bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning models reveal microbial signatures in healthy human tissues, challenging the sterility of human organs
Authors: Skoulakis Anargyros , Skoufos Giorgos , Ovsepian Armen , Hatzigeorgiou Artemis G. 
Published: January 2025

BackgroundThe presence of microbes within healthy human internal organs still remains under question. Our study endeavors to discern microbial signatures within normal human internal tissues using data from the Genotype-Tissue Expression (GTEx) consortium. Machine learning (ML) models were developed to classify each tissue type based solely on microbial profiles, with the identification of tissue-specific microbial signatures suggesting the presence of distinct microbial communities inside tissues.MethodsWe analyzed 13,871 normal RNA-seq samples from 28 tissues obtained from the GTEx consortium. Unaligned sequencing reads with the human genome were processed using AGAMEMNON, an algorithm for metagenomic microbial quantification, with a reference database comprising bacterial, archaeal, and viral genomes, alongside fungal transcriptomes. Gradient-boosting ML models were trained to classify each tissue against all others based on its microbial profile. To validate the findings, we analyzed 38 healthy living tissue samples (samples from healthy tissues obtained from living individuals, not deceased) from an independent study, as the GTEx samples were derived from post-mortem biopsies.ResultsTissue-specific microbial signatures were identified in 11 out of the 28 tissues while the signatures for 8 tissues (Muscle, Heart, Stomach, Colon tissue, Testis, Blood, Liver, and Bladder tissue) demonstrated resilience to in silico contamination. The models for Heart, Colon tissue, and Liver displayed high discriminatory performance also in the living dataset, suggesting the presence of a tissue-specific microbiome for these tissues even in a living state. Notably, the most crucial features were the fungus Sporisorium graminicola for the heart, the gram-positive bacterium Flavonifractor plautii for the colon tissue, and the gram-negative bacterium Bartonella machadoae for the liver.ConclusionThe presence of tissue-specific microbial signatures in certain tissues suggests that these organs are not devoid of microorganisms even in healthy conditions and probably they harbor low-biomass microbial communities unique to each tissue. The discoveries presented here confront the enduring dogma positing the sterility of internal tissues, yet further validation through controlled laboratory experiments is imperative to substantiate this hypothesis. Exploring the microbiome of internal tissues holds promise for elucidating the pathophysiology underlying both health and a spectrum of diseases, including sepsis, inflammation, and cancer.
Multi-institutional evaluation comparing guidance from International Ki67 Working Group vs National Health Commission of China on immunohistochemistry-based Ki67 assessment alongside the Quantitative Dot Blot method
Authors: Wang Yin , Zou Jiarui , Cao Qinghua , Dai Guihong , Fan Panhong , Gong Xue , Jiang Jinyan , Kong Yanqing , Liu Chao , Liu Chunhui , Lu Chenjia , Li Meiren , Lang Zhiqiang , Lin Yang , Peng Yan , Shi Haiyan , Wang Yuhuan , Wang Jiu , Xie Bichen , Yang Bing , Yu Guohua , Zhang Cuiping , Zhang Hengming , Zhou Luting , Zhang Zilan , Zhu Zhenli , Hao Junmei 
Published: January 2025

