bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does drainage or resection predict subsequent interventions and long-term quality of life in patients with Grade IV pancreatic injuries: A population-based analysis
Authors: Ball Chad G. , Biffl Walter L. , Vogt Kelly , Hameed S. Morad , Parry Neil G. , Kirkpatrick Andrew W. , Kaminsky Matthew 
Published: June 2021

BACKGROUND
Clinical equipoise remains significant for the treatment of Grade IV pancreatic injuries in stable patients (i.e., drainage vs. resection). The literature is poor in regards to experience, confirmed main pancreatic ductal injury, nuanced multidisciplinary treatment, and long-term patient quality of life (QOL). The primary aim was to evaluate the management and outcomes (including long-term QOL) associated with Grade IV pancreatic injuries.

METHODS
All severely injured adult patients with pancreatic trauma (1995–2020) were evaluated (Grade IV injuries compared). Concordance of perioperative imaging, intraoperative exploration, and pathological reporting with a main pancreatic ductal injury was required. Patients with resection of Grade IV injuries were compared with drainage alone. Long-term QOL was evaluated (Standard Short Form-36).

RESULTS
Of 475 pancreatic injuries, 36(8%) were confirmed as Grade IV. Twenty-four (67%) underwent a pancreatic resection (29% pancreatoduodenectomy; 71% extended distal pancreatectomy [EDP]). Patient, injury and procedure demographics were similar between resection and drainage groups (p > 0.05). Pancreas-specific complications in the drainage group included 92% pancreatic leaks, 8% pseudocyst, and 8% walled-off pancreatic necrosis. Among patients with controlled pancreatic fistulas beyond 90 days, 67% required subsequent pancreatic operations (fistulo-jejunostomy or EDP). Among patients whose fistulas closed, 75% suffered from recurrent pancreatitis (67% eventually undergoing a Frey or EDP). All patients in the resection group had fistula closure by 64 days after injury. The median number of pancreas-related health care encounters following discharge was higher in the drainage group (9 vs. 5; p = 0.012). Long-term (median follow-up = 9 years) total QOL, mental and physical health scores were higher in the initial resection group (p = 0.031, 0.022 and 0.017 respectively).

CONCLUSION
The immediate, intermediate and long-term experiences for patients who sustain Grade IV pancreatic injuries indicate that resection is the preferred option, when possible. The majority of drainage patients will require additional, delayed pancreas-targeted surgical interventions and report poorer long-term QOL.

LEVEL OF EVIDENCE
Epidemiology/Prognostic, Level III.
Pregnancy, fertility concerns, and fertility preservation procedures in French breast cancer survivors in the FEERIC national study (on behalf of the Seintinelles research network)
Authors: Mangiardi-Veltin Manon , Sebbag Clara , Rousset-Jablonski Christine , Ray-Coquard Isabelle , Berkach Clémentine , Laot Lucie , Wang Yuting , Abdennebi Inès , Labrosse Julie , Sautter Camille , Toussaint Aullène , Sablone Laura , Laas Enora , Khallouch Sarah , Coussy Florence , Santulli Pietro , Chapron Charles , Bobrie Angelique , Jacot William , Sella Nadir , Dumas Elise , Sénéchal-Davin Claire , Espie Marc , Giacchetti Sylvie , Maitrot Lorraine , Plu-Bureau Geneviève , Coutant Charles , Guerin Julien , Asselain Bernard , Fumoleau Pierre , Rodrigues Manuel , Decanter Christine , Mailliez Audrey , Delrieu Lidia ,   Seintinelles research network, Reyal Fabien , Hamy Anne-Sophie 
Published: June 2021

