bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-resolution genomics identifies pneumococcal diversity and persistence of vaccine types in children with community-acquired pneumonia in the UK and Ireland
Authors: Malhotra-Kumar Surbhi , Rodriguez Juan-Pablo , Xavier Basil , Stohr Wolfgang , Heirstraeten Liesbet Van , Lammens Christine , Finn Adam , Goossens Herman , Bielicki Julia , Sharland Michael 
Published: May 2023

Abstract
Background Streptococcus pneumoniae is a global cause of community-acquired pneumonia (CAP) and invasive disease in children that requires antibiotic treatment. As part of the CAP-IT trial (grant No. 13/88/11; https://www.capitstudy.org.uk/), we analyzed nasopharyngeal swabs from children with clinically diagnosed CAP, and found no differences in pneumococcal susceptibility between patients receiving oral amoxicillin treatment for shorter or longer durations and at higher or lower antibiotic doses. Here, we perform high-resolution genomics to understand pneumococcal diversity and to unravel potential mechanisms underlying persistence of pneumococcal (vaccine) serotypes.Methods Three-hundred and ninety pneumococci cultured from 1132 nasopharyngeal swabs from 718 children were whole-genome sequenced (Illumina) and tested for susceptibility to penicillin and amoxicillin. Recombination analysis was performed using long-read sequenced isolates (PacBio) and publicly available sequences.Results In 390 unique pneumococcal isolates, non-susceptibility to penicillin (n = 61, 15.6%) and amoxicillin (n = 10, 2.6%) was low and independent of the amoxicillin treatment dosage and duration. Serotypes 15B/C, 11A, 15A and 23B1 were most prevalent. PCV13 serotypes 3, 19A, and 19F were also identified (n = 25, 6.4%), and recombination analysis and genome-wide comparisons with historical isolates dating from 1995 identified several potential capsule switch events in these highly recombinant vaccine serotypes 19A and 19F, in contrast to serotype 3 genomes (n = 13, 3.3%) that showed high genomic stability over the last 20 years. All 23B1 isolates (n = 27, 6.9%) were penicillin non-susceptible, and one was the result of a potential capsule-switch in 19F.Conclusions Our data suggest that vaccination strategies, but not amoxicillin use, are more likely to drive pneumococcal serotype prevalence among children in the UK and prompts consideration of PCVs with additional serotype coverage that are likely to further decrease invasive disease in this target population. Emergence of 23B1, a non-vaccine genotype with penicillin non-susceptibility, might provide a persistence strategy for vaccine serotypes, highlighting the need for continued genomic surveillance.
Skeletal muscle index-to-body mass index ratio as a predictor of postsurgical bleeding after mastectomy in patients with breast cancer
Authors: Morikawa Hiroki , Oba Takaaki , Kiyosawa Nami , Iji Ryoko , Amitani Masatsugu , Chino Tatsunori , Shimizu Tadafumi , Ono Mayu , Ito Tokiko , Kanai Toshiharu , Maeno Kazuma , Ito Ken-ichi 
Published: May 2023

Abstract
Background Postsurgical bleeding is a major complication of mastectomy in patients with breast cancer. However, the risk factors for postsurgical bleeding have not been well studied. Although obesity or reduced skeletal muscle mass is an indicator of cancer surgery complications, its impact on postsurgical bleeding after mastectomy remains unknown.Methods In total, 563 patients with breast cancer who underwent mastectomy were included in this study. We evaluated the preoperative body mass index (BMI), skeletal muscle index (SMI), and SMI-to-BMI ratio and analyzed the association between these values and the incidence of postsurgical bleeding.Results Postsurgical bleeding occurred in 33 (5.6%) patients. Mean BMI was significantly higher in the bleeding group (26.3 ± 4.7) than in the no bleeding group (23.0 ± 4.1) (p < 0.001), whereas mean SMI was lower in the former group (45.0 ± 8.5) than in the latter group (48.0 ± 8.5) (p = 0.08). The bleeding group had significantly lower SMI-to-BMI ratio (1.71 ± 0.16) than the no bleeding group (2.10 ± 0.23) (p < 0.001). Among these three parameters, SMI-to-BMI ratio had the highest area under the curve value in their receiver operating characteristic curves (0.73 for BMI, 0.59 for SMI, 0.92 for SMI-to-BMI ratio). Furthermore, on multivariate analysis, SMI-to-BMI ratio was an independent risk factor for postsurgical bleeding (hazard ratio, 38.4; 95% confidence interval, 13.9–136.2; p < 0.001).Conclusions SMI-to-BMI ratio is a superior predictive factor of postsurgical bleeding after mastectomy to either BMI or SMI alone.
Effects of short-chain per- and polyfluoroalkyl substances (PFAS) on human cytochrome P450 (CYP450) enzymes and human hepatocytes: an in vitro study
Authors: Solan Megan E. , Lavado Ramon 
Published: May 2023

