physical activity levels in post-bariatric patients exposed to social distancing measures are necessary during the Covid-19 pandemic.

What is already known about this subject?

Reduced physical activity is associated with poor health-related outcomes in patient undergoing bariatric surgery.

The impact of the social distancing measures due to Covid-19 pandemic on objectively-measured physical activity in this condition remains unknown.

What are the new findings in your manuscript?

Adherence to social distancing due to Covid-19 pandemic was associated with decreased objectively measured physical activity and increased sedentary behavior in patients who had undergone bariatric surgery.

Questionnaire data widely underestimated sedentary behavior when compared to accelerometry data.

How might your results change the direction of research or the focus of clinical practice?

Given the increased burden of cardiovascular diseases related to inactivity and sedentary behavior, strategies to increase physical activity in post-bariatric patients are clinically relevant during the Covid-19 pandemic.

The use of validated accelerometers is recommended to screen and track physical activity during the pandemic.
Assessment of Infection Prevention and Control Protocols, Procedures, and Implementation in Response to the COVID-19 Pandemic in Twenty-three Long-term Care Facilities in Fulton County, Georgia
Authors: Telford Carson T. , Bystrom Cyndra , Fox Teresa , Wiggins-Benn Sherry , McCloud Meshell , Holland David P. , Shah Sarita
Published: August 2020

Through infection prevention and control (IPC) site visits to 23 LTCFs in Fulton County, Georgia, comparison between the Higher- and Lower-prevalence groups revealed significant differences in PPE and Social Distancing, with five specific indicators driving these differences.
Comparison of COVID-19 Infections Among Healthcare Workers and Non-Healthcare Workers
Authors: Kim Rachel , Nachman Sharon , Fernandes Rafael , Meyers Kristen , Taylor Maria , LeBlanc Debra , Singer Adam J
Published: August 2020

Objectives

Healthcare workers face distinct occupational challenges that affect their personal health, especially during a pandemic. In this study we compare the characteristics and outcomes of Covid-19 patients who are and who are not healthcare workers (HCW).

Methods

We retrospectively analyzed a cohort of adult patients with known HCW status and a positive SARS-CoV-2 PCR test presenting to a large academic medical center emergency department (ED) in New York State. We routinely collect data on occupation and exposures to suspected Covid-19. The primary outcome was hospital admission. Secondary outcomes were ICU admission, need for invasive mechanical ventilation (IMV), and mortality. We compared baseline characteristics and outcomes of Covid-19 adult patients based on whether they were or were not HCW using univariable and multivariable analyses.

Results

From March 1 2020 through June 2020, 2,842 adult patients (mean age 53+/-19 years, 53% male) with positive SARS-CoV-2 PCR tests and known HCW status visited the ED. This included 193 (6.8%) known HCWs and 2,649 (93.2%) non-HCWs. Compared with non-HCW, HCWs were younger (43 vs 53 years, P<0.001), more likely female (118/193 vs 1211/2649, P<0.001), and more likely to have a known Covid-19 exposure (161/193 vs 946/2649, P<0.001), but had fewer comorbidities. On presentation to the ED, HCW also had lower frequencies of tachypnea (12/193 vs 426/2649, P<0.01), hypoxemia (15/193 vs 564/2649, P<0.01), bilateral opacities on imaging (38/193 vs 1189/2649, P<0.001), and lymphocytopenia (6/193 vs 532/2649, P<0.01) compared to non-HCWs. Direct discharges home from the ED were more frequent in HCW 154/193: 80% vs 1275/2649: 48% p<0.001). Hospital admissions (38/193 20% vs 1264/2694 47%, P<0.001), ICU admissions (7/193 3% vs 321/2694 12%, P<0.001), need for IMV (6/193 3% vs 321/2694 12%, P<0.001) and mortality (2/193 1% vs 219/2694 8%, P<0.01) were lower than among non-HCW. After controlling for age, sex, comorbidities, presenting vital signs and radiographic imaging, HCW were less likely to be admitted (OR 0.6, 95%CI 0.3-0.9) than non HCW.

