bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community structure of soil mites under different crops and its response to environmental factors in the buffer zone of Shibing Karst World Natural Heritage
Authors: Yin Xiumei , Gong Tong , Liu Wenjun , Chen Hu , Fei Yifan 
Published: May 2023

Abstract
To reveal the differences in the community structure of soil mites under different crop environments in the buffer zone of the Shibing Karst World Natural Heritage Site, soil mites from corn fields (CF), pear tree lands (PL), tobacco fields (TF), grape fields (GF), and plum gardens (PG) were collected in the buffer zone in January 2022. Through the identification of mite specimens and data analysis, differences in the number of families, genera, individuals, individual density, diversity, similarity of communities, ecological groups of oribatid mites, and responses to environmental factors of soil mites under different crop environments were determined. The results showed that: (1) A total of 6941 soil mites were captured in the study area, belonging to 130 genera, 75 families, and 3 orders. The number of soil mite genera (CF and TF > PL > PG > GF) and number of soil mite individuals (PG > PL > GF > TF > CF) showed characteristics of differential distribution and surface soil aggregation in the five habitats. (2) Scheloribates, Protorobotritia, and Tectocepheus were the dominant genera in the study area. Lohmannia, Scheloribates, and Tectocepheus, representative species that indicate a good soil environment, were distributed in the sample plots of CF, PL, and PG to varying degrees, indicating that the ecological environment of these three crops was healthy. (3) The diversity index of PG was the highest, and similarity analysis of the five habitats revealed that they were at a medium level of similarity. (4) The ecological groups of oribatid mites in the different crop environments were dominated by the overall (O) type, which is a combination of Macropylina, Gymnonota, and Poronota. (5) The community structure of soil mites was sensitive to bulk density (BD), natural water content (NWC), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available potassium (AK), and soil organic matter (SOM). Based on the above results, there were differences in the community structures of soil mites under different crop environments in the study area. The identification of the dominant mite genera can preliminarily indicate the environmental conditions of different crops, and a special correlation exists between the community structure of mites and environmental factors. Studying the community structure of mites in different crop environments in the Shibing Karst World Natural Heritage Site buffer zone is important in ensuring the ecological protection and sustainable development of the buffer zone. Furthermore, the results of this study support the role of the buffer zone as an ecological protection barrier for the heritage site.
Birth Weight in Consecutive Pregnancies and Maternal Cardiovascular Disease Mortality Among Spontaneous and Iatrogenic Term Births: A Population-Based Cohort Study
Authors: Sima Yeneabeba Tilahun , Skjaerven Rolv , Kvalvik Liv Grimstvedt , Morken Nils-Halvdan , Klungsøyr Kari , Mannseth Janne , Sørbye Linn Marie 
Published: May 2023

AbstractKnowledge on the association between offspring birth weight and long-term risk of maternal cardiovascular disease (CVD) mortality is often based on firstborn infants without consideration of women’s consecutive births. We studied long-term CVD mortality according to offspring birth weight patterns among women with spontaneous and iatrogenic term deliveries in Norway (1967–2020). We constructed birth weight quartiles (Qs) by combining standardized birth weight with gestational age in quartiles (Q1, Q2/Q3, and Q4) for the women’s first 2 births. Mortality was estimated using Cox regression and expressed as hazard ratios (HRs) with 95% confidence intervals (CIs). Changes in offspring birth weight quartiles were associated with long-term maternal CVD mortality. Compared with women who had 2 term infants in Q2/Q3, women with a first offspring in Q2/Q3 and a second in Q1 had higher mortality risk (HR = 1.33, 95% CI: 1.18, 1.50), while risk was lower if the second offspring was in Q4 (HR = 0.78, 95% CI: 0.67, 0.91). The risk increase associated with having a first infant in Q1 was eliminated if the second offspring was in Q4 (HR = 0.99, 95% CI: 0.75, 1.31). These patterns were similar for women with iatrogenic and spontaneous deliveries. Inclusion of information from subsequent births revealed heterogeneity in maternal CVD mortality which was not captured when using only information based on the first offspring.
NTpred: a robust and precise machine learning framework forin silicoidentification of Tyrosine nitration sites in protein sequences
Authors: Datta Sourajyoti , Nabeel Asim Muhammad , Dengel Andreas , Ahmed Sheraz 
Published: May 2023

