bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advancing personalized cancer therapy: Onko_DrugCombScreen—a novel Shiny app for precision drug combination screening
Authors: Yang Jingyu , Wang Meng , Dönitz Jürgen , Chapuy Björn , Beißbarth Tim 
Published: January 2025

Abstract
Identifying and validating genotype-guided drug combinations for a specific molecular subtype in cancer therapy represents an unmet medical need and is important in enhancing efficacy and reducing toxicity. However, the exponential increase in combinatorial possibilities constrains the ability to identify and validate effective drug combinations. In this context, we have developed Onko_DrugCombScreen, an innovative tool aiming at advancing precision medicine based on identifying significant drug combination candidates in a target cancer cohort compared to a comparison cohort. Onko_DrugCombScreen, inspired by the molecular tumor board process, synergizes drug knowledgebase analysis with various statistical methodologies and data visualization techniques to pinpoint drug combination candidates. Validated through a TCGA-BRCA case study, Onko_DrugCombScreen has demonstrated its proficiency in discerning established drug combinations in a specific cancer type and in revealing potential novel drug combinations. By enhancing the capability of drug combination discovery through drug knowledgebases, Onko_DrugCombScreen represents a significant advancement in personalized cancer treatment by identifying promising drug combinations, setting the stage for the development of more precise and potent combination treatments in cancer care. The Onko_DrugCombScreen Shiny app is available at https://rshiny.gwdg.de/apps/onko_drugcombscreen/. The Git repository can be accessed at https://gitlab.gwdg.de/MedBioinf/mtb/onko_drugcombscreen.
Chemical Constituents and Particle Size Distribution of Mainstream Emission from Electronic Waterpipe
Authors: Klupinski Theodore P , Adetona Anna , Ivanov Alexander , Richardson Aaron , Strozier Erich D , Aume Laura L S , Karam Hani , Makselan Stephanie D , McCauley Martha , Mullins Larry , Stiffler Billie , Lucas Eric A , Kim Hyoshin 
Published: January 2025

Abstract

Introduction
An electronic waterpipe (electronic hookah) uses an electronic heating element to promote the vaporization and aerosolization of an e-liquid in a waterpipe. There is little or no published information characterizing the toxicant levels or particle size distributions of electronic waterpipe mainstream emission.

Methods
Controlled laboratory experiments were performed to evaluate electronic waterpipe mainstream emission for 40 test conditions: 10 e-liquid products × 2 power settings × 2 puffing topographies. Data were collected for amounts of three volatile toxicants and selected semi-volatile compounds, mass of total particulate matter, and particle size distribution within the size range of 5–1000 nm.

Results
Amounts of the volatile toxicants acetaldehyde, acrolein, and benzene measured in mainstream emission were 33–505 µg/session, 27–415 µg/session, and 0.69–2.44 µg/session, respectively. The amounts of acetaldehyde and acrolein, when reported in units of µg/puff, are generally similar to some literature-reported amounts in e-cigarette mainstream emission and tobacco waterpipe smoke. A bimodal or trimodal particle size distribution was typically observed, and substantial concentrations of nanoparticles were detected. The amounts (in µg/puff) of the volatile toxicants and several quantitative measures of particle size distribution were significantly affected by power setting and puffing topography.

Conclusions
Given the hazards of acetaldehyde and acrolein and the distinctive toxicological profile of nanoparticles, electronic waterpipe use may present significant toxicity concerns. Operation of an electronic waterpipe is a complex process in which physics, fluid dynamics, and chemistry interact to yield mainstream emission for which the composition is sensitive to changes from various sources.

IMPLICATIONS
This publication, to our knowledge, is the first to report the amounts of toxicants and particle size distributions in electronic waterpipe mainstream emission. The results reported herein suggest that there may be significant toxicity concerns associated with electronic waterpipe use as indicated by the levels of volatile toxicants and the presence of nanoparticles in electronic waterpipe mainstream emission. This knowledge is valuable to support the research community and tobacco regulatory agencies in understanding the impact that electronic waterpipe use may have on public health.
Asset Pricing in the Information Age: Employee Expectations and Stock Returns
Authors: Sheng Jinfei 
Published: January 2025

