bluuebunny/crossref_metadata_2025_split huggingface dataset:
Readmission for infection after blunt splenic injury: A national comparison of management techniques
Authors: Cioci Alessia C. , Parreco Joshua P. , Lindenmaier Laurence B. , Olufajo Olubode A. , Namias Nicholas , Askari Reza , DeRosa Luis , Rattan Rishi 
Published: December 2019

BACKGROUND
As nonoperative management (NOM) of blunt splenic injury (BSI) increases, understanding risks, especially infectious complications, becomes more important. There are no national studies on BSI outcomes that track readmissions across hospitals. Prior studies demonstrate that infection is a major cause of readmission after trauma and that a significant proportion is readmitted to different hospitals. The purpose of this study was to compare nationwide outcomes of different treatment modalities for BSI including readmissions to different hospitals.

METHODS
The Nationwide Readmissions Database for 2010 to 2014 was queried for patients 18 years to 64 years old admitted nonelectively with a primary diagnosis of BSI. Organ space infection; a composite infectious incidence of surgical site infection (SSI), urinary tract infection, and pneumonia; and sepsis were identified in three groups: NOM, splenic artery embolization (SAE), and operative management (OM). Rates of infection were quantified during index admission and 30-day and 1-year readmission. Multivariable logistic regression was performed. Results were weighted for national estimates.

RESULTS
Of the 37,986 patients admitted for BSI, 54.1% underwent NOM, 12.2% SAE, and 33.7% OM. Compared with OM and NOM, SAE had the highest rates of organ space SSI at 1 year (3.9% vs. 2.2% vs. 1.7%, p < 0.001). Compared with NOM, at 1 year, SAE had higher rates of infection (17.2% vs. 8.1%, p < 0.001) and sepsis (3.2% vs. 1.1%, p < 0.001). Compared with NOM, SAE had an increased risk of infection (odds ratio [OR], 1.24; 95 confidence interval [95% CI], 1.10–1.39; p < 0.001) and sepsis (OR, 1.37; 95% CI, 1.06–1.76; p < 0.001) at 1 year. At 1 year, SAE had increased risk of organ space SSI (OR, 1.99; 1.60–2.47; p < 0.001) but OM did not.

CONCLUSION
Blunt splenic injury treated with SAE is at increased risk of both immediate and long-term infectious complications. Despite being considered splenic preservation, surgeons should be aware of these risks and incorporate such knowledge into their practice accordingly.

LEVEL OF EVIDENCE
Epidemiological study, level IV.
Preoperative computed tomography is poor in detecting tumors of the appendix among patients with acute appendicitis: A cohort study of 5,224 appendectomies
Authors: Kangaspunta Helmi , Tahkola Kyösti , Wirta Erkki-Ville , Kotaluoto Sannamari , Laukkarinen Johanna , Ukkonen Mika 
Published: December 2019

BACKGROUND
Neoplastic processes are among the known etiologies for acute appendicitis. While conservative treatment with antibiotics alone has been proposed as a treatment for uncomplicated appendicitis, the presence of tumors should be excluded when offering patients this option. The aim of this study was to assess the accuracy of computed tomography (CT) in detecting appendiceal tumors.

METHOD
Consecutive patients operated on for acute appendicitis between January 2007 and October 3, 2018, in our university hospital were included. Whenever appendiceal tumor was histopathologically confirmed, CT interpretations and surgical reports were carefully reviewed. All CT scans were reanalyzed by consultant body radiologists. Discrepancies between the preliminary and final radiological interpretations were noted.

RESULTS
A total of 5,224 patients underwent appendectomy, of whom 4,766 had histopathologically confirmed acute appendicitis. Eighty-four patients (median, 61 (13–89) years; 54% female) were diagnosed with appendiceal tumor. Fifty-two patients (62%) had uncomplicated appendicitis. Although incidence of tumors was associated with older age, tumors were found in all ages. The share of tumors increased from 1.7% to 3.0%/year during the study. The most common tumors were neuroendocrine tumors (n = 33), low-grade appendiceal mucinous neoplasms (n = 14), and adenocarcinomas (n = 11). Sixty-one patients (73%) underwent preoperative CT. Computed tomography interpretation during on-call hours suspected tumor in only one case (3.4%) with invasive tumor, and in five cases (16%) with noninvasive tumor.

