bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a reliable preoperative risk stratification system for phacoemulsification
Authors: Mylona Ioanna , Dermenoudi Maria , Glynatsis Mikes , Ziakas Nikolaos , Tsinopoulos Ioannis 
Published: April 2020

Purpose:
To present a statistically validated risk classification system for intraoperative complications in cataract surgery.

Setting:
2nd Department of Ophthalmology, Aristotle University of Thessaloniki, Thessaloniki, Greece.

Design:
Prospective observational study.

Methods:
All patients underwent phacoemulsification surgery by experienced, high-volume surgeons for cases with intraoperative complications. The presence of several risk factors was statistically assessed with the help of multiple correspondence analysis to determine the more reliable rank categorization for severity and to calculate a total risk score.

Results:
This study included 1572 consecutive patients. The proposed system had 3 risk groups and a no-risk group and had high statistical reliability. A comparison of this system against a previously asserted empirical system showed higher internal reliability.

Conclusions:
Previous efforts to construct a risk classification system for intraoperative complications in cataract surgery have been empirically defined and tested against practice-as-usual. The system in this study quantified risk more accurately and provided an experienced clinician with a reliable means of assessing the preoperational likelihood of intraoperative complications.
Plastic Surgery and the COVID-19 Pandemic
Authors: Ozturk Cemile Nurdan , Kuruoglu Doga , Ozturk Can , Rampazzo Antonio , Gurunian (Gurunluoglu) Raffi 
Published: April 2020

Background
A novel coronavirus disease (COVID-19) was first reported in December 2019 in China and was soon declared a pandemic by the World Health Organization. Many elective and nonessential surgeries were postponed worldwide in an effort to minimize spread of disease, as well as to conserve resources. Our goal with this article is to review current practice guidelines in setting of the COVID-19 pandemic, based on available data and literature.

Methods
Websites pertaining to surgical and medical societies, and government agencies were reviewed, along with recently published literature to identify recommendations related to COVID-19 and plastic surgery procedures.

Results
Clinical practice modifications are recommended during the pandemic in outpatient and perioperative settings. Use of personal protective equipment is critical for aerosol-generating procedures, such as surgery in the head and neck area. Care for trauma and malignancy should continue during the pandemic; however, definitive reconstruction could be delayed for select cases. Specific recommendations were made for surgical treatment of cancer, trauma, and semiurgent reconstructive procedures based on available data and literature.

Conclusions
The risk and benefit of each reconstructive procedure should be carefully analyzed in relation to necessary patient care, minimized COVID-19 spread, protection of health care personnel, and utilization of resources. Recommendations in this article should be taken in the context of each institute's resources and prevalance of COVID-19 in the region. It should be emphasized that the guidelines provided are a snapshot of current practices and are subject to change as the pandemic continues to evolve.
Autosomal Dominant Polycystic Kidney Disease Is a Risk Factor for Posttransplantation Diabetes Mellitus: An Updated Systematic Review and Meta-analysis
Authors: Culliford Alice , Phagura Nuvreen , Sharif Adnan 
Published: April 2020

Background.
Autosomal dominant polycystic kidney disease (ADPKD) is linked with risk for posttransplantation diabetes mellitus (PTDM), but this association has methodologic limitations like diagnostic criteria. The aim of this study was to use contemporary diagnostic criteria for PTDM and explore any risk association for kidney transplant recipients with ADPKD.

Methods.
We undertook a retrospective analysis of 1560 nondiabetic kidney transplant recipients between 2007 and 2018 at a single center, of whom 248 (15.9%) had ADPKD. Local/national data were linked for every patient, with manual data capture of PTDM diagnosis by International Consensus Recommendations. We then pooled our data with eligible studies after an updated systematic review and performed a meta-analysis to estimate the pooled effect.

