bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial Composition of Haemaphysalis longicornis in Shaanxi Province, Determined Through Next-Generation Sequencing
Authors: Wang Yuhua , Lu Zhenhua , Xu Linli , He Zhen , Liu Jiacheng , Yang Zurong , Shao Zhongjun , Long Yong 
Published: October 2024

Background:Ticks are parasitic organisms that can transmit a wide range of pathogenic microorganisms. They are the second most common vectors of diseases affecting humans and animals. The occurrence and transmission of tick-borne diseases has recently shown increasing or fluctuating trends.Methods:DNA was extracted after the collection of tick samples. A library targeting the V4 hypervariable region of the 16S rRNA gene was constructed. After quality control, next-generation sequencing was performed with the Illumina NextSeq platform to analyze microbial diversity within the ticks.Results:Samples were gathered between May 2023 and July 2023. A total of 77 ticks from five distinct regions were selected for next-generation sequencing. Molecular identification confirmed that all sequenced samples belonged toHaemaphysalis longicornis. The most abundant bacteria belonged to the phylumProteobacteria, which was present in all samples. Variations in sample richness and evenness were observed among sampling sites (Shannon index,P= 0.019). The bacterial diversity in LT exhibited the highest value, with an average of 2.449.RickettsiaandCoxiellawere the predominant bacterial species, both of which are classified as tick-borne pathogens. The linear discriminant analysis effect size revealed significant differences in microbial composition among groups, except for the PC and LY groups, and identified distinct biomarkers for each group.Conclusions:Our findings indicated the high relative abundance of both pathogenic bacteria and non-pathogenic endosymbionts inH. longicornisand the potential for pathogen transmission to residents. However, further validation through human case studies is necessary. Health care providers should be aware of the possibility of the occurrence of these diseases.
МОРФОЛОГИЯ ЧАСТИЦ И ФАЗОВЫЕ СОСТАВЫ НАНОСТРУКТУРИРОВАННЫХ СИСТЕМ COPT И COPD В ОБЛАСТЯХ, “БОГАТЫХ” БЛАГОРОДНЫМИ МЕТАЛЛАМИ
Authors: ЗАХАРОВ Ю.А. , ТИХОНОВА И.Н. , ПУГАЧЕВ В.М. , ПОПОВА А.Н. , ЗАХАРОВ Н.С. , ДОДОНОВ В.Г. , РУССАКОВ Д.М. 
Published: October 2024

Методами рентгенофазового и рентгеноструктурного анализа, малоуглового рентгеновского рассеяния и просвечивающей электронной микроскопии высокого разрешения изучены и впервые сопоставлены морфология наночастиц, структурно-фазовые свойства и фазовые трансформации при нагревании “богатых” благородными металлами наноструктурированных систем CoPt и CoPd, полученных совместным восстановлением гидразин-гидратом смесей водных растворов прекурсоров. Полученные результаты представляют интерес при разработке основ материаловедения биметаллических наносплавов, а также относятся к ключевым в понимании процессов, приводящих к формированию при нагревании наносплавов FePt, CoPt и FePd интерметаллидов с высокоупорядоченной структурой L10, обладающих рекордными для биметаллов магнитными и магнитооптическими свойствами.
The morphology of nanoparticles, structural-phase properties, and phase transformations that occur during heating in the nanostructured CoPt and CoPd systems rich in precious metals, obtained by co-reduction of aqueous precursor solutions by hydrazine hydrate, were studied by X-ray phase analysis and X-ray structural analysis, small-angle X-ray scattering, and high-resolution transmission electron microscopy. The results obtained are of interest for the development of the fundamentals of materials science of bimetallic nanoalloys, and provide a key to understand the processes of the formation of FePt, CoPt and FePd nanoalloys while heating intermetallic compounds with a highly ordered structure L10, which possess record-setting magnetic and magneto-optical properties.
КАТАЛИТИЧЕСКОЕ ГИДРИРОВАНИЕ СО В ПРИСУТСТВИИ КАТАЛИЗАТОРОВ НА ОСНОВЕ ЛИГНИНА, ПОЛУЧЕННЫХ ГИДРОТЕРМАЛЬНЫМ СИНТЕЗОМ
Authors: ИВАНЦОВ М.И. , СВИДЕРСКИЙ С.А. , КРЫСАНОВА К.О. , СОТНИКОВА А.Е. , КУЛИКОВА М.В. 
Published: October 2024