CONCLUSION
Appendiceal tumors are possible findings in appendix specimens, and most patients had uncomplicated acute appendicitis. In light of findings we conclude that CT cannot be used to exclude neoplastic etiology underlying acute appendicitis.

LEVEL OF EVIDENCE
Diagnostic, level IV.
The American Association for the Surgery of Trauma renal injury grading scale: Implications of the 2018 revisions for injury reclassification and predicting bleeding interventions
Authors: Keihani Sorena , Rogers Douglas M. , Putbrese Bryn E. , Anderson Ross E. , Stoddard Gregory J. , Nirula Raminder , Luo-Owen Xian , Mukherjee Kaushik , Morris Bradley J. , Majercik Sarah , Piotrowski Joshua , Dodgion Christopher M. , Schwartz Ian , Elliott Sean P. , DeSoucy Erik S. , Zakaluzny Scott , Sherwood Brenton G. , Erickson Bradley A. , Baradaran Nima , Breyer Benjamin N. , Fick Cameron N. , Smith Brian P. , Okafor Barbara U. , Askari Reza , Miller Brandi D. , Santucci Richard A. , Carrick Matthew M. , Allen LaDonna , Norwood Scott , Hewitt Timothy , Burks Frank N. , Heilbrun Marta E. , Gross Joel A. , Myers Jeremy B. 
Published: December 2019

BACKGROUND
In 2018, the American Association for the Surgery of Trauma (AAST) published revisions to the renal injury grading system to reflect the increased reliance on computed tomography scans and non-operative management of high-grade renal trauma (HGRT). We aimed to evaluate how these revisions will change the grading of HGRT and if it outperforms the original 1989 grading in predicting bleeding control interventions.

METHODS
Data on HGRT were collected from 14 Level-1 trauma centers from 2014 to 2017. Patients with initial computed tomography scans were included. Two radiologists reviewed the scans to regrade the injuries according to the 1989 and 2018 AAST grading systems. Descriptive statistics were used to assess grade reclassifications. Mixed-effect multivariable logistic regression was used to measure the predictive ability of each grading system. The areas under the curves were compared.

RESULTS
Of the 322 injuries included, 27.0% were upgraded, 3.4% were downgraded, and 69.5% remained unchanged. Of the injuries graded as III or lower using the 1989 AAST, 33.5% were upgraded to grade IV using the 2018 AAST. Of the grade V injuries, 58.8% were downgraded using the 2018 AAST. There was no statistically significant difference in the overall areas under the curves between the 2018 and 1989 AAST grading system for predicting bleeding interventions (0.72 vs. 0.68, p = 0.34).

CONCLUSION
About one third of the injuries previously classified as grade III will be upgraded to grade IV using the 2018 AAST, which adds to the heterogeneity of grade IV injuries. Although the 2018 AAST grading provides more anatomic details on injury patterns and includes important radiologic findings, it did not outperform the 1989 AAST grading in predicting bleeding interventions.

LEVEL OF EVIDENCE
Prognostic and Epidemiological Study, level III.
Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations
Authors: Ramaker Ryne C. , Hardigan Andrew A. , Goh Say-Tar , Partridge E. Christopher , Wold Barbara , Cooper Sara J. , Myers Richard M. 
Published: December 2019

AbstractDNA associated proteins (DAPs) classically regulate gene expression by binding to regulatory loci such as enhancers or promoters. As expanding catalogs of genome-wide DAP binding maps reveal thousands of loci that, unlike the majority of conventional enhancers and promoters, associate with dozens of different DAPs with apparently little regard for motif preference, an understanding of DAP association and coordination at such regulatory loci is essential to deciphering how these regions contribute to normal development and disease. In this study, we aggregated publicly available ChIP-seq data from 469 human DAPs assayed in three cell lines and integrated these data with an orthogonal dataset of 352 non-redundant,in vitro-derived motifs mapped to the genome within DNase hypersensitivity footprints in an effort to characterize regions of the genome that have exceptionally high numbers of DAP associations. We subsequently performed a massively parallel mutagenesis assay to search for sequence elements driving transcriptional activity at such loci and explored plausible biological mechanisms underlying their formation. We establish a generalizable definition for High Occupancy Target (HOT) loci and identify putative driver DAP motifs in HEPG2 cells, including HNF4A, SP1, SP5, and ETV4, that are highly prevalent and exhibit sequence conservation at HOT loci. The number of different DAPs associated with an element is positively associated with evidence of regulatory activity and, by systematically mutating 245 HOT loci, we localized regulatory activity to a central core region that depends on the motif sequences of our previously nominated driver DAPs. In sum, this work leverages the increasingly large number of DAP motif and ChIP-seq data publicly available to explore how DAP associations contribute to genome-wide transcriptional regulation.
Kinetic improvement of an algal diacylglycerol acyltransferase 1 via fusion with an acyl-CoA binding protein
Authors: Xu Yang , Caldo Kristian Mark P. , Falarz Lucas , Jayawardhane Kethmi , Chen Guanqun 
Published: December 2019