Abstract
Firms with more positive employee expectations tend to earn higher future returns, delivering annualized abnormal returns ranging from 8% to 11%. Employees’ forward-looking expectations are a stronger return predictor than employee satisfaction, which is backward-looking. Employee expectations can predict returns because they reflect information about firms’ fundamentals that has not yet been reflected in traditional data sources, such as earnings reports. Hedge funds actively trade on this information, consistent with a decay in forecasting power over longer holding horizons. Overall, this paper highlights the importance of labor in asset pricing, specifically from the perspective of employee expectations. (JEL G12, G14)
Towards the definition of disease phenotypes in pediatric SAPHO syndrome: a national multicentric study
Authors: Matucci-Cerinic Caterina , Attico Anna , Malattia Clara , Consolaro Alessandro , Rosina Silvia , Breda Luciana , La Bella Saverio , Cattalini Marco , Ricci Francesca , Conti Giovanni , Civino Adele , Baldini Letizia , Licciardi Francesco , Insalaco Antonella , La Torre Francesco , Pastore Serena , Filocamo Giovanni , Beretta Gisella Beatrice , Biscaro Francesca , Miniaci Angela , Simonini Gabriele , Marrani Edoardo , Pistorio Angela , Ruperto Nicolino , Volpi Stefano , Caorsi Roberta , Viglizzo Gianmaria , Gattorno Marco ,   on behalf of REUMAPED
Published: January 2025

Abstract

Objectives
To confirm the presence of different disease phenotypes of pediatric SAPHO syndrome (pSAPHO) based on their skin manifestations in a large cohort of Italian patients.

Methods
pSAPHO were enrolled in the Eurofever Registry and the data retrospectively analysed. Patients were divided depending on their skin manifestations into an Acne-Hidradenitis suppurativa (HS) group and a Palmoplantar Pustulosis-Psoriasis Vulgaris (PPP-PV) group and were compared with patients without skin manifestations (chronic non-bacterial osteomyelitis, CNO). Comparison of frequencies between groups was performed by the means of χ2 test or by Fischer’s Exact test.

Results
54 pSAPHO with skin manifestations (35 acne-HS, 19 PPP-PV) were enrolled and compared with 167 CRMO. In the Acne-HS, 82.9% were males, in the PPP-PV, 84.2% were females, while in the CNO group there were no gender differences (p&lt; 0.0001). The 3 groups differed significantly for age at disease onset: acne-HS median 13.3 years, PPP-PV median 10.2 years, CNO median 9.5 years (p= 0.0001). An axial pattern was more frequent in acne-HS (91.4%) and PPP-PV group (89.4%) compared with CNO (46%) (p&lt; 0.0001). Both acne-HS (82.9%), and PPP-PV (63.2%) required more frequently a biologic therapy than CNO (36.8%), but acne-HS presented a refractory skin disease requiring steroids and different lines of treatment, while PPP-PV responded well to biologics.

Conclusions
Our data have identified two different phenotypes of pSAPHO based on skin manifestations, with different sex, age and response to treatments. These two groups have peculiar clinical features different from the CNO group. A new classification encompassing these phenotypes is warranted.
Disparities in unmet need for family planning: a comparative study of urban and rural women in Kano State, Nigeria
Authors: Ibinaiye Taiwo , Adelekan Babatunde , Bajoga Ummulkhulthum , Ezikeanyi Sampson , Chijide Joachim , Opiyo Collins , Dasogot Andat , Kuawu Koessan 
Published: January 2025

Abstract
This study investigated urban–rural differences in the prevalence of unmet need for family planning among women of reproductive age in Kano State, Nigeria, and identified factors contributing to these disparities. Rural–urban disparities in unmet need for family planning outcomes and women’s characteristics were assessed. Univariate multilevel mixed-effect logistic regression models were employed to quantify the association between rural/urban residences and each unmet need for family planning and related outcomes. In urban areas, factors associated with unmet need for family planning included husband/partner (OR: 0.25, 95% CI 0.07 to 0.88, p=0.031) and joint decision-making about medical treatment (OR: 0.27, 95% CI 0.09 to 0.80, p=0.018). In rural areas, middle wealth categories (OR: 1.92, 95% CI 1.07 to 3.47, p=0.029), women with 3–4 (OR: 5.41, 95% CI 1.07 to 27.1, p=0.040) and ≥5 birth events (OR: 8.44, 95% CI 1.74 to 40.82, p=0.008) and those who work but are not paid in cash (OR: 0.46, 95% CI 0.21 to 0.99, p=0.049) were associated with unmet need for family planning. Tailored interventions considering socioeconomic, cultural and geographical factors are essential to reduce barriers to family planning services and promote informed decision-making among women in Kano State.
The Changes of Lymphocytes and Immune Molecules in Irradiated Mice by Different Doses of Radiation
Authors: Yang Tingyu , Gao Rong , Gao Yehui , Huang Mingyue , Cui Jialu , Lin Lin , Cheng Hongbo , Dang Wanyun , Gao Yue , Ma Zengchun 
Published: January 2025

