bluuebunny/crossref_metadata_2025_split huggingface dataset:
Erwinia wuhanensis sp. nov. isolated from human blood
Authors: Zhang Yingmiao , Zhan Yu , Wang Hui , Yang Jing , Lu Zhongxin 
Published: June 2024

Abstract

A novel Erwinia strain BC051422T was isolated from the blood of a patient at the Central Hospital of Wuhan, Wuhan, PR China in 2022. The strain was found to be Gram stain negative, facultatively anaerobic, motile, and rod-shaped. A preliminary analysis based on the 16S rRNA gene sequence and multi-locus sequence analysis of the atpD, infB, rpoB, and gyrB gene revealed that this strain is closely related to members of the genus Erwinia. The strain was subjected to whole genome sequencing and both average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values between strain BC051422T and type strains of all known species in Erwiniaceae were 68.8 to 83.4% and 19.2 to 35.5%, respectively, which are lower than the 95% (ANI) and 70% (isDDH) cut-off for delineation of bacterial species. The major cellular fatty acids of strain BC051422T is C16:0, C16:1 ω7c/C16:1 ω6c, and C17: 0 cyclo, which are similar to other Erwinia species. The genomic DNA G + C content of strain was 55.95 mol%. Strain BC051422T can be differentiated from other Erwinia species by its ability to ferment sucrose, but is negative for mannose, rhamnose, melibiose, and sorbitol. Genotypic and phenotypic characteristics indicate that strain BC051422T represent a novel species of the genus Erwinia, for which the names Erwinia wuhanensis sp. nov. is proposed. The type strain of Erwinia wuhanensis sp. nov. is BC051422T (= GDMCC 1.4074T = JCM 36319T).
Online Nonparametric Supervised Learning for Massive Data
Authors: Chaouch Mohamed , Al-Hamed Omama M. 
Published: June 2024

Abstract

Despite their benefits in terms of simplicity, low computational cost and data requirement, parametric machine learning algorithms, such as linear discriminant analysis, quadratic discriminant analysis or logistic regression, suffer from serious drawbacks including linearity, poor fit of features to the usually imposed normal distribution and high dimensionality. Batch kernel-based nonparametric classifier, which overcomes the linearity and normality of features constraints, represents an interesting alternative for supervised classification problem. However, it suffers from the well-known ''curse of dimension". The problem can be alleviated by the explosive sample size in the era of big data, while large-scale data size presents some challenges in the storage of data and the calculation of the classifier. These challenges make the classical batch nonparametric classifier no longer applicable. This motivates us to develop a fast algorithm adapted to the real-time calculation of the nonparametric classifier in massive as well as streaming data frameworks. This online classifier includes two steps. First, we consider an online principle components analysis to reduce the dimension of the features with a very low computation cost. Then, a stochastic approximation algorithm is deployed to obtain a real-time calculation of the nonparametric classifier. The proposed methods are evaluated and compared to some commonly used machine learning algorithms for real-time fetal well-being monitoring. The study revealed that, in terms of accuracy, the offline (or Batch), as well as, the online classifiers are serious competitors to the random forest algorithm. Moreover, we show that the online classifier gives the best trade-off accuracy/computation cost compared to the offline classifier.
Developing a medication-safety self-assessment tool for rural primary care units - A case from Finnish Lapland
Authors: Sova Päivi , Celikkayalar Ercan , Sneck Sami , Holmström Anna-Riia 
Published: June 2024

