bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comprehensive assessment of carbapenem use across 90 Veterans Health Administration hospitals with defined stewardship strategies for carbapenems
Authors: Suzuki Hiroyuki , Perencevich Eli , Goto Michihiko , Alexander Bruce , Nair Rajeshwari , Puig-Asensio Mireia , Ernst Erika , Livorsi Daniel J 
Published: January 2021

Abstract

Objectives
Carbapenems are an important target for antimicrobial stewardship (AS) efforts. In this study, we sought to compare different hospital-based strategies for improving carbapenem use.

Methods
We analysed a cohort of all patients hospitalized at Veterans Health Administration (VHA) acute care hospitals during 2016 and a mandatory survey that characterized each hospital’s carbapenem-specific AS strategy into one of three types: no strategy (NS), prospective audit and feedback (PAF) or restrictive policies (RP). Carbapenem use was compared using risk-adjusted generalized estimating equations that accounted for clustering within hospitals. Two infectious disease (ID) physicians independently performed manual chart reviews in 425 randomly selected cases. Auditors assessed carbapenem appropriateness with an assessment score on Day 4 of therapy.

Results
There were 429 062 admissions in 90 sites (24 NS, 8 PAF, 58 RP). Carbapenem use was lower at PAF than NS sites [rate ratio (RR) 0.6 (95% CI 0.4–0.9); P = 0.01] but similar between RP and NS sites. Carbapenem prescribing was considered appropriate/acceptable in 215 (50.6%) of the reviewed cases. Assessment scores were lower (i.e. better) at RP than NS sites (mean 2.3 versus 2.7; P &lt; 0.01) but did not differ significantly between NS and PAF sites. ID consultations were more common at PAF/RP than NS sites (51% versus 29%; P &lt; 0.01). ID consultations were associated with lower (i.e. better) assessment scores (mean 2.3 versus 2.6; P &lt; 0.01).

Conclusions
In this VHA cohort, PAF strategies were associated with lower carbapenem use and ID consultation and RP strategies were associated with more appropriate carbapenem prescribing. AS and ID consultations may work complementarily and hospitals could leverage both to optimize carbapenem use.
Mortality attributable to third-generation cephalosporin resistance in Gram-negative bloodstream infections in African hospitals: a multi-site retrospective study
Authors: Dramowski Angela , Ong’ayo Gerald , Rehman Andrea M , Whitelaw Andrew , Labi Appiah-Korang , Obeng-Nkrumah Noah , Ndir Awa , Magwenzi Marcelyn T , Onyedibe Kenneth , Wolkewitz Martin , de Kraker Marlieke E A , Scott J Anthony G , Aiken Alexander M ,   MBIRA study collaborators, Mujuru Hilda , Odipo Emily , Mwarumba Salim , Mturi Neema , Gordon N Claire , Diop Amadou , Ndiaye Aissatou Thilor , Shwe David , Diala Udochukwu M , Okolo Mark , Grundmann Hajo 
Published: January 2021

Abstract

Background
Bloodstream infections (BSI) caused by Enterobacteriaceae show increasing frequency of resistance to third-generation cephalosporin (3GC) antibiotics on the African continent but the mortality impact has not been quantified.

Methods
We used historic data from six African hospitals to assess the impact of 3GC resistance on clinical outcomes in Escherichia coli and Klebsiella pneumoniae BSI. We matched each bacteraemic patient to two uninfected patients. We compared outcomes between 3GC-susceptible and 3GC-resistant BSI and their respective uninfected controls using Cox regression models.

Results
For 1431 E. coli BSI patients, we matched 1152 (81%) 3GC-susceptible and 279 (19%) 3GC-resistant cases to 2263 and 546 uninfected inpatient controls. For 1368 K. pneumoniae BSI patients, we matched 502 (37%) 3GC-susceptible and 866 (63%) 3GC-resistant cases to 982 and 1656 uninfected inpatient controls. We found that 3GC-resistant E. coli had similar hazard ratios (HRs) for in-hospital mortality over their matched controls as compared to susceptible infections over their controls (ratio of HRs 1.03, 95% CI 0.73–1.46). Similarly, 3GC-resistance in K. pneumoniae BSI was not associated with mortality (ratio of HR 1.10, 95% CI 0.80–1.52). Estimates of mortality impact varied by site without a consistent pattern.

