bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mortality Rates of Severe Dengue Viral Infection Before and After Implementation of a Revised Guideline for Severe Dengue
Authors: Laoprasopwattana Kamolwish , Khantee Puttichart , Saelim Kantara , Geater Alan 
Published: November 2021

Objectives:
To compare the mortality rate of severe dengue (SD) before and after implementation of a revised SD guideline.

Methods:
Medical records of SD patients <15 years of age hospitalized during 1998–2020 were reviewed. The revised SD guidelines were implemented in 2016, including intensive monitoring of vital signs and intra-abdominal pressure, the release of intra-abdominal pressure in cases of abdominal compartment syndrome (ACS) and the use of N-acetyl cysteine in cases of acute liver failure.

Results:
On initial admission, organ failure including severe bleeding, acute respiratory failure, acute kidney injury and acute liver failure was not significantly different between 78 and 23 patients treated in the pre- and postrevised guideline periods, respectively. After hospitalization, the proportions of patients who developed profound shock (68.8% vs. 41.2%), multiorgan failures (60.4% vs. 73.3%), ACS (37.2% vs. 26.1%) and fatal outcome (33.3% vs. 13.0%) were also not significantly different between the pre- and postrevised guideline periods, respectively. In subgroup analysis, the mortality rates in patients with multiorgan failure (44.1% vs. 15.8%), acute respiratory failure and active bleeding (78.1% vs. 37.5%) and ACS (82.8% vs. 33.3%), respectively, were significantly higher in the pre- than the postrevised guideline periods. The durations of time before the liver function tests returned to normal levels, and the mortality rates in acute liver failure patients treated with and without N-acetyl cysteine were not significantly different.

Conclusions:
Although following the revised guidelines could not prevent organ failure, the mortality rates in patients with multiorgan failure and/or ACS decreased significantly when following the revised guidelines.
Calculated functional joint center positions are highly variable in individuals with unilateral transtibial amputation walking with identical prosthetic ankle-foot devices
Authors: De Asha Alan R. , Barnett Cleveland T. 
Published: November 2021

Background:
Biomechanical modeling of the lower limbs, including prosthetic componentry, makes a number of assumptions that influence the data obtained and their subsequent interpretation. Calculated prosthetic ankle functional joint center (FJC) positions vary between devices and have been suggested as a possible method of comparing device function.

Objectives:
The study aimed to assess the variability of joint center position estimates, calculated using an FJC methodology, in all three planes. This was assessed in participants with unilateral transtibial amputation using an identical prosthetic ankle-foot device during walking on a flat surface.

Study design:
Case series.

Technique:
Three-dimensional motion capture recorded the position of markers placed on the shank and ankle-foot device of five individuals with unilateral transtibial amputation, as they completed 10 trials of level walking using the same ankle-foot device. The FJC between the prosthetic foot and shank segments were calculated for each trial.

Results:
The calculated FJC positions were highly variable across individual participants and within each individual. This variability was observed across all three planes of movement and resulted in calculated joint center positions created beyond the physical boundaries of the prosthetic device.

Conclusions:
Biomechanical data are affected by lower limb and prosthetic device modeling assumptions. Definition of a prosthetic “ankle” joint using an FJC method results in highly variable “ankle” joint center positions when applied to a prosthetic ankle-foot device. Their use should be discouraged to avoid misleading interpretations of data.
Rectal chlamydia infections: implications for reinfection risk, screening, and treatment guidelines
Authors: Lau Andrew , Hocking Jane S. , Kong Fabian Y.S. 
Published: November 2021

Purpose of review
Rectal chlamydia is a prevalent sexually transmissible infection in both men who have sex with men (MSM) and in women. Screening is recommended for MSM but remains controversial for women. The optimal treatment for rectal chlamydia is now conclusive but interpreting and managing positive results remains challenging. Infections among MSM are increasing and strategies are needed to reduce incident infections. This review summarizes recent developments for the screening and management of rectal chlamydia and its implications on reinfection.

