bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering disease-related multicellular pathway modules on large-scale single-cell transcriptomes with scPAFA
Authors: Huang Zhuoli , Zheng Yuhui , Wang Weikai , Zhou Wenwen , Zhang Yanbo , Wei Chen , Zhang Xiuqing , Jin Xin , Yin Jianhua 
Published: November 2024

AbstractPathway analysis is a crucial analytical phase in disease research on single-cell RNA sequencing (scRNA-seq) data, offering biological interpretations based on prior knowledge. However, currently available tools for generating cell-level pathway activity scores (PAS) exhibit computational inefficacy in large-scale scRNA-seq datasets. Additionally, disease-related pathways are often identified through cross-condition comparisons within specific cell types, overlooking potential patterns that involve multiple cell types. Here, we present single-cell pathway activity factor analysis (scPAFA), a Python library designed for large-scale single-cell datasets allowing rapid PAS computation and uncovering biologically interpretable disease-related multicellular pathway modules, which are low-dimensional representations of disease-related PAS alterations in multiple cell types. Application on colorectal cancer (CRC) datasets and large-scale lupus atlas over 1.2 million cells demonstrated that scPAFA can achieve over 40-fold reductions in the runtime of PAS computation and further identified reliable and interpretable multicellular pathway modules that capture the heterogeneity of CRC and transcriptional abnormalities in lupus patients, respectively. Overall, scPAFA presents a valuable addition to existing research tools in disease research, with the potential to reveal complex disease mechanisms and support biomarker discovery at the pathway level.
Prüfungsthema: Klimaassoziierte und saisonale Gesundheitsrisiken
Authors: Schmid Eva C. 
Published: November 2024

SummaryLiebe Heilpraktikeranwärterinnen, liebe Heilpraktikeranwärter – mit diesen Karteikarten wollen wir Sie bei der Vorbereitung auf die mündliche Heilpraktikerüberprüfung unterstützen. Viel Erfolg beim Lernen wünscht Ihnen HP Eva C. Schmid!
Was wissen Sie über … saisonale Gesundheitsrisiken und Fieber?
Authors: Schmid Eva C. 
Published: November 2024

SummaryLiebe Leserinnen, liebe Leser, testen Sie Ihr Wissen und frischen Sie Ihre Kenntnisse auf. Bitte kreuzen Sie jeweils eine Antwort an. Viel Spaß beim Beantworten wünscht Ihnen HP Eva C. Schmid!
Jedes Molekül macht ein Gefühl
Authors: Zimmermann Eliane 
Published: November 2024

SummaryGerüche interagieren direkt mit Emotionen und lassen sich in Form von ätherischen Ölen, zum Beispiel über Raumsprays oder Ultraschall-Vernebler (unter Vermeidung von Verkeimung), schnell und einfach in der Raumluft verteilen. Belastende Gerüche, wie sie unter anderem in der Pflege von Langzeit- und Palliativpatienten entstehen, lassen sich über die Raumbeduftung wirksam abmildern. Fast alle ätherischen Öle wirken laut einer Reihe im Artikel vorgestellter Studien in der Raumluft deutlich keimwidrig (insbesondere auf Bakterien und Pilze), aber zum Teil auch immunmodulierend (zum Beispiel Hinoki-Zypresse), angstlösend (Lavendel, Orange) oder konzentrationssteigernd (Rosmarin, Pfefferminze, Zitrone).
Wenn das Klima in den Körper dringt
Authors: Böcel-Witt Martina 
Published: November 2024

SummaryDringen äußere pathogene Faktoren, insbesondere Wind, Kälte, Hitze oder Feuchtigkeit in den Körper ein, zeigen sie sich zunächst als akutes Krankheitsbild (vor allem Wind-Hitze, -Kälte und -Feuchtigkeit – Erkältung in der westlichen Terminologie) und müssen wieder über die Oberfläche ausgeleitet werden. Nach dem Schichtenmodell können äußere – insbesondere klimatische – Faktoren in bestimmte Organe eindringen, wie am Beispiel der Blasenentzündung mit Feuchte-Kälte in der Blase gezeigt wird. Die TCM verwendet ausgewählte Rezepturen und Akupunkturpunkte, die auf den spezifischen äußeren pathogenen Faktor wirken – im vorgestellten Fall wird damit eine akute Erkältung erfolgreich behandelt.
Gewappnet für den Klimawandel
Authors: Bierbach Elvira 
Published: November 2024