AbstractPost-translational modifications (PTMs) either enhance a protein’s activity in various sub-cellular processes, or degrade their activity which leads toward failure of intracellular processes. Tyrosine nitration (NT) modification degrades protein’s activity that initiates and propagates various diseases including neurodegenerative, cardiovascular, autoimmune diseases and carcinogenesis. Identification of NT modification supports development of novel therapies and drug discoveries for associated diseases. Identification of NT modification in biochemical labs is expensive, time consuming and error-prone. To supplement this process, several computational approaches have been proposed. However these approaches fail to precisely identify NT modification, due to the extraction of irrelevant, redundant and less discriminative features from protein sequences. This paper presents the NTpred framework that is competent in extracting comprehensive features from raw protein sequences using four different sequence encoders. To reap the benefits of different encoders, it generates four additional feature spaces by fusing different combinations of individual encodings. Furthermore, it eradicates irrelevant and redundant features from eight different feature spaces through a Recursive Feature Elimination process. Selected features of four individual encodings and four feature fusion vectors are used to train eight different Gradient Boosted Tree classifiers. The probability scores from the trained classifiers are utilized to generate a new probabilistic feature space, which is used to train a Logistic Regression classifier. On the BD1 benchmark dataset, the proposed framework outperforms the existing best-performing predictor in 5-fold cross validation and independent test evaluation with combined improvement of 13.7% in MCC and 20.1% in AUC. Similarly, on the BD2 benchmark dataset, the proposed framework outperforms the existing best-performing predictor with combined improvement of 5.3% in MCC and 1.0% in AUC. NTpred is publicly available for further experimentation and predictive use at: https://sds_genetic_analysis.opendfki.de/PredNTS/.
Accelerated nanopore basecalling with SLOW5 data format
Authors: Samarakoon Hiruna , Ferguson James M , Gamaarachchi Hasindu , Deveson Ira W 
Published: May 2023

Abstract

Motivation
Nanopore sequencing is emerging as a key pillar in the genomic technology landscape but computational constraints limiting its scalability remain to be overcome. The translation of raw current signal data into DNA or RNA sequence reads, known as ‘basecalling’, is a major friction in any nanopore sequencing workflow. Here, we exploit the advantages of the recently developed signal data format ‘SLOW5’ to streamline and accelerate nanopore basecalling on high-performance computing (HPC) and cloud environments.

Results
SLOW5 permits highly efficient sequential data access, eliminating a potential analysis bottleneck. To take advantage of this, we introduce Buttery-eel, an open-source wrapper for Oxford Nanopore’s Guppy basecaller that enables SLOW5 data access, resulting in performance improvements that are essential for scalable, affordable basecalling.

Availability and implementation
Buttery-eel is available at https://github.com/Psy-Fer/buttery-eel.
3DMolMS: prediction of tandem mass spectra from 3D molecular conformations
Authors: Hong Yuhui , Li Sujun , Welch Christopher J , Tichy Shane , Ye Yuzhen , Tang Haixu 
Published: May 2023

Abstract

Motivation
Tandem mass spectrometry is an essential technology for characterizing chemical compounds at high sensitivity and throughput, and is commonly adopted in many fields. However, computational methods for automated compound identification from their MS/MS spectra are still limited, especially for novel compounds that have not been previously characterized. In recent years, in silico methods were proposed to predict the MS/MS spectra of compounds, which can then be used to expand the reference spectral libraries for compound identification. However, these methods did not consider the compounds’ 3D conformations, and thus neglected critical structural information.

Results
We present the 3D Molecular Network for Mass Spectra Prediction (3DMolMS), a deep neural network model to predict the MS/MS spectra of compounds from their 3D conformations. We evaluated the model on the experimental spectra collected in several spectral libraries. The results showed that 3DMolMS predicted the spectra with the average cosine similarity of 0.691 and 0.478 with the experimental MS/MS spectra acquired in positive and negative ion modes, respectively. Furthermore, 3DMolMS model can be generalized to the prediction of MS/MS spectra acquired by different labs on different instruments through minor fine-tuning on a small set of spectra. Finally, we demonstrate that the molecular representation learned by 3DMolMS from MS/MS spectra prediction can be adapted to enhance the prediction of chemical properties such as the elution time in the liquid chromatography and the collisional cross section measured by ion mobility spectrometry, both of which are often used to improve compound identification.