PurposeRecommendations from the National Health Commission of China (NHCC) and the International Ki67 Working Group (IKWG) were issued to guide immunohistochemistry (IHC)-based Ki67 scoring for breast cancer patients in daily clinical practice. They were evaluated in this multi-institutional study alongside the results from the Quantitative Dot Blot (QDB) method.MethodsThree alternative adjacent sections from 40 primary ER+ breast cancer resection blocks were randomly assigned a number from 1 to 120 for Ki67 staining and reviewed by 21 pathologists, while the other three alternative sections were sent for QDB analysis of Ki67 protein levels. Ki67 scores were grouped by 5/30% (IKWG), 10/30% (NHCC) and 20/30% (NHCC appendix 9, NHCCa9), respectively while QDB results were grouped by C5–C95 of 2.31 nmol/g defined in previous study as low-, equivocal-, and high-risk groups.ResultsThe overall Intraclass Correlation Coefficient (ICC) was 0.785 for IHC evaluations from 21 pathologists, with Fleiss Kappa values of 0.555, 0.628, and 0.480 when Ki67 scores were grouped by guidance from IKWG, NHCC, and NHCCa9, respectively. In comparison, the ICC and Fleiss kappa values for the QDB analysis were 0.939 and 0.831, respectively. When IHC and QDB results were cross-referenced, more specimens were grouped as high-risk by QDB than IHC, and NHCCa9 led to the highest percentage of disagreement between the two methods.ConclusionThe IKWG recommendation was harder to achieve categorized agreement among pathologists than the NHCC recommendation, yet it led to the best agreement with the QDB to define the low-risk group. The QDB method offers significantly improved consistency compared to the current IHC-based Ki67 assessment.
Application of Cold Atmospheric Pressure Plasma Jet Results in Achievement of Universal Antibacterial Properties on Various Plant Seeds
Authors: Orlowski Jakub , Motyka-Pomagruk Agata , Dzimitrowicz Anna , Pohl Pawel , Terefinko Dominik , Lojkowska Ewa , Jamroz Piotr , Sledz Wojciech 
Published: January 2025

In view of a constant growth in the human population on Earth, the provision of a necessary amount of high-quality food looks challenging. As over 10% of the crop yields are annually lost due to the presence of phytopathogens, the development of novel, eco-friendly methods of pest eradication might contribute to avoiding nutritional shortages. Here, we propose a controlled application of cold atmospheric pressure plasma (CAPP) generated in the form of an atmospheric pressure plasma jet (APPJ), for which we conducted multivariate optimization of the working parameters with the use of the design of experiments (DoE) in addition to the response surface methodology (RSM). After estimating the optimal operating conditions of APPJ, we determined the inactivation rates caused by 2 min CAPP exposure towards bacterial phytopathogens from three species Dickeya solani, Pectobacterium atrosepticum and Pectobacterium carotovorum artificially inoculated on the surface of plant seeds from four species. Logarithmic reductions, as a key result of this work, were enclosed in the range of 1.61–4.95 in the case of Cucumis sativus, Pisum sativum, and Vigna radiata, while for the bacteria-inoculated Zea mays seeds, lower antibacterial properties of APPJ equaling 0.86–1.12 logs were noted. The herein applied exposure to APPJ did not reveal any statistically significant detrimental effects on the germination of plant seeds, seed coat integrity, or early plant growth. Even plant growth promotion by 20.96% was observed for the APPJ-exposed Zea mays seeds. By applying colorimetric assays and optical emission spectrometry (OES), we determined the oxidative potential in addition to identifying the reactive oxygen species (ROS) •OH, •HO2, •O2−, O3, and 1O2 and the reactive nitrogen species (RNS) N, NO2, and NO3 responsible for the antibacterial properties of APPJ. In summary, universal antiphytopathogenic properties of the APPJ treatment reached due to proper optimization of the working conditions were revealed against three bacterial strains from the family Pectobacteriaceae inoculated on the seeds from diverse plant species. The data presented herein may contribute to future development of the plasma agriculture field and provide alternatives to pesticides or the prevention-based control methods towards plant pathogenic bacteria.
Performance Assessment of a Coupled Circulation–Wave Modelling System for the Northwest Atlantic
Authors: Hughes Colin J. , Sheng Jinyu , Perrie William , Liu Guoqiang 
Published: January 2025