SummaryHitzeperioden, Starkregen, Überschwemmungen und mehr: Es ist zu erwarten, dass Extremwetterereignisse als Folge des Klimawandels weiter zunehmen werden. Entsprechend ist mit einem Anstieg klimatischer Gesundheitsbedrohungen zu rechnen. Die Polykrise der letzten Jahre hat dazu beigetragen, dass sich auch das gesellschaftliche Klima stark verändert hat in Richtung mehr Stress, Aggression und Erschöpfung. Die im Beitrag vorgestellten Informationen und Maßnahmen sollen Heilpraktiker dazu ermutigen, möglichst selbstwirksam auf den Klimawandel und seine Folgen zu reagieren – sei es in der Aufklärung und Behandlung der Patienten oder im Praxismanagement.
Activation of Hippocampal Neuronal NADPH Oxidase NOX2 Promotes
Depressive-Like Behaviour and Cognition Deficits in Chronic Restraint Stress
Mouse Model
Authors: Zuo Zejie , Zhang Hongyang , Li Zhihui , Qi Fangfang , Hu Haojie , Yang Junhua , Yao Zhibin 
Published: November 2024

Abstract
Background Nicotinamide adenosine dinucleotide phosphate oxidases (NOX)
play important roles in mediating stress-induced depression. Three NOX isotypes
are expressed mainly in the brain: NOX2, NOX3 and NOX4. In this study, the
expression and cellular sources of these NOX isoforms was investigated in the
context of stress-induced depression.
Methods Chronic restraint stress (CRS)-induced depressive-like behaviour
and cognitive deficits were evaluated by tail suspension tests, forced swimming
tests and the Morris water maze test. Hippocampal NOX expression was determined
by immunofluorescence staining and western blotting. The hippocampal levels of
the brain-derived neurotrophic factor (BDNF) mRNA were determined via
quantitative real-time –polymerase chain reaction. Glucocorticoid levels in the
hippocampus were measured using ELISA kits.
Results In the mouse CRS model, a significant increase in NOX2 expression
was observed in the hippocampus, whereas no significant changes in NOX3 and NOX4
expression were detected. Next, NOX2 expression was primarily localised to
neurons (NeuN+) but not microglia (Iba-1+) or astrocytes
(GFAP+). Treatment with gp91ds-tat, a specific NOX2 inhibitor,
effectively mitigated the behavioural deficits induced by CRS. The decreased
expression of the BDNF mRNA in the hippocampus of CRS mice was restored upon
gp91ds-tat treatment. A positive correlation was identified between neuronal
NOX2 expression and serum glucocorticoid levels.
Conclusions Our study indicated that neuronal NOX2 may be a critical
mediator of depression-like behaviours and spatial cognitive deficits in mice
subjected to CRS. Blockade of NOX2 signalling may be a promising therapeutic
strategy for depression.
Hydrotherapie bei Wetterfühligkeit und gesundheitlichen Folgen des Klimawandels
Authors: Gündling Peter W. 
Published: November 2024

SummaryVielen bekannt sind Unpässlichkeiten und Beschwerden bei Wetterwechsel wie Klagen über Kopfschmerzen und Kreislaufstörungen. Folge dieser äußeren Reize durch Temperatur- und Luftdruckschwankungen sind Regulationsstörungen des vegetativen Nervensystems. Naturheilverfahren, die der Stimulation und Regeneration der Selbstheilungskräfte dienen, sind als Adaptiva zur Prophylaxe dieser Funktionsstörungen die erste Wahl. Als typische unspezifische Regulationsmaßnahmen sind speziell Wasseranwendungen in besonderer Art und Weise geeignet, diese Fehlregulationen und die der hormonellen Steuerungsmechanismen auszugleichen.
Computed Tomography and Magnetic Resonance Imaging Features of Gracilis Myopathy in Dogs
Authors: Gunovska Hana , Llanos Cesar , Fitzgerald Ella , Alcoverro Emili , Flatz Katharina , Gomes César , Gomes Sergio A. 
Published: November 2024