Conclusions
In a retrospective analysis, including the use of matched uninfected patients, there did not appear to be an impact of 3GC-resistance on mortality in E. coli or K. pneumoniae BSI in African hospitals, as compared with susceptible BSI with equivalent species. Better information on the actual use of antibiotics in treating infections in African hospitals would improve these impact estimates.
Supervised machine learning to support the diagnosis of bacterial infection in the context of COVID-19
Authors: Rawson Timothy M , Hernandez Bernard , Wilson Richard C , Ming Damien , Herrero Pau , Ranganathan Nisha , Skolimowska Keira , Gilchrist Mark , Satta Giovanni , Georgiou Pantelis , Holmes Alison H 
Published: January 2021

Abstract

Background
Bacterial infection has been challenging to diagnose in patients with COVID-19. We developed and evaluated supervised machine learning algorithms to support the diagnosis of secondary bacterial infection in hospitalized patients during the COVID-19 pandemic.

Methods
Inpatient data at three London hospitals for the first COVD-19 wave in March and April 2020 were extracted. Demographic, blood test and microbiology data for individuals with and without SARS-CoV-2-positive PCR were obtained. A Gaussian Naive Bayes, Support Vector Machine (SVM) and Artificial Neural Network were trained and compared using the area under the receiver operating characteristic curve (AUCROC). The best performing algorithm (SVM with 21 blood test variables) was prospectively piloted in July 2020. AUCROC was calculated for the prediction of a positive microbiological sample within 48 h of admission.

Results
A total of 15 599 daily blood profiles for 1186 individual patients were identified to train the algorithms; 771/1186 (65%) individuals were SARS-CoV-2 PCR positive. Clinically significant microbiology results were present for 166/1186 (14%) patients during admission. An SVM algorithm trained with 21 routine blood test variables and over 8000 individual profiles had the best performance. AUCROC was 0.913, sensitivity 0.801 and specificity 0.890. Prospective testing on 54 patients on admission (28/54, 52% SARS-CoV-2 PCR positive) demonstrated an AUCROC of 0.960 (95% CI: 0.90–1.00).

Conclusions
An SVM using 21 routine blood test variables had excellent performance at inferring the likelihood of positive microbiology. Further prospective evaluation of the algorithms ability to support decision making for the diagnosis of bacterial infection in COVID-19 cohorts is underway.
Evaluation of Sensitivity to Phoxim and Cypermethrin in an Endoparasitoid,Meteorus pulchricornis(Wesmael) (Hymenoptera: Braconidae), and Its Parasitization Efficiency Under Insecticide Stress
Authors: Sheng Sheng , Wang Jiao , Zhang Xiao-rui , Liu Zhi-xiang , Yan Meng-wen , Shao Ying , Zhou Jin-cheng , Wu Fu-an , Wang Jun 
Published: January 2021

AbstractInsecticides can have consequences for beneficial arthropods. Insect parasitoids can contact insecticides through direct exposure spray droplets or residues on crop foliage. Here, we focus on better understand the response of Meteorus pulchricornis (Wesmael), a parasitoid wasp of lepidopteran pests, and its detoxification mechanisms on stress caused by phoxim and cypermethrin. Hence, we determined the dose–mortality curves and estimating the sublethal concentrations (LC30 and LC50). Then, we applied the sublethal concentrations against adult parasitoids to assess its survival, parasitism efficacy, and also developmental and morphometric parameters of their offspring. Simultaneously, we check the activities of glutathione S-transferase (GST), acetylcholinesterase (AChE), and peroxidase (POD) after sublethal exposure of both insecticides, which has measured until 48 h after treatment. Overall, phoxim and cypermethrin exhibited acute lethal activity toward the parasitoid with LC50 values 4.608 and 8.570 mg/liter, respectively. Also, we detect that LC30 was able to trigger the enzymatic activity of GST, AChE, and POD, suggesting a potential detoxification mechanism. However, even when subjected to sublethal exposure, our results indicate strong negatives effects, in particular for phoxim, which has affected the parasitism efficacy and also the developmental and morphometric parameters of M. pulchricornis offspring. Therefore, it can be concluded that both phoxim and cypermethrin have negative impacts on M. pulchricornis and we suggest cautioning their use and the need for semifield and field assessments to confirm such an impact.
Historic Assessment and Analysis of the Mass Production ofLaricobiusspp. (Coleoptera: Derodontidae), Biological Control Agents for the Hemlock Woolly Adelgid, at Virginia Tech
Authors: Foley Jeremiah R , Jubb Carrie S , Cole D Austin , Mausel David , Galloway Ashley Lamb , Brooks Rachel , Salom Scott M 
Published: January 2021