We present a modified version of a coupled circulation–wave modelling system for the northwest Atlantic (CWMS-NWA) by including additional physics associated with wave–current interactions. The latest modifications include a parameterization of Langmuir turbulence and surface flux of turbulent kinetic energy from wave breaking in vertical mixing. The performance of the modified version of CWMS-NWA during Hurricane Arthur in 2014 is assessed using in situ measurements and satellite data. Several error statistics are used to evaluate the model performance, including correlation (R), root mean square error (RMSE), normalized model variance of model errors (γ2) and relative bias (RB). It is found that the simulated surface waves (R ≈ 94.0%, RMSE ≈ 27.5 cm, γ2≈ 0.16) and surface elevations (R ≈ 97.3%, RMSE ≈ 24.0 cm, γ2≈ 0.07) are in a good agreement with observations. The large-scale circulation, hydrography and associated storm-induced changes in the upper ocean during Arthur are reproduced satisfactorily by the modified version of CWMS-NWA. Relative to satellite observations of the daily averaged sea surface temperature (SST), the model reproduces large-scale features as demonstrated by the error metrics: R ≈ 97.8%, RMSE ≈ 1.6 °C and RB ≈ 8.6 × 10−3°C.
On the Uniform Projection and Covering Problems in Descriptive Set Theory Under the Axiom of Constructibility
Authors: Kanovei Vladimir , Lyubetsky Vassily 
Published: January 2025

The following two consequences of the axiom of constructibility V=L will be established for every n≥3: 1. Every linear Σn1 set is the projection of a uniform planar Πn−11 set. 2. There is a planar Πn−11 set with countable cross-sections not covered by a union of countably many uniform Σn1 sets. If n=2 then claims 1 and 2 hold in ZFC alone, without the assumption of V=L.
L'hydrosystème du Lez : une gestion active pour un karst à enjeux
Authors: Maréchal Jean-Christophe , Vestier Arnaud , Dörfliger Hervé , Dörfliger Nathalie 
Published: January 2025

Une gestion multi-usages des aquifères karstiques est susceptible de répondre de manière intégrée à des problématiques en apparence antagonistes : besoins supplémentaires pour l'Alimentation en Eau Potable (AEP), réduction des risques d'inondation et contribution à la préservation des milieux aquatiques. L'hydrosystème du Lez fait l'objet depuis 1982 d'une «gestion active» de la ressource en eau, à savoir la sollicitation des réserves du karst pour le prélèvement de débits supérieurs aux débits d'étiage durant les périodes de fort stress hydrique. Elle fait suite à une première période d'exploitation de type gravitaire (gestion passive avant 1968) suivie d'une gestion active par pompage au sein de la vasque de la source (entre 1968 et 1982).
Cette exploitation du réservoir est rendue possible par un contexte hydrogéologique qui permet une bonne reconstitution des réserves de l'aquifère karstique lors des précipitations postérieures à la période estivale. Cette configuration générale de l'hydrosystème Lez soulève en conséquence un certain nombre de questions relatives aux processus hydrogéologiques et hydrologiques qui contrôlent l'évolution qualitative et quantitative de la ressource en eau souterraine au gré du cycle hydrologique, mais également sur de plus longues périodes de temps en fonction des changements globaux qui affecteront cet hydrosystème. Le projet Lez-Gestion Multi-Usages (Lez-GMU) a pour ambitions, à l'échelle de l'hydrosystème Lez, de 1) parfaire la connaissance du milieu karstique d'un point de vue géologique et hydrogéologique, 2) établir une cartographie de la vulnérabilité intrinsèque de l'aquifère du Lez, 3) évaluer les variations spatio-temporelles de la qualité des eaux souterraines 4) produire un inventaire et un état des lieux de la biodiversité souterraine, 5) caractériser le régime hydrologique du fleuve Lez ainsi que 6) la propagation de l'onde de crue à travers Montpellier, l'un des objectifs majeurs étant de 7) réévaluer la ressource en eau exploitable et vérifier le bon état quantitatif de la masse d'eau sous l'effet de différents scénarios d'exploitation, y compris issus de modèles climatiques pour le climat futur. Les résultats et réponses à ces questions scientifiques abordés dans ce projet sont présentés point par point dans la suite de ce numéro.
Analyse par tomographie électrique du site et de la Grotte Préhistorique d’Azé (Saône-et-Loire, France)
Authors: Barriquand Lionel , Kaufmann Olivier , Auboeuf Bernard , Blanchard David , Deceuster John , Dechamps Sylvain , Guillot Ludovic 
Published: January 2025

