bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relevance of oncobiome in breast cancer evolution in an Argentine cohort
Authors: Dandeu Leonardo Néstor Rubén , Lachovsky Joel , Sidlik Sofía , Marenco Pablo , Orschanski Daniela , Aguilera Pablo , Vázquez Martín , Carballo María del Pilar , Fernández Elmer , Penas-Steinhardt Alberto , Chasseing Norma Alejandra , Labovsky Vivian 
Published: February 2025

ABSTRACT

Breast cancer is the leading cause of cancer deaths in women worldwide, with about 20,000 cases annually in Argentina. While age, diet, and genetics are known risk factors, most breast cancer cases have unknown causes, necessitating the discovery of new risk factors. The aim of this study was the analysis of the prognostic relevance of the oncobiome in Argentinean breast cancer patients. Sequencing of the V4 region 16S rRNA gene was performed on 34 primary breast tumor samples, using bioinformatic and statistical analyses to identify bacteria and hypothetical pathways. Each sample presented a unique microbial profile, with
Proteobacteria
being the most abundant phylum. Tumors >2 cm showed greater alpha diversity with increased nucleotide biosynthesis. Moreover, progesterone-receptor tumors showed differences in beta diversity, being progesterone receptor-positive tumors that had the highest expression of
Acinetobacter
and
Moraxella
. In disease progression, the phylum
Chloroflexi
was prevalent in tumors of surviving patients.
Acinetobacter
and
Cloacibacterium
genera were significantly higher in patients without events and those without metastasis. We found that nucleotide and cell-structure biosynthesis, and lipid metabolism pathways were enriched in tumors with poor progression, whereas amino-acid degradation was increased in tumors of surviving patients. This finding is an indication that tumor cells are taking advantage of this effect of the microbiome during tumor progression. We conclude that oncobiome is dysbiotic in these patients, with distinct patterns in those with poor progression. Suggesting a link between the oncobiome and cancer progression, paving the way for new therapies to improve patient quality of life and survival.

IMPORTANCE
This is the first study to investigate the relevance of the oncobiome in the evolution of breast cancer in a cohort of Argentine patients. It also highlights the need for further research in this area to improve our understanding of the role of the microbiome in this disease and potentially identify new therapeutic targets or prognostic indicators. Understanding the complex interaction between the microbiome, the tumor microenvironment, and the pathogenesis of breast cancer holds the promise of more personalized and effective treatment approaches in the future.
Fiber, microbiomes, and SCFAs: insights from companion animal models to inform personalized nutrition
Authors: Frame Leigh A. 
Published: February 2025

ABSTRACT

A recent study by A. Bhosle, M. I. Jackson, A. M. Walsh, E. A. Franzosa, et al. (mSystems 10:e00452-24, 2024,
https://doi.org/10.1128/msystems.00452-24
) enhances our understanding of dietary fiber’s impact on the gut microbiome and metabolome in companion animals, uncovering individual variations in microbial and metabolic responses. By examining short-chain fatty acid (SCFA) profiles in response to fiber, the authors reveal potential therapeutic benefits of tailored dietary interventions, such as enhanced gut and immune health. These findings resonate with human microbiome research, where dietary fiber has shown health benefits through microbial diversity and SCFA production. The study emphasizes the potential for breed-specific responses to fiber, given the variation in microbiome composition and physiology across breeds. Such insights align with emerging concepts of personalized nutrition, offering an opportunity to develop precision dietary strategies that address specific health needs in both veterinary and human contexts. This foundational research positions dietary fiber as a valuable tool in preventive health, providing a roadmap for future studies to refine individualized approaches for gut microbiome modulation.
Relationship between sleep disorders and depressive symptoms among young women in Japan: a web-based cross-sectional study
Authors: Tashiro Tsubasa , Maeda Noriaki , Mizuta Rami , Abekura Takeru , Oda Sakura , Onoue Satoshi , Arima Satoshi , Suzuki Yuta , Urabe Yukio 
Published: February 2025