Abstract

Background
In rural areas, primary care faces several challenges, and medication therapy is one of the most complex processes in primary care. With a specific, proactive, medication-safety self-assessment tool designed for rural primary care units, healthcare professionals could identify development needs in their medication processes.
Methods
The Delphi consensus method with two Delphi rounds was used to create a medication-safety self-assessment tool for rural primary care units in Finnish Lapland. A preliminary tool was designed based on three national and international risk management tools. Statements of the preliminary tool were evaluated with a two-round Delphi panel by 12 experts in primary care and patient safety. Evaluated aspects were suitability for primary care settings, patient safety relevance, and necessity of the statements to be included in the developed rural, primary care, medication-safety self-assessment tool.
Results
In the first Delphi round, a consensus was reached on 39% of the statements (n = 118/304), of which 86% (n = 101/118) were included, and 14% (n = 17/118) were excluded from the final primary care medication- safety self-assessment tool. In the second round, 84% of the statements (n = 141/167) reached a consensus, of which 70% (n = 98/141) were excluded and 30% (n = 43/141) included in the final tool. The included 144 statements were divided into 12 thematic sub-groups: 1. Patient information, 2. Drug information, 3. Communication of drug orders and other drug information; 4. Drug labeling, packaging and nomenclature; 5. Drug storage and distribution, 6. Medication device acquisition and use, 7. Environmental factors, workflow and staffing patterns; 8. Staff competency and education, 9. Patient education, 10. Preventive risk management, 11. Learning from medication safety incidents, and 12. Electronic health record.
Conclusions
The developed medication-safety self-assessment tool is targeted for proactive medication risk management in rural primary care settings. While experts reached a consensus for the PMSSA tool contents, adoption of the tool to suit the rural primary care environments in different countries should be further investigated.
Assessment of Ecotoxic Metal Leaching Behaviour of Coal Gangue using a Sequential Extraction Procedure
Authors: Nash William , Fahmi Reza , Ramos Violeta , Crane Rich 
Published: June 2024

Abstract

The environmental leaching characteristics of the ecotoxic metals Cr, Co, Ni, Cu, Zn, As, Se, Ag, Cd, Tl and Pb within six coal gangue samples from mines located in Poland are assessed herein using the BCR-2 sequential extraction procedure. The samples’ bulk mineralogical and chemical compositions are determined by petrographic examination, X-ray fluorescence spectroscopy, X-ray diffraction and inductively-coupled mass spectrometry (following acid digestion). In general, of the metals studied Cd (predominantly oxidizable but often exchangeable) and Pb (predominantly reducible) pose the greatest hazard to the environment. Ni (predominantly oxidizable) and Cr (predominantly reducible) are also highly abundant and potentially mobile. Zn and Cu are abundant and predominantly exchangeable in half of the samples examined. Leaching of all metals is likely to be accelerated by the samples’ acid-forming propensity, which arises from their considerable (though variable) inventories of framboidal pyrite. This is especially the case for the wastes from Bogdanka and Piast mines, since they possess an order of magnitude more sulfidic material than the other samples (up to 1.9 wt%). Management of repositories containing these wastes will require specific measures to prevent such acid generation and ecotoxic metal release into the environment. Specifically, encapsulation within acid-neutralizing (e.g. calcite-bearing) materials is essential for these wastes, but is also recommended for those from mines Jankowice, Marcel, Staszik and Chwalowice.
Pasting and Texture Properties of Commercial Plant Proteins and Its Mixtures
Authors: Kaspchak Elaine , Muntilha Anna Paula , Nabeshima Elizabeth Harumi , Sadahira Mitie Sônia 
Published: June 2024

Abstract

Protein mixtures are usually applied in plant based products development in order to achieve amino acids balance and properly technological performance. Therefore, the aim of this work was to study the pasting and texture properties of commercial proteins commonly used in food products (pea, lentil, fava bean, rice and soybean) and its binary and ternary mixtures. The pasting properties were studied by Rapid Visco Analyser (RVA) and the texture by Texture Profile Analysis (TPA) method using a texturometer. Results showed that protein mixtures exhibit distinct behaviors when compared to single proteins. Single lentil and soy protein presented the highest final viscosity (847 and 806 cP, respectively) whilst the rice the lowest final viscosity (10 cP). Related to texture, faba bean and soy exhibited the highest gel hardness (1.52 and 1.50 N, respectively). For binary and ternary mixtures, in general, the viscosity and texture profiles parameters decreased. Rice-containing mixtures showed the lowest final viscosity (30.5–62.0 cP), while lentil and faba bean mixtures had the highest final viscosities and gel strengths (579 cP and 1.77 N, respectively). From the ternary mixtures, samples containing lentil, fava bean, and rice displayed superior gel strength (0.9 N) due to a synergistic interaction. This work provides information about vegetable proteins and its mixtures that can be used for a better design of plant based food products.
Evaluating the impact of extended dosing intervals on mRNA COVID-19 vaccine effectiveness in adolescents
Authors: Tsang Tim K. , Sullivan Sheena G. , Meng Yu , Lai Francisco Tsz Tsun , Fan Min , Huang Xiaotong , Lin Yun , Peng Liping , Zhang Chengyao , Yang Bingyi , Ainslie Kylie E. C. , Cowling Benjamin J. 
Published: June 2024