Une campagne de prospections géophysiques par tomographie en résistivité électrique a été effectuée afin d’améliorer la connaissance du site des grottes d’Azé. Cette technique d’investigation du sous-sol consiste à déplacer un quadripôle le long d’un profil linéaire et à mesurer l’intensité du courant injecté et de la différence de potentiel générée entre les électrodes de réception. Ces données permettent de calculer la résistivité électrique des terrains et de reconstituer ses variations tout au long du profil.
Cinq profils ont été établis : les trois premiers ont couvert le parc des grottes ; de longueurs identiques, 235 m, parallèles les uns aux autres ils ont permis de sonder le parc sur une profondeur de 30 m au centre du profil. Les modèles de résistivité obtenus ont mis en évidence l’existence d’une troisième grotte de taille importante complètement remplie de sédiments. De déterminer l’ampleur de la coulée de solifluxion qui est à l’origine de la fermeture de la grotte de la Rivière Souterraine mais également de mettre en évidence d’autres phénomènes karstiques. Le quatrième profil traversait entièrement la vallée de la Mouge en contrebas des grottes. Associé avec le troisième profil, il a montré un écoulement d’eau pouvant correspondre à une cavité servant de drain aux eaux d’infiltration de la Grotte Préhistorique. Il a aussi montré l’existence des paléo-lits de la Mouge. Le dernier profil établi débute devant le porche d’entrée de la Grotte Préhistorique au sud et se termine au fond de la galerie de Chauffailles 300 m plus au nord. Il traverse les salles où se trouvent les gisements paléontologiques d’Azé 1-1, Azé 1-2 et Azé 1-3. Les résultats obtenus montrent clairement les relations entre la galerie supérieure dite Grotte Préhistorique (où se trouvent Azé 1-1, Azé 1-2 et Azé 1-3) et une galerie inférieure distincte correspondant dans sa partie nord à la galerie de Chauffailles et dans sa partie sud à la galerie des Aiglons et donc au gisement paléontologique d’Azé 1-5. Les relations entre ces deux galeries sont limitées. La taphonomie des différents gisements d’Azé 1-2, 1-3, 1-4, 1-5 et 1-6 est directement liée aux relations qui existent ou pas entre ces deux réseaux. Ces résultats ont permis de proposer un modèle en trois dimensions de la cavité.
L’aquifère karstique, objet d’études mathématiques ou naturalistes ?
Authors: Collignon Bernard 
Published: January 2025

Study of Karst Aquifer : Natural Science or Mathematical Modelling ?
Hydrogeological science has developed since Darcy on the basis of a simple model for aquifers in a porous medium [Darcy, 1856], developed from experiments on sand filters in fountains in the city of Dijon. Countless field observations then confirmed that aquifers in porous media behave as a homogeneous and isotropic medium, in which velocity and pressure fields are linked by simple laws. The success of this type of mathematical modelling has been amazing : in a few decades, poorly synthesized empirical knowledge has been overtaken. Hydrogeology has become a quantitative science, endowed with predictive capacities (regarding exploitable yield, piezometric level, and propagation speed of pollutants, heat transfer…). Meanwhile, karst aquifers have stubbornly withstood all the modelling tests. The karst extreme heterogeneity is the main cause of these difficulties. This heterogeneity manifests itself at all scales, from the rock matrix to underground rivers, via a network of joints and cracks that largely escape observation. To overcome these difficulties, two main types of approaches were tried : the “ black box” approach and the naturalistic approach. Their performance and field of application will be compared, but it has to be said that there is still a lot of progress to be made before real karst aquifer engineering can take place. This contrasts sharply with the hydrogeology of porous media : on the one hand, a science with a real predictive capacity and, on the other hand, an abundant literature, but which does not usually make it possible to predict how the aquifer will react at a given point. The karst hydrogeologist is still at the bottom of Plato’s cave (it’s a shame) and tries to interpret fleeting shadows to predict how they will move in the future.
La grotte aux Points d’Aiguèze, petite soeur de la grotte Chauvet, et les recherches menées dans le cadre du projet « Datation Grottes Ornées »
Authors: Monney Julien 
Published: January 2025