Работа посвящена разработке нового типа железосодержащего катализатора (Кт) на основе лигнина для процесса гидрирования монооксида углерода. Каталитические системы получали методом гидротермального синтеза и изучали комплексом физико-химических методов (ИК-Фурье спектроскопия, спектроскопия комбинационного рассеяния, низкотемпературная адсорбция азота, элементный анализ, атомно-абсорбционный анализ, рентгенофазовый анализ, рентгеновская фотоэлектронная спектроскопия, просвечивающая электронная микроскопия). Показано, что сформированные катализаторы представляют собой мелкозернистый непирофорный негигроскопичный порошок черного цвета. Установлено, что каталитические системы проявляют высокую активность в процессе гидрирования монооксида углерода: конверсия близка к 100 %, производительность по углеводородам С5+ достигает 131.6 г/(кг Кт•ч).
The work is concerned with the development of a new type of iron-containing catalyst (Ct) based on lignin for the hydrogenation of carbon monoxide. Catalytic systems were obtained by hydrothermal synthesis and studied using a set of physicochemical methods (Fourier transform IR spectroscopy, Raman spectroscopy, low-temperature nitrogen adsorption, elemental analysis, atomic absorption analysis, X-ray phase analysis, X-ray photoelectron spectroscopy, transmission electron microscopy). Brunauer-Emmett-Teller (BET) surface area analysis, elemental analysis, atomic absorption analysis, X-ray fluorescence (XRF), transmission electron microscopy (TEM). It is shown that the formed catalysts are fine-grained, non-pyrophoric, non-hygroscopic, black powders. The catalytic systems are determined to exhibit high activity in carbon monoxide hydrogenation: the conversion is close to 100 %, the productivity with respect to C5+ hydrocarbons reaches 131.6 g/(kg Ct ∙ h).
ИССЛЕДОВАНИЕ ГОРЕНИЯ БИОУГЛЕЙ, ПОЛУЧЕННЫХ ГИДРОТЕРМАЛЬНОЙ КАРБОНИЗАЦИЕЙ И ТОРРЕФИКАЦИЕЙ ОПИЛА
Authors: ПУДОВА Я.Д. , КРЫСАНОВА К.О. 
Published: October 2024

Исследовано влияние температурных режимов термохимической обработки (гидротермальной карбонизации и торрефикации) опила лиственных пород на свойства биоуглей и характеристики процесса их горения. Рассмотрены массовые выходы биоугля с точки зрения протекающих при термохимической обработке процессов, а также изменение элементного состава в результате этих процессов. Определены оптимальный способ и температурный режим термохимической обработки. Методом ИК-Фурье спектроскопии, совмещенной с термогравиметрическим анализом, выявлено влияние способа и температуры термохимической обработки опила на состав газообразных продуктов горения биоуглей. Обнаружены две основные стадии горения биоуглей - фаза удаления и сжигания летучих веществ (до 400 °С) и фаза сжигания полукокса (после 400 °С). Проведенный в процессе горения ИК-Фурье-анализ позволил определить выделяющиеся компоненты газовой смеси и наблюдать процессы термохимического распада компонентов биоугля в режиме реального времени. Исследование горения биоуглей показало, что повышение температуры обработки опила снижает образование газообразных продуктов на первой стадии горения и способствует росту количества диоксида углерода на второй стадии.
The effect of the temperature regimes of hardwood sawdust thermochemical treatment (hydrothermal carbonization and torrefaction) on biochar properties and combustion characteristics are investigated. The mass yields of biochars were considered from the viewpoint of the processes that take place during thermochemical treatment, along with the changes in the elemental composition resulting from these processes. The optimal method and temperature regime of thermochemical treatment were determined. The effect of the method and temperature of sawdust thermochemical treatment on the composition of gaseous products from biochar combustion was assessed by FTIR spectroscopy combined with thermogravimetric analysis. Two main stages of biochar combustion were detected: the phase of removal and combustion of volatile substances (up to 400 °C) and the phase of semi-coke combustion (above 400 °C). The analysis carried out by means of FTIR spectroscopy during combustion allowed us to determine the released components of the gaseous mixture and to observe thermochemical decomposition of biochar components in the real time mode. Investigation of biochar combustion showed that an increase in sawdust processing temperature reduces the formation of gaseous products at the first stage of combustion and promotes an increase in the amount of carbon dioxide at the second stage.
Leaving Against Medical Advice From Children’s Hospitals
Authors: Campbell Jeffrey I. , Tolliver Destiny G. , He Yuan , Wang Rita Y. , Shapiro Joseph , Shanahan Kristen , Mell Anthony , Luercio Marcella , Shah Snehal N. , Hall Matt , Goel Anuj K. , Melvin Patrice , Ward Valerie L. , Berry Jay 
Published: October 2024