SUMMARYMicroalgal oils in the form of triacylglycerols (TAGs) are broadly used as nutritional supplements and biofuels. Diacylglycerol acyltransferase (DGAT) catalyzes the final step of acyl-CoA-dependent biosynthesis of TAG and is considered a key target for manipulating oil production. Although a growing number ofDGAT1s have been identified and over-expressed in some algal species, the detailed structure-function relationship, as well as the improvement of DGAT1 performance via protein engineering, remain largely untapped. Here, we explored the structure-function features of the hydrophilic N-terminal domain of DGAT1 from the green microalgaChromochloris zofingiensis(CzDGAT1). The results indicated that the N-terminal domain of CzDGAT1 was less disordered than those of the higher eukaryotic enzymes and its partial truncation or complete removal could substantially decrease enzyme activity, suggesting its possible role in maintaining enzyme performance. Although the N-terminal domains of animal and plant DGAT1s were previously found to bind acyl-CoAs, replacement of CzDGAT1 N-terminus by an acyl-CoA binding protein (ACBP) could not restore enzyme activity. Interestingly, the fusion of ACBP to the N-terminus of the full-length CzDGAT1 could enhance the enzyme affinity for acyl-CoAs and augment protein accumulation levels, which ultimately drove oil accumulation in yeast cells and tobacco leaves to higher levels than the full-length CzDGAT1. Overall, our findings unravel the distinct features of the N-terminus of algal DGAT1 and provide a strategy to engineer enhanced performance in DGAT1 via protein fusion, which may open a vista in generating improved membrane-bound acyl-CoA-dependent enzymes and boosting oil biosynthesis in plants and oleaginous microorganisms.SIGNIFICANCE STATEMENTHere, we explored the N-terminus of a microalgal DGAT1, a membrane-bound enzyme determining oil biosynthesis, usingin silicoanalysis, truncation mutagenesis, protein fusion andin vitroandin vivocharacterization, and demonstrated its distinct structure-function features from the higher eukaryotic enzymes. We further engineered enhanced performance in DGAT1 via N-terminal fusion of ACBP, and obtained a kinetically improved enzyme with augmented protein production levels, which could boost oil accumulation in yeast and plant vegetative tissues.
Ecological and evolutionary drivers of hemoplasma infection and bacterial genotype sharing in a Neotropical bat community
Authors: Becker Daniel J. , Speer Kelly A. , Brown Alexis M. , Fenton M. Brock , Washburne Alex D. , Altizer Sonia , Streicker Daniel G. , Plowright Raina K. , Chizhikov Vladimir E. , Simmons Nancy B. , Volokhov Dmitriy V. 
Published: December 2019

AbstractMost emerging pathogens can infect multiple species, underscoring the importance of understanding the ecological and evolutionary factors that allow some hosts to harbor greater infection prevalence and share pathogens with other species. However, our understanding of pathogen jumps is primarily based around viruses, despite bacteria accounting for the greatest proportion of zoonoses. Because bacterial pathogens in bats (Order: Chiroptera) can have conservation and human health consequences, studies that examine the ecological and evolutionary drivers of bacterial prevalence and barriers to pathogen sharing are crucially needed. We here studied hemotropicMycoplasmaspp. (i.e., hemoplasmas) across a species-rich bat community in Belize over two years. Across 469 bats spanning 33 species, half of individuals and two-thirds of species were hemoplasma positive. Infection prevalence was higher for males and for species with larger body mass and colony sizes. Hemoplasmas displayed high genetic diversity (21 novel genotypes) and strong host specificity. Evolutionary patterns supported co-divergence of bats and bacterial genotypes alongside phylogenetically constrained host shifts. Bat species centrality to the network of shared hemoplasma genotypes was phylogenetically clustered and unrelated to prevalence, further suggesting rare—but detectable—bacterial sharing between species. Our study highlights the importance of using fine phylogenetic scales when assessing host specificity and suggests phylogenetic similarity may play a key role in host shifts for not only viruses but also bacteria. Such work more broadly contributes to increasing efforts to understand cross-species transmission and epidemiological consequences of bacterial pathogens.
Seq2DFunc: 2-dimensional convolutional neural network on graph representation of synthetic sequences from massive-throughput assay
Authors: Guo Haotian , Song Xiaohu , Lindner Ariel B. 
Published: December 2019