Abstract
Short-chain have been developed as alternatives to legacy long-chain PFAS, but they may still pose risks due to their potential to interact with biomolecules. Cytochrome P450 (CYP450) enzymes are essential for xenobiotic metabolism, and disruptions of these enzymes by PFAS can have significant human health implications. The inhibitory potential of two legacy long-chain (PFOA and PFOA) and five short-chain alternative PFAS (PFBS, PFHxA, HFPO-DA, PFHxS, and 6:2 FTOH) were assessed in recombinant CYP1A2, − 2B6, -2C19, -2E1, and − 3A4 enzymes. Most of the short-chain PFAS, except for PFHxS, tested did not result in significant inhibition up to 100 µM. PFOS inhibited recombinant CYP1A2, -2B6, -2C19, and − 3A4 enzymes. However, concentrations where inhibition occurred, were all higher than the averages reported in population biomonitoring studies, with IC50 values higher than 10 µM. We also evaluated the activities of CYP1A2 and CYP3A4 in HepaRG monolayers following 48 h exposures of the short-chain PFAS at two concentrations (1 nM or 1 µM) and with or without an inducer (benzo[a]pyrene, BaP, for CYP1A2 and Rifampicin for CYP3A4). Our findings suggest that both 1 nM and 1 µM exposures to short-chain PFAS can modulate CYP1A2 activity, with some acting as inducers and others as inhibitors. Except for PFHxS, the short-chain PFAS appear to have little effect on CYP3A4 activity. Understanding the effects of PFAS exposure on biotransformation can shed light on the mechanisms of PFAS toxicity and aid in developing effective strategies for managing chemical risks, enabling regulators to make more informed decisions.
Jet noise and wing installation effects of circular, beveled and rectangular nozzles
Authors: Christophe Julien , de Decker Julien , Schram Christophe 
Published: May 2023

Abstract
With the growth of modern turbofan engines, their integration under the wing becomes challenging and induces aerodynamic and acoustic interactions between the jet exhaust and the airframe. Jet noise reduction techniques have been widely studied over the past decades but their efficiency has still to be demonstrated once installed. The present lab-scale jet experiments at Mach 0.6 compare the noise radiated by beveled and rectangular installed nozzles to circular ones on a quarter-sphere radiation map using a microphone antenna. For all radiation angles, modified nozzles show an amplitude decrease of the jet-plate interaction tones of the noise spectra attributed to a strong coupling between the jet shear layers and the sound scattering at the plate trailing edge. Circular nozzles achieve a noise reduction for all radiation angles with a maximum decrease up to 2~dB at receiver locations perpendicular to the plate. While rectangular nozzles show a similar behavior, a sound increase is observed for listeners parallel to the plate when the height-to-width ratio is small.
Tropical Atlantic variability in EC-EARTH: impact of the radiative forcing
Authors: Volpi Danila , García-Serrano Javier , Palmeiro Froila M. , Gil-Reyes Laura , Haarsma Reindert J. 
Published: May 2023

Abstract
Understanding the impact of radiative forcing on climate variability and change in the Tropical Atlantic is crucial for different socio-economic sectors, given their substantial impacts in both local and remote regions. Standard transient historical and scenario simulations do not allow to properly evaluate the effect of a changing climate on the variability. To overcome this limitation and as an alternative to a large ensemble, two 250-year-long atmosphere-ocean coupled simulations with EC-EARTH 3.3 (CMIP6 version) have been performed with fixed radiative forcing at year 2000 and 2050, representative of present and future climate conditions respectively. The changes in the leading modes of Tropical Atlantic variability (TAV), including the Atlantic Niño/Niña and the Subtropical North Atlantic pattern, have been assessed in three target seasons: spring (MAM), summer (JJ) and early winter (ND). While the change in sea surface temperature (SST) climatology shows homogeneous warming, the difference between future and present SST variability exhibits a distinct behaviour, consistent along the seasonal cycle, with a decrease in the equatorial region and an increase at subtropical latitudes. This study explores the processes associated with the suppressed/enhanced TAV, with particular focus on the less-explored early-winter season. In agreement with previous studies, the Atantic Meridional Overturning Circulation (AMOC) shows a weakening in strength, but the results also show an increase in variability. The AMOC-related deepening of the equatorial thermocline and the flattening linked to weakened trade winds are consistent with the suppressed SST variability of the Atlantic Niño/Niña. On the other hand, the enhanced SST variability at subtropical latitudes is mainly associated with an increase in turbulent heat flux variability, with a minor contribution of mixed layer depth variability. The former is dominated by the latent heat flux, whose key component appears to be the specific humidity linked to an increase in precipitation variability.
Performance of zeolite and trace elements on biogas production from alkaline hydrogen peroxide pretreated sweet sorghum bagasse slurry
Authors: Li Xuemei , xiao Ying , Zhang Rui , Sun Chen , Cao Weixing 
Published: May 2023