Results.
Comparing ADPKD versus non-ADPKD kidney transplant recipients, PTDM risk was not significantly different at our center (19.4% versus 14.9%, respectively; P = 0.085). ADPKD patients who developed PTDM were older, borderline heavier, and less likely to be recipients of living kidney donor compared with ADPKD patients who remained free of PTDM. Systematic review of the literature identified 14 eligible studies, of which 8 had a PTDM diagnosis consistent with Consensus recommendations. In the meta-analysis, we observed an increased odds ratio (OR) of kidney transplant recipients with ADPKD developing PTDM regardless of all study inclusion (OR, 1.98; 95% confidence interval, 1.43-2.75) or restricted study inclusion based on robust PTDM diagnostic criteria (OR, 1.81; 95% confidence interval, 1.16-2.83).

Conclusions.
ADPKD kidney transplant candidates should be counseled of their increased risk for PTDM, with further work warranted to investigate any underlying metabolic pathophysiology.
Estimating the early death toll of COVID-19 in the United States
Authors: Weinberger Daniel M. , Cohen Ted , Crawford Forrest W. , Mostashari Farzad , Olson Don , Pitzer Virginia E , Reich Nicholas G , Russi Marcus , Simonsen Lone , Watkins Anne , Viboud Cecile 
Published: April 2020

ABSTRACTBackgroundEfforts to track the severity and public health impact of the novel coronavirus, COVID-19, in the US have been hampered by testing issues, reporting lags, and inconsistency between states.Evaluating unexplained increases in deaths attributed to broad outcomes, such as pneumonia and influenza (P&I) or all causes, can provide a more complete and consistent picture of the burden caused by COVID-19.MethodsWe evaluated increases in the occurrence of deaths due to P&I above a seasonal baseline (adjusted for influenza activity) or due to any cause across the United States in February and March 2020. These estimates are compared with reported deaths due to COVID-19 and with testing data.ResultsThere were notable increases in the rate of death due to P&I in February and March 2020. In a number of states, these deaths pre-dated increases in COVID-19 testing rates and were not counted in official records as related to COVID-19. There was substantial variability between states in the discrepancy between reported rates of death due to COVID-19 and the estimated burden of excess deaths due to P&I. The increase in all-cause deaths in New York and New Jersey is 1.5-3 times higher than the official tally of COVID-19 confirmed deaths or the estimated excess death due to P&I.ConclusionsExcess P&I deaths provide a conservative estimate of COVID-19 burden and indicate that COVID-19-related deaths are missed in locations with inadequate testing or intense pandemic activity.RESEARCH IN CONTEXTEvidence before this studyDeaths due to the novel coronavirus, COVID-19, have been increasing sharply in the United States since mid-March. However, efforts to track the severity and public health impact of COIVD-19 in the US have been hampered by testing issues, reporting lags, and inconsistency between states. As a result, the reported number of deaths likely represents an underestimate of the true burden.Added Value of this studyWe evaluate increases in deaths due to pneumonia across the United States and relate these increases to the number of reported deaths due to COVID-19 in different states and evaluate the trajectories of these increases in relation to the volume of testing and to indicators of COVID-19 morbidity. This provides a more complete picture of mortality due to COVID-19 in the US and demonstrates how delays in testing led to many coronavirus deaths not being counted in certain states.Implications of all the available evidenceThe number of deaths reported to be due to COVID-19 represents just a fraction of the deaths linked to the pandemic. Monitoring trends in deaths due to pneumonia and all-causes provides a more complete picture of the tool of the disease.
Inequalities in COVID19 mortality related to ethnicity and socioeconomic deprivation
Authors: Rose Tanith C. , Mason Kate , Pennington Andy , McHale Philip , Buchan Iain , Taylor-Robinson David C. , Barr Ben 
Published: April 2020