AbstractIn recent years, a pipeline of massively parallel reporter assay (MPRA), and next-generation sequencing (NGS) provided large-scale datasets to investigate biological mechanisms in detail. However, bigger data often leads to larger complexity. As a result, theories derived from low-throughput experiments lose explanatory power, requiring new methods to create predictive models. Here we focus on modeling functions of nucleic acid sequences, as a study case of massive-throughput assays. We report a deep learning approach, training a two-dimensional convolutional neural network (CNN) on an ordered graph representation of nucleic acid sequences to predict their functions (Seq2DFunc). To compare the performance of Seq2DFunc with conventional methods, we obtained customized database on a CRISPR RNA processing assay. For this specific assay, analyses of sequence and RNA structure determinants failed to explain the results regardless of dataset size. 1-dimensional CNN of raw sequences generate generally failed to converge at < 10,000 or fewer sequences. By contrast, Seq2DFunc trained on ∼ 7,000 sequences still provided 86% accuracy. Given a sufficient dataset (∼ 120,000 sequences) for training, Seq2DFunc (96% accuracy, 0.93 f1-score) still outperformed the best 1D CNN (92% accuracy, 0.83 f1-score). We anticipate Seq2DFunc can be a versatile downstream tool for deciphering massive-throughput assays for many fundamental studies. In addition, the use of smaller dataset is especially beneficial to reduce the experiment budget or required sequencing depth.
Influence of native endophytic bacteria on the growth and bacterial crown rot tolerance of papaya (Carica papaya)
Authors: Rivarez Mark Paul Selda , Parac Elizabeth P. , Dimasingkil Shajara Fatima M. , Mirnia Eka , Magdalita Pablito M. 
Published: December 2019

AbstractThe native plant microbiome is composed of diverse communities that influence its overall health, with some species known to promote plant growth and pathogen resistance. Here, we show the antimicrobial and growth promoting activities of autoclaved culture metabolites (ACMs) from native endophytic bacteria (NEB) in a papaya cultivar that is tolerant to bacterial crown rot (BCR) caused byErwinia mallotivora. Initially, bacterial colonization in recovering tissues of this cultivar was observed before onset of tissue regeneration or ‘regrowth’. We further isolated and characterized these bacteria and were able to identify two culturable stem NEB under generaKosakonia(EBW), related to Enterobacter, andSphingomonas(EBY). We also identified root NEB (BN, BS and BT) under genusBacillus. Inhibition assays indicated that ACMs from these NEB promptly (18-30h) and efficiently inhibited (60-65%)E. mallotivoraproliferationin vitro. Interestingly, when ACMs from BN and EBW were inoculated in surface-sterilized papaya seeds, germination was variably retarded (20-60% reduction) depending on plant genotype, but plant biomass accumulation was significantly stimulated, at around two-fold increase. Moreover, greenhouse experiments show that ACMs from all isolates, especially EBW, significantly reduced BCR incidence and severity in susceptible genotype, at around two-fold. In general, our observations of pathogen antagonism, plant growth promotion leading to disease reduction by ACMs of native endophytic bacteria suggested its contribution to increased fitness of papaya and tolerance against the (re)emerging BCR disease.
Heterogeneous habenular neuronal ensembles during selection of defensive behaviors
Authors: Lecca Salvatore , Namboodiri Vijay MK , Restivo Leonardo , Gervasi Nicolas , Pillolla Giuliano , Stuber Garret D. , Mameli Manuel 
Published: December 2019