Abstract
Objectives Gracilis myopathy is a well-recognized syndrome of weight-bearing gait abnormality; however, detailed description of computed tomography (CT) and magnetic resonance imaging (MRI) features of gracilis myopathy is lacking in the literature. This study aims to describe in detail CT and MRI features of gracilis myopathy.
Study design This is a retrospective study. Medical records of dogs with characteristic gait and available pelvic limb MRI or CT, presenting to four referral institutions, were reviewed.
Results Seven cases with MRI (3/7) or CT (4/7) were included, all German Shepherd dogs. MRI findings in all cases included a well-defined, T1-/T2-/proton density-weighted hypointense band along the axial margin of the gracilis muscle, shorter affected muscles, thickening and T2W/STIR hyperintensity with contrast enhancement at the symphyseal tendon, and concurrent focal indentation of the axial border of the gracilis muscle. CT findings included a hyperattenuating band (4/4), single instances of contrast enhancement at the origin of the muscle, thickening of the tendon at the origin and insertion, and concurrent thickening at the musculotendinous muscle.
Conclusion CT and MRI can present advantages in correctly identifying the specific muscles affected within the gracilis–semitendinosus muscle complex. Both modalities can localize anatomically lesions in detail, for instance at the origin or insertion of the muscle, which could present advantages in novel treatment strategies for this condition.
Ex Vivo Biomechanical Comparison of Four Techniques to Tibiotarsus Osteosynthesis in Adult Laying Hens (Gallus gallus domesticus)
Authors: de Carvalho Anderson Luiz , Formenton Ana Bárbara Krummenauer , Campos Joanna Kulczynski , Fraga Junior Vilson Ferreira , Monteiro Eduardo Raposo , Vassoler Jakson Mandredini , Ferreira Márcio Poletto , Alievi Marcelo Meller 
Published: November 2024

Abstract
Objective To assess the biomechanical parameters of intact tibiotarsi (INT) and tibiotarsi with a 5-mm segmental diaphyseal defect repaired using four osteosynthesis techniques: a locking plate (LP), a plate–rod combination, an external skeletal fixator (one end-threaded positive-profile pin per fragment) with an intramedullary pin tie-in (TIF 1), and an external skeletal fixator (two end-threaded positive-profile pins per fragment) with an intramedullary pin tie-in (TIF 2).
Study Design Sixty tibiotarsi from 30 adult laying hens were allocated into five groups for nondestructive dynamic torsion and four-point bending tests, followed by failure tests. Nondestructive dynamic tests evaluated stiffness over time in torsion and bending. Torsion destructive tests provided maximum torque and rotation values, whereas the four-point bending tests provided the yield load, maximum bending load, and maximum displacement.
Results The INT group showed higher torsional stiffness and maximum torque but similar bending stiffness, torsional strength, and bending strength in one or more groups. LP and TIF 2 exhibited the highest similarity frequencies among the treatment groups, whereas the TIF 1 group displayed lower stiffness and strength for most of the evaluated parameters.
Conclusion Similar results for LP and TIF-2 groups suggest the biomechanical equivalence of these methods for tibiotarsal osteosynthesis in adult hens.
Implementation of pharmacogenomics: Experience at Ochsner Health
Authors: Oliver Catherine B , Naik Dhara , Kirkikis Mark , Ghaffari Mary , Oyen Lance J , Thomas Karen C 
Published: November 2024

Abstract

Purpose
Pharmacogenomics is the study of how individual responses to medication are influenced by genetics. As medication experts, pharmacists are uniquely suited to practicing this application of precision medicine. Fundamental operational aspects of developing a pharmacy clinical pharmacogenomics practice are described, and the specific experience of a multisite health system in developing a pharmacogenomics service is discussed.

Summary
Considerations for the development of a clinical pharmacy–driven pharmacogenomics service include understanding testing selection, targeting the appropriate patient population, exploration of reimbursement, design of the practice, and education of the pharmacogenomics workforce. Testing can be preemptive or reactive, can occur in house or as a send-out service, and can be panel based or specific to a single gene. Pharmacogenomics is applicable to many medicine specialties, making deployment of services to strategic groups essential. Reimbursement for pharmacogenomics is variable and may pose a barrier to implementation. The demand for pharmacogenomics education for pharmacy students and as a formal postgraduate career path is growing. Pharmacogenomics service planning and implementation details for a multisite health system are described.