Availability and implementation
The codes of 3DMolMS are available at https://github.com/JosieHong/3DMolMS and the web service is at https://spectrumprediction.gnps2.org.
NHGNN-DTA: a node-adaptive hybrid graph neural network for interpretable drug–target binding affinity prediction
Authors: He Haohuai , Chen Guanxing , Chen Calvin Yu-Chian 
Published: May 2023

Abstract

Motivation
Large-scale prediction of drug–target affinity (DTA) plays an important role in drug discovery. In recent years, machine learning algorithms have made great progress in DTA prediction by utilizing sequence or structural information of both drugs and proteins. However, sequence-based algorithms ignore the structural information of molecules and proteins, while graph-based algorithms are insufficient in feature extraction and information interaction.

Results
In this article, we propose NHGNN-DTA, a node-adaptive hybrid neural network for interpretable DTA prediction. It can adaptively acquire feature representations of drugs and proteins and allow information to interact at the graph level, effectively combining the advantages of both sequence-based and graph-based approaches. Experimental results have shown that NHGNN-DTA achieved new state-of-the-art performance. It achieved the mean squared error (MSE) of 0.196 on the Davis dataset (below 0.2 for the first time) and 0.124 on the KIBA dataset (3% improvement). Meanwhile, in the case of cold start scenario, NHGNN-DTA proved to be more robust and more effective with unseen inputs than baseline methods. Furthermore, the multi-head self-attention mechanism endows the model with interpretability, providing new exploratory insights for drug discovery. The case study on Omicron variants of SARS-CoV-2 illustrates the efficient utilization of drug repurposing in COVID-19.

Availability and implementation
The source code and data are available at https://github.com/hehh77/NHGNN-DTA.
Intraoperative bowel perfusion assessment methods and their effects on anastomotic leak rates: meta-analysis
Authors: Renna Maxwell S , Grzeda Mariusz T , Bailey James , Hainsworth Alison , Ourselin Sebastien , Ebner Michael , Vercauteren Tom , Schizas Alexis , Shapey Jonathan 
Published: May 2023

AbstractBackgroundAnastomotic leak is one of the most feared complications of colorectal surgery, and probably linked to poor blood supply to the anastomotic site. Several technologies have been described for intraoperative assessment of bowel perfusion. This systematic review and meta-analysis aimed to evaluate the most frequently used bowel perfusion assessment modalities in elective colorectal procedures, and to assess their associated risk of anastomotic leak. Technologies included indocyanine green fluorescence angiography, diffuse reflectance spectroscopy, laser speckle contrast imaging, and hyperspectral imaging.MethodsThe review was preregistered with PROSPERO (CRD42021297299). A comprehensive literature search was performed using Embase, MEDLINE, Cochrane Library, Scopus, and Web of Science. The final search was undertaken on 29 July 2022. Data were extracted by two reviewers and the MINORS criteria were applied to assess the risk of bias.ResultsSome 66 eligible studies involving 11 560 participants were included. Indocyanine green fluorescence angiography was most used with 10 789 participants, followed by diffuse reflectance spectroscopy with 321, hyperspectral imaging with 265, and laser speckle contrast imaging with 185. In the meta-analysis, the total pooled effect of an intervention on anastomotic leak was 0.05 (95 per cent c.i. 0.04 to 0.07) in comparison with 0.10 (0.08 to 0.12) without. Use of indocyanine green fluorescence angiography, hyperspectral imaging, or laser speckle contrast imaging was associated with a significant reduction in anastomotic leak.ConclusionBowel perfusion assessment reduced the incidence of anastomotic leak, with intraoperative indocyanine green fluorescence angiography, hyperspectral imaging, and laser speckle contrast imaging all demonstrating comparable results.
Localized adaptive waveform inversion: regularizations for Gabor deconvolution and 3-D field data application
Authors: Yong Peng , Brossier Romain , Métivier Ludovic , Virieux Jean 
Published: May 2023