AbstractOptimal selection of threat-driven defensive behaviors is paramount to an animal’s survival. The lateral habenula (LHb) is a key neuronal hub coordinating behavioral responses to aversive stimuli. Yet, how individual LHb neurons represent defensive behaviors in response to threats remains unknown. Here we show that, in mice, a visual threat promotes distinct defensive behaviors, namely runaway (escape) and action-locking (immobile-like). Fiber photometry of bulk LHb neuronal activity in behaving animals revealed an increase and decrease of calcium signal time-locked with runaway and action-locking, respectively. Imaging single-cell calcium dynamics across distinct threat-driven behaviors identified independently active LHb neuronal clusters. These clusters participate during specific time epochs of defensive behaviors. Decoding analysis of this neuronal activity unveiled that some LHb clusters either predict the upcoming selection of the defensive action or represent the selected action. Thus, heterogeneous neuronal clusters in LHb predict or reflect the selection of distinct threat-driven defensive behaviors.
A High-Throughput Extraction and Analysis Method for Steroidal Glycoalkaloids in Tomato
Authors: Dzakovich Michael P. , Hartman Jordan L. , Cooperstone Jessica L. 
Published: December 2019

AbstractTomato steroidal glycoalkaloids (tSGAs) are a class of cholesterol-derived metabolites uniquely produced by the tomato clade. These compounds provide protection against biotic stress due to their fungicidal and insecticidal properties. Although commonly reported as being anti-nutritional, bothin vitroas well as pre-clinical animal studies have indicated that some tSGAs may have a beneficial impact on human health. However, the paucity of quantitative extraction and analysis methods presents a major obstacle for determining the biological and nutritional functions of tSGAs. To address this problem, we developed and validated the first comprehensive extraction and UHPLC-MS/MS quantification method for tSGAs. Our extraction method allows for up to 16 samples to be extracted simultaneously in 20 minutes with 93.0 ± 6.8% and 100.8 ± 13.1% recovery rates for tomatidine and alpha-tomatine, respectively. Our ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method was able to chromatographically separate analytes derived from 16 tSGAs representing 9 different tSGA masses, as well as two internal standards, in 13 minutes. Tomato steroidal glycoalkaloids that did not have available standards were annotated using high resolution mass spectrometry as well as product ion scans that provided fragmentation data. Lastly, we utilized our method to survey a variety of commonly consumed tomato-based products. Total tSGA concentrations ranged from 0.7 to 3.4 mg/serving and represent some of the first reported tSGA concentrations in tomato-based products. Our validation studies indicate that our method is sensitive, robust, and able to be used for a variety of applications where concentrations of biologically relevant tSGAs need to be quantified.
Simulating intervertebral disc cell behavior within 3D multifactorial environments
Authors: Baumgartner L. , Reagh J.J. , González Ballester M.A. , Noailly J. 
Published: December 2019

AbstractMotivationLow back pain is responsible for more global disability than any other condition. Its incidence is closely related to intervertebral disc (IVD) failure, which is likely caused by an accumulation of microtrauma within the IVD. Crucial factors in microtrauma development are not entirely known yet, probably because their exploration in vivo or in vitro remains tremendously challenging. In-silico modelling is, therefore, definitively appealing, and shall include approaches to integrate influences of multiple cell stimuli at the microscale. Accordingly, this study introduces a hybrid Agent-based (AB) model in IVD research and exploits network modelling solutions in systems biology to mimic the cellular behavior of Nucleus Pulposus cells exposed to a 3D multifactorial biochemical environment, based on mathematical integrations of existing experimental knowledge. Cellular activity reflected by mRNA expression of Aggrecan, Collagen type I, Collagen type II, MMP-3 and ADAMTS were calculated for inflamed and non-inflamed cells. mRNA expression over long periods of time is additionally determined including cell viability estimations. Model predictions were eventually validated with independent experimental data.ResultsAs it combines experimental data to simulate cell behavior exposed to a multifactorial environment, the present methodology was able to reproduce cell death within 3 days under glucose deprivation and a 50% decrease in cell viability after 7 days in an acidic environment. Cellular mRNA expression under non-inflamed conditions simulated a quantifiable catabolic shift under an adverse cell environment, and model predictions of mRNA expression of inflamed cells provide new explanation possibilities for unexpected results achieved in experimental research.Contactlaura.baumgartner@upf.edu