bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phospholipase C epsilon-1 (PLCƐ1) mediates macrophage activation and protection against tuberculosis
Authors: Gupta Ananya , Thirunavukkarasu Shyamala , Rangel-Moreno Javier , Ahmed Mushtaq , Swanson Rosemary V. , Mbandi Stanley Kimbung , Smrcka Alan V. , Kaushal Deepak , Scriba Thomas J. , Khader Shabaana A. 
Published: March 2024

ABSTRACT

Tuberculosis (TB) caused by
Mycobacterium tuberculosis
(
Mtb
) infects up to a quarter of the world’s population. Although immune responses can control
Mtb
infection, 5%–10% of infected individuals can progress to active TB disease (progressors). A myriad of host factors regulate disease progression in TB and a better understanding of immune correlates of protection and disease is pivotal for the development of new therapeutics. Comparison of human whole blood transcriptomic metadata with that of macaque TB progressors and
Mtb
-infected diversity outbred mice (DO) led to the identification of differentially regulated gene (DEG) signatures, associated with TB progression or control. The current study assessed the function of Phospholipase C epsilon (
PLCƐ1
), the top downregulated gene across species in TB progressors, using a gene-specific knockout mouse model of
Mtb
infection and in vitro
Mtb
-infected bone marrow-derived macrophages.
PLCƐ1
gene expression was downregulated in TB progressors across species.
PLCε1
deficiency in the mouse model resulted in increased susceptibility to
Mtb
infection
,
coincident accumulation of lung myeloid cells, and reduced ability to mount antibacterial responses. However,
PLCε1
was not required for the activation and accumulation of T cells in mice. Our results suggest an important early role for
PLCƐ1
in shaping innate immune response to TB and may represent a putative target for host-directed therapy.
Complete genome of
Microbacterium plantarum
CoE-159-22, isolated from traditionally produced Montenegrin cheese
Authors: Daza Prieto Beatriz , Raicevic Nadja , Hyden Patrick , Mösenbacher Tobias , Ladstätter Johann , Stöger Anna , Cabal Adriana , Mach Robert L. , Martinovic Aleksandra , Ruppitsch Werner 
Published: March 2024

ABSTRACT

Microbacterium plantarum
(
M. plantarum
) was recently described as a new species isolated from copper globemallow (
Sphaeralcea angustifolia
). Here, we report the complete genome of
M. plantarum
CoE-159-22, which was obtained from traditionally produced Montenegrin cheese.
A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics
Authors: Eisenhofer Raphael , Nesme Joseph , Santos-Bay Luisa , Koziol Adam , Sørensen Søren Johannes , Alberdi Antton , Aizpurua Ostaizka 
Published: March 2024

ABSTRACT

Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 fecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: (i) 20 Gbp of Illumina short-read data, (ii) 40 Gbp of short-read data, (iii) 20 Gbp of PacBio HiFi long-read data, and (iv) 40 Gbp of hybrid (20 Gbp of short-read +20 Gbp of long-read) data. No strategy was best for all metrics; instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific and depends on how researchers assess the trade-off between the quantity and quality of recovered genomes.

IMPORTANCE
Mice are an important model organism for understanding the gut microbiome. When studying these gut microbiomes using DNA techniques, researchers can choose from technologies that use short or long DNA reads. In this study, we perform an extensive benchmark between short- and long-read DNA sequencing for studying mice gut microbiomes. We find that no one approach was best for all metrics and provide information that can help guide researchers in planning their experiments.
On Embedding of Besov Spaces of Zero Smoothness into Lorentz Spaces
Authors: Stolyarov D. M. 
Published: March 2024

Abstract
We show that the zero smoothness Besov space $$B_{p,q}^{0,1}$$ does not embed into the Lorentz space $$L_{p,q}$$ unless $$p=q$$; here $$p,q\in (1,\infty)$$. This answers in the negative a question posed by O. V. Besov.
What is cystic fibrosis screen positive inconclusive diagnosis? And what is it not?
Authors: Devoy Emily , Hughes Dominic , Alharbi Asma Falah , Francis Jacqueline , Davies Jane