Abstract
In order to alleviate the inhibition of sodium ions and phenols on methanogenesis by anaerobic digestion of sweet sorghum bagasse pretreated with alkaline hydrogen peroxide, zeolite and trace elements (TEs) were added to sweet sorghum bagasse slurry (PSSBS) for biogas production. The influence of zeolite dosage and TE on the anaerobic digestion performance was revealed from the perspective of biogas production, as well as the cellulase and dehydrogenase activities. The results showed that zeolite and TE increased methane production and shorten the lag time. The maximum methane yield of 274.5 mL/gVS from PSSBS + 5 g/L zeolite + 1 mL TE could be obtained and 58.4% higher than that of untreated sweet sorghum bagasse. Addition of zeolite and TE was beneficial to increase the activities of cellulase and dehydrogenase of the digestate. This work would provide a theoretical reference for the resource utilization of sweet sorghum bagasse for clean industrial application in future.
An integrated proteomic classifier to distinguish benign from malignant pulmonary nodules
Authors: dong junqiang , Jia Bin , Wang Tingting , Pan Liangxuan , Du Xiaoyao , Yang Jing , Gao Fei , Guo Bianqin , Liao Lujian 
Published: May 2023

Abstract
Background
Pulmonary nodule with a diameter ranging 8-30 mm has a high rate of occurrence, and distinguishing benign from malignant nodules can greatly improve the prevention and management of lung cancer. However, sensitive and specific liquid-biopsy methods have yet to achieve satisfactory clinical goals.
Methods
We enrolled three cohorts and a total of 185 patients diagnosed with pulmonary nodules for this study. Utilizing data-independent acquisition (DIA) mass spectrometry, we quantified the expression of plasma proteome from patients diagnosed with benign (BE) and malignant (MA) pulmonary nodules. We then performed logistic regression analysis to classify benign from malignant nodules, using cohort 1 as discovery data set and cohort 2 and 3 as independent validation data sets.
Results
We quantified a total of 451 proteins from the plasma, with 15 up-regulated and 5 down-regulated proteins from patients diagnosed as having malignant nodules. Logistic regression identified a six-protein panel comprised of APOA4, CD14, PFN1, APOB, PLA2G7, and IGFBP2 that classifies benign and malignant nodules with improved accuracy. In cohort 1, the area under curve (AUC) of the training and testing reached 0.87 and 0.91, respectively. We have achieved a sensitivity of 100%, specificity of 40%, positive predictive (PPV) of 62.5%, and negative predictive value (NPV) of 100%. In two independent cohorts, the 6-biomarker panel showed a sensitivity, specificity, PPV, and NPV of 96.2%, 35%, 65.8%, and 87.5% respectively in cohort 2, and that of 91.4%, 54.2%, 74.4%, and 81.3% respectively in cohort 3.
Conclusions
Our study identified new panel of plasma protein biomarkers for distinguishing benign from malignant pulmonary nodules that worth further development into a clinically valuable assay.
Do elderly patients with colorectal cancer benefit from surgery and different therapeutic patterns? A real-world study based on SEER database
Authors: Zhang Lei , Hu Chenhao , Zhang Zhe , She Junjun , Shi Feiyu 
Published: May 2023