Recent findings
Reinfections in MSM may be occurring due to resumption of sex soon after treatment whereas repeat infections in women may occur due to autoinoculation in the absence of sex. Doxycycline is now first-line treatment but its role in chemoprophylaxis remains unclear. False positive results remain an issue, but the development of viability assays may prove useful in future to determine true infections.

Summary
Doxycycline is the first-line treatment for rectal chlamydia and in women may prevent infections at the urogenital site. Viability assays can help to reduce antibiotic use once developed. The role of routine screening of rectal chlamydia in women remains unclear and this debate may soon include asymptomatic infections in MSM.
Error reduction in trauma care: Lessons from an anonymized, national, multicenter mortality reporting system
Authors: Hamad Doulia M. , Mandell Samuel P. , Stewart Ronald M. , Patel Bhavin , Guttman Matthew P. , Williams Phillip , Thomas Arielle , Jerath Angela , Bulger Eileen M. , Nathens Avery B. 
Published: November 2021

BACKGROUND
Twenty years ago, the landmark report To Err Is Human illustrated the importance of system-level solutions, in contrast to person-level interventions, to assure patient safety. Nevertheless, rates of preventable deaths, particularly in trauma care, have not materially changed. The American College of Surgeons Trauma Quality Improvement Program developed a voluntary Mortality Reporting System to better understand the underlying causes of preventable trauma deaths and the strategies used by centers to prevent future deaths. The objective of this work is to describe the factors contributing to potentially preventable deaths after injury and to evaluate the effectiveness of strategies identified by trauma centers to mitigate future harm, as reported in the Mortality Reporting System.

METHODS
An anonymous structured web-based reporting template based on the Joint Commission on Accreditation of Healthcare Organizations taxonomy was made available to trauma centers participating in the Trauma Quality Improvement Program to allow for reporting of deaths that were potentially preventable. Contributing factors leading to death were evaluated. The effectiveness of mitigating strategies was assessed using a validated framework and mapped to tiers of effectiveness ranging from person-focused to system-oriented interventions.

RESULTS
Over a 2-year period, 395 deaths were reviewed. Of the mortalities, 33.7% were unanticipated. Errors pertained to management (50.9%), clinical performance (54.7%), and communication (56.2%). Human failures were cited in 61% of cases. Person-focused strategies like education were common (56.0%), while more effective system-based strategies were seldom used. In 7.3% of cases, centers could not identify a specific strategy to prevent future harm.

CONCLUSION
Most strategies to reduce errors in trauma centers focus on changing the performance of providers rather than system-level interventions such as automation, standardization, and fail-safe approaches. Centers require additional support to develop more effective mitigations that will prevent recurrent errors and patient harm.

LEVEL OF EVIDENCE
Therapeutic/Care Management, level V.
Diversification of plasmids in a genus of pathogenic and nitrogen-fixing bacteria
Authors: Weisberg Alexandra J. , Miller Marilyn , Ream Walt , Grünwald Niklaus J. , Chang Jeff H. 
Published: November 2021

Members of the agrobacteria–rhizobia complex (ARC) have multiple and diverse plasmids. The extent to which these plasmids are shared and the consequences of their interactions are not well understood. We extracted over 4000 plasmid sequences from 1251 genome sequences and constructed a network to reveal interactions that have shaped the evolutionary histories of oncogenic virulence plasmids. One newly discovered type of oncogenic plasmid is a mosaic with three incomplete, but complementary and partially redundant virulence loci. Some types of oncogenic plasmids recombined with accessory plasmids or acquired large regions not known to be associated with pathogenicity. We also identified two classes of partial virulence plasmids. One class is potentially capable of transforming plants, but not inciting disease symptoms. Another class is inferred to be incomplete and non-functional but can be found as coresidents of the same strain and together are predicted to confer pathogenicity. The modularity and capacity for some plasmids to be transmitted broadly allow them to diversify, convergently evolve adaptive plasmids and shape the evolution of genomes across much of the ARC.
This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
Asymmetric and adaptive reward coding via normalized reinforcement learning
Authors: Louie Kenway 
Published: November 2021