ObjectivesJapanese people are known to get the least amount of sleep in the world, and in particular, the increase in sleep deprived young women is a serious problem. Sleep deprivation is considered to be associated with depression, but the factors involved in this problem are unclear. This study aimed to examine the association between sociodemographic factors, lifestyle choices, sleep-related characteristics and depressive symptoms in young Japanese women.DesignWeb-based cross-sectional study.ParticipantsWe distributed an online survey aiming to recruit young Japanese women ages 18 to 29 from 8 November 2022 to 2 February 2023.Primary and secondary outcome measuresSociodemographic, lifestyle, health, and sleep characteristics were compared among participants according to the presence or absence of depressive symptoms, as assessed by the Patient Health Questionnaire 2 (Cut-off value: 3 points).ResultsOverall, 540 participants aged between 19 and 29 years were enrolled in the study. The overall prevalence of depressive symptoms was 15.6%. The group with depressive symptoms had a higher rate of current smoking status at 38.5% (unadjusted OR 3.716, 95% CI 1.624 to 8.502). Multiple logistic analyses revealed that depressive symptoms were associated with increased sleep onset latency (β=0.282; p=0.048; OR, 1.325; 95% CI, 1.003 to 1.752) and daytime dysfunction (β=0.550; p<0.001; OR, 1.733; 95% CI, 1.281 to 2.343) after adjusting for the effects of smoking habits.ConclusionsDepressive symptoms were found to be associated with sleep disorders in young Japanese women, and paying attention to sleep onset latency and daytime dysfunction which are one of the strongest related factors to depressive symptoms could be a clue to improving sleep disorders and depressive symptoms.
Efficacy of Chinese traditional quadruple single pill combination versus valsartan/hydrochlorothiazide for the treatment of hypertension (COSPQ-BP): study protocol for randomised controlled study
Authors: Jia Shanshan , Zhang Xin , Yang Xiangyu , Ye Runyu , Yao Yuanyuan , Liu Lu , Zuo Xianghao , Li Yanan , Yan Yu , Liu Kai , Wang Si , Meng Qingtao , Chen Xiaoping 
Published: February 2025

Introduction
Hypertension constitutes the primary health burden of cardiovascular diseases, and the global control of blood pressure (BP) remains insufficient. Single pill combinations (SPCs) are employed as a means to streamline the management of poor BP control due to non-adherence and treatment inertia. The compound reserpine and triamterene tablets constitute a quadruple SPC, comprising reserpine 0.1 mg, dihydralazine 12.5 mg, hydrochlorothiazide 12.5 mg and triamterene 12.5 mg. It is widely employed in primary medical institutions and has favourable efficacy, tolerability and cost-effectiveness.

Methods and analysis
The COSPQ-BP trial is a 12-week prospective randomised controlled trial to enrol 1332 patients with primary mild-to-moderate hypertension. Participants who meet the inclusion criteria will be randomly assigned to a 1:1 ratio to an intervention group (compound reserpine and triamterene tablets) or a control group (valsartan/hydrochlorothiazide). The primary outcome will be mean changes from baseline in 24-hour ambulatory systolic BP after intervention for 12 weeks. The secondary outcomes have been predetermined and will primarily encompass the following: (1) changes in other BP measures, as well as changes in blood lipids, blood glucose and uric acid at 12 weeks and (2) evaluation of the impact of starting antihypertensive therapy with compound reserpine and triamterene tablets or valsartan/hydrochlorothiazide on the depressive and anxiety statess of patients.

Ethics and dissemination
The study protocol (version number: V5.0, version date: 17 January 2023) has been approved by the ethics committee (Biomedical Ethics Committee of West China Hospital of Sichuan University, approval number: Review (51) in 2023). Written informed consent will be obtained from each participant by researchers. The findings of this study will be disseminated through conference presentations and peer-reviewed publications.