BACKGROUND
Leaving the hospital against medical advice (AMA) reflects a breakdown in the family-clinician relationship and creates ethical dilemmas in inpatient pediatric care. There are no national data on frequency or characteristics of leaving AMA from US children’s hospitals.

METHODS
We performed a retrospective cohort study of hospital discharges for children under 18 years old from January 1, 2018 to December 31, 2022 in 43 children’s hospitals in the Pediatric Health Information System (PHIS) database. The primary outcome was leaving AMA. Exposures were demographic, geographic, and clinical characteristics. We used multivariable mixed effects logistic regression models to assess independent factors associated with leaving AMA and all-cause 14-day hospital readmission.

RESULTS
Among 3 672 243 included inpatient encounters, 2972 (0.08%) ended in leaving AMA. Compared with non-Hispanic white patients, non-Hispanic Black patients had higher odds of leaving AMA (adjusted odds ratio [aOR] 1.31 [95% confidence interval (CI) 1.19–1.44]), whereas Hispanic patients (aOR 0.66 [95% CI 0.59–0.75]) had lower odds of leaving AMA. Hospitalizations for patients with noncommercial insurance were more likely to end in leaving AMA. Leaving AMA was associated with increased odds of 14-day inpatient readmission (aOR 1.41 [95% CI 1.24–1.61]) compared with patients who did not leave AMA. There was substantial interhospital variability in standardized rates of leaving AMA (range 0.18–2.14 discharges per 1000 inpatient encounters).

CONCLUSIONS
Approximately 1 in 1235 inpatient encounters ended in leaving AMA. Non-Hispanic Black patients had increased odds of leaving AMA. Leaving AMA was associated with increased odds of 14-day readmission.
Self-Supervised Learning for Feature Extraction from Glomerular Images and Disease Classification with Minimal Annotations
Authors: Abe Masatoshi , Niioka Hirohiko , Matsumoto Ayumi , Katsuma Yusuke , Imai Atsuhiro , Okushima Hiroki , Ozaki Shingo , Fujii Naohiko , Oka Kazumasa , Sakaguchi Yusuke , Inoue Kazunori , Isaka Yoshitaka , Matsui Isao 
Published: October 2024

Key Points

Self-supervised learning extracts meaningful glomerular features without teacher labels.Self-distillation with no labels–pretrained model outperformed conventional supervised learning in disease and clinical parameter classification.Self-distillation with no labels model enabled deep learning on small datasets, reducing annotation efforts.

Background
Deep learning has great potential in digital kidney pathology. However, its effectiveness depends heavily on the availability of extensively labeled datasets, which are often limited because of the specialized knowledge and time required for their creation. This limitation hinders the widespread application of deep learning for the analysis of kidney biopsy images.

Methods
We applied self-distillation with no labels (DINO), a self-supervised learning method, to a dataset of 10,423 glomerular images obtained from 384 periodic acid–Schiff-stained kidney biopsy slides. Glomerular features extracted from the DINO-pretrained backbone were visualized using principal component analysis. We then performed classification tasks by adding either k-nearest neighbor classifiers or linear head layers to the DINO-pretrained or ImageNet-pretrained backbones. These models were trained on our labeled classification dataset. Performance was evaluated using metrics such as the area under the receiver operating characteristic curve (ROC-AUC). The classification tasks encompassed four disease categories (minimal change disease, mesangial proliferative GN, membranous nephropathy, and diabetic nephropathy) and clinical parameters such as hypertension, proteinuria, and hematuria.