AbstractLearning is widely modeled in psychology, neuroscience, and computer science by prediction error-guided reinforcement learning (RL) algorithms. While standard RL assumes linear reward functions, reward-related neural activity is a saturating, nonlinear function of reward; however, the computational and behavioral implications of nonlinear RL are unknown. Here, we show that nonlinear RL incorporating the canonical divisive normalization computation introduces an intrinsic and tunable asymmetry in prediction error coding. At the behavioral level, this asymmetry explains empirical variability in risk preferences typically attributed to asymmetric learning rates. At the neural level, diversity in asymmetries provides a computational mechanism for recently proposed theories of distributional RL, allowing the brain to learn the full probability distribution of future rewards. This behavioral and computational flexibility argues for an incorporation of biologically valid value functions in computational models of learning and decision-making.
Increasing Animal Cognition Research in Zoos
Authors: Garcia-Pelegrin Elias , Clark Fay E. , Miller Rachael 
Published: November 2021

AbstractAnimal cognition covers various mental processes including perception, learning, decision-making and memory, and animal behavior is often used as a proxy for measuring cognition. Animal cognition/behavior research has multiple benefits; it provides fundamental knowledge on animal biology and evolution but can also have applied conservation and welfare applications. Zoos provide an excellent yet relatively untapped resource for animal cognition research, because they house a wide variety of species - many of which are under threat - and allow close observation and relatively high experimental control compared to the wild. Multi-zoo collaboration leads to increased sample size and species representation, which in turn leads to more robust science. However, there are salient challenges associated with zoo-based cognitive research, which are subject-based (e.g., small sample sizes at single zoos, untrained/unhabituated subjects, site effects) and human-based (e.g., time restrictions, safety concerns, and perceptions of animals interacting with unnatural technology or apparatus). We aim to increase the understanding and subsequent uptake of animal cognition research in zoos, by transparently outlining the main benefits and challenges. Importantly, we use our own research (1) a study on novelty responses in hornbills, and (2) a multi-site collaboration called the ‘ManyBirds’ project to demonstrate how challenges may be overcome. These potential options include using ‘drop and go’ apparatuses that require no training, close human contact or animal separation. This article is aimed at zoo animal care and research staff, as well as external researchers interested in zoo-based studies.RESEARCH HIGHLIGHTSZoos are an excellent yet relatively untapped resource for animal cognition research.Zoo cognition research has historically been challenging, and traditional laboratory paradigms often do not translate well to the majority of zoos.Salient challenges of zoo-based cognitive research can be overcome by using less restrictive test apparatuses, limiting animal training and isolation, and subscribing to multi-zoo collaborative programs.
Partial lockdown on unvaccinated individuals promises breaking of fourth COVID-19 wave in Bavaria
Authors: Krebs Tobias , Moeckel Michael J. 
Published: November 2021

AbstractPurpose of this reportThe aim of this rapid communication is a projection of the development of the fourth COVID-19 wave in the federal state of Bavaria in Germany, taking into account different lockdown scenarios especially for unvaccinated individuals. In particular, the number of infections and the occupancy of intensive care facilities are considered.Applied MethodsWe use the agent-based epidemiological simulator Covasim for discussing various epidemiological scenarios. Firstly, we adapt and calibrate our model to reproduce the historical course of the COVID-19 pandemic in Bavaria. For this, we model and integrate numerous public health interventions imposed on the local population. As for some of the political actions rigorous quantification is currently not available, we fit those unknown (free) model parameters to published data on the measured epidemiological dynamics. Finally, we define and analyse scenarios of different lockdown scenarios with restrictions for unvaccinated individuals in different areas of life.Key messageThe results of our simulations show that in all scenarios considered, the number of infections, but also the number of severe cases, exceed previous maximum values. Interventions, especially restrictions on contacts of unvaccinated persons, can still mitigate the impact of the fourth COVID-19 wave on populations substantially. Excluding unvaccinated students from attending classes has only a small impact on the public health burden. However, many severe cases can be prevented by reducing community and/or work related contacts of unvaccinated people, e.g, by achieving high home office rates.
A conserved long intergenic non-coding RNA containing snoRNA sequences, lncCOBRA1, affects Arabidopsis germination and development
Authors: Kramer Marianne C. , Kim Hee Jong , Palos Kyle R. , Garcia Benjamin A. , Lyons Eric , Beilstein Mark A. , Nelson Andrew D.L. , Gregory Brian D. 
Published: November 2021