Abstract
The effects of different radiation doses on T and B lymphocyte functional subsets and the changes of immune cells and immune molecules were observed in mice at different times post-irradiation to provide a theoretical basis for the changes of immune cells affected by radiation. In this study, the changes of T and B immune cells and immune-related molecules were observed at 1, 3, 7, 14, and 21 d after single irradiation of 2 Gy, 4 Gy, and 6 Gy. The results showed that white blood cells (WBC), lymphocytes (LYMPH), and lymphocyte percentage (LYMPH%) in peripheral blood of mice were significantly reduced and reached the lowest point 3 d after irradiation. Flow cytometry results showed that the percentages of CD3+T and CD8+/CD3+T lymphocytes in spleen and thymus were significantly decreased, and the percentages of CD19+B lymphocytes in spleen and CD4+/CD3+T lymphocytes in thymus were also decreased. However, the percentages of splenic NK cells, CD4+/CD3+T cells, and CD4+/CD8+ ratios in spleen and thymus were increased. Most of the indicators fell to the lowest or highest point 3 d after irradiation, indicating that immune function was suppressed at this time. From 7 to 21 d after irradiation, most immune cells gradually recovered. Single irradiation of 2 Gy, 4 Gy, and 6 Gy increased the contents of IL-1β, IL-2, IL-6, IL-17, TNF-α, TGF-β, and IFN-γ in serum of mice and decreased the contents of anti-inflammatory factors IL-4 and IL-10. The serum levels of immunoglobulin IgA, IgG, IgM and complement C3, C4 were significantly increased after irradiation. Our study showed that a single dose of 2 Gy, 4 Gy, and 6 Gy induced immunosuppression in mice, and maximum immunosuppression was achieved 3 d after irradiation. At this time, CD19+B lymphocytes were the most sensitive, followed by CD3+T lymphocytes, and NK cells were the most resistant. The radiosensitivity of CD8+/CD3+T lymphocytes was slightly higher than that of CD4+/CD3+T lymphocytes.
Nutrition in the critically ill in resource-limited settings/low- and middle-income countries
Authors: Mer Mervyn , Dünser Martin W. 
Published: January 2025

Purpose of review
To share current concepts and provide an overview of the contextual issues and nutrition practices in critically ill patients in resource-limited settings (RLSs)/low- and middle-income countries (LMICs). Most of the world's population reside in these settings which also carries the greatest burden of critical illness.

Recent findings
There is a paucity of evidence on nutrition practice in critically ill patients in RLSs and international guidelines are largely based on evidence derived from high-income countries (HICs). While some recommendations are adaptable to RLSs, many are not feasible or directly transferable. Despite the challenges that may prevail, pragmatic solutions can address many of the difficulties to enhance nutrition practice and improve patient outcomes.

Summary
This review provides a contemporary synopsis of nutrition practice in critically ill patients in RLSs covering the relevance of optimal nutrition, gives insights into relevant contextual issues and challenges in RLSs, evaluates recent scientific evidence and available literature pertinent to critically ill patients in RLSs, addresses nutrition guidelines, discusses some pragmatic options and solutions, deals with relevant and important complications that may arise, and offers suggestions and future considerations to enhance nutrition practice in critically ill patients in these settings.
Ubiquitous microbial contaminants associated with scientific ocean drilling
Authors: Labonte Jessica , Campbell Kathryn L. , Walker Jordan R. , Rodriguez-Pilco Milena A. 
Published: January 2025