AbstractObjectiveTo study fertility concerns and oncofertility practices at time of breast cancer (BC) diagnosis.DesignThe FEERIC study (Fertility, Pregnancy, Contraception after BC in France) is a prospective, multicenter study.SettingWeb-based collaborative research platform Seintinelles.Patients517 patients with prior BC diagnosis free from relapse and aged 18 to 43 years at inclusion (from 12th March 2018 to 27th June 2019).InterventionBaseline online self-administered questionnaires.Main Outcome MeasureFertility preservation procedures at BC diagnosis.ResultsMedian age at BC diagnosis was 33.6 years and 424 patients (82.0%) received chemotherapy. Overall, 236 (45.6%) patients were offered specialized oncofertility counseling, 124 (24.0%) underwent one or more FP procedures with material preservation (oocytes n=108, 20.9%; embryos n=31, 6.0%; both oocytes and embryos n=13, 2.5%; ovarian cryopreservation n=6, 1.2%) and 78 patients received gonadotropin-releasing hormone agonists (15.1%). With a median follow-up of 26.7 months after the end of treatments,133 pregnancies (25.7%) had occurred in 85 patients (16.4%), including 20 unplanned pregnancies (15.0%). Most of the pregnancies were spontaneous (n=113, 87.6%), while 16 (12.4%) required medical interventions. Patients who had an unplanned pregnancy were less likely to have received fertility counseling (p=0.02) and contraceptive counseling (p=0.08) at BC diagnosis.ConclusionMost of the patients were not offered proper specialized oncofertility counseling at the time of BC diagnosis. Spontaneous pregnancies after BC were very much more frequent than pregnancies resulting from the use of cryopreserved gametes. Adequate contraceptive counseling seems as important as information about fertility and might prevent unplanned pregnancies.
Does reactogenicity after a second injection of the BNT162b2 vaccine predict spike IgG antibody levels in healthy Japanese subjects?
Authors: Takeuchi Masaaki , Higa Yukie , Esaki Akina , Nabeshima Yosuke , Nakazono Akemi 
Published: June 2021

AbstractAdverse reactions are more common after the second injection of messenger RNA vaccines such as Pfizer/BioNTech’s BNT162b2. We hypothesized that the degree and severity of reactogenicity after the second injection reflects the magnitude of antibody production against the SARS CoV-2 virus spike protein (spike IgG). Blood samples were obtained from 67 healthy Japanese healthcare workers three weeks after the first injection and two weeks after the second injection of the BNT162b2 vaccine to measure spike IgG levels. Using questionnaires, we calculated an adverse event (AE) score (0-11) for each participant. The geometric mean of spike IgG titers increased from 1,047 antibody units (AU/mL) (95% CI: 855−1282 AU/mL) after the first injection to 17,378 AU/mL (14,622−20,663 AU/mL) after the second injection. The median AE score increased from 2 to 5. Spike IgG levels after the second injection were negatively correlated with age and positively correlated with spike IgG after the first injection. AE scores after the second injection were not significantly associated with log-transformed spike IgG after the second injection, when adjusted for age, sex, and log-transformed spike IgG after the first injection. Although the sample size was relatively small, reactogenicity after the second injection may not accurately reflect antibody production.
Developing and testing two arts-based knowledge translation tools for parents about pediatric acute gastroenteritis
Authors: Scott Shannon D. , Le Anne , Hartling Lisa 
Published: June 2021

AbstractCharacterized by vomiting, fever, abdominal pain and diarrhea, acute gastroenteritis (AGE) is a common illness in pediatric populations. In Canada, pediatric AGE accounts for 200,000 emergency visits, 20,000 hospital admissions, and 30 deaths a year. Yet, there continues to be significant practice variations in the treatment of AGE. Knowledge translation (KT) can help close the research-practice gap. In particular, art and stories are powerful mediums that cut across age, culture, language, literacy, and gender barriers.The purpose of this study was to work with parents to develop an e-Book and whiteboard animation video for parents on pediatric AGE. Using a multi-method research process, we developed a 2 minute 57 second video and 39-page e-Book for pediatric AGE. Both tools underwent usability testing with parents in three Canadian emergency department waiting rooms in urban, rural, and remote regions. Focus groups were also conducted with parents in each of the three regions.Overall, parents felt that digital and paper-based KT tools would be beneficial knowledge dissemination mediums. Our study showed that parents positively rated an e-Book and whiteboard animation video for pediatric AGE. These findings demonstrate how working together with key stakeholders can facilitate the development of KT tools for parents that are usable, relevant, and increase parental confidence. Furthermore, the type of KT tool developed is an important decision that may depend on parental preferences as well as when and where parents access the tools.This report should be cited asScott, S.D., Le, A., Hartling, L. (2021). Developing and testing two arts-based knowledge translation tools for parents about pediatric acute gastroenteritis. Internal Technical Report. ECHO Research, University of Alberta.Available at: http://www.echokt.ca/research/technical-reports/
Microbial communities network structure across strong environmental gradients: How do they compare to macroorganisms?
Authors: Arboleda-Baena C.M , Freilich M. A , Pareja C.B , Logares R , De la Iglesia R , Navarrete S.A 
Published: June 2021

