bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accelerating Surgical Site Infection Abstraction With a Semi-automated Machine-learning Approach
Authors: Skube Steven J. , Hu Zhen , Simon Gyorgy J. , Wick Elizabeth C. , Arsoniadis Elliot G. , Ko Clifford Y. , Melton Genevieve B. 
Published: October 2020

Objective:
To demonstrate that a semi-automated approach to health data abstraction provides significant efficiencies and high accuracy.

Background:
Surgical outcome abstraction remains laborious and a barrier to the sustainment of quality improvement registries like ACS-NSQIP. A supervised machine learning algorithm developed for detecting SSi using structured and unstructured electronic health record data was tested to perform semi-automated SSI abstraction.

Methods:
A Lasso-penalized logistic regression model with 2011–3 data was trained (baseline performance measured with 10-fold cross-validation). A cutoff probability score from the training data was established, dividing the subsequent evaluation dataset into “negative” and “possible” SSI groups, with manual data abstraction only performed on the “possible” group. We evaluated performance on data from 2014, 2015, and both years.

Results:
Overall, 6188 patients were in the 2011–3 training dataset and 5132 patients in the 2014–5 evaluation dataset. With use of the semi-automated approach, applying the cut-off score decreased the amount of manual abstraction by >90%, resulting in < 1% false negatives in the “negative” group and a sensitivity of 82%. A blinded review of 10% of the “possible” group, considering only the features selected by the algorithm, resulted in high agreement with the gold standard based on full chart abstraction, pointing towards additional efficiency in the abstraction process by making it possible for abstractors to review limited, salient portions of the chart.

Conclusion:
Semi-automated machine learning-aided SSI abstraction greatly accelerates the abstraction process and achieves very good performance. This could be translated to other post-operative outcomes and reduce cost barriers for wider ACS-NSQIP adoption.
Natural Language Processing in Surgery
Authors: Mellia Joseph A. , Basta Marten N. , Toyoda Yoshiko , Othman Sammy , Elfanagely Omar , Morris Martin P. , Torre-Healy Luke , Ungar Lyle H. , Fischer John P. 
Published: October 2020

Objective:
The aim of this study was to systematically assess the application and potential benefits of natural language processing (NLP) in surgical outcomes research.

Summary Background Data:
Widespread implementation of electronic health records (EHRs) has generated a massive patient data source. Traditional methods of data capture, such as billing codes and/or manual review of free-text narratives in EHRs, are highly labor-intensive, costly, subjective, and potentially prone to bias.

Methods:
A literature search of PubMed, MEDLINE, Web of Science, and Embase identified all articles published starting in 2000 that used NLP models to assess perioperative surgical outcomes. Evaluation metrics of NLP systems were assessed by means of pooled analysis and meta-analysis. Qualitative synthesis was carried out to assess the results and risk of bias on outcomes.

Results:
The present study included 29 articles, with over half (n = 15) published after 2018. The most common outcome identified using NLP was postoperative complications (n = 14). Compared to traditional non-NLP models, NLP models identified postoperative complications with higher sensitivity [0.92 (0.87–0.95) vs 0.58 (0.33–0.79), P < 0.001]. The specificities were comparable at 0.99 (0.96–1.00) and 0.98 (0.95–0.99), respectively. Using summary of likelihood ratio matrices, traditional non-NLP models have clinical utility for confirming documentation of outcomes/diagnoses, whereas NLP models may be reliably utilized for both confirming and ruling out documentation of outcomes/diagnoses.

Conclusions:
NLP usage to extract a range of surgical outcomes, particularly postoperative complications, is accelerating across disciplines and areas of clinical outcomes research. NLP and traditional non-NLP approaches demonstrate similar performance measures, but NLP is superior in ruling out documentation of surgical outcomes.
Laryngeal and Pharyngeal Squamous Cell Carcinoma After Antireflux Surgery in the 5 Nordic Countries
Authors: Yanes Manar , Santoni Giola , Maret-Ouda John , Ness-Jensen Eivind , Färkkilä Martti , Lynge Elsebeth , Pukkala Eero , Romundstad Pål , Tryggvadóttir Laufey , Euler-Chelpin My von , Lagergren Jesper 
Published: October 2020

Objective:
The aim of this study was to clarify whether antireflux surgery prevents laryngeal and pharyngeal squamous cell carcinoma.