AbstractLaricobius nigrinus (Coleoptera: Derodontidae) Fender and Laricobius osakensis (Coleoptera: Derodontidae) Montgomery and Shiyake have been mass produced by Virginia Tech as biological control agents for the hemlock woolly adelgid (HWA), Adelges tsugae (Hemiptera: Adelgidae) Annand, for the past 15 and 9 yr, respectively. Herein, we describe modifications of our rearing procedures, trends and analyses in the overall production of these agents, and the redistribution of these agents for release to local and federal land managers. Based on these data, we have highlighted three major challenges to the rearing program: 1) high mortality during the subterranean portion of its life cycle (averaging 63% annually) reducing beetle production, 2) asynchrony in estivation emergence relative to the availability of their host HWA minimizing food availability, and 3) unintended field collections of Laricobius spp. larvae on HWA provided to lab-reared larvae complicating rearing procedures. We further highlight corresponding avenues of research aimed at addressing each of these challenges to further improve Laricobius spp. production.
Fine Particulate Matter Air Pollution and Mortality Risk Among US Cancer Patients and Survivors
Authors: Coleman Nathan C , Ezzati Majid , Marshall Julian D , Robinson Allen L , Burnett Richard T , Pope C Arden 
Published: January 2021

Abstract

Background
Exposure to fine particulate matter (PM2.5) air pollution has been linked to increased risk of mortality, especially cardiopulmonary and lung cancer mortality. It is unknown if cancer patients and survivors are especially vulnerable to PM2.5 air pollution exposure. This study evaluates PM2.5 exposure and risk for cancer and cardiopulmonary mortality in cohorts of US cancer patients and survivors.

Methods
A primary cohort of 5 591 168 of cancer patients and a 5-year survivor cohort of 2 318 068 was constructed using Surveillance, Epidemiology, and End Results Program data from 2000 to 2016, linked with county-level estimates of long-term average concentrations of PM2.5. Cox proportional hazards models were used to estimate PM2.5-mortality hazard ratios controlling for age-sex-race combinations and individual and county-level covariables.

Results
Of those who died, 26% died of noncancer causes, mostly from cardiopulmonary disease. Minimal PM2.5-mortality associations were observed for all-cause mortality (hazard ratio [HR] = 1.01, 95% confidence interval [CI] = 1.00 to 1.03) per 10 µg/m3 increase in PM2.5. Substantial adverse PM2.5-mortality associations were observed for cardiovascular (HR = 1.32, 95% CI = 1.26 to 1.39), chronic obstructive pulmonary disease (HR = 1.10, 95% CI = 1.01 to 1.20), influenza and pneumonia (HR = 1.55, 95% CI = 1.33 to 1.80), and cardiopulmonary mortality combined (HR = 1.25, 95% CI = 1.21 to 1.30). PM2.5-cardiopulmonary mortality hazard ratio was higher for cancer patients who received chemotherapy or radiation treatments.

Conclusions
Air pollution is adversely associated with cardiopulmonary mortality for cancer patients and survivors, especially those who received chemotherapy or radiation treatment. Given ubiquitous and involuntary air pollution exposures and large numbers of cancer patients and survivors, these results are of substantial clinical and public health importance.
Cecal volvulus complicated by evisceration case report
Authors: Johnson Kylie , Williams Ben , Steen Eric 
Published: January 2021