Conclusion
The practice of pharmacogenomics presents a remarkable opportunity for clinical pharmacists and health systems to improve patient care outcomes and experiences.
Robust self-supervised learning strategy to tackle the inherent sparsity in single-cell RNA-seq data
Authors: Park Sejin , Lee Hyunju 
Published: November 2024

Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful tool for elucidating cellular heterogeneity and tissue function in various biological contexts. However, the sparsity in scRNA-seq data limits the accuracy of cell type annotation and transcriptomic analysis due to information loss. To address this limitation, we present scRobust, a robust self-supervised learning strategy to tackle the inherent sparsity of scRNA-seq data. Built upon the Transformer architecture, scRobust employs a novel self-supervised learning strategy comprising contrastive learning and gene expression prediction tasks. We demonstrated the effectiveness of scRobust using nine benchmarks, additional dropout scenarios, and combined datasets. scRobust outperformed recent methods in cell-type annotation tasks and generated cell embeddings that capture multi-faceted clustering information (e.g. cell types and HbA1c levels). In addition, cell embeddings of scRobust were useful for detecting specific marker genes related to drug tolerance stages. Furthermore, when we applied scRobust to scATAC-seq data, high-quality cell embedding vectors were generated. These results demonstrate the representational power of scRobust.
TIPS: a novel pathway-guided joint model for transcriptome-wide association studies
Authors: Wang Neng , Ye Zhenyao , Ma Tianzhou 
Published: November 2024

Abstract
In the past two decades, genome-wide association studies (GWAS) have pinpointed numerous SNPs linked to human diseases and traits, yet many of these SNPs are in non-coding regions and hard to interpret. Transcriptome-wide association studies (TWAS) integrate GWAS and expression reference panels to identify the associations at gene level with tissue specificity, potentially improving the interpretability. However, the list of individual genes identified from univariate TWAS contains little unifying biological theme, leaving the underlying mechanisms largely elusive. In this paper, we propose a novel multivariate TWAS method that Incorporates Pathway or gene Set information, namely TIPS, to identify genes and pathways most associated with complex polygenic traits. We jointly modeled the imputation and association steps in TWAS, incorporated a sparse group lasso penalty in the model to induce selection at both gene and pathway levels and developed an expectation-maximization algorithm to estimate the parameters for the penalized likelihood. We applied our method to three different complex traits: systolic and diastolic blood pressure, as well as a brain aging biomarker white matter brain age gap in UK Biobank and identified critical biologically relevant pathways and genes associated with these traits. These pathways cannot be detected by traditional univariate TWAS + pathway enrichment analysis approach, showing the power of our model. We also conducted comprehensive simulations with varying heritability levels and genetic architectures and showed our method outperformed other established TWAS methods in feature selection, statistical power, and prediction. The R package that implements TIPS is available at https://github.com/nwang123/TIPS.
MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data
Authors: Bosilj Martin , Suljič Alen , Zakotnik Samo , Slunečko Jan , Kogoj Rok , Korva Misa 
Published: November 2024

Abstract
Over the past decade, there have been many improvements in the field of metagenomics, including sequencing technologies, advances in bioinformatics and the development of reference databases, but a one-size-fits-all sequencing and bioinformatics pipeline does not yet seem achievable. In this study, we address the bioinformatics part of the analysis by combining three methods into a three-step workflow that increases the sensitivity and specificity of clinical metagenomics and improves pathogen detection. The individual tools are combined into a user-friendly workflow suitable for analysing short paired-end (PE) and long reads from metagenomics datasets—MetaAll. To demonstrate the applicability of the developed workflow, four complicated clinical cases with different disease presentations and multiple samples collected from different biological sites as well as the CAMI Clinical pathogen detection challenge dataset were used. MetaAll was able to identify putative pathogens in all but one case. In this case, however, traditional microbiological diagnostics were also unsuccessful. In addition, co-infection with Haemophilus influenzae and Human rhinovirus C54 was detected in case 1 and co-infection with SARS-Cov-2 and Influenza A virus (FluA) subtype H3N2 was detected in case 3. In case 2, in which conventional diagnostics could not find a pathogen, mNGS pointed to Klebsiella pneumoniae as the suspected pathogen. Finally, this study demonstrated the importance of combining read classification, contig validation and targeted reference mapping for more reliable detection of infectious agents in clinical metagenome samples.
Nmix: a hybrid deep learning model for precise prediction of 2’-O-methylation sites based on multi-feature fusion and ensemble learning
Authors: Geng Yu-Qing , Lai Fei-Liao , Luo Hao , Gao Feng 
Published: November 2024