SUMMARYRecently, we have developed a localized adaptive waveform inversion (LAWI) method to tackle the cycle-skipping issue in velocity reconstruction through seismic waveform inversion. The LAWI method employs a local matching filter, computed using Gabor deconvolution, to measure the instantaneous time-shift between observed and calculated data. Unlike the adaptive waveform inversion (AWI) approach, the LAWI method can take the non-stationarity between observed and calculated data into account. In this work, we investigate two types of regularization based on prior information about the expected filter, which could be a minimum-norm filter or a delta-shape filter, with regard to their effects on the robustness and resolution of inversion. We demonstrate on synthetic data the advantages and disadvantages of these two types of prior information, where the delta-type LAWI may handle multiple observed phases not initially predicted by the starting velocity model. Therefore, we apply the delta-type LAWI to a high-quality 3-D field data set in the North Sea, eliminating the need for data-windowing tuning, which can be tedious and time-consuming for 3-D data. Under different workflows with varying reliable initial models and frequency bands of the pressure data considered, we show that the LAWI approach is robust, effective and efficient for reconstructing the P-wave velocity, while other approaches such as AWI and graph-space optimal-transport method may require meticulous data-tuning strategies to converge to the correct model. Well logs and data fits, primarily from early arrivals, give us confidence that this LAWI approach could be applied to various acquisitions and subsurface targets, thanks to its phase-driven principle.
Checkmate: Chess Artifacts and Artworks Made and Played in Extremis
Authors: Perry Rachel , Jackl Klara , Lochekhina Galina 
Published: May 2023

Abstract
A game of war, chess was played and pictured in a time of war by men and women, Jews and non-Jews in hiding, in the ghettos, and even behind the barbed wire of the transit, concentration, and extermination camps across Nazi-occupied Europe. Throughout the Second World War, instead of “throwing the game” and giving up, victims of National Socialism devised ingenious ways to improvise chess sets out of found materials and detritus—carved wood, folded paper, etched tin, and modeled bread. They also drew and painted chess games to document and allegorize their lives in extremis. Through a close reading of chess artifacts and artworks, this article reveals how access to materials and time, status within camp hierarchies, ethnic and national identities, and wartime experiences impacted the various ways these groups used the game of chess under difficult playing conditions. Insisting upon the central role of creativity and play, it argues that both material artifacts and artwork inform our knowledge of how individuals living under Nazi oppression thought and felt.
Molecular ecology of highest priority critically important antibiotic resistant Escherichia coli from mammals housed at an urban zoo
Authors: Sealey Jordan E , Saunders Richard , Horspool Teresa , Barrows Michelle G , Avison Matthew B 
Published: May 2023

Abstract

Objectives
Zoos are environments where species of highly valued animals are kept largely separated from others and the wider world. We report the molecular ecology of critically important antibiotic resistant (ABR) Escherichia coli carried by 28 mammalian species housed in a zoo located in an urban residential district.

Methods
Over 3 months we collected 167 faecal samples from captive mammals and processed for E. coli resistant to third-generation cephalosporins (3GC-R) and fluoroquinolones (FQ-R). Isolates were sequenced using Illumina.

Results
We identified high rates of faecal sample-level positivity, with 50%, 57% and 36% of mammalian species excreting 3GC-R, FQ-R or dual 3GC-R/FQ-R E. coli, respectively. Isolates represented multiple ST and ABR mechanisms; CTX-M-15 and CMY-2 dominated for 3GC-R, and target-site mutation caused 75% of FQ-R. We identified multiple examples of ABR E. coli transmission between mammalian species in separate enclosures, and a variant of the epidemic plasmid pCT within the zoo. There was no evidence for ABR E. coli leaving the zoo, based on comparative analysis with E. coli from humans, cattle and dogs isolated from the 50 × 50 km region in which the zoo is located. Amoxicillin/clavulanate was the most widely used antibiotic in the zoo, and we identified four widely disseminated amoxicillin/clavulanate resistance mechanisms, including a previously unreported inhibitor-resistant TEM, and the carbapenemase OXA-181.