Points cave (Aiguèze, Gard, France), little sister of chauvet cave, and the “ cave art dating” project.
In 2008, the “Cave Art Dating” project (in French : Projet “ Datation Grottes Ornées” (DGO) undertook archaeological research at Les Deux-Ouvertures cave (St-Martind’Ardèche ; France). This research was intended to renew the chronological knowledge regarding the periods of use and decoration of the palaeolithic rock art caves in the Ardèche River region. In parallel with still ongoing studies at les Deux-Ouvertures and some fieldwork at la Tête-du-Lion cave in 2009, research has also been conducted since 2011 at Points cave (in French : “Grotte aux Points d’Aiguèze”) to which this special issue of Karstologia is dedicated. While many studies are still underway, be it on the field and / or in the laboratory, this special issue allows to make a first, and somehow preliminary, assessment of the results obtained between 2011 and 2015 at Points cave. It is meant to provide a first chronological framework for this site and to discuss its implications at a wider scale (cf. Monney & Jaillet, this volume). Through a state of the art of chronological data available at that time for the palaeolithic rock art caves of the region, it also offers the opportunity to remind the context in which these studies were launched in 2008 and to stress the scientific issues and methodological principles that federated the various studies undertaken at Points cave.
Identification des apports du karst par thermographie infra-rouge aéroportée : campagnes de mesures de 2013 sur la Cèze
Authors: Marteau Baptiste , Ré-Bahuaud Jordan , Wawrzyniak Vincent 
Published: January 2025

Location of karstic inputs from airborne thermal infra-red imaging : 2013 field survey on the Cèze river.
A proper and adequate representation of River-Aquifer (R-A) exchanges is important for an effective management of water resource and aquatic ecosystems as it influences both quantitative and qualitative aspects of groundwater and river water. Among the different tools at hand, InfraRed Thermal imaging (TIR) allows a fine mapping of surface temperature in order to characterize groundwater inputs. The purpose of this article is to demonstrate the relevance of using TIR imaging to characterize hydraulic exchanges between groundwater and surface water in karst areas. In the present work, a study is carried out to analyse the R-A exchanges over the lower part of the Cèze River lower valley (Gard – France). The main objectives of this study are (1) to identify the locations where groundwater discharges into the Cèze River and (2) to quantify the total discharge of the Cèze River including inputs from these springs. Maximum output from the TIR images can be possible (1) if the temperature contrast between surface and groundwater is significant, and (2) if river discharge is not too high in comparison to groundwater inputs from karstic springs. Results from airborne measurements achieved in April and August 2013 show the potential of using TIR images to quantify and identify the location of groundwater inputs along the river.
HUBUNGAN BEBAN KERJA, STRES KERJA DAN KOMPETENSI DENGAN KINERJA PERAWAT DALAM PENDOKUMENTASIAN ASUHAN KEPERAWATAN
Authors: Mayenti Fitra , Meri Dilgu , Gusniwati Yuli 
Published: January 2025