Conclusions

Compared with non HCW, HCW with Covid-19 were younger, had less severe illness, and were less likely to be admitted.
Extraction of accurate cytoskeletal actin velocity distributions from noisy measurements
Authors: Miller Cayla M. , Korkmazhan Elgin , Dunn Alexander R.
Published: August 2020

Dynamic remodeling of the actin cytoskeleton is essential for many cellular processes. Tracking the movement of individual actin filaments can in principle shed light on how this complex behavior arises at the molecular level. However, the information that can be extracted from these measurements is often limited by low signal-to-noise ratios. We developed a Bayesian statistical approach to estimate true, underlying velocity distributions from the tracks of individual actin-associated fluorophores with quantified localization uncertainties. We found that filamentous (F)-actin velocity distributions in fibroblasts and endothelial cells were well described by a statistical jump process, in which filaments exist in mechanical equilibria punctuated by abrupt, jump-like movements. A model with exponentially distributed jump length- and time-scales recapitulated actin filament velocity distributions measured for the cell cortex, integrin-based adhesions, and stress fibers, suggesting that a common physical model can potentially describe actin filament dynamics in a variety of cellular contexts.
SARS-CoV-2 manipulates the SR-B1-mediated HDL uptake pathway for its entry
Authors: Wei Congwen , Wan Luming , Yan Qiulin , Wang Xiaolin , Zhang Jun , Zhang Yanhong , Sun Jin , Yang Xiaopan , Gong Jing , Fan Chen , Yang Xiaoli , Wang Yufei , Wang Xuejun , Li Jianmin , Yang Huan , Li Huilong , Zhang Zhe , Wang Rong , Du Peng , Zong Yulong , Yin Feng , Zhang Wanchuan , Peng Yumeng , Lin Haotian , Zhang Rui , Chen Wei , Gao Qi , Cao Yuan , Zhong Hui
Published: August 2020

The recently emerged pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly, leading to a global COVID-19 pandemic. Binding of the viral spike protein (SARS-2-S) to cell surface receptor angiotensin-converting enzyme 2 (ACE2) mediates host cell infection. In the present study, we demonstrate that in addition to ACE2, the S1 subunit of SARS-2-S binds to HDL and that SARS-CoV-2 hijacks the SR-B1-mediated HDL uptake pathway to facilitate its entry. SR-B1 facilitates SARS-CoV-2 entry into permissive cells by augmenting virus attachment. MAb (monoclonal antibody)-mediated blocking of SARS-2-S-HDL binding and SR-B1 antagonists strongly inhibit HDL-enhanced SARS-CoV-2 infection. Notably, SR-B1 is co-expressed with ACE2 in human pulmonary and extrapulmonary tissues. These findings revealed a novel mechanism for SARS-CoV-2 entry and could provide a new target to treat SARS-CoV-2 infection.
Lineage transcription factors co-regulate subtype-specific genes providing a roadmap for systematic identification of small cell lung cancer vulnerabilities
Authors: Pozo Karine , Kollipara Rahul K. , Kelenis Demetra P. , Rodarte Kathia E. , Zhang Xiaoyang , Minna John D. , Johnson Jane E.
Published: August 2020

Lineage-defining transcription factors (LTFs) play key roles in tumor cell growth, making them highly attractive, but currently “undruggable”, small cell lung cancer (SCLC) vulnerabilities. Delineating LTF genomic binding sites and associated chromatin features would provide important insights into SCLC dependencies. Here we map super-enhancers (SEs) across multiple patient-derived SCLC preclinical models, and find SE patterns are sufficient to classify the models into the recently defined, LTF-based, SCLC subtypes. 3D-chromatin conformation analysis identified genes associated with SEs that define subtype-specific tumor signatures with genes functioning in diverse processes. Focusing on ASCL1-high SCLC (SCLC-A), we found ASCL1 physically interacts with NKX2-1 and PROX1. These factors bind overlapping genomic regions, and co-regulate a set of genes, including genes encoding cell surface proteins, SCN3A and KCNB2 enriched in SCLC-A. Genetic depletion of NKX2-1 or PROX1 alone, or in combinations with ASCL1, did not inhibit SCLC growth more than that achieved by depleting ASCL1 alone. We demonstrate the SE signature supports the LTF classification of SCLC, identify NKX2-1 and PROX1 as ASCL1 co-factors, and substantiate the central importance of ASCL1 as a key dependency factor in the majority of SCLC. The LTF and SE gene sets provide a molecular roadmap for future ASCL1 therapeutic targeting studies.
Ex vivodetection of SARS-CoV-2-specific CD8+ T cells: rapid induction, prolonged contraction, and formation of functional memory
Authors: Schulien Isabel , Kemming Janine , Oberhardt Valerie , Wild Katharina , Seidel Lea M. , Killmer Saskia , Sagar  , Daul Franziska , Lago Marilyn Salvat , Decker Annegrit , Luxenburger Hendrik , Binder Benedikt , Bettinger Dominik , Sogukpinar Oezlem , Rieg Siegbert , Panning Marcus , Huzly Daniela , Schwemmle Martin , Kochs Georg , Waller Cornelius F. , Nieters Alexandra , Duerschmied Daniel , Emmerich Florian , Mei Henrik , Schulz Axel , Llewellyn-Lacey Sian , Price David A. , Boettler Tobias , Bengsch Bertram , Thimme Robert , Hofmann Maike , Neumann-Haefelin Christoph
Published: August 2020