Deep-sea subsurface samples typically have low microbial biomass, making them more susceptible to contamination. Potential contaminants can be introduced during any step of the scientific process, including drilling (contamination from the drilling fluid and lubricants, seawater), sample preparation (contamination from air and human handling), and DNA extraction, amplification, and sequencing (contamination from reagents). International Ocean Discovery Program (IODP) samples that are dedicated for microbiological analyses (known as MBIO samples) are routinely tested for contamination by injecting known concentrations of fluorescent microspheres or tracers directly into the drilling fluids. These tracers are a great tool to determine the level of drilling fluid contamination on board, but they are not consistently used and contamination of the samples could occur during other steps of sample processing and analysis. Moreover, there is an increased risk of contamination dominating the results of microbial surveys using polymerase chain reaction (PCR) amplification of marker genes. Here, we built a database of common contaminants through the screening of contamination controls from available 16S rRNA gene amplicon datasets from past IODP expeditions. These controls included various lubricants used on board, drilling fluids, seawater, DNA extraction blanks, and PCR blanks. The order Burkholderiales dominated most of the very low biomass samples, including negative controls, indicating the order’s ubiquity and its potential to be overamplified with common 16S rRNA amplification protocols. We amplified the 16S rRNA gene from preserved IODP legacy microbiological core samples and tested their level of contamination using the database. We also looked at published studies that did not sequence negative controls. Our results demonstrate that the type of drilling, amount of manipulation of the sample prior to preservation, and sample depth, often associated with biomass, can influence the level of contamination within subsurface samples. This work provides an analysis framework for microbial taxonomic survey studies from low biomass subsurface samples for future scientific ocean drilling expeditions.
Source Reconstruction Without an MRI using Optically Pumped Magnetometer based Magnetoencephalography
Authors: Rhodes Natalie , Rier Lukas , Boto Elena , Hill Ryan , Brookes Matthew J. 
Published: January 2025

AbstractSource modelling in magnetoencephalography (MEG) maps the spatial origins of electrophysiological signals in the brain. Typically, this requires an anatomical MRI scan of the subject’s head, from which a model of the neuromagnetic field (the forward model) is derived. Wearable MEG – based on optically pumped magnetometers (OPMs) – enables MEG measurement from participants who struggle to cope with conventional scanning environments (e.g. children), enabling study of novel cohorts. However, its value is limited if an MRI scan is still required for source modelling. Here we describe a method of warping template MRIs to 3D structured-light scans of the head, to generate “pseudo-MRIs”. We apply our method using data from 20 participants during a sensory task, measuring induced (beta band) responses and whole-brain functional connectivity. Results show that the group average locations of peak task-induced beta modulation were separated by 2.75 mm, when comparing real- and pseudo-MRI approaches. Group averaged time-frequency spectra were also highly correlated (Pearson correlation 0.99) as were functional connectome matrices (0.87), and global connectivity (0.98). In sum, our results demonstrate that source-localized OPM-MEG data, modelled with and without an individual MRI scan can be similar. This will be useful for future studies where MRI data capture is challenging.
Glycaemic variability underlies myocyte dysfunction and myocardial injury risk in diabetes
Authors: Cao Yuanzhao , Redd Meredith A. , Outhwaite Jennifer E. , Mizikovsky Dalia , Shim Woo Jun , Fang Chen , Wu Zhixuan , Daygon Dara , Stark Terra , Palfreyman Robin , Chiu Han Sheng , Tan Clarissa , Thomas Ulrich , Dragicevic Elena , Sng Julian , Barrett Helen , Dorey Emily , Shah Sonia , Short Kirsty R. , Palpant Nathan J. 
Published: January 2025

SUMMARYHeart disease is the leading cause of morbidity and mortality in individuals with diabetes, due largely to risks associated with ischaemic injuries such as myocardial infarction (MI). We use human population genetic data to demonstrate that current biomarkers of hyperglycaemia do not account for risk of post-MI mortality in diabetes patients. This study therefore systematically evaluates glycaemic stress underpinning cardiovascular risk in diabetes. Usingin vivoandin vitromodels, we demonstrate that glycaemic variability rather than hyperglycaemia alone is a dominant risk factor for heart muscle dysfunction and myocardial injury sensitivity in diabetes. These findings provide new preclinical models for mechanistic and drug discovery studies and inform strategies for managing cardiovascular outcomes in patients with diabetes.
Cotyledon opening during seedling deetiolation is determined by ABA-mediated splicing regulation
Authors: Martín Guiomar , Larran Alvaro , Qüesta Julia , Duque Paula 
Published: January 2025