Abstract

Extending the dosing interval of a primary series of mRNA COVID-19 vaccination has been employed to reduce myocarditis risk in adolescents, but previous evaluation of impact on vaccine effectiveness (VE) is limited to risk after second dose. Here, we quantified the impact of the dosing interval based on case notifications and vaccination uptake in Hong Kong from January to April 2022. We estimated that the hazard ratio (HR) and odds ratio (OR) of infections after the second dose for extended (28 days or more) versus regular (21–27 days) dosing intervals ranged from 0.86 to 0.99 from calendar-time proportional hazards models, and from 0.85 to 0.87 from matching approaches, respectively. Adolescents in the extended dosing groups (including those who did not receive a second dose in the study period) had a higher hazard of infection than those with a regular dosing interval during the intra-dose period (HR: 1.66; 95% CI: 1.07, 2.59; p = 0.02) after the first dose. Implementing an extended dosing interval should consider multiple factors including the degree of myocarditis risk, the degree of protection afforded by each dose, and the extra protection achievable using an extended dosing interval.
Design and implementation of the first proton beamline in VEGA-3 Petawatt laser system.
Authors: Cebriano Teresa , Curcio Alessandro , Aginako Jon Imanol Apiñaniz , Blanco Diego De Luis , Morabito Antonia , Frías María Dolores Rodríguez , Salgado-Lopez Carlos , Volpe Luca , Gatti Giancarlo 
Published: June 2024

Abstract

Laser-Plasma ion acceleration is acquiring importance on a daily basis due to incipient applicability in certain research fields.However, the energy and divergence control of these brilliant sources can be considered a bottleneck in the developmentof some applications. In this work, we present the commissioning of a compact proton beamline based on a triplet ofquadrupoles dedicated to focus and collect short and energetic pulses, open to the user community. The focused proton beamcharacterization has been carried out by imaging of scintillation detectors with different particle filters. Experimental resultshave been compared with numerical simulations performed with Monte Carlo code (MCNP6) and T-STEP that have been usedto perform the deposited energy, the particle tracking, and the particle distribution in different focal configurations, respectively.Charges of nC (∼1010protons with energies up to 17.25 MeV) have been measured at the focal planes compacting the thebeam to spot sizes of a few millimetres in RMS (root mean square). The percentage fluctuation of the transported chargesvalues has been studied. The beam rigidity has been measured by transverse moving of the quadrupoles and subsequentbeam centroid shift, allowing to cross correlate the deflected energy with the energy ranges resulting from the filtering process.Finally, the versatility of the system, which is also suitable for operating at high repetition rate (HRR), has been demonstratedby proton beam lithography tests using a mask.
Liquidity index of the Lublin loess as a function of cone resistance qc from CPTU test
Authors: Nepelski Krzysztof , Lal Agnieszka , Krzysiak Monika , Skrzypczak Izabela , Ochab Piotr , Gosk Wojciech 
Published: June 2024

Abstract

The paper presents the results of the calibration of an interpretive formula for the determination of IL based on cone resistance qc for loess soils of eolian facies. The studies were carried out on characteristic soils that occur in the Lublin region. For this purpose, three CPTU static soundings were selected in which a representative soil profile with a total length of 21 m was extracted. Boreholes were then drilled in close vicinity, at distances ranging within 1.0 m, and samples for laboratory testing were collected at intervals of 0.25 m. A total of 86 samples were tested and the liquidity index of each was determined. The IL values specified in the laboratory examinations were paired with the cone resistances qc averaged over the depth range corresponding to the sampling. The qc- IL distribution was then analysed and a formula correlating both parameters was derived. The cone resistance depends not only on water content but also on a number of other factors, including porosity, overconsolidation ratio, cementation, fraction distribution, degree of saturation, grain shape and alignment. Therefore, the estimation of IL from CPTU tests should be regarded as an approximation, while an accurate identification of the subsoil requires further investigations. Nevertheless, such information provides valuable knowledge in the initial stages of subsoil recognition, e.g. during design work.
TSH receptor and IGF1 receptor expression in Circulating Fibrocytes in the pathogenesis of Graves’ Orbitopathy
Authors: Basak Madhurima , Bhattacharjee Dipanjan , Kar Anish , De Sriparna , Chakraborty Bidhan , Das Madhusudan , Chowdhury Jyothi , Chowdhury Subhankar 
Published: June 2024