Abstract
Currently, the treatment guidelines for colorectal cancer (CRC) in elder patients remained unclear. This study aims to investigate whether elder patients (≥70 years) with CRC benefit from surgery and different therapeutic patterns. A total of 90,347 eligible CRC patients older than 70 years were collected from the Surveillance, Epidemiology, and End Results(SEER) database. All the patients were divided into the surgery group and the no-surgery group. After being matched by propensity score matching (PSM) at a 1:1 ratio, 23,930 patients were included in our analysis. The Kaplan-Meier method and log-rank test were applied to compare overall survival (OS) and cancer-specific survival (CSS). In the age-stratified analysis (70–74; 75–79; 80–84; ≥85), the OS and CSS rates of patients in the surgery group were significantly higher than those of patients in the no-surgery group (all P < 0.001). Further analysis showed that surgery plus chemotherapysignificantly improved OS and CSS in elder colon cancer patients with III stage and IV stage compared to surgery alone. Surgery plus chemoradiotherapy significantly improved OS and CSS in elder rectal cancer patients with II stage, III stage and IV stage compared to other therapeutic patterns. Among these CRC patients with aged ≥70 years reported in the SEER database, treatment with surgical resection is significantly associated with an improved OS and CSS. Moreover, adjuvant therapyshowed a significant prognostic advantage for elder advanced CRC patients underwent surgery.
Evaluating Caregiver-Clinician Communication for Tracheostomy Placement in the Neonatal Intensive Care Unit: A Qualitative Inquiry
Authors: Bushroe Kylie , Crisp Kelly , Politi Mary , Brennan Steven , Housten Ashley 
Published: May 2023

Abstract
Objective Identify stakeholders’ tracheostomy decision-making information priorities in the Neonatal Intensive Care Unit (NICU).
Study Design English-speaking caregivers and clinicians who participated in NICU tracheostomy discussions between January 2017 and December 2021 were eligible. They reviewed a pediatric tracheostomy communication guide prior to meeting. Interviews focused on tracheostomy decision-making experiences, communication preferences, and guide perceptions. Interviews were recorded, transcribed, and analyzed using iterative inductive/deductive coding to inform thematic analysis.
Results Ten caregivers and nine clinicians were interviewed. Caregivers were surprised by the severity of their child’s diagnosis and the intensive home care required, but proceeded with tracheostomy because it was the only chance for survival. All recommended that tracheostomy information be introduced early and in phases. Inadequate communication limited caregivers’ understanding of post-surgical care and discharge requirements. All felt a guide could standardize communication.
Conclusions Caregivers seek detailed information regarding expectations after tracheostomy placement in the NICU and at home.
Phase Separation in Mixtures of Prion-Like Low Complexity Domains is Driven by the Interplay of Homotypic and Heterotypic Interactions
Authors: Pappu Rohit , Farag Mina , Borcherds Wade , Bremer Anne , Mittag Tanja 
Published: May 2023

Abstract
Prion-like low-complexity domains (PLCDs) are involved in the formation and regulation of distinct biomolecular condensates that form via coupled associative and segregative phase transitions. We previously deciphered how evolutionarily conserved sequence features drive phase separation of PLCDs through homotypic interactions. However, condensates typically encompass a diverse mixture of proteins with PLCDs. Here, we combine simulations and experiments to study mixtures of PLCDs from two RNA binding proteins namely, hnRNPA1 and FUS. We find that 1:1 mixtures of the A1-LCD and FUS-LCD undergo phase separation more readily than either of the PLCDs on their own. The enhanced driving forces for phase separation of mixtures of A1-LCD and FUS-LCD arise partly from complementary electrostatic interactions between the two proteins. This complex coacervation-like mechanism adds to complementary interactions among aromatic residues. Further, tie line analysis shows that stoichiometric ratios of different components and their sequence-encoded interactions jointly contribute to the driving forces for condensate formation. These results highlight how expression levels might be tuned to regulate the driving forces for condensate formation in vivo. Simulations also show that the organization of PLCDs within condensates deviates from expectations based on random mixture models. Instead, spatial organization within condensates will reflect the relative strengths of homotypic versus heterotypic interactions. We also uncover rules for how interaction strengths and sequence lengths modulate conformational preferences of molecules at interfaces of condensates formed by mixtures of proteins. Overall, our findings emphasize the network-like organization of molecules within multicomponent condensates, and the distinctive, composition-specific conformational features of condensate interfaces.
Reliability and Usability of Telemedicine Evaluations for Facial Dystonia
Authors: Pongpanich Punnaka , Hirunwiwatkul Parima , Jariyakosol Supharat , Assavapongpaiboon Buravej , Krittanupong Supaporn , Tulvatana Wasee 
Published: May 2023