Conclusions
We conclude that the zoo studied here is a ‘melting pot’ for the selection and circulation of 3GC-R and FQ-R E. coli, but these circulating E. coli appear captive within the zoo.
Differential response to antibiotic therapy in staphylococcal infective endocarditis: contribution of an ex vivo model
Authors: Lalanne Sébastien , Cattoir Vincent , Guerin François , Verdier Marie-Clémence , Revest Matthieu 
Published: May 2023

Abstract

Objectives
Staphylococcal infective endocarditis (IE) remains a hard-to-treat infection with high mortality. Both the evaluation of new innovative therapies and research on alternative models mimicking human IE are therefore urgently needed to improve the prognosis of patients with diagnosed IE. Dalbavancin is a novel anti-staphylococcal lipoglycopeptide but there are limited data supporting its efficacy on biofilm infections. This antibiotic could be an alternative to current therapies for the medical treatment of IE but it needs to be further evaluated.

Methods
Here we developed an original ex vivo model of Staphylococcus aureus IE on human heart valves and assessed biofilm formation on them. After validating the model, the efficacy of two antistaphylococcal antibiotics, vancomycin and dalbavancin, was compared by measuring and visualizing their respective ability to inhibit and eradicate late-formed biofilm.

Results
Determination of the minimum biofilm inhibitory (MbIC) and eradicating (MbEC) concentrations in our ex vivo model identified dalbavancin as a promising drug with much lower MbIC and MBEC than vancomycin (respectively &lt;0.01 versus 28 mg/L and 0.03 versus 32 mg/L).

Conclusions
These data highlight a strong bactericidal effect of dalbavancin, particularly on an infected heart valve compared with vancomycin. Dalbavancin could be a realistic alternative treatment for the management of staphylococcal IE.
Impact of a prospective audit and feedback antimicrobial stewardship programme on carbapenem consumption: a quasi-experimental study (IPANEMA study)
Authors: Ronda Mar , Padullés Ariadna , Grau Imma , Tubau Fe , Satorra Pau , Shaw Evelyn , Vigués Francesc , Carratalà Jordi 
Published: May 2023

Abstract

Objectives
To test the hypothesis that a prospective audit and feedback (PAF) intervention combined with electronic tools will reduce carbapenem use without negatively affecting patient outcomes.

Methods
A quasi-experimental, pre-intervention and intervention study was performed conducted in the urology department of a university hospital. The intervention involved implementing a PAF within an antimicrobial stewardship programme with the aid of an electronic tool. The primary outcome was carbapenem use, assessed by DDD/100 patient-days (PD). Secondary outcomes included evaluating the effect of the intervention on overall antibiotic use measured by DDD/100 PD and days of therapy (DOT)/100 PD, as well as patient safety. The chi-squared test or t-test was used, and the Poisson model was employed to assess the association between the intervention and outcomes.

Results
A 9% decrease in carbapenem DDD/100 PD was observed during the intervention period (IR = 0.91; 95% CI = 0.85–0.97, P = 0.007). The proportion of patients who received carbapenem treatment dropped from 17.8% to 16.5% [incidence ratio (IR) = 0.95; 95% CI = 0.86–2.05, P = 0.31]. Carbapenem DOT/100 PD decreased from 12.4 to 11.0 (IR = 0.89; 95% CI = 0.83–0.94, P &lt; 0.001). Overall antibiotic DDD/100 PD decreased by 3% (IR = 0.97; 95% CI = 0.94–0.99, P = 0.001) and DOT/100 PD by 7% (IR = 0.93; 95% CI = 0.91–0.95, P &lt; 0.001). The incidence of infections caused by carbapenemase-producing microorganisms, Enterococcus faecium bacteraemia and Clostridioides difficile-associated diarrhoea episodes was similar in the pre-intervention and intervention periods. ESBL incidence rate decreased, but the differences were not statistically significant (3.94/1000 PD versus 2.88/1000 PD, P = 0.111). Length of hospital stay, in-hospital all-cause mortality, and 30 day readmission incidence remained unchanged.

Conclusions
The implementation of PAF combined with an electronic tool was an effective and safe intervention for reducing carbapenem use.