Abstract

Purpose
Graves’ Orbitopathy (GO), an autoimmune disorder linked to Graves’ Disease (GD), manifests through inflammation in orbital tissues and extraocular muscles (EOMs), driven by key receptors like TSHR and IGF1R. It was observed that a certain individual with GD will develop clinically significant orbitopathy and reason behind this still unclear. This study aimed to elucidate this connection by: i) Assessing IGF1R expression and its correlation with TSHR on circulating fibrocytes. ii) Investigating fibrocyte conversion to fibroblasts upon serum treatment. iii) Analysing cytokine and chemokine expression in fibrocytes post-serum exposure within the Indian population.
Methods and Results
Flow cytometry analysis of IGF1R in peripheral blood from 30 GO, 30 GD, and 20 healthy controls (HC) revealed significantly elevated IGF1R+ fibrocytes in GO (11%) versus GD (2.4%) and HC (0.1%). Immunocytochemistry of TSHR and IGF1R on cultured fibrocytes confirmed colocalization of TSHR and IGF1R on fibrocytes, notably higher in GO. Treating HC-derived fibrocytes with GO patient serum triggered fibroblast transformation, marked by increased fibrotic markers (CD90, alpha SMA). Moreover, sandwich ELISA of cytokines and chemokines like IL-6, IL-8, TNF-α, MCP-1, and HA demonstrated elevated levels of those cytokines and chemokines in GO serum-treated HC-fibrocytes.
Conclusion
These results highlight the potential pathogenicity of TSHR and IGF1R on fibrocytes in GO, suggesting their role in orbital tissue remodelling and inflammation. The observed receptor colocalization may drive GO pathogenesis, providing insights into targeted therapeutic strategies for this debilitating condition.
Influence of frailty and specific comorbidities on oncological outcomes in metastatic hormone-sensitive and castration resistant prostate cancer
Authors: Wenzel Mike , Hoeh Benedikt , Siech Carloin , Humke Clara , Welte Maria , Ahrens Marit , Würnschimmel Christoph , Tilki Derya , Steuber Thomas , Graefen Markus , Kluth Luis , Chun Felix , Mandel Philipp 
Published: June 2024

Abstract

Background:
Demographic changes will lead to higher proportions of metastatic hormone-sensitive (mHSPC) and castration resistant metastatic prostate cancer (mCRPC) patients with higher frailty index and multiple comorbidities.
Methods:
We relied on an institutional tertiary-care database to explore the effect of frailty (Eastern Cooperative Oncology Group [ECOG]), as well as cardiovascular (CVD) and secondary malignancy (SecCa) comorbidities on overall survival (OS) and time to mCRPC in mHSPC and OS in mCRPC patients with Kaplan-Meyer estimates and Cox regression models.
Results:
Of 802 mHSPC patients, 61% were ECOG0 vs. 32% ECOG1 vs. 6.5% ECOG ≥ 2. Significant differences in baseline patient and baseline mHSPC characteristics were observed for all three groups (all p ≤ 0.05). In time to mCRPC analyses and OS analyses of mHSPC and mCRPC patients, significant disadvantages were observed for ECOG 1/≥2 patients, relative to ECOG0, even after multivariable adjustment. Moreover, 31% of included patients had history/active CVD, which yielded significant median OS differences in mHSPC patients (95 vs. 63 months, multivariable hazard ratio: HR: 1.77, p < 0.01), but not in mCRPC patients (p = 0.085). After stratification according to SecCa, 14% had a SecCa which led to significant median OS differences in mCRPC patients (50 vs. 37 months, p < 0.01) but not in mHSPC patients (76 vs. 64 months, p = 0.089). Patients with higher frailty index and comorbidities showed significant differences in therapy lines.
Conclusions:
Frailty and specific comorbidities significantly influence cancer-control outcomes in mHSPC, as well as mCRPC patients, even after controlling for adverse tumor characteristics.
Coenzyme A protects against ferroptosis via CoAlation of thioredoxin reductase 2
Authors: Chi Jen-Tsan , Lin Chao Chieh , Lin Yi-Tzu , Chen Ssu-Yu , Setayeshpour Yasaman , Chen Yubin , Dunn Denise , Soderblom Erik , Zhang Guo-Fang , Filonenko Valeriy , Jeong Suh Young , Floyd Scott , Hayflick Susan , Gout Ivan 
Published: June 2024