Abstract

This study aimed to investigate telemedicine reliability and usability for facial dystonia. Eighty-two telemedicine recordings from 43 adults with blepharospasm (12,27.9%) and hemifacial spasm (31,72.1%) were obtained (mean age 64.5+9.3 years, 32 female (64.4%)). Two recorded in-hospital telemedicine visits were arranged on the same day as in-person visits at baseline and 4-6 weeks. The third non-recorded home-based telemedicine visit was held 2 days prior to the third in-person visit at 12-14 weeks. After 8 weeks, the neuro-ophthalmologists who performed the in-person visits also evaluated the telemedicine videos records. Spasm gradings by Jankovic Rating Scale (low, grades 0-2; high, grades 3-4), signs and symptoms indicating botulinum toxin complications were collected. Intra-rater agreements in assessing spasm gradings were moderate (severity: kappa=0.42, 95%CI 0.21 to 0.62, frequency: kappa=0.41, 95%CI 0.21 to 0.61) with substantial agreement in detecting lagophthalmos (kappa=0.61, 95%CI 0.36 to 0.86). Adding symptoms to signs increased sensitivity and negative predictive value in detecting lagophthalmos (66.7% to 100% and 94.3% to 100%) and drooping lips (37.5% to 75% and 93.6% to 96.4%), respectively. High mean usability score of 6.5(SD0.8) out of 7 was determined by “Thai version Telehealth Usability Questionnaire.” Therefore, telemedicine could be an alternative platform to evaluate facial dystonia.
Metagenomic analysis reveals the composition and function of intestinal microbiota were affected by different sampling methods and digestive tract segments in monogastric and polygastric animals
Authors: Su Lei , Guo Jindan , Shi Weixiong , Tong Wei , Li Xue , Yang Bochao , Chen Yubao , Xiang Zhiguang , Qin Chuan 
Published: May 2023

Abstract
Background: As a domesticated species vital to humans, cow and donkey are raised worldwide as a source of agricultural industry and food production. The digestion and absorption must rely on the division of labor and cooperation of all the digestive tract segments and microbes. The microbiota plays an important role in the health, diseases, athletic performance, weight and digestion of food in animals. The composition and function of microbial community are closely related to the animals’ physiological structure. Moreover, experimental techniques, like the sampling method, could also influence the identification results.
Results: Here, using approximately 300 GB of metagenomic sequencing data from digestive tract samples from 91 samples that represent six (donkeys) and nine (cows) digestive tract segment with swab and fecal samples of monogastric (donkeys) and polygastric (cows) animals. We assembled 4,004,115 (cow) and 2,938,653 (donkey) microbial metagenome assembled contigs, and obtained 9,060,744 genes with an average of 553bp (range 102bp ~ 10,912bp) were obtained by clustering at 95% identity and 90% coverage. There were certainly influences on the microbiota with two sampling methods and fecal sample was recommended due to more abundant diversity of species compared with swab sample. Besides, microbiota in the stomach was significantly different from other segments and colon held the most abundant bacteria in the other intestine. In addition, the microbial community structure of donkey was obviously different from cow for both dominant and endemic microbes. There were 1,942 genera that were characterized by high Lactobacillus, Clostridium and Prevotella in the donkey while 1,744 genera were recognized in the cow. Differ from the donkey, different segments of the cow had different dominate genera such Prevotellafor the stomach, Kandleria for the small intestine and Clostridium for the hindgut.
Conclusions: Overall, we solved the scientific problem of fecal sample could more objectively reflect the intestinal microbial community. Meanwhile, the microbial composition showed the shared and distinct features of digestive tract segments in different type animals. Our experimental design and dataset provides a valuable resource for discovery of performance-enhancing microbes and systematic studies of cow and donkey microbiome.
Arithmetic optimization algorithm with mathematical operator for spherical minimum spanning tree
Authors: Mi Xiaodong , Luo Qifang , Wei Yuanfei , Zhou Yongquan , Huang Huajuan 
Published: May 2023

Abstract
In this paper, to effectively reinforce the exploration and exploitation of Arithmetic optimization algorithm (AOA) and reasonably achieve their balance. A novel mathematical operator-based arithmetic optimization algorithm (MAOA) is proposed, firstly, we use mathematical symmetry operator and median operator to improve the exploitation and exploration ability of the population, respectively. Secondly, we use sine and cosine operator to effectively reinforce the exploration and exploitation of AOA algorithms and reasonably achieve their balance. Finally, the MAOA algorithm is used to solve the spherical mining spanning tree (sphere MST) and communication network problems. Experimental results show that the proposed MAOA has achieved excellent results in terms of global performance, accuracy, robustness, and convergence speed.