CD8+ T cells are critical for the elimination and long-lasting protection of many viral infections, but their role in the current SARS-CoV-2 pandemic is unclear. Emerging data indicates that SARS-CoV-2-specific CD8+ T cells are detectable in the majority of individuals recovering from SARS-CoV-2 infection. However, optimal virus-specific epitopes, the role of pre-existing heterologous immunity as well as their kinetics and differentiation program during disease control have not been defined in detail. Here, we show that both pre-existing and newly induced SARS-CoV-2-specific CD8+ T-cell responses are potentially important determinants of immune protection in mild SARS-CoV-2 infection. In particular, our results can be summarized as follows: First, immunodominant SARS-CoV-2-specific CD8+ T-cell epitopes are targeted in the majority of individuals with convalescent SARS-CoV-2 infection. Second, MHC class I tetramer analyses revealed the emergence of phenotypically diverse and functionally competent pre-existing and newly induced SARS-CoV-2-specific memory CD8+ T cells that showed similar characteristics compared to influenza-specific CD8+ T cells. Third, SARS-CoV-2-specific CD8+ T-cell responses are more robustly detectable than antibodies against the SARS-CoV-2-spike protein. This was confirmed in a longitudinal analysis of acute-resolving infection that demonstrated rapid induction of the SARS-CoV-2-specific CD8+ T cells within a week followed by a prolonged contraction phase that outlasted the waning humoral immune response indicating that CD8+ T-cell responses might serve as a more precise correlate of antiviral immunity than antibody measurements after convalescence. Collectively, these data provide new insights into the fine specificity, heterogeneity, and dynamics of SARS-CoV-2-specific memory CD8+ T cells, potentially informing the rational development of a protective vaccine against SARS-CoV-2.
A power amplification dyad in seahorses
Authors: Avidan Corrine , Day Steven W , Holzman Roi
Published: August 2020

Ubiquitous constraints derived from the muscle’s structure limit the power capacity of fast contracting muscles. Correspondingly, organisms evolved elastic elements that store energy which, when released, can be used to rapidly accelerate appendages. Such latch-mediated spring actuation (LaMSA) systems comprise of a single elastic element and are used to actuate a single mass. Here we reveal a dual LaMSA system in seahorses, in which two elastic elements actuate two masses: the head as they rapidly swing it towards the prey, and the water mass sucked into the mouth to prevent the prey from escaping. This power-amplified system enhances the speeds of both head rotation and suction flows by x10 compared to similarly-sized fish. Furthermore, the dual system provides temporal coordination between head rotation and suction flows, a novel function for LaMSA. These findings extend the known function, capacity and design of LaMSA systems.
Thymidylate synthase drives the phenotypes of epithelial-to-mesenchymal transition in non-small cell lung cancer
Authors: Siddiqui Mohammad Aarif , Gollavilli Paradesi Naidu , Ramesh Vignesh , Parma Beatrice , Schwab Annemarie , Vazakidou Maria Eleni , Natesan Ramakrishnan , Saatci Ozge , Rapa Ida , Bironzo Paolo , Schuhwerk Harald , Asangani Irfan Ahmed , Sahin Ozgur , Volante Marco , Ceppi Paolo
Published: August 2020

Background

Epithelial-to-mesenchymal transition (EMT) enhances motility, stemness and chemoresistance of carcinomas and is an important determinant of metastasis. Little is known about how various pathways coordinate to elicit EMT’s different functional aspects. Even lesser has been studied in this context in non-small cell lung cancer (NSCLC), where EMT is a key event during early tumorigenesis. Thymidylate synthase (TS), a proliferation enzyme, has been previously correlated with EMT transcription factor ZEB1 in NSCLC and is associated with resistance against anti-folate chemotherapy. In this study we establish a functional correlation between TS, EMT, chemotherapy and metastasis and identify a network that might propel the TS mediated EMT phenotype.