ABSTRACTLong non-coding RNAs (lncRNAs) are an increasingly studied group of non-protein-coding transcripts with a wide variety of molecular functions gaining attention for their roles in numerous biological processes. Nearly 6,000 lncRNAs have been identified in Arabidopsis thaliana but many have yet to be studied. Here, we examine a class of previously uncharacterized lncRNAs termed CONSERVED INBRASSICA RAPA (lncCOBRA) transcripts that were previously identified for their high level of sequence conservation in the related crop species Brassica rapa, their nuclear-localization and protein-bound nature. In particular, we focus on lncCOBRA1 and demonstrate that its abundance is highly tissue and developmental specific, with particularly high levels early in germination. lncCOBRA1 contains two snoRNAs domains within it, making it the first sno-lincRNA example in a non-mammalian system, though we find that it is processed differently than its mammalian counterparts. We further show that plants lacking lncCOBRA1 display patterns of delayed gemination and are overall smaller than wild-type plants. Lastly, we identify the proteins that interact with lncCOBRA1 and examine the protein-protein interaction network of lncCOBRA1-interacting proteins.
Intrathecal sc-AAV9-CB-GFP: Systemic Distribution Predominates Following Single-Dose Administration in Cynomolgus Macaques
Authors: Meseck Emily K. , Guibinga Ghiabe , Wang Stephen , McElroy Cameron , Hudry Eloise , Mansfield Keith 
Published: November 2021

ABSTRACTBiodistribution of self-complementary adeno-associated virus-9 (scAAV9)–chicken β promoter–green fluorescent protein (GFP) was assessed in juvenile cynomolgus macaques infused intrathecally via lumbar puncture or the intracisterna magna (1.0×1013 or 3.0×1013 vg/animal), with necropsy 28 days later. Our results characterized central nervous system biodistribution compared with systemic organs/tissues by droplet digital polymerase chain reaction for DNA and in situ hybridization. GFP expression was characterized by Meso Scale Discovery electrochemiluminescence immunosorbent assay and immunohistochemistry (IHC). Biodistribution was widespread but variable, with vector DNA and GFP expression greatest in the spinal cord, dorsal root ganglia (DRG), and certain systemic tissues (e.g., liver), with low concentrations in many brain regions despite direct cerebrospinal fluid administration. Transduction and expression were observed primarily in perivascular astrocytes in the brain, with a paucity in neurons. Greater GFP expression was observed in hepatocytes, striated myocytes, cardiomyocytes, spinal cord lower motor neurons, and DRG sensory neurons by IHC. These results suggest caution for use of scAAV9-based intrathecal delivery with the current expression cassette as a modality for neurologic diseases that require widespread brain neuronal expression. This capsid/expression cassette combination may be better suited for diseases that express a secreted protein and/or do not require widespread brain neuronal transduction.
Convergent evolution of “genome guardian” functions in a parasite-specific p53 homolog
Authors: Wendt George , Shiroor Divya A. , Adler Carolyn E. , Collins James J. 
Published: November 2021

SignificanceP53 is a widely studied tumor suppressor that is found throughout metazoans, including invertebrates that do not develop malignancies. The prevailing theory for why this is the case is that P53 originally evolved to protect the germline of early metazoans from genotoxic stress such as UV radiation. In this study, we examine the function of two P53 homologs in the parasitic flatworm Schistosoma mansoni. The first is orthologous to canonical P53, and regulates stem cell maintenance and differentiation. The second P53 gene is a parasite-specific paralog that is required for the normal response to genotoxic stress. This implies that the ability to respond to genotoxic stress in parasitic flatworms may have arisen from convergent evolution.
Deep proteome profiling with reduced carry over using superficially porous microfabricated nanoLC columns
Authors: Stejskal Karel , de Beeck Jeff Op , Matzinger Manuel , Dürnberger Gerhard , Boychenko Alexander , Jacobs Paul , Mechtler Karl 
Published: November 2021