Results
Principal component analysis visualization revealed distinct principal components corresponding to different glomerular structures, demonstrating the capability of the DINO-pretrained backbone to capture morphologic features. In disease classification, the DINO-pretrained transferred model (ROC-AUC=0.93) outperformed the ImageNet-pretrained fine-tuned model (ROC-AUC=0.89). When the labeled data were limited, the ImageNet-pretrained fine-tuned model's ROC-AUC dropped to 0.76 (95% confidence interval, 0.72 to 0.80), whereas the DINO-pretrained transferred model maintained superior performance (ROC-AUC, 0.88; 95% confidence interval, 0.86 to 0.90). The DINO-pretrained transferred model also exhibited higher AUCs for the classification of several clinical parameters. External validation using two independent datasets confirmed DINO pretraining's superiority, particularly when labeled data were limited.

Conclusions
The application of DINO to unlabeled periodic acid–Schiff-stained glomerular images facilitated the extraction of histologic features that could be effectively used for disease classification.
Impact of the tumor microenvironment of breast cancer on prognosis and treatment
Authors: Titov K. S. , Chulkova S. V. , Zapirov H. M. , Lorie Z. V. , Kiselevskiy M. V. 
Published: October 2024

According to world Health Organization, breast cancer (BC) ranks first among cancer diseases in women in many developed countries of the world and in the Russian Federation. Over the past 20 years, the incidence of breast cancer in the world has increased and continues to increase. This phenomenon dictates the need for a more in-depth molecular biological, genetic and immunological study of the mechanisms of development and progression of this heterogeneous malignant tumor.Recently, there has been increasing interest in the world not on lyin the direct causes of tumor development, but also in factors contributing to its progression, such as the cellular microenvironment of the tumor, the composition of which has a great influence on cancer development, treatment and prognosis. In the cellular microenvironment of the tumor, mononuclear cells are assessed, the proportion of which determines the severity and direction of the immuneresponse. Their importance for choosing the priority type of drug therapy and assessing its effectiveness is shown. The article provide scurrent data on subpopulations of T cells (CD8+, CD4+), B cells (CD20+), and natural killer. Their role in the development and progression of breast cancer is discussed depending on their phenotype. Modern research pays attention to a minor subpopulation of T lymphocytes – TCR-Vδ1+ cells. This subpopulation is represented predominantly in tumor tissue and has an immunosuppressive effect on T-effectors. At the present stage, inflammatory cells – macrophages and neutrophils – are of no less interest. Their role in tumor progression is widely debated. It is known that the differentiation of macrophages into M1 or M2 phenotypes is determined by the tumor microenvironment. The predominance of macrophages with protumor activity promotes tumor progression and cancer metastasis. Additionally, macrophages can stimulate the migration of neutrophils, which, in turn, support the metastasis of breast cancer through the production of matrix metalloproteinases. Matrix metalloproteinase 9 has been reported to promote the formation of vascular endothelial growth factor, which explains the protumor properties of neutrophils. In the context of growing tumor immunotherapy, assessment of tumor microenvironmental factors is promising both in relation to monitoring the effectiveness of breast cancer therapy and in relation to the search for potential therapeutic targets. The review systematizes and summarizes information on this issue to date.
The first experience of multi-modal in vivo PET/SPECT/CT and MRI imaging of laboratory mice with melanoma B16F10 (short message)
Authors: Skribitsky V. A. , Finogenova Yu. A. , Shpakova K. E. , Lipengolts A. A. , Smirnova A. V. , Skripachev I. A. , Nevzorov D. I. , Pronin A. I. , Grigorieva E. Yu. 
Published: October 2024