Methods

Published datasets were analysed to evaluate significance of TS in NSCLC fitness and prognosis. mCherry based promoter reporter assay was used to sort Calu-1 and A549 NSCLC cells in TSHIGHand TSLOW. Metastatic potential of TS knock-down was assayed in syngeneic C57BL/6 mice.

Results

Low TS levels were prognostic and predicted chemotherapy response. NSCLC cell lines with higher TS promoter activity were more mesenchymal-like. RNA-seq from these cells, and shRNA mediated TS knocked down cells, identified EMT as one of the most differentially regulated pathways. EMT transcription factors HOXC6 and HMGA2 were identified as upstream regulator of TS whereas, AXL, SPARC and FOSL1 were identified as downstream effectors. TS knock-down reduced the metastatic colonisationin vivo.

Conclusion

These results establish the role of TS as a theranostic NSCLC marker integrating survival, chemo-resistance and EMT, and identifies a regulatory network that could be exploited to target EMT-driven NSCLC.
Q-SNARE Syntaxin 7 confers actin-dependent rapidly replenishing synaptic vesicles upon high activity
Authors: Mori Yasunori , Takenaka Koichiro , Fukazawa Yugo , Takamori Shigeo
Published: August 2020

Replenishment of readily releasable synaptic vesicles (SVs) with vesicles in the recycling pool is important for sustained transmitter release during repetitive stimulation. Kinetics of replenishment and available pool size define synaptic performance. However, whether all SVs in the recycling pool are recruited for release with equal probability is unknown. Here, using comprehensive optical imaging for various presynaptic endosomal SNARE proteins in cultured hippocampal neurons, we demonstrate that part of the recycling pool bearing the endosomal Q–SNARE Syntaxin 7 (Stx7) is preferentially mobilized for release during high–frequency repetitive stimulation. Recruitment of the SV pool marked with the Stx7–reporter requires high intra–terminal Ca2+concentrations and actin polymerization. Furthermore, disruption of Stx7 function by overexpressing the N–terminal domain selectively abolished this pool. Thus, our data indicate that endosomal membrane fusion involving Stx7 is essential for adaptation of synapses to respond high-frequency repetitive stimulation.
Comparing spatial null models for brain maps
Authors: Markello Ross D. , Misic Bratislav
Published: August 2020

Technological and data sharing advances have led to a proliferation of high-resolution structural and functional maps of the brain. Modern neuroimaging research increasingly depends on identifying correspondences between the topographies of these maps; however, most standard methods for statistical inference fail to account for their spatial properties. Recently, multiple methods have been developed to generate null distributions that preserve the spatial autocorrelation of brain maps and yield more accurate statistical estimates. Here, we comprehensively assess the performance of ten published null frameworks in statistical analyses of neuroimaging data. To test the efficacy of these frameworks in situations with a known ground truth, we first apply them to a series of controlled simulations and examine the impact of data resolution and spatial autocorrelation on their family-wise error rates. Next, we use each framework with two empirical neuroimaging datasets, investigating their performance when testing (1) the correspondence between brain maps (e.g., correlating two activation maps) and (2) the spatial distribution of a feature within a partition (e.g., quantifying the specificity of an activation map within an intrinsic functional network). Finally, we investigate how differences in the implementation of these null models may impact their performance. In agreement with previous reports, we find that naive null models that do not preserve spatial autocorrelation consistently yield elevated false positive rates and unrealistically liberal statistical estimates. While spatially-constrained null models yielded more realistic, conservative estimates, even these frameworks suffer from inflated false positive rates and variable performance across analyses. Throughout our results, we observe minimal impact of parcellation and resolution on null model performance. Altogether, our findings highlight the need for continued development of statistically-rigorous methods for comparing brain maps. The present report provides a harmonised framework for benchmarking and comparing future advancements.
Metabarcoding, direct stomach observation and stable isotope analysis reveal a highly diverse diet for the invasive green crab in Atlantic Patagonia
Authors: Cordone Georgina , Lozada Mariana , Vilacoba Elisabet , Thalinger Bettina , Bigatti Gregorio , Lijtmaer Darío A. , Steinke Dirk , Galván David E.
Published: August 2020