Kinerja merupakan hasil kerja perawat secara nyata yang dikerjakan sesuai dengan tanggung jawabnya. Faktor yang berhubungan dengan kinerja perawat adalah beban kerja, stress kerja dan kompetensi. Beban kerja merupakan sekumpulan kegiatan yang harus diselesaikan oleh perawat diruangan. Beban kerja perawat yang berlebih akan bepengaruh terhadap kualitas kerja perawat tersebut, sehingga dapat menyebabkan perawat tersebut mudah stress. Selain beban kerja dan stress kerja, kompetensi perawat merupakan faktor yang mempengaruhi kinerja perawat, kompetensi merupakan kemampuan atau keahlian seseorang perawat dalam mejalankan tugas dan tanggungjawabnya sebagai perawat professional dilingkungan tempat bekerja. Penelitian ini bertujuan untuk mengetahui hubungan beban kerja, stress kerja dan kompetensi dengan kinerja perawat dalam pendokumentasian asuhan keperawatan di RSUD Indrasari. Jenis penelitian yang digunakan adalah penelitian kuantitatif dengan pendekatan cross sectional. Jumlah sampel dalam penelitian ini sebanyak 79 orang. Metode pengambilan sampel yang digunakan adalah Probability Sampling dengan Proportionate Stratified random sampling. Data diolah dan dianalisis secara univariat dan bivariat dengan sistem komputerisasi, menggunakan uji pearson chi-square. Hasil penelitian menunjukkan beban kerja perawat mayoritas kategori sedang yakni 64,6%, stres kerja perawat mayoritas kategori sedang yakni 62%, kompetensi perawat mayoritas kategori sedang yakni 57%, dan kinerja perawat mayoritas kategori sedang yakni 67,1%. Hasil uji statistik menunjukkan bahwa terdapat hubungan yang signifikan antara beban kerja (0,001, stres kerja (0,001), kompetensi (0,002) dengan kinerja perawat dalam pendokumentasian asuhan keperawatan. Rekomendasi pada pihak manajemen rumah sakit untuk mengutamakan kebutuhan perawat dalam peningkatkan kompetensi dan meningkatkan fasilitas dalam rangka meningkatkan mutu pelayanan kesehatan terhadap pasien.
دراسة تاثير مدة التطبيق على متغير الوزن العام لطالبات التربية الرياضية
Authors: حسن علي مهدي 
Published: January 2025

اشتملت الدراسة على خمسة ابواب اذ تضمن الباب الاول المقدمة واهمية البحث وكذلك اهداف البحث وهما :-1- معرفة الوزن العام لطالبات التربية الرياضية / كلية التربية للبنات / جامعة الكوفة قبل فترة التطبيق وبعده .2- دراسة تاثير مدة التطبيق على متغير الوزن العام لطالبات قسم التربية الرياضية / جامعة الكوفة .وتضمن الباب الاول فرضا واحدا وهو :-1- مدة التطبيق لها تاثيرات ذات دلالة احصائية على متغير الوزن العام للطالبات في قسم التربية الرياضية / جامعة الكوفة .اما الباب الثاني تضمن الدراسات النظرية وشملت الموضوعات التالية (بعض العوامل المؤثرة على وزن الطالبات , اهداف التغذية , معايير الغذاء , الانشطة البدنية والتخطيط لمجموعة غذائية . اما الباب الثالث شمل منهج البحث واجراءاته الميدانية , اذ تم اختيار المنهج الوصفي لملائمته طبيعة المشكلة والاهداف وايضا تم تحديد عينة البحث من طالبات قسم التربية الرياضية / جامعة الكوفة المرحلة الرابعة .وتم اتباع الاجراءات التالية لتطبيق العمل وهي اخذ قياسات الوزن للطالبات في بداية مدة التطبيق للعام الدراسي 2008/2009 وتم تكرار القياس في نهاية مدة التطبيق 14/4/2009 . بعد ذلك تم جمع البيانات الخاصة بوزن الطالبات ومعالجتها بالوسائل الاحصائية ومنها قانون الاختبار التائي .وفي الباب الرابع تم عرض وتحليل ومناقشة النتائج الخاصة بالوزن اذ اظهرت فارقا معنويا لمتغير الوزن بعد التطبيق وعلى اساس النتائج تم وضع مجموعة من الاستنتاجات ومنها :-1- ان مدة التطبيق لها تاثيرات مباشرة على متغير الوزن لدى طالبات قسم التربية الرياضية . وعلى ضوء الاستنتاجات وضع الباحث مجموعة من التوصيات ومنها :-يجب مراقبة وزن الطالبات من قبل المدرسيين باستمرار .