AbstractBackgroundInitial reports suggest that ethnic minorities may be experiencing more severe coronavirus disease 2019 (COVID19) outcomes. We therefore assessed the association between ethnic composition, income deprivation and COVID19 mortality rates in England.MethodsWe performed a cross-sectional ecological analysis across England’s upper-tier local authorities. We assessed the association between the proportion of the population from Black, Asian and Minority Ethnic (BAME) backgrounds, income deprivation and COVID19 mortality rates using multivariable negative binomial regression, adjusting for population density, proportion of the population aged 50–79 and 80+ years, and the duration of the epidemic in each area.FindingsLocal authorities with a greater proportion of residents from ethnic minority backgrounds had statistically significantly higher COVID19 mortality rates, as did local authorities with a greater proportion of residents experiencing deprivation relating to low income. After adjusting for income deprivation and other covariates, each percentage point increase in the proportion of the population from BAME backgrounds was associated with a 1% increase in the COVID19 mortality rate [IRR=1.01, 95%CI 1.01–1.02]. Each percentage point increase in the proportion of the population experiencing income deprivation was associated with a 2% increase in the COVID19 mortality rate [IRR=1.02, 95%CI 1.01–1.04].InterpretationThis study provides evidence that both income deprivation and ethnicity are associated with greater COVID19 mortality. To reduce these inequalities, Government needs to target effective control and recovery measures at these disadvantaged communities, proportionate to their greater needs and vulnerabilities, during and following the pandemic.FundingNational Institute of Health Research; Medical Research Council
Searching the Sigmoid-type trend in Lock Down period covid19 data of India and its different states
Authors: Mondal Supriya , Ghosh Sabyasachi 
Published: April 2020

AbstractWe have worked on imported covid19 cases of India, detected after declaration of lock down. They are marked as hidden travelers, who are detected later during 1-2 weeks period of lock down. We have investigated the impact of those travelers on selective 15 states, having large number cases. Among them 5 states have faced a noticeable effect on their data profile, although its overall effect in country level is quite negligible. Searching the Sigmoid trends of all 15 states, we have identified 3 categories depending upon latest data of new case with respect to the peak value of Sigmoid functions. Based on our optimistic predicted curves, ongoing lock down period might be enough for getting marginal values of new cases for KL, HR, JK, TN and AP but the reamining of 15 states might need a third phase of lock down or alternative preventive measures.
Curricular change in a medical school: a new method for analysis of students’ academic pathways
Authors: Sánchez Damián Canales , Godínez Tomás Bautista , Salinas J. Gerardo Moreno , García-Minjares Manuel , Sánchez-Mendiola Melchor 
Published: April 2020

AbstractBackgroundCurricular changes in medical schools occur due to advances in medical sciences, but its evaluation is limited and fragmented, with scant data of students’ success as they progress through the program. Longitudinal follow-up can be “natural experiments” to explore innovative methodologies.ObjectiveTo propose a method for analyzing students’ academic pathways, and identify changes associated with a medical school curricular reform.MethodsWe analyzed the academic pathways of students throughout the program in two different curricula (1993 and 2010), at the National Autonomous University of Mexico (UNAM) Faculty of Medicine. Advancement of each student in the program was calculated with the “academic trajectory” using the accumulated credits in a defined time period, and the percentage of students that completed the credits for each stage of the curriculum. The theoretical framework is based on the “life course” approach, applying concepts of trajectory, transition and state. Data was analyzed with R software and TraMineR algorithm.ResultsFive student cohorts of the older curriculum were studied (classes of 1994, 1995, 1996, 2004 and 2005), and two cohorts of the new curriculum (2011, 2012), a population of 6829 students. Students in the newer curriculum had a faster, more timely and efficient advancement in academic pathways, than cohorts in the older one. There was a higher percentage of students with “regular” trajectory (without failed courses) in the newer curriculum. Regularity is a straightforward metric that allows identification of complex curricular changes’ associated effects.ConclusionsAnalysis of students’ academic pathways offers valuable information to evaluate curricular changes, which is difficult to obtain with traditional cross-sectional studies. The study does not provide proof of causality regarding the educational impact of different programs, although it can be useful to complement the array of program evaluation strategies in higher education.
A collection of designed peptides to target SARS-Cov-2 – ACE2 interaction: PepI-Covid19 database
Authors: Molina Ruben , Oliva Baldo , Fernandez-Fuentes Narcis 
Published: April 2020