Abstract

The Cystine-xCT transporter-Glutathione (GSH)-GPX4 axis is the canonical pathway to protect against ferroptosis. While not required for ferroptosis-inducing compounds (FINs) targeting GPX4, FINs targeting the xCT transporter require mitochondria and its lipid peroxidation to trigger ferroptosis. However, the mechanism underlying the difference between these FINs is still unknown. Given that cysteine is also required for coenzyme A (CoA) biosynthesis, here we show that CoA supplementation specifically prevents ferroptosis induced by xCT inhibitors but not GPX4 inhibitors. We find that, auranofin, a thioredoxin reductase inhibitor, abolishes the protective effect of CoA. We also find that CoA availability determines the enzymatic activity of thioredoxin reductase, but not thioredoxin. Importantly, the mitochondrial thioredoxin system, but not the cytosolic thioredoxin system, determines CoA-mediated ferroptosis inhibition. Our data show that the CoA regulates the in vitro enzymatic activity of mitochondrial thioredoxin reductase (TXNRD2) by covalently modifying the thiol group of cysteine (CoAlation) on Cys-483. Replacing Cys-483 with alanine on TXNRD2 abolishes its in vitro enzymatic activity and ability to protect cells from ferroptosis. Targeting xCT to limit cysteine import and, therefore, CoA biosynthesis reduced CoAlation on TXNRD2, an effect that was rescued by CoA supplementation. Furthermore, the fibroblasts from patients with disrupted CoA metabolism demonstrate increased mitochondrial lipid peroxidation. In organotypic brain slice cultures, inhibition of CoA biosynthesis leads to an oxidized thioredoxin system, mitochondrial lipid peroxidation, and loss in cell viability, which were all rescued by ferrostatin-1. These findings identify CoA-mediated post-translation modification to regulate the thioredoxin system as an alternative ferroptosis protection pathway with potential clinical relevance for patients with disrupted CoA metabolism.
Small for gestational age in twin pregnancies and the risk of offspring pediatric neurologic morbidity
Authors: Haleluya Noa leybovitz , Wainstock Tamar , Pariente Gali , Sheiner Eyal 
Published: June 2024

Abstract

Objectives
Small for gestational age (SGA) singletons are at increased risk for neurodevelopmental abnormalities. Scarce data exist regarding the long-term implications of SGA in twins. We opted to study the association between SGA of one twin and long- term neurologic related morbidity in dichorionic diamniotic twins.
Study design:
A population-based retrospective cohort study including consecutive dichorionic diamniotic twins, born between the years 1991–2021 at a tertiary medical center was conducted. Total and subtypes of neurologic related pediatric hospitalizations among SGA versus non-SGA twins were compared. A Kaplan-Meier survival curve was used to compare the cumulative neurologic morbidity incidence, and a Cox proportional hazards model was constructed to adjust for confounders.
Results
The study population included 4,222 newborns; 180 (4.3%) were SGA. Rate of long- term neurologic related hospitalizations was comparable between the two groups (8.7% vs. 8.0%, p = 0.755; Kaplan-Meier survival curve Log- rank p = 0.652). Using a Cox proportional hazards model, controlling for gender and birth order, no association was found between SGA and the risk for subsequent neurologic pediatric morbidity of the offspring (Adjusted HR = 1.0, 95% CI 0.6–1.8, p = 0.973).
Conclusions
SGA is not associated with an increased risk for long-term pediatric neurologic morbidity in dichorionic diamniotic twins.
FitScore: A Fast Machine Learning-Based Score for 3D Virtual Screening Enrichment
Authors: Gehlhaar Daniel K. , Mermelstein Daniel J. 
Published: June 2024

Abstract

Enhancing virtual screening enrichment has become an urgent problem in computational chemistry, driven by increasingly large databases of commercially available compounds, without a commensurate drop in in vitro screening costs. Docking these large databases is possible with cloud-scale computing. However, rapid docking necessitates compromises in scoring, often leading to poor enrichment and an abundance of false positives in docking results. This work describes a new scoring function composed of two parts – a knowledge-based component that predicts the probability of a particular atom type being in a particular receptor environment; and a tunable weight matrix that converts the probability predictions into a dimensionless score suitable for virtual screening enrichment. This score, the FitScore, represents the compatibility between the ligand and the binding and is capable of a high degree of enrichment across standardized docking test sets.