Summary Background Data:
Gastroesophageal reflux disease (GERD) seems to increase the risk of laryngeal and pharyngeal squamous cell carcinoma.

Methods:
All-Nordic (Denmark, Finland, Iceland, Norway, and Sweden) population-based cohort study of adults with documented GERD in 1980 to 2014. First, cancer risk after antireflux surgery was compared to the expected risk in the corresponding background population	by calculating standardized incidence ratios (SIRs) with 95% confidence intervals (CIs). Second, cancer risk among antireflux surgery patients was compared to nonoperated GERD patients using multivariable Cox regression, providing hazard ratios (HR) with 95% CIs, adjusted for sex, age, calendar period, and diagnoses related to tobacco smoking, obesity, and alcohol overconsumption.

Results:
Among 814,230 GERD patients, 47,016 (5.8%) underwent antireflux surgery. The overall SIRs and HRs of the combined outcome laryngeal or pharyngeal squamous cell carcinoma (n=39) were decreased after antireflux surgery [SIR=0.62 (95% CI 0.44–0.85) and HR=0.55 (95% CI 0.38–0.80)]. The point estimates were further decreased >10 years after antireflux surgery [SIR=0.48 (95% CI 0.26–0.80) and HR=0.47 (95% CI 0.26–0.85)]. The risk estimates of laryngeal squamous cell carcinoma were particularly decreased >10 years after antireflux surgery [SIR=0.28 (95% CI 0.08–0.72) and HR=0.23 (95% CI 0.08–0.69)], whereas no such decrease over time after surgery was found for pharyngeal squamous cell carcinoma. Analyses of patients with severe GERD (reflux esophagitis or Barrett esophagus) showed similar results.

Conclusion:
Antireflux surgery may decrease the risk of laryngeal squamous cell carcinoma and possibly also of pharyngeal squamous cell carcinoma.
Laparoscopic Appendectomy Performed by Surgical Interns: Is it Too Early?
Authors: Valinoti Agustin C. , Dreifuss Nicolas H. , Angeramo Cristian A. , Schlottmann Francisco 
Published: October 2020

Background:
Laparoscopic appendectomy (LA) is a common procedure among surgical trainees. However, first-year residents’ involvement in this procedure is scarcely studied. We aimed to determine the safety and outcomes of LA performed by surgical interns early in their first year of surgical training.

Materials and Methods:
A retrospective review of all patients who underwent LA for acute appendicitis from 2006 to 2019 was performed. All patients operated by surgical interns were included. The sample was divided into 2 groups: LA performed during the first (G1) and last 3 months (G2) of their first year of residency. Demographics, operative variables, and postoperative outcomes were compared between groups.

Results:
A total of 2009 LA were performed during the study period; 1647 (82%) were done by surgical interns. A total of 934 LA were performed at both ends of the year; 505 belonged to G1 and 429 to G2. Each surgical intern performed a mean of 40 LA. Demographics, complicated appendicitis rates, and presence of peritonitis were comparable between groups. Operative time was longer in G1 (G1: 61 vs. G2: 52 min, P<0.0001). Major morbidity (G1: 2.1% vs. G2: 3.4%, P=0.2), postoperative intra-abdominal abscess rates (G1: 2.8% vs. G2: 2.8%, P=0.66), median length of hospital stay (G1: 1.9 vs. G2: 1.8 d, P=0.59), and readmission rates (G1: 1.6% vs. G2: 2%, P=0.73) were similar between groups. There was no mortality in the series.

Conclusions:
LA can be safely performed by supervised surgical interns early in their training. Despite a longer operative time, postoperative outcomes were favorable and similar as those achieved at the end of surgical internship.
Respiratory tract explant infection dynamics of influenza A virus in California sea lions, northern elephant seals, and rhesus macaques
Authors: Liu Hongwei , Plancarte Magdalena , Ball Erin. E. , Weiss Christopher M. , Gonzales-Viera Omar , Holcomb Karen , Ma Zhong-Min , Allen A. Mark , Reader J. Rachel , Duignan Pádraig J. , Halaska Barbie , Khan Zenab , Kriti Divya , Dutta Jayeeta , van Bakel Harm , Jackson Kenneth , Pesavento Patricia A. , Boyce Walter M. , Coffey Lark L. 
Published: October 2020