AbstractThe way strong environmental gradients shape multispecific assemblages has allowed us to examine a suite of ecological and evolutionary hypotheses about structure, regulation, and community responses to fluctuating environments. But whether the highly diverse co-occurring, free-living microorganisms are shaped in similar ways as macroscopic organisms, across the same gradients, has yet to be addressed in most ecosystems. The ‘everything is everywhere’ hypothesis suggests they are not, at least not to the same extent. Here we characterize the structure of intertidal microbial biofilm communities and compare the intensity of zonation at the ‘species’ level, changes in taxonomic diversity and composition at the community level, and network attributes, with those observed in co-occurring macroalgae and invertebrates. At the level of species and OTUs, for dominant macro and microorganisms respectively, microbes showed less variability across the tidal gradient than macroorganisms. At the community-level, however, microbes and macro-organisms showed similarly strong patterns of tidal zonation, with major changes in composition and relative abundances across tides. Moreover, the proportion of ‘environmental specialists’ in different tidal zones was remarkably similar in micro and macroscopic communities, and taxonomic richness and diversity followed similar trends, with lower values in the high intertidal zone. Network analyses showed similar connectivity and transitivity, despite the large differences in absolute richness between the groups. A high proportion of positive co-occurrences within all tidal zones and mostly negative links between the high and low tidal zones were observed among habitat specialist taxa of micro-and macro-organisms. Thus, our results provide partial support to the idea that microbes are less affected by environmental variability than macroscopic counterparts. At the species-level, the most common microbe species exhibit less variation across tides than most common macroscopic organisms, suggesting the former perceive a more homogeneous environment and/or are more resistant to the associated stress. At the community-level, most indicators of community and network structure across the gradient are similar between microbes and macro-organisms, suggesting that despite orders of magnitude differences in richness and size, these two systems respond to stress gradients, giving rise to zonation patterns.
MP-NeRF: A Massively Parallel Method for Accelerating Protein Structure Reconstruction from Internal Coordinates
Authors: Alcaide Eric , Biderman Stella , Telenti Amalio , Maher M. Cyrus 
Published: June 2021

AbstractThe conversion of proteins between internal and cartesian coordinates is a limiting step in many pipelines, such as molecular dynamics simulations and machine learning models. This conversion is typically carried out by sequential or parallel applications of the Natural extension of Reference Frame (NeRF) algorithm. This work proposes a massively parallel NeRF implementation which, depending on the polymer length, achieves speedups between 400-1200x over the previous state-of-the-art. It accomplishes this by dividing the conversion into three main phases: parallel composition of the monomer backbone, assembly of backbone subunits, and parallel elongation of sidechains; and by batching these computations into a minimal number of efficient matrix operations. Special emphasis is placed on reusability and ease of use. We open source the code (available at https://github.com/EleutherAI/mp_nerf) and provide a corresponding python package.
A habitat class to land cover translation model for mapping Area of Habitat of terrestrial vertebrates
Authors: Lumbierres Maria , Dahal Prabhat Raj , Di Marco Moreno , Butchart Stuart H. M. , Donald Paul F. , Rondinini Carlo 
Published: June 2021