Trial registration
This study was registered at the Chinese Clinical Trials Registry (ChiCTR2300067920). The COSPQ-BP trial is currently enrolling. The study period will be from 1 January 2024 to 31 December 2025.
Can physical and psychological factors predict pain recurrence or an exacerbation of persistent non-specific low back pain? A protocol for a systematic review and meta-analysis
Authors: Wongwitwichote Kanya , Yu Cho Wai Geoffrey , Mansfield Michael , Deane Janet , Falla Deborah 
Published: February 2025

IntroductionLow back pain (LBP) is a global health concern. Approximately two-thirds of those who recover from LBP experience a relapse within a year, with many chronic cases encountering acute flare-ups (exacerbation). This systematic review will synthesise and analyse whether physical and/or psychological features can predict recurrent episodes of LBP or exacerbation of pain.Methods and analysisThis systematic review protocol follows the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols guidelines. Comprehensive literature searches will be conducted in MEDLINE, EMBASE, APA PsycInfo, PubMed, CINAHL Plus, Web of Science, Scopus and ZETOC, spanning from each database’s inception through to January 2025. Google Scholar and grey literature sources, including OpenGrey, will also be searched to ensure comprehensive coverage. Two independent reviewers will screen titles, abstracts and full texts, assessing the risk of bias with a modified Quality in Prognosis Studies tool. The overall certainty of evidence will be evaluated using an adapted Grading of Recommendations Assessment, Development and Evaluation approach. If sufficient data homogeneity is present, a meta-analysis will be performed; otherwise, findings will be synthesised narratively. The results will identify the ability of physical and/or psychological factors to predict pain recurrence or acute exacerbation in case of persistent non-specific LBP.Ethics and disseminationThis study protocol does not present any ethical concerns. The findings from the systematic review will be submitted for publication in a peer-reviewed journal and will also be presented at relevant conferences.PROSPERO registration numberCRD42024599514.
Will it Fit? Verifying Heap Space Bounds of Concurrent Programs under Garbage Collection
Authors: Moine Alexandre , Charguéraud Arthur , Pottier François 
Published: February 2025

We present IrisFit, a Separation Logic with space credits for reasoning about heap space in a concurrent call-by-value language equipped with tracing garbage collection and shared mutable state.
We point out a fundamental difficulty in the analysis of the worst-case heap space complexity of concurrent programs in the presence of tracing garbage collection: if garbage collection phases and program steps can be arbitrarily interleaved, then there exist undesirable scenarios where a root held by a sleeping thread prevents a possibly large amount of memory from being freed.
To remedy this problem and eliminate such undesirable scenarios, we propose several language features, namely possibly-blocking memory allocation, polling points, and protected sections. Polling points are meant to be automatically inserted by the compiler; protected sections are delimited by the programmer and represent regions where no polling points must be inserted.
The heart of our contribution is IrisFit, a novel program logic that can establish worst-case heap space complexity bounds and whose reasoning rules can take advantage of the presence of protected sections. IrisFit is formalized inside the Coq proof assistant, on top of the Iris Separation Logic framework. We prove that IrisFit offers both a safety guarantee—programs cannot crash and cannot exceed a heap space limit—and a liveness guarantee—provided enough polling points have been inserted, every memory allocation request is satisfied in bounded time. We illustrate the use of IrisFit via several case studies, including a version of Treiber's stack whose worst-case behavior relies on the presence of protected sections.
Side Channel Attacks on GPRS Standard Encryption Algorithms
Authors: Wu Zheng , Ding Lin , Li Zhengting , Wang Xinhai , Guan Ziyu 
Published: February 2025

GEA-1 and its successor GEA-2 are stream ciphers that were selected as the General Packet Radio Service (GPRS) standard encryption algorithms, used to protect the communication between phones and base stations from eavesdropping. These stream ciphers, once widely used for GPRS encryption in the late 1990s and early 2000s, are surprisingly still supported in many current mobile phones and in numerous developing regions even today. GEA-2a is a more secure, improved version of GEA-2 designed by Ding et al. in 2022. Side channel attack (SCA) utilizes easily accessible information from cryptographic devices, such as power consumption, electromagnetic radiation, and runtime, to obtain secret information in the cryptographic systems. Side channel attack is a powerful attack method that has been successfully applied in many stream ciphers, such as TRIVIUM and GRAIN-128-AEAD. In this paper, We put forward a automated framework that can mount side channel attack on stream ciphers with structures similar to the GPRS standard encryption algorithms GEA-1 and GEA-2. We use the Satisfiability Model Theory (SMT) for modeling, while considering the software and hardware implementation of the algorithms, and use Microsoft’s open-source solver Z3 to solve the constructed instances. The experimental results indicate that the internal states of GEA-1, GEA-2 and GEA-2a in keystream generation phase can be recovered practically under HW/32 model. For models where the solution time is too long, by guessing a small number of bits, the state bits can be fully recovered within an acceptable time. Our automated framework is effective in both noiseless and noisy trace scenarios.
Sample size estimations based on human microbiome temporal stability over six months: a shallow shotgun metagenome sequencing analysis
Authors: Zouiouich Semi , Wan Yunhu , Vogtmann Emily , Porras Carolina , Abnet Christian C. , Shi Jianxin , Sinha Rashmi 
Published: February 2025