AbstractThe angiotensin-converting enzyme 2 is the cellular receptor used by SARS coronavirus SARS-CoV and SARS-CoV-2 to enter the cell. Both coronavirus use the receptor-binding domain (RBD) of their viral spike protein to interact with ACE2. The structural basis of these interactions are already known, forming a dimer of ACE2 with a trimer of the spike protein, opening the door to target them to prevent the infection. Here we present PepI-Cov19 database, a repository of peptides designed to target the interaction between the RDB of SARS-CoV-2 and ACE2 as well as the dimerization of ACE2 monomers. The peptides were modelled using our method PiPreD that uses native elements of the interaction between the targeted protein and cognate partner that are subsequently included in the designed peptides. These peptides recapitulate stretches of residues present in the native interface plus novel and highly diverse conformations that preserve the key interactions on the interface. PepI-Covid19 database provides an easy and convenient access to this wealth of information to the scientific community with the view of maximizing its potential impact in the development of novel therapeutic agents.
Robust gene expression-based classification of cancers without normalization
Authors: Jiang Aixiang , Hilton Laura K. , Tang Jeffrey , Rushton Christopher K. , Grande Bruno M. , Scott David W. , Morin Ryan D. 
Published: April 2020

AbstractBinary classification using gene expression data is commonly used to stratify cancers into molecular subgroups that may have distinct prognoses and therapeutic options. A limitation of many such methods is the requirement for comparable training and testing data sets. Here, we describe and demonstrate aself-training implementation ofprobabilityratio-based classificationpredictionscore (PRPS-ST) that facilitates the porting of existing classification models to other gene expression data sets. We demonstrate its robustness through application to two binary classification problems in diffuse large B-cell lymphoma using a diverse variety of gene expression data types and normalization methods.
Antibody repertoire and gene expression dynamics of diverse human B cell states during affinity maturation
Authors: King Hamish W , Orban Nara , Riches John C , Clear Andrew J , Warnes Gary , Teichmann Sarah A , James Louisa K 
Published: April 2020

AbstractIn response to antigen challenge, B cells clonally expand, undergo selection and differentiate to produce mature B cell subsets and high affinity antibodies. However, the interplay between dynamic B cell states and their antibody-based selection is challenging to decipher in primary human tissue. We have applied an integrated analysis of bulk and single-cell antibody repertoires paired with single-cell transcriptomics of human B cells undergoing affinity maturation. We define unique gene expression and antibody repertoires of known and novel B cell states, including a pre-germinal centre state primed to undergo class switch recombination. We dissect antibody class-dependent gene expression of germinal centre and memory B cells to find that class switching prior to germinal centre entry dictates the capacity of B cells to undergo antibody-based selection and differentiate. Together, our analyses provide unprecedented resolution into the gene expression and selection dynamics that shape B cell-mediated immunity.
BCL-XL is essential for the protection from secondary anemia caused by radiation-induced fatal kidney damage
Authors: Brinkmann Kerstin , Waring Paul , Glaser Stefan , Wimmer Verena , Nhu Duong , Whitehead Lachlan , Delbridge Alex RD , Lessene Guillaume , Herold Marco J , Kelly Gemma L , Grabow Stephanie , Strasser Andreas 
Published: April 2020

AbstractStudies of gene-targeted mice identified the roles of the different pro-survival BCL-2 proteins during embryogenesis, but less is known about the roles of these proteins in adults, including in the response to cytotoxic stresses, such as treatment with anti-cancer agents. We investigated the role of BCL-XL in adult mice using a strategy where prior bone marrow transplantation allowed for loss of BCL-XL exclusively in non-hematopoietic tissues to prevent anemia caused by BCL-XL-deficiency in erythroid cells. Unexpectedly, the combination of total-body γ-irradiation (TBI) and genetic loss ofBcl-xcaused secondary anemia resulting from chronic renal failure due to apoptosis of renal tubular epithelium with secondary obstructive nephropathy. These findings identify a critical protective role of BCL-XL in the adult kidney and inform on the use of BCL-XL inhibitors in combinations with DNA damage-inducing drugs for cancer therapy.SummaryThe inducible loss of BCL-XL in all cells of adult mice causes primary anemia due to apoptosis of erythroid and megakaryocytic cell populations. In contrast γ-radiation plus loss of BCL-XL in all cells except hematopoietic cells causes secondary anemia resulting from kidney damage.
Characterization of brown adipose tissue thermogenesis in the naked mole-rat (Heterocephalus glaber), a poikilothermic mammal
Authors: Oiwa Yuki , Oka Kaori , Yasui Hironobu , Higashikawa Kei , Bono Hidemasa , Kawamura Yoshimi , Miyawaki Shingo , Watarai Akiyuki , Kikusui Takefumi , Shimizu Atsushi , Okano Hideyuki , Kuge Yuji , Kimura Kazuhiro , Okamatsu-Ogura Yuko , Miura Kyoko 
Published: April 2020