AbstractArea of Habitat (AOH) is defined as the ‘habitat available to a species, that is, habitat within its range’ and is produced by subtracting areas of unsuitable land cover and elevation from the range. Habitat associations are documented using the IUCN Habitats Classification Scheme, and unvalidated expert opinion has been used so far to match habitat to land-cover classes generating a source of uncertainty in AOH maps. We develop a data-driven method to translate IUCN habitat classes to land-cover based on point locality data for 6,986 species of terrestrial mammals, birds, amphibians and reptiles. We extracted the land-cover class at each point locality and matched it to the IUCN habitat class(es) assigned to each species occurring there. Then we modelled each land cover class as a function of IUCN habitat using logistic regression models. The resulting odds ratios were used to assess the strength of the association of each habitat land-cover class. We then compared the performance of our data-driven model with those from a published expert knowledge translation table. The results show that some habitats (e.g. forest and desert) could be more confidently assigned to land-cover classes than others (e.g. wetlands and artificial). We calculated the association between habitat classes and land-cover classes as a continuous variable, but to map AOH, which is in the form of a binary presence/absence, it is necessary to apply a threshold of association. This can be chosen by the user according to the required balance between omission and commission errors. We demonstrate that a data-driven translation model and expert knowledge perform equally well, but the model provides greater standardization, objectivity and repeatability. Furthermore, this approach allows greater flexibility in the use of the results and allows uncertainty to be quantified. Our model can be developed regionally or for different taxonomic groups.
Reward influences the allocation but not the availability of resources in visual working memory
Authors: Brissenden James A. , Adkins Tyler J. , Hsu Yu Ting , Lee Taraz G. 
Published: June 2021

AbstractVisual working memory possesses strict capacity constraints which place limits on the availability of resources for encoding and maintaining information. Studies have shown that prospective rewards improve performance on visual working memory tasks, but it remains unclear whether rewards increase total resource availability or rather influence the allocation of resources without affecting availability. Participants performed a continuous report visual working memory task with oriented grating stimuli. On each trial, participants were presented with a priority cue, which signaled the item most likely to be probed, and a reward cue, which signaled the magnitude of a performance-contingent reward. We showed that rewards decreased recall error for cued items and increased recall error for non-cued items. We further demonstrated that rewards produced a tradeoff in the probability of successfully encoding a cued versus a non-cued item rather than a tradeoff in recall precision or the probability of binding errors. Lastly, we showed that rewards only affected resource allocation when participants were given the opportunity to engage proactive control prior to encoding. These findings indicate that rewards influence the flexible allocation of resources during selection and encoding in visual working memory, but do not augment total capacity.
TrackSOM: mapping immune response dynamics through sequential clustering of time- and disease-course single-cell cytometry data
Authors: Putri Givanna H. , Chung Jonathan , Edwards Davis N. , Marsh-Wakefield Felix , Dervish Suat , Koprinska Irena , King Nicholas J.C. , Ashhurst Thomas M. , Read Mark N. 
Published: June 2021

AbstractMapping the dynamics of immune cell populations over time or disease-course is key to understanding immunopathogenesis and devising putative interventions. We present TrackSOM, an algorithm which delineates cellular populations and tracks their development over a time- or disease-course of cytometry datasets. We demonstrate TrackSOM-enabled elucidation of the immune response to West Nile Virus infection in mice, uncovering heterogeneous sub-populations of immune cells and relating their functional evolution to disease severity. TrackSOM is easy to use, encompasses few parameters, is quick to execute, and enables an integrative and dynamic overview of the immune system kinetics that underlie disease progression and/or resolution.
The cell adhesion molecule Sdk1 shapes assembly of a retinal circuit that detects localized edges
Authors: Rochon Pierre-Luc , Theriault Catherine , Olguin Aline Giselle Rangel , Krishnaswamy Arjun 
Published: June 2021