AbstractTo understand susceptibility of wild California sea lions and Northern elephant seals to influenza A virus (IAV), we developed anex vivorespiratory explant model and used it to compare infection kinetics for multiple IAV subtypes. We first established the approach using explants from colonized rhesus macaques, a model for human IAV. Trachea, bronchi, and lungs from 11 California sea lions, 2 Northern elephant seals and 10 rhesus macaques were inoculated within 24 hours post-mortem with 6 strains representing 4 IAV subtypes. Explants from the 3 species showed similar IAV infection kinetics with peak viral titers 48-72 hours post-inoculation that increased by 2-4 log10plaque forming units (PFU)/explant relative to the inoculum. Immunohistochemistry localized IAV infection to apical epithelial cells. These results demonstrate that respiratory tissue explants from wild marine mammals support IAV infection. In the absence of the ability to perform experimental infections of marine mammals, thisex vivoculture of respiratory tissues mirrors thein vivoenvironment and serves as a tool to study IAV susceptibility, host-range, and tissue tropism.ImportanceAlthough influenza A virus can infect marine mammals, a dearth of marine mammal cell lines and ethical and logistical challenges prohibiting experimental infections of living marine mammals means that little is known about IAV infection kinetics in these species. We circumvented these limitations by adapting a respiratory tract explant model first to establish the approach with rhesus macaques and then for use with explants from wild marine mammals euthanized for non-respiratory medical conditions. We observed that multiple strains representing 4 IAV subtypes infected trachea, bronchi, and lungs of macaques and marine mammals with variable peak titers and kinetics. Thisex vivomodel can define infection dynamics for IAV in marine mammals. Further, use of explants from animals euthanized for other reasons reduces use of animals in research.
Mapping sites of carboxymethyllysine modification on proteins reveals its consequences for proteostasis and cell proliferation
Authors: Di Sanzo Simone , Spengler Katrin , Leheis Anja , Kirkpatrick Joanna M. , Rändler Theresa L. , Baldensperger Tim , Parca Luca , Marx Christian , Wang Zhao-Qi , Glomb Marcus A. , Ori Alessandro , Heller Regine 
Published: October 2020

SummaryPosttranslational mechanisms play a key role in modifying the abundance and function of cellular proteins. Among these, modification by advanced glycation end products (AGEs) has been shown to accumulate during aging and age-associated diseases but specific protein targets and functional consequences remain largely unexplored. Here, we devised a proteomic strategy to identify specific sites of carboxymethyllysine (CML) modification, one of the most abundant AGEs. We identified over 1000 sites of CML modification in mouse and primary human cells treated with the glycating agent glyoxal. By using quantitative proteomics, we found that protein glycation triggers a proteotoxic response and directly affects the protein degradation machinery. We show that glyoxal induces cell cycle perturbation in primary endothelial cells and that CML modification reduces acetylation of tubulins and impairs microtubule dynamics. Our data demonstrate the relevance of AGE modification for cellular function and pinpoint specific protein networks that might become compromised during aging.HighlightsA peptide enrichment strategy allows mapping of CML modification in cells and tissuesCML modification competes with ubiquitination or acetylation of lysinesGlyoxal treatment destabilizes the 26S proteasomeGlyoxal arrests cell cycle and impairs microtubule dynamics via altering the tubulin code
CRISPR screening identifies novel PARP inhibitor classification based on distinct base excision repair pathway dependencies
Authors: Breuer Gregory A. , Bezney Jonathan , Fons Nathan R. , Sundaram Ranjini K. , Feng Wanjuan , Gupta Gaorav P. , Bindra Ranjit S. 
Published: October 2020