The European green crabCarcinus maenasand its sister speciesC. aestuariiare highly invasive species causing damage to coastal ecosystems and contributing to severe economic losses worldwide.C. maenaswas first detected at the Atlantic Patagonian coast in 2001. In this work, we studied the diet of the green crab in a recently invaded location in Golfo Nuevo, using three complementary techniques: direct stomach observation, metabarcoding of gut content and stable isotope analysis. Direct stomach observation and metabarcoding showed that green crabs have a broad omnivorous diet, ingesting most of the phyla present in the study area. Gut content metabarcoding allowed a detailed description of algal diversity and revealed other taxa that went unnoticed in the visual stomach analysis. Stable isotope analysis showed that the major contribution to the crabs’ diet was from the phytoplankton chain (by bivalve consumption) and not directly from algae. This study approach combining three complementary techniques also allowed us to detect some differences in the diet between sexes, which suggests that male and female crabs are not as ecologically equivalent as previously thought. Besides, we detected sequences corresponding toC. aestuariisuggesting that the green crab Patagonian population is a hybrid of both sister species. These findings are key to understanding the impacts green crabs can have on the local ecosystem.
Fibroblast Mechanotransduction Network Predicts Targets for Mechano-Adaptive Infarct Therapies
Authors: Rogers Jesse D. , Richardson William J.
Published: August 2020

Regional control of fibrosis after myocardial infarction is critical for maintaining structural integrity in the infarct while preventing collagen accumulation in non-infarcted areas. Cardiac fibroblasts modulate matrix turnover in response to biochemical and biomechanical cues, but the complex interactions between signaling pathways confounds efforts to develop therapies for regional scar formation. Here, we employed a logic-based ordinary differential equation model of fibroblast mechano-chemo signal transduction to predict matrix protein expression in response to canonical biochemical stimuli and mechanical tension. Functional analysis of mechano-chemo interactions showed extensive pathway crosstalk with tension amplifying, dampening, or reversing responses to biochemical stimuli. Comprehensive drug target screens in low- and high-tension contexts identified 13 mechano-adaptive therapies that promote matrix accumulation in regions where it is needed and reduce matrix levels in regions where it is not needed. Our predictions demonstrate this approach’s utility for discovering context-specific mechanisms mediating fibrosis and druggable targets for spatially resolved therapies.
The dynamic nature of the human Origin Recognition Complex revealed through five cryoEM structures
Authors: Jaremko Matt J. , On Kin Fan , Thomas Dennis R. , Stillman Bruce , Joshua-Tor Leemor
Published: August 2020

Genome replication is initiated from specific origin sites established by dynamic events. The Origin Recognition Complex (ORC) is necessary for orchestrating the initiation process by binding to origin DNA, recruiting CDC6, and assembling the MCM replicative helicase on DNA. Here we report five cryoEM structures of the human ORC (HsORC) that illustrate the native flexibility of the complex. The absence of ORC1 revealed a compact, stable complex of ORC2-5. Introduction of ORC1 opens the complex into several dynamic conformations. Two structures revealed dynamic movements of the ORC1 AAA+ and ORC2 winged-helix domains that likely impact DNA incorporation into the ORC core. Additional twist and pinch motions were observed in an open ORC conformation revealing a hinge at the ORC5·3 interface that may facilitate ORC binding to DNA. Finally, a structure of ORC was determined with endogenous DNA bound in the core revealing important differences between human and yeast origin recognition.
Swimming direction of the glass catfish is responsive to magnetic stimulation
Authors: Hunt Ryan D. , Ashbaugh Ryan C. , Reimers Mark , Udpa Lalita , De Jimenez Gabriela Saldana , Moore Michael , Gilad Assaf A. , Pelled Galit
Published: August 2020