Abstract
Background: Biological factors impact the human microbiome, highlighting the need for reasonably estimating sample sizes in future population studies. Methods: We assessed the temporal stability of fecal microbiome diversity, species composition, and genes and functional pathways through shallow shotgun metagenome sequencing. Using intraclass correlation coefficients (ICC), we measured biological variability over six months. We estimated case numbers for 1:1 or 1:3 matched case-control studies, considering significance levels of 0.05 and 0.001 with 80% power, based on the collected fecal specimens per participant. Results: The fecal microbiome's temporal stability over six months varied (ICC &lt;0.6) for most alpha and beta diversity metrics. Heterogeneity was seen in species, genes, and pathways stability (ICC 0.0–0.9). Detecting an odds ratio of 1.5 per standard deviation required 1,000–5,000 cases (0.05 significance for alpha and beta; 0.001 for species, genes, pathways) with equal cases and controls. Low-prevalent species needed 15,102 cases; high-prevalent species required 3,527. Similar needs applied to genes and pathways. In a 1:3 matched case-control study with one fecal specimen, 10,068 cases were needed for low-prevalent species; 2,351 for high-prevalent species. For odds ratios of 1.5 with multiple specimens, cases needed for low-prevalent species were 15,102 (one specimen), 8,267 (two specimens), and 5,989 (three specimens). Conclusions: Detecting disease associations requires a large number of cases. Repeating prediagnostic samples and matching cases to more controls could decrease the needed number of cases for such detections. Impact: Our results will help future epidemiologic studies design and implement well-powered microbiome studies.
Magnetic resonance imaging measures of fat distribution and risk of cancer
Authors: Peila Rita , Rohan Thomas E. 
Published: February 2025

Abstract
Background Excess adiposity has been associated with an increased risk of several types of cancer. The relationship of fat tissue distribution in the body with these outcomes is less well known. Using data from the UK Biobank imaging substudy, we evaluated the prospective relationship between MRI-derived measurements of adipose tissue distribution and the risk of the major site-specific cancers associated with obesity. Methods Between 2014 and 2023, MRI measurements on adipose tissue distribution and volume were obtained from 49,044 (52.2% women) cancer-free UK Biobank participants. Quantitative MRI data included volumes of visceral and subcutaneous adipose tissues (VAT and ASAT), total abdominal fat/height squared (TAT/h2), and muscle fat infiltration (MFI). Cox proportional hazard models adjusted for cancer-specific risk factors were used to generate hazard ratios (HRs) and 95% confidence intervals (CI). Results Incident cancer cases of the breast (N+179), endometrium (n=30), colorectum (n=145), and kidney (n=50) were ascertained over a median follow-up of 4.5 years. In women, VAT, TAT/h2, and MFI were positively associated with risk of postmenopausal breast cancer, and ASAT was associated with increased risk of endometrial cancer. In men, VAT and TAT/h2 were positively associated with risk of colorectal cancer, while ASAT was associated with increased risk of kidney cancer. Conclusions The present study showed that increasing volumes of VAT, ASAT and MFI were associated with cancer at specific organ-sites, indicating a potential role for adipose tissue distribution in influencing cancer risk. Impact Both visceral and subcutaneous fat may have an impact on the risk of certain cancers.
Safety and efficacy of copanlisib in combination with nivolumab: a Phase Ib study in patients with advanced solid tumors
Authors: Carneiro Benedito A. , Jotte Robert M. , Gabrail Nashat Y. , Wentzel Kristopher , Huang Funan , Chaturvedi Shalini , Weispfenning Anke , Hiemeyer Florian , Morcos Peter N. , Mongay Soler Lidia , Childs Barrett H. , Hansen Aaron R. 
Published: February 2025