Abstract
This case of bowel obstruction with multiple postoperative complications provides unique insight into the challenges faced by providers caring for intellectually disabled patients with acute surgical abdominal pathology and poor compliance. In this case, the component separation was utilized as a method of facilitated wound closure and compliance in a postoperative course highlighted by both dehiscence and wound infection. The patient, only able to communicate the presence of abdominal pain due to his disability, was surgically managed for a bowel obstruction secondary to a cecal volvulus. The difficulty in initial communication and patient noncompliance help illustrate the individualized care these patients require. This report will demonstrate both the challenges present in the management of intellectually disabled patients with abdominal wounds, as well as the use of component separation in providing both initial wound closure and continued wound integrity with the goal of reducing postoperative complications in patients with decreased compliance.
Usage of Plasma Presepsin, C-Reactive Protein, Procalcitonin and Proadrenomedullin to Predict Bacteremia in Febril Neutropenia of Pediatric Hematological Malignancy Patients
Authors: Arıkan Kamile , Karadag-Oncel Eda , Aytac Selin , Cetin Mualla , Cengiz Ali Bülent , Gümrük Fatma , Kara Ates , Ceyhan Mehmet 
Published: January 2021

Abstract

Objective
To investigate the value of presepsin and proadrenomedullin (proADM) as new markers for febrile neutropenia, by comparing them with conventional markers.

Methods
Plasma specimens for presepsin, proADM, C-reactive protein (CRP), and procalcitonin (PCT) were collected every 3 days during each episode of febrile neutropenia.

Results
A total of 39 patients experiencing a collective 47 episodes of febrile neutropenia with hematological malignant neoplasms, as well as 40 healthy control patients without infectious disease, were enrolled in this study. Levels of the studied analytes in the presepsin 1 group (with baseline values taken at admission), presepsin 2 group (values recorded on the 3rd day of febrile neutropenia), and presepsin 3 group (values recorded on the 6th day of hospitalization) were all higher in the subgroups with bacteremia. C-reactive protein 1 (baseline value taken at admission), procalcitonin 1 (as recorded at admission), and procalcitonin 2 (recorded on the 3rd day of febrile neutropenia) were higher in the subroups with bacteremia (P =.03, P = .04, and P = .04, respectively). In multivariate logistic regression analysis, presepsin 1 and/or PCT 1/CRP 1 combined analysis was superior in predicting bacteremia.

Conclusion
Presepsin could be used in combination with other biomarkers to detect bacteremia.
Estimation of the size and structure of the broad line region using Bayesian approach
Authors: Mandal Amit Kumar , Rakshit Suvendu , Stalin C S , Petrov R G , Mathew Blesson , Sagar Ram 
Published: January 2021

ABSTRACT
Understanding the geometry and kinematics of the broad line region (BLR) of active galactic nuclei (AGN) is important to estimate black hole masses in AGN and study the accretion process. The technique of reverberation mapping (RM) has provided estimates of BLR size for more than 100 AGN now; however, the structure of the BLR has been studied for only a handful number of objects. Towards this, we investigated the geometry of the BLR for a large sample of 57 AGN using archival RM data. We performed systematic modelling of the continuum and emission line light curves using a Markov chain Monte Carlo method based on Bayesian statistics implemented in PBMAP (Parallel Bayesian code for reverberation−MAPping data) code to constrain BLR geometrical parameters and recover velocity integrated transfer function. We found that the recovered transfer functions have various shapes such as single-peaked, double-peaked, and top-hat suggesting that AGN have very different BLR geometries. Our model lags are in general consistent with that estimated using the conventional cross-correlation methods. The BLR sizes obtained from our modelling approach is related to the luminosity with a slope of 0.583 ± 0.026 and 0.471 ± 0.084 based on H β and H α lines, respectively. We found a non-linear response of emission line fluxes to the ionizing optical continuum for 93 ${{\ \rm per\ cent}}$ objects. The estimated virial factors for the AGN studied in this work range from 0.79 to 4.94 having a mean at 1.78 ± 1.77 consistent with the values found in the literature.
Vibrio cholerae FruR facilitates binding of RNA polymerase to the fru promoter in the presence of fructose 1-phosphate
Authors: Yoon Chang-Kyu , Kang Deborah , Kim Min-Kyu , Seok Yeong-Jae 
Published: January 2021