Several marine species have developed a magnetic perception that is essential for navigation and detection of prey and predators. One of these species is the transparent glass catfish that contains an ampullary organ dedicated to sense magnetic fields. Here we examine the behavior of the glass catfish in response to static magnetic fields which will provide valuable insight on function of this magnetic response. By utilizing state of the art animal tracking software and artificial intelligence approaches, we quantified the effects of magnetic fields on the swimming direction of glass catfish. The results demonstrate that glass catfish placed in a radial arm maze, consistently swim away from magnetic fields over 20 µT and show adaptability to changing magnetic field direction and location.
SEMplMe: A tool for integrating DNA methylation effects in transcription factor binding affinity predictions
Authors: Nishizaki Sierra S. , Boyle Alan P.
Published: August 2020

Motivation

Aberrant DNA methylation in transcription factor binding sites has been shown to lead to anomalous gene regulation that is strongly associated with human disease. However, the majority of methylation-sensitive positions within transcription factor binding sites remain unknown. Here we introduce SEMplMe, a computational tool to generate predictions of the effect of methylation on transcription factor binding strength in every position within a transcription factor’s motif.

Results

SEMplMe uses ChIP-seq and whole genome bisulfite sequencing to predict effects of methylation within binding sites. SEMplMe validates known methylation sensitive and insensitive positions within a binding motif, identifies cell type specific transcription factor binding driven by methylation, and outperforms SELEX-based predictions for CTCF. These predictions can be used to identify aberrant sites of DNA methylation contributing to human disease.

Availability and Implementation

SEMplMe is available fromhttps://github.com/Boyle-Lab/SEMplMe.

Contact

apboyle@umich.edu

Supplementary Information

Supplementary data are available atBioinformaticsonline.
Sub-optimal Discontinuous Current-Clamp switching rates lead to deceptive mouse neuronal firing
Authors: Manuel Marin
Published: August 2020

Abstract

Intracellular recordings using sharp microelectrodes often rely on a technique called Discontinuous Current-Clamp to accurately record the membrane potential while injecting current through the same microelectrode. It is well known that a poor choice of DCC switching rate can lead to under-or over-estimation of the cell potential, however, its effect on the cell firing is rarely discussed. Here, we show that sub-optimal switching rates lead to an overestimation of cell excitability. We performed intracellular recordings of mouse spinal motoneurons and recorded their firing in response to pulses and ramps of current in Bridge and DCC mode at various switching rates. We demonstrate that using an incorrect (too low) DCC frequency leads not only to an underestimation of the input resistance, but also, paradoxically, to an artificial overestimation of the firing of these cells: neurons fire at lower current, and at higher frequencies than at higher DCC rates, or than the same neuron recorded in Bridge mode. These effects are dependent on the membrane time constant of the recorded cell, and special care needs to be taken in large cells with very short time constants. Our work highlights the importance of choosing an appropriate DCC switching rate to obtain not only accurate membrane potential readings but also an accurate representation of the firing of the cell.

Significance Statement

Discontinuous Current-Clamp is a technique often used during intracellular recordings in vivo. However, incorrect usage of this technique can lead to incorrect interpretations. Poor choice of the DCC switching rate can lead to under- or over-estimation of the cell potential. In addition, we show here that sub-optimal switching rates lead to an overestimation of the cell excitability.
Bisbee: A proteomics validated analysis package for detecting differential splicing, identifying splice outliers, and predicting splice event protein effects
Authors: Halperin Rebecca F. , Hegde Apurva , Lang Jessica D. , Raupach Elizabeth A. ,   C4RCD Research Group, Legendre Christophe , Liang Winnie S. , LoRusso Patricia M. , Sekulic Aleksandar , Sosman Jeffrey A. , Trent Jeffrey M. , Rangasamy Sampathkumar , Pirrotte Patrick , Schork Nicholas J.
Published: August 2020

Here we present a novel statistical approach to splicing outlier and differential splicing detection, implemented in a software package called Bisbee. We leverage Bisbee’s prediction of protein level effects to benchmark using matched RNAseq and mass spectrometry data from normal tissues. Bisbee exhibits improved sensitivity and specificity over existing approaches. We applied Bisbee to confirm a pathogenic splicing event in a rare disease and to identify tumor-specific splice isoforms associated with an oncogenic splice factor mutation. We also identified common tumor associated splice isoforms replicated in an independent dataset, demonstrating the utility of Bisbee in discovering disease relevant splice variants.