Abstract
Purpose: Copanlisib in combination with immune checkpoint inhibitors (ICIs) demonstrated synergy and favorable anti-tumor immune responses in preclinical models. This study evaluated copanlisib plus nivolumab in adults with advanced solid tumors. Patients and Methods: In this Phase Ib, non-randomized, open-label, dose-escalation study, patients received intravenous nivolumab 240 mg (day 15 of cycle 1 and days 1 and 15 of subsequent cycles) plus intravenous copanlisib (45 or 60 mg on days 1, 8, and 15 of each cycle) in 28-day cycles. The primary objective was to determine the maximum tolerated dose and/or recommended Phase II dose (RP2D) of copanlisib plus nivolumab. Secondary objectives were safety, tolerability, and efficacy. Exploratory objectives included evaluation of potentially predictive biomarkers. Results: Overall, 16 patients were treated (copanlisib: 45 mg [n=5]; 60 mg [n=11]). The most common cancer types at baseline were bladder (25.0%) and oropharyngeal (18.8%). No dose-limiting toxicities were observed; copanlisib 60 mg was deemed the RP2D in combination with nivolumab 240 mg. Grade 3 and 4 treatment-emergent adverse events were reported in 56.3% and 12.5% of patients, respectively; one grade 5 event was reported (unrelated to treatment). Overall, 18.8% of patients achieved a partial response. Evaluations of potential biomarkers did not correlate with response, but copanlisib-modulated biomarker changes were observed before nivolumab administration and were consistent and dose-dependent. Conclusions: No new safety concerns were identified with this combination, and preliminary efficacy indicated an anti-tumor effect. Data supported an immunomodulatory effect of copanlisib, suggesting that this combination may enhance the efficacy of ICIs.
The March 2023 MJO and Its Impacts on the Subsequent Coastal El Niño
Authors: Wei Yuntao , Mu Mu , Lian Tao , Hsu Huang-Hsiung , Ren Hong-Li , Wang Jie , Ji Chaopeng , Tao Lingjiang 
Published: February 2025

Abstract
The year 2023 has witnessed sequential geneses of a record-breaking Madden–Julian oscillation (MJO) and an unprecedented coastal El Niño in March–April, thus offering another opportunity to further understand the dynamics of MJO–El Niño interactions. Here, we show that the March 2023 MJO is quite unusual as it starts from the South China Sea due to the dry intrusion of extratropical cold northerly winds and moist preconditioning effects of equatorial Rossby waves, propagates eastward fast as a double Kelvin wave system, and expands over the entire tropical Pacific largely as a Kelvin wave response to its strong suppressed convection over the Maritime Continent. Because of these unusual features, the MJO exerts widespread westerly wind forcing to the ocean surface, with two maxima over the western and far eastern tropical Pacific. Due mainly to the depressed local Ekman upwelling under MJO westerly, the upper ocean gets warmer than normal near the coast of South America, thereby helping trigger the 2023 coastal El Niño. Using an El Niño ensemble forecasting system, we quantify that the MJO westerly over the far eastern Pacific explains approximately 30% of coastal warming signals off Peru. Although only marginally increasing the end-of-year Niño-3.4 index, the March MJO can induce small-scale oceanic westward-propagating disturbances, which significantly decrease the intermember spread of the forecasted basin-scale 2023/24 El Niño. These results highlight the pivotal importance of tropical–extratropical interactions in initiating those MJOs from outside the Indian Ocean and also point out the potential roles of MJOs in dynamical El Niño evolution and prediction.

Significance Statement
By examining a record-breaking Madden–Julian oscillation (MJO) and an unprecedented coastal El Niño occurring sequentially in March–April 2023 using observations and climate model ensemble forecasting experiments, the authors have indicated a chain of upscale feedbacks: extratropical cold surges and equatorial waves jointly initiate the MJO, which then helps (∼30%) trigger coastal warming signals off Peru through dynamical ocean responses. Moreover, small-scale westward-propagating disturbances are generated in the model with MJO perturbations added in March, which considerably reduce the end-of-year intermember spread of the forecasted basin-scale 2023/24 El Niño. These findings significantly advance our basic understanding of the MJO initiation from outside the Indian Ocean and the dynamical El Niño evolution and prediction.