Abstract
In most bacteria, efficient use of carbohydrates is primarily mediated by the phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS), which concomitantly phosphorylates the substrates during import. Therefore, transcription of the PTS-encoding genes is precisely regulated by transcriptional regulators, depending on the availability of the substrate. Fructose is transported mainly through the fructose-specific PTS (PTSFru) and simultaneously converted into fructose 1-phosphate (F1P). In Gammaproteobacteria such as Escherichia coli and Pseudomonas putida, transcription of the fru operon encoding two PTSFru components, FruA and FruB, and the 1-phosphofructokinase FruK is repressed by FruR in the absence of the inducer F1P. Here, we show that, contrary to the case in other Gammaproteobacteria, FruR acts as a transcriptional activator of the fru operon and is indispensable for the growth of Vibrio cholerae on fructose. Several lines of evidence suggest that binding of the FruR-F1P complex to an operator which is located between the –35 and –10 promoter elements changes the DNA structure to facilitate RNA polymerase binding to the promoter. We discuss the mechanism by which the highly conserved FruR regulates the expression of its target operon encoding the highly conserved PTSFru and FruK in a completely opposite direction among closely related families of bacteria.
The metabolite methylglyoxal-mediated gene expression is associated with histone methylglyoxalation
Authors: Fu Zheng-Wei , Li Jian-Hui , Feng Yu-Rui , Yuan Xiao , Lu Ying-Tang 
Published: January 2021

Abstract
Methylglyoxal (MG) is a byproduct of glycolysis that functions in diverse mammalian developmental processes and diseases and in plant responses to various stresses, including salt stress. However, it is unknown whether MG-regulated gene expression is associated with an epigenetic modification. Here we report that MG methylglyoxalates H3 including H3K4 and increases chromatin accessibility, consistent with the result that H3 methylglyoxalation positively correlates with gene expression. Salt stress also increases H3 methylglyoxalation at salt stress responsive genes correlated to their higher expression. Following exposure to salt stress, salt stress responsive genes were expressed at higher levels in the Arabidopsis glyI2 mutant than in wild-type plants, but at lower levels in 35S::GLYI2 35S::GLYII4 plants, consistent with the higher and lower MG accumulation and H3 methylglyoxalation of target genes in glyI2 and 35S::GLYI2 35S::GLYII4, respectively. Further, ABI3 and MYC2, regulators of salt stress responsive genes, affect the distribution of H3 methylglyoxalation at salt stress responsive genes. Thus, MG functions as a histone-modifying group associated with gene expression that links glucose metabolism and epigenetic regulation.
Product-market integration with endogenous firm heterogeneity
Authors: Ledezma Ivan 
Published: January 2021

Abstract
This paper proposes a general equilibrium oligopoly model in which firm heterogeneity is endogenously reproduced through technology adoption decisions. The model can explain persistent oligopolistic market structures and prices in spite of free entry and market enlargement. Moreover, strong selection might deteriorate average cost efficiency due to strategic interactions. Integrating identical countries can be welfare-improving. But distributional issues and tensions between welfare and scale economies may arise. The theory can be motivated by recent evidence on oligopolistic market structures resisting globalization forces.
Algorithm for calculating high disease activity in SLE
Authors: Hoi Alberta , Nim Hieu T , Koelmeyer Rachel , Sun Ying , Kao Amy , Gunther Oliver , Morand Eric 
Published: January 2021

Abstract

Background
The ability to identify lupus patients in high disease activity status (HDAS) without knowledge of the SLEDAI could have application in selection of patients for treatment escalation or enrolment in trials. We sought to generate an algorithm that could calculate via model fitting the presence of HDAS using simple demographic and laboratory values.

Methods
We examined the association of high disease activity (HDA) with demographic and laboratory parameters using prospectively collected data. An HDA visit is recorded when SLEDAI-2K ≥10. We utilized the use of combinatorial search to find algorithms to build a mathematical model predictive of HDA. Performance of each algorithm was evaluated using multi-class area under the receiver operating characteristic curve and the final model was compared with the naïve Bayes classifier, and analysed using the confusion matrix for accuracy and misclassification rate.

Results
Data on 286 patients, followed for a median of 5.1 years were studied for a total of 5680 visits. Sixteen laboratory parameters were found to be significantly associated with HDA. A total of 216 algorithms were evaluated and the final algorithm chosen was based on seven pathology measures and three demographic variables. It has an accuracy of 88.6% and misclassification rate of 11.4%. When compared with the naïve Bayes classifier [area under the curve (AUC) = 0.663], our algorithm has a better accuracy with AUC = 0.829.

Conclusion
This study shows that building an accurate model to calculate HDA using routinely available clinical parameters is feasible. Future studies to independently validate the algorithm will be needed to confirm its predictive performance.