Background. For in vivo determination of size and metabolic characteristics of model tumors in laboratory animals, it is recommended to use imaging methods: positron emission tomography (PET), single-photon emission computed tomography (SPECT), computed tomography (CT) and magnetic resonance imaging (MRI). Due to the limited availability of hybrid scanners, it is necessary to investigate the feasibility of obtaining tomograms on separate devices with subsequent geometric comparison of images.Aim. To investigate the feasibility of multimodal imaging of mice with subcutaneous melanoma B16F10.Materials and methods. PET, SPECT and CT were performed using a preclinical VECTor 6 tomograph (MILabs, the Netherlands), MRI was performed using a preclinical nanoScan® 3T tomograph (Mediso, Hungary). The following modality combinations were studied: MRI and PET / CT with 18F-fluorodeoxyglucose; MRI and PET / CT with 18F-boronphenylalanine; MRI and PET / SPECT / CT with 18F-fluoroethyltyrosine (18F-FET) and 177lutetium – prostate-specific membrane antigen (177Lu-PSMA). Mice were immobilized in a custom-made device during scanning and during movement between tomographs. PET and MRI, SPECT and MRI images were fused in the program InterView FUSION 3.09.008.0000 through an intermediate stage of fusion with CT.Results. Multimodal PET / CT / MRI and PET / SPECT / CT / MRI images of tumor-bearing mice were obtained for the first time in Russia. PET / MRI data confirmed development of the tumor from 6 × 4 × 4 mm in size. PET / SPECT / CT / MRI enabled to image visceral organs with high accumulation of radionuclide tracers: pancreas with 18F-FET (standardized uptake value 2.6) and kidneys with 177Lu-PSMA (standardized uptake value 4.4), while the obtained images of organs did not merge and did not overlap.Conclusion. Multimodal imaging enables the selection of experimental animals with tumors of specific size and metabolic activity for the study of new radiopharmaceuticals, including those with vector delivery.
Gradual Loss of UV Tolerance with Increasing Habitat Depths in Deep-Freshwater Amphipods (Amphipoda, Crustacea) of Ancient Lake Baikal
Authors: Kondrateva Elizaveta , Gurkov Anton , Rzhechitskiy Yaroslav , Saranchina Alexandra , Diagileva Anastasiia , Drozdova Polina , Vereshchagina Kseniya , Shatilina Zhanna , Sokolova Inna , Timofeyev Maxim 
Published: October 2024

Solar ultraviolet (UV) is among the most important ecological factors shaping the composition of biota on the planet surface, including upper layers of waterbodies. Inhabitants of dark environments recently descending from surface organisms provide natural opportunities to study the evolutionary losses of UV adaptation mechanisms and better understand how those mechanisms function at the biochemical level. Ancient Lake Baikal is the only freshwater reservoir, where deep-water fauna emerged, and its diverse endemic amphipods (Amphipoda, Crustacea) now inhabit the whole range from highly transparent littoral to dark depths of over 1600 m, which makes them a convenient model to study UV adaptation. Here we show that adults of deep-water Baikal amphipods Ommatogammarus flavus and O. albinus indeed have high sensitivity to environmentally relevant UV levels in contrast to littoral species Eulimnogammarus cyaneus and E. verrucosus. The UV intolerance was more pronounced in deeper-dwelling O. albinus and was explainable by lower levels of carotenoids and carotenoid-binding proteins. Signs of oxidative stress were not found but specifically UV-B seemingly led to accumulation of toxic compounds. Overall, the obtained results demonstrate that UV is an important factor limiting distribution of deep-water amphipods into the littoral zone of Lake Baikal.
A spatial-temporal graph attention network for protein-ligand binding affinity prediction based on molecular geometry
Authors: Li Gaili , Yuan Yongna , Zhang Ruisheng 
Published: October 2024

Abstract

Accurately estimating the binding strength between proteins and ligands is fundamental in the field of pharmaceutical research and innovation. Previous research has largely concentrated on 1D or 2D molecular descriptors, often neglecting the pivotal 3D features of molecules that profoundly impact drug properties and target binding. This oversight has resulted in diminished predictive performance in molecule-related analyses. A comprehensive grasp of molecular properties necessitates the integration of both local and global molecular information. In this paper, we introduce a deep-learning model, termed PLGAs, which represents molecular systems as graphs based on the three-dimensional configurations of protein-ligand complexes. PLGAs consist of two components: Graph Convolution Networks (GCN) and a Global Attention Mechanism (GAM) network. Specifically, GCNs learn both the graph structure and node attribute information, capturing local and global information to better represent node features. GAM is then used to gather interactive edges by reducing information loss and amplifying global interactions. PLGAs were tested on the standard PDBbind refined set (v.2019) and core set (v.2016). The model demonstrated a Spearman's correlation coefficient of 0.823 on the refined set and an RMSE (Root Mean Square Error) of 1.211 kcal/mol between experimental and predicted affinities on the core set, surpassing several advanced contemporary binding affinity prediction methods. We further evaluated the efficacy of various components within our model, and the marked improvements in accuracy underscore the potential of PLGAs to significantly enhance the drug development process.