AbstractRNA 2’-O-methylation (Nm) is a crucial post-transcriptional modification with significant biological implications. However, experimental identification of Nm sites is challenging and resource-intensive. While multiple computational tools have been developed to identify Nm sites, their predictive performance, particularly in terms of precision and generalization capability, remains deficient. We introduced Nmix, an advanced computational tool for precise prediction of Nm sites in human RNA. We constructed the largest, low-redundancy dataset of experimentally verified Nm sites and employed an innovative multi-feature fusion approach, combining one-hot, Z-curve and RNA secondary structure encoding. Nmix utilizes a meticulously designed hybrid deep learning architecture, integrating 1D/2D convolutional neural networks, self-attention mechanism and residual connection. We implemented asymmetric loss function and Bayesian optimization-based ensemble learning, substantially improving predictive performance on imbalanced datasets. Rigorous testing on two benchmark datasets revealed that Nmix significantly outperforms existing state-of-the-art methods across various metrics, particularly in precision, with average improvements of 33.1% and 60.0%, and Matthews correlation coefficient, with average improvements of 24.7% and 51.1%. Notably, Nmix demonstrated exceptional cross-species generalization capability, accurately predicting 93.8% of experimentally verified Nm sites in rat RNA. We also developed a user-friendly web server (https://tubic.org/Nm) and provided standalone prediction scripts to facilitate widespread adoption. We hope that by providing a more accurate and robust tool for Nm site prediction, we can contribute to advancing our understanding of Nm mechanisms and potentially benefit the prediction of other RNA modification sites.
Differential functional change in olfactory bulb and olfactory eloquent areas in Parkinson’s disease
Authors: Luo Yu , Miao Xinyuan , Rajan Suraj , Paez Adrian G , Zhou Xinyi , Rosenthal Liana S , Pantelyat Alexander , Kamath Vidyulata , Hua Jun 
Published: November 2024

Abstract
Olfactory dysfunction, or hyposmia, frequently occurs as a prodromal symptom and ongoing sign of Parkinson’s disease. Functional MRI is a powerful tool for studying functional changes in the olfactory brain regions in patients with Parkinson’s disease. However, existing studies show inconsistent results and no study has measured olfactory functional MRI abnormalities in the human olfactory bulb directly. This is mainly due to the well-known susceptibility artefacts in conventional functional MRI images that affect several key olfactory-eloquent brain regions, and especially the olfactory bulb. In this study, olfactory functional MRI was performed using a recently developed functional MRI approach that can minimize susceptibility artefacts and measure robust functional MRI signals in the human olfactory bulb during olfactory stimulation. Experiments were performed on high magnetic field (7 T) in 24 early (&lt;5 years of parkinsonian symptoms) Parkinson’s disease patients and 31 matched healthy controls. Our data showed increased functional MRI signal changes (ΔS/S) in the olfactory bulb in patients with early Parkinson’s disease, which correlated with behavioural olfactory measures. Temporally, functional MRI signals in the olfactory bulb returned to the pre-stimulus state earlier after reaching peak amplitude in patients with early Parkinson’s disease, implicating a faster olfactory habituation effect. The piriform cortex showed reduced numbers of activated voxels in patients with early Parkinson’s disease, which correlated with behavioural olfactory assessment. Several secondary olfactory regions including the orbitofrontal cortex, temporal pole and amygdala exhibited reduced numbers of activated voxels and increased functional MRI signal changes in patients with early Parkinson’s disease. Our data also showed that functional MRI results are highly dependent on voxel selection in the functional analysis. In summary, we demonstrate differential spatial and temporal characteristics of olfactory functional MRI signals between the primary and secondary olfactory regions in patients with early Parkinson’s disease. These results may assist the development of novel quantitative biomarkers (especially in the early stages of Parkinson’s disease) to track and predict disease progression, as well as potential treatment targets for early intervention.