ABSTRACTDNA repair deficiencies have become an increasingly promising target for novel therapeutics within the realm of clinical oncology. Recently, several inhibitors of Poly(ADP-ribose) Polymerases (PARPs) have received approval for the treatment of cancers primarily with deleterious mutations in the homologous recombination (HR) proteins, BRCA1 and BRCA2. Despite numerous clinical trials which have been completed or are currently ongoing, the mechanism of action by which PARP inhibitors selectively kill tumor cells is poorly understood. While many believe “trapping” of PARP proteins to DNA at sites of damage is the most important determinant driving cytotoxicity by these drugs, clinically effective inhibitors exist with a diverse range of PARP-trapping qualities. These findings suggest that characterization of inhibitors as strong versus weak trappers does not properly capture the intra-class characteristics of these drugs. Here, we use a novel, targeted DNA damage response (DDR) CRISPR/Cas9 screening library to reveal heterogenous genetic dependencies on the base excision repair (BER) pathway for PARP inhibitors, which is not correlated with PARP trapping ability or catalytic inhibition of PARP. These findings demonstrate that inhibition of PARylation and induction of PARP trapping are not the only factors contributing to distinct biological activity for different PARP inhibitors, and they provide insight into the optimal choice of PARP inhibitors for use in the setting of specific DDR defects.AUTHOR SUMMARYTargeted cancer therapies rely on our general understanding of which genetic mutations are involved in both sensitivity and resistance to such anticancer agents. In this study, we describe the use of functional genetic screening to evaluate the role of various DNA repair proteins in response to inhibitors of PARP, a quintessential example of targeted therapy. While PARP inhibitors are best known for their utility in cancers with homologous recombination defects, we show that some inhibitors within this class may have additional functionality in cancers with deficient base excision repair. These findings highlight not only the importance of PARP inhibitor selection in the appropriate context, but also the mechanistic differences that exist within this class of inhibitors. It is our hope that our findings will inspire future work evaluating the use of specific PARP inhibitor selection in designing clinical trials to further expand the use of PARP inhibitors beyond tumors with homologous recombination deficiencies.
Fundamental limits on the rate of bacterial growth
Authors: Belliveau Nathan M. , Chure Grifin , Hueschen Christina L. , Garcia Hernan G. , Kondev Jane , Fisher Daniel S. , Theriot Julie A. , Phillips Rob 
Published: October 2020

AbstractRecent years have seen an experimental deluge interrogating the relationship between bacterial growth rate, cell size, and protein content, quantifying the abundance of proteins across growth conditions with unprecedented resolution. However, we still lack a rigorous understanding of what sets the scale of these quantities and when protein abundances should (or should not) depend on growth rate. Here, we seek to quantitatively understand this relationship across a collection ofEscherichia coliproteomic data covering ≈ 4000 proteins and 36 growth rates. We estimate the basic requirements for steady-state growth by considering key processes in nutrient transport, cell envelope biogenesis, energy generation, and the central dogma. From these estimates, ribosome biogenesis emerges as a primary determinant of growth rate. We expand on this assessment by exploring a model of proteomic regulation as a function of the nutrient supply, revealing a mechanism that ties cell size and growth rate to ribosomal content.
Temporal changes in plasma membrane lipid content induce endocytosis to regulate developmental epithelial-to-mesenchymal transition
Authors: Piacentino Michael L. , Hutchins Erica J. , Andrews Cecelia J. , Bronner Marianne E. 
Published: October 2020

AbstractEpithelial-to-mesenchymal transition (EMT) is a dramatic change in cellular physiology during development and metastasis which involves coordination between cell signaling, adhesion, and membrane protrusions. These processes all involve dynamic changes in the plasma membrane, yet how membrane lipid content regulates membrane function during developmental EMT remains incompletely understood. By screening for differential expression of lipid-modifying genes over the course of EMT in avian neural crest, we have identified the ceramide-producing enzyme neutral sphingomyelinase 2 (nSMase2) as a critical regulator of a developmental EMT. nSMase2 expression begins at the onset of EMT, andin vivoknockdown experiments demonstrate that nSMase2 is necessary for neural crest migration. Further, we find that nSMase2 promotes Wnt and BMP signaling, and is required to activate the mesenchymal gene expression program. Mechanistically, we show that nSMase2 is sufficient to induce endocytosis, and that inhibition of endocytosis mimics nSMase2 knockdown. Our results support a model in which nSMase2 is expressed at the onset of neural crest EMT to produce ceramide and induce membrane curvature, thus increasing endocytosis of Wnt and BMP signaling complexes and activating pro-migratory gene expression. These results highlight the critical role of plasma membrane lipid metabolism in regulating transcriptional changes during developmental EMT programs.
Differential effects of prediction error and adaptation along the auditory cortical hierarchy during deviance processing
Authors: Schlossmacher Insa , Dilly Jacky , Protmann Ina , Hofmann David , Dellert Torge , Roth-Paysen Marie-Luise , Moeck Robert , Bruchmann Maximilian , Straube Thomas 
Published: October 2020