AbstractDuring seedling deetiolation, plants adjust their development to expose photosynthetic tissues to sunlight, enabling the transition from heterotrophic to autotrophic growth. While various plant hormones are known to influence this process, the role of abscisic acid (ABA) remains unclear. Here, we reveal that ABA plays a major role in controlling the dynamics of cotyledon aperture during seedling deetiolation. In darkness, ABA accumulates in the cotyledons to effectively repress their opening. However, light exposure reverses this effect, allowing the cotyledons to open. Our findings indicate that the ABA-mediated regulation of cotyledon dynamics is accompanied by genome-wide rearrangements in both transcriptional and splicing patterns. We demonstrate that the ABA-dependent adjustments of cotyledon and splicing dynamics in response to light depend on the positive role of two splicing factors, RS40 and RS41. Moreover, we identify transcriptional and posttranscriptional mechanisms that repress the activity of these proteins in the dark. Altogether, this work sheds light on the interplay between light and ABA, highlighting a new developmental outcome: cotyledon opening, and identifying a novel layer of gene regulation: alternative splicing.
Spatial transcriptomic analysis of HIV and tuberculosis coinfection in a humanized mouse model reveals specific transcription patterns, immune responses and early morphological alteration signaling
Authors: Adduri Sitaramaraju , Bohorquez Jose Alejandro , Adejare Omoyeni , Rincon Diego , Tucker Torry , Konduru Nagarjun V , Yi Guohua 
Published: January 2025

AbstractMycobacterium tuberculosis(Mtb) and human immunodeficiency virus (HIV) coinfection is one of the biggest public health concerns worldwide. Both pathogens are adept at modulating immune response and, in the case ofMtb, even inducing structural modification of the affected tissue. The present study aimed at understanding the early phenotypical and functional changes in immune cell infiltration in the affected organ, using a humanized mouse model. The humanized mice were infected with either HIV orMtbin single infection, or with both pathogens in coinfection. Three weeks after the infection, lung samples were collected, and spatial transcriptomics analysis was performed. This analysis revealed high infiltration of CD4+T cells inMtbinfection, but not in HIV or coinfection. Coinfected mice also showed a minimal number of NK cells compared to the other groups. In addition to infection status, histological features also influenced the immune cell infiltration pattern in the lungs. Two distinct airway regions with distinct immune cell abundance patterns were detected by spatial transcriptome profiling. A lymphoid cell aggregate detected in coinfection lung exhibited distinct transcript profile. The cellular architecture in the lymphoid cell aggregate did not follow the spatial patterns seen in mature granulomas. However, lymphoid cell aggregates exhibited granuloma gene expression signatures, and pathways associated with reactive oxygen species production, oxidative phosphorylation, and TGFβ and interferon signaling similar to granulomas. This study revealed specific transcription patterns, immune responses and morphological alteration signaling in the early stage of HIV andMtbinfections.
Single cell-resolved transcriptional dynamics of human subcutaneous adipose tissue during lifestyle- and bariatric surgery-induced weight loss
Authors: Loft Anne , Rydbirk Rasmus , Klinggaard Ellen Gammelmark , Van Hauwaert Elvira Laila , Wernberg Charlotte Wilhelmina , Møller Andreas Fønss , Dam Trine Vestergaard , Hassan Mohamed Nabil , Maniyadath Babukrishna , Nielsen Ronni , Krag Aleksander , Kalucka Joanna , Schmidt Søren Fisker , Lauridsen Mette Enok Munk , Madsen Jesper Grud Skat , Mandrup Susanne 
Published: January 2025

AbstractDuring sustained weight gain, human white adipose tissue undergoes dramatic remodeling that may compromise adipose tissue function and lead to obesity comorbidities such as cardiometabolic disease. These comorbidities can be at least partially reversed by weight loss; however, the degree to which human adipose tissue is remodeled during weight loss is currently unclear. Here, we have used snRNA-seq combined with bulk RNA-seq and 3D light microscopy to investigate the cellular and transcriptional alterations in abdominal subcutaneous adipose tissue (ASAT) from a unique cohort of obese individuals undergoing initially modest (8-10%) lifestyle-induced weight loss followed by a more dramatic (20-45%) bariatric surgery-induced weight loss. We show that in response to this weight loss, ASAT in both males and females underwent dramatic compositional and transcriptional remodeling. Most notably, surgery-indued weight loss led to an increase in the adipose vascular compartment, a dramatic reduction in proinflammatory immune cells, and a tissue-wide reduction in inflammatory gene signatures. In response to modest weight loss, we observed an increase in specific progenitor populations and an induction of proadipogenic genes, indicating that this process is important for the early adaptation of AT to weight loss that might contribute to the early overall beneficial effects on insulin sensitivity and systemic inflammation.