AbstractNearly 50 different mouse retinal ganglion cell (RGC) types sample the visual scene for distinct features. RGC feature selectivity arises from its synapses with a specific subset of amacrine (AC) and bipolar cell (BC) types, but how RGC dendrites arborize and collect input from these specific subsets remains poorly understood. Here we examine the hypothesis that RGCs employ molecular recognition systems to meet this challenge. By combining calcium imaging and type-specific histological stains we define a family of circuits that express the recognition molecule Sidekick 1 (Sdk1) which include a novel RGC type (S1-RGC) that responds to local edges. Genetic and physiological studies revealed that Sdk1 loss selectively disrupts S1-RGC visual responses which result from a loss of excitatory and inhibitory inputs and selective dendritic deficits on this neuron. We conclude that Sdk1 shapes dendrite growth and wiring to help S1-RGCs become feature selective.
MCGA: a multi-strategy conditional gene-based association framework integrating with isoform-level expression profiles reveals new susceptible and druggable candidate genes of schizophrenia
Authors: Li Xiangyi , Jiang Lin , Xue Chao , Li Mulin Jun , Li Miaoxin 
Published: June 2021

AbstractLinkage disequilibrium and disease-associated variants in non-coding regions make it difficult to distinguish truly associated genes from redundantly associated genes for complex diseases. In this study, we proposed a new conditional gene-based framework called MCGA that leveraged an improved effective chi-squared statistic to control the type I error rates and remove the redundant associations. MCGA initially integrated two conventional strategies to map genetic variants to genes, i.e., mapping a variant to its physically nearby gene and mapping a variant to a gene if the variant is a gene-level expression quantitative trait locus (eQTL) of the gene. We further performed a simulation study and demonstrated that the isoform-level eQTL was more powerful than the gene-level eQTL in the association analysis. Then the third strategy, i.e., mapping a variant to a gene if the variant is an isoform-level eQTL of the gene, was also integrated with MCGA. We applied MCGA to predict the potential susceptibility genes of schizophrenia and found that the potential susceptibility genes identified by MCGA were enriched with many neuronal or synaptic signaling-related terms in the Gene Ontology knowledgebase and antipsychotics-gene interaction terms in the drug-gene interaction database (DGIdb). More importantly, nine susceptibility genes were the target genes of multiple approved antipsychotics in DrugBank. Comparing the susceptibility genes identified by the above three strategies implied that strategy based on isoform-level eQTL could be an important supplement for the other two strategies and help predict more candidate susceptibility isoforms and genes for complex diseases in a multi-tissue context.
Nuclear-cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number
Authors: Gyorfy Matheus Fernandes , Miller Emma R. , Conover Justin L. , Grover Corrinne E. , Wendel Jonathan F. , Sloan Daniel B. , Sharbrough Joel 
Published: June 2021

SummaryThe plant genome is partitioned across three distinct subcellular compartments: the nucleus, mitochondria, and plastids. Successful coordination of gene expression among these organellar genomes and the nuclear genome is critical for plant function and fitness. Whole genome duplication events (WGDs) in the nucleus have played a major role in the diversification of land plants and are expected to perturb the relative copy number (stoichiometry) of nuclear, mitochondrial, and plastid genomes. Thus, elucidating the mechanisms whereby plant cells respond to the cytonuclear stoichiometric imbalance that follow WGDs represents an important yet underexplored question in understanding the evolutionary consequences of genome doubling. We used droplet digital PCR (ddPCR) to investigate the relationship between nuclear and organellar genome copy numbers in allopolyploids and their diploid progenitors in both wheat andArabidopsis. Polyploids exhibit elevated organellar genome copy numbers per cell, largely preserving the cytonuclear stoichiometry observed in diploids despite the change in nuclear genome copy number. To investigate the timescale over which cytonuclear stoichiometry may respond to WGD, we also estimated organellar genome copy number inArabidopsissynthetic autopolyploids and in a haploid-induced diploid line. We observed corresponding changes in organellar genome copy number in these laboratory-generated lines, indicating that at least some of the cellular response to cytonuclear stoichiometric imbalance is immediate following WGD. We conclude that increases in organellar genome copy numbers represent a common response to polyploidization, suggesting that maintenance of cytonuclear stoichiometry is an important component in establishing polyploid lineages.Significance StatementWhole genome duplications (WGD) have the potential to alter the stoichiometric balance between nuclear and organellar genomes. We used two separate diploid-polyploid complexes to show that plant cells with WGD exhibit elevated mitochondrial and plastid genome copy numbers, both immediately in lab-generated lines and in natural polyploids.