AbstractNeural mismatch responses have been proposed to rely on different mechanisms, including prediction error-related activity and adaptation to frequent stimuli. However, the cortical hierarchical structure of these mechanisms is unknown. To investigate this question, we used functional magnetic resonance imaging (fMRI) and an auditory oddball design with a suited control condition that enabled us to delineate the contributions of prediction error- or adaptation-related brain activation during deviance processing. We found that while prediction-error related processes increased with the hierarchical position of the brain area, adaptation declined. This suggests that the relative contribution of different mechanisms in deviance processing varies across the cortical hierarchy.
Accounting's role in resisting wage theft: a labour process theory analysis
Authors: Yang Da , Dumay John , Tweedie Dale 
Published: October 2020

PurposeIn 2015, one university student in KC – a small town in regional Australia – unknowingly launched a resistance movement and national debate on modern wage theft. We apply labour process theory to analyse accounting's role in this case.Design/methodology/approachWe study multiple instances of wage theft in one Australian town. This case site reveals how wage theft can emerge in a developed economy with well-established legal and institutional constraints. We use Thompson's “core” labour process theory to analyse accounting's role via two interrelated dialectics: (1) structure and agency and, (2) control and resistance.FindingsAccounting was “weaponised” by both sides of the controversy: as a tool of employer control and as a vehicle for student resistance. Digital technologies enabled employee resistance to form unconsciously and organically. Proponents mobilised informally, with information and accounting the ammunition.Social implicationsWage theft affects industrialised as well as developing economies, especially “precarious” workers. We show how accounting can conceal exploitation, but also how – with the right support – accounting can help vulnerable workers enforce their rights and entitlements.Originality/valueThe paper uncovers novel dynamics of exploitation and resistance at work under contemporary economic and technological conditions. Labour process theory can provide a more dialectical perspective on accounting's role in these dynamics, including the emancipatory potential of informal and opportunistic counter-accounts.
Adoption and implementation of building information modelling (BIM) in small and medium-sized enterprises (SMEs): a review and conceptualization
Authors: Saka Abdullahi B. , Chan Daniel W.M. 
Published: October 2020

PurposeDespite the SMEs representing a large percentage of firms in the construction industry, there has been an under-representation of SMEs’ perspective in BIM research studies. This paper aims to systematically review the few extant studies with a view of synthesizing the findings.Design/methodology/approachHermeneutic philosophy using the interpretivist epistemology approach with a touch of metasynthesis was adopted to critically review and analyse extant studies published over the last decade.FindingsThe findings revealed a scarcity of BIM studies in SMEs, the status of adoption, identified barriers, benefits and drivers. A conceptual model was then developed based on the literature review and theoretical lenses of innovation diffusion model, technology–organization–environment framework and institutional theory. The paper presents pertinent propositions to drive BIM in the SMEs.Originality/valueThis paper holistically reviews extant BIM studies from the perspective of SMEs that are the backbone of the construction industry. It synthesizes extant studies and sets scenes for further studies.
Modified accident causation model for highway construction accidents (ACM-HC)
Authors: Tong Ruipeng , Zhao Hui , Zhang Na , Li Hongwei , Wang Xiaolong , Yang Hongqing 
Published: October 2020

PurposeThe purpose of this study is to establish a modified accident causation model for highway construction accidents (ACM-HC) and describe the establishment process of the ACM-HC.Design/methodology/approachBased on the 2–4 Model, a framework of the ACM-HC was constructed, and the accident causal factors (CF) were extracted from four aspects of human, material, environment and management. In addition, association rule mining (ARM) was introduced to analyze accident investigation reports to obtain the interrelationships between the factors. Based on the framework, factors and ARM results, the ACM-HC was established. Finally, the ACM-HC was verified with a tunnel collapse accident.FindingsBoth the external and internal causes of contractor cause accidents. The flaws of safety management of other stakeholders are external causes. In terms of the internal causes, there are four stages: direct causes, indirect causes, radical causes and root causes. More specifically, the direct causes refer to the unsafe acts and the unsafe conditions; ineffective safety supervision and poor individual factors of frontline workers constitute the indirect causes; the radical causes lie in the flaws of construction procedures and technical schemes; the root causes are related to the poor individual factors of decision makers and managers.Originality/valueThe ACM-HC expresses the causes, sequence and mechanism of highway construction accidents in a visual way. In addition, this study describes a process of using a qualitative–quantitative hybrid approach to establish a modified ACM, which provides a different perspective for the establishment of an ACM.