AbstractThe naked mole-rat (NMR) is a poikilothermic mammal that forms eusocial colonies consisting of one breeding queen, several breeding kings, and subordinates. Despite their poikilothermic feature, NMRs possess brown adipose tissue (BAT), which in homeothermic mammals induces thermogenesis in cold environments. However, NMR-BAT thermogenic potential is controversial, and its physiological roles are unknown. Here, we show that NMR-BAT has beta-3 adrenergic receptor (ADRB3)-dependent thermogenic potential, which contributes to thermogenesis in the isolated queen in non-cold environments. NMR-BAT expressed several brown adipocyte marker genes and showed noradrenaline-dependent thermogenic activityin vitroandin vivo. Although our ADRB3 inhibition experiments revealed that NMR-BAT thermogenesis slightly delays the decrease in body temperature in a cold environment, it was insufficient to maintain the body temperatures of the NMRs. In a non-cold environment, NMRs are known to increase their body temperature by a heat-sharing behavior. Interestingly, we found that the body temperatures of NMRs isolated from the colony were also significantly higher than the ambient temperature. We also show that queens, but not subordinates, induce BAT thermogenesis in isolated, non-cold conditions. Our research provides novel insights into the role and mechanism of thermoregulation in this unique poikilothermic mammal.
High-resolution cryo-EM structure of urease from the pathogenYersinia enterocolitica
Authors: Righetto Ricardo D. , Anton Leonie , Adaixo Ricardo , Jakob Roman P. , Zivanov Jasenko , Mahi Mohamed-Ali , Ringler Philippe , Schwede Torsten , Maier Timm , Stahlberg Henning 
Published: April 2020

AbstractUrease converts urea into ammonia and carbon dioxide and makes urea available as a nitrogen source for all forms of life except animals. In human bacterial pathogens, ureases also aid in the invasion of acidic environments such as the stomach by raising the surrounding pH. Here, we report the structure of urease from the pathogenYersinia enterocoliticaat better than 2 Å resolution from cryo-electron microscopy.Y. enterocoliticaurease is a dodecameric assembly of a trimer of three protein chains, ureA, ureB and ureC. The high data quality enables detailed visualization of the urease bimetal active site and of the impact of radiation damage. Our data are of sufficient quality to support drug development efforts.
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation
Authors: Niederer Rachel O. , Rojas-Duran Maria F. , Zinshteyn Boris , Gilbert Wendy V. 
Published: April 2020

AbstractTranslational control shapes the proteome in normal and pathophysiological conditions. Current high-throughput approaches reveal large differences in mRNA-specific translation activity but cannot identify the causative mRNA features. We developed direct analysis of ribosome targeting (DART) and used it to dissect regulatory elements within 5′ untranslated regions that confer thousand-fold differences in ribosome recruitment in biochemically accessible cell lysates. Using DART, we identified novel translational enhancers and silencers, determined a functional role for most alternative 5′ UTR isoforms expressed in yeast, and revealed a general mode of increased translation via direct binding to a core translation factor. DART enables systematic assessment of the translational regulatory potential of 5′ UTR variants, whether native or disease-associated, and will facilitate engineering of mRNAs for optimized protein production in various systems.HighlightsDART illuminates thousand-fold differences in 5′ UTR-specific translation activitySNPs and alternative 5′ UTR isoforms affect ribosome recruitment significantlyInhibitory effects of RNA structures are highly dependent on 5′ UTR context5′ UTR motifs bind initiation factors directly, broadly stimulating translation