ABSTRACTIn the field of LC-MS based proteomics, increases in sampling depth and proteome coverage have mainly been accomplished by rapid advances in mass spectrometer technology. The comprehensiveness and quality of data that can be generated do however also depend on the performance provided by nano liquid chromatography (nanoLC) separations. Proper selection of reversed-phase separation columns can be important to provide the MS instrument with peptides at the highest possible concentration and separated at the highest possible resolution. In the current contribution, we evaluate the use of prototype generation 2 μPAC nanoLC columns which use C18 functionalized superficially porous micro pillars as a stationary phase. When comparing to traditionally used fully porous silica stationary phases, more precursors could be characterized when performing single shot data-dependent LC-MS/MS analyses of a human cell line tryptic digest. Up to 30% more protein groups and 60% more unique peptides were identified for short gradients (10 min) and limited sample amounts (10-100 ng of cell lysate digest). With LC-MS gradient times of 10, 60, 120 and 180 min, we respectively identified 2252, 6513, 7382 and 8174 protein groups with 25, 500, 1000 and 2000 ng of sample loaded on column. Reduction of sample carry over to the next run (up to 2 to 3%) and decreased levels of methionine oxidation (up to 3-fold) were identified as additional figures of merit. When analyzing a disuccinimidyl dibutyric urea (DSBU) crosslinked synthetic library, 29 to 59 more unique crosslinked peptides could be identified at a experimentally validated false discovery rate (FDR) of 1-2%.
Less is worse than none: ineffective adaptive foraging can destabilise food webs
Authors: Ho Hsi-Cheng , Pawar Samraat , Tylianakis Jason M. 
Published: November 2021

AbstractConsumers can potentially adjust their diet in response to changing resource abundances, thereby achieving better foraging payoffs. Although previous work has explored how such adaptive foraging scales up to determine the structure and dynamics of food webs, consumers may not be able to perform perfect diet adjustment due to sensory or cognitive limitations. Whether the effectiveness of consumers’ diet adjustment alters food-web consequences remains unclear.Here, we study how adaptive foraging, specifically the effectiveness (i.e. rate) with which consumers adjust their diet, influences the structure, dynamics, and overall species persistence in synthetic food webs.We model metabolically-constrained optimal foraging as the mechanistic basis of adaptive diet adjustment and ensuing population dynamics within food webs. We compare food-web dynamical outcomes among simulations sharing initial states but differing in the effectiveness of diet adjustment.We show that adaptive diet adjustment generally makes food-web structure resilient to species loss. Effective diet adjustment that maintains optimal foraging in the face of changing resource abundances facilitates species persistence in the community, particularly reducing the extinction of top consumers. However, a greater proportion of intermediate consumers goes extinct as optimal foraging becomes less-effective and, unexpectedly, slow diet adjustment leads to higher extinction rates than no diet adjustment at all. Therefore, food-web responses cannot be predicted from species’ responses in isolation, as even less-effective adaptive foraging benefits individual species (better than non-adaptive) but can harm species’ persistence in the food web as a whole (worse than non-adaptive).Whether adaptive foraging helps or harms species coexistence has been contradictory in literature Our finding that it can stabilise or destabilise the food web depending on how effectively it is performed help reconcile this conflict. Inspired by our simulations, we deduce that there may exist a positive association between consumers’ body size and adaptive-foraging effectiveness in the real world. We also infer that such effectiveness may be higher when consumers cognise complete information about their resources, or when trophic interactions are driven more by general traits than by specific trait-matching. We thereby suggest testable hypotheses on species persistence and food-web structure for future research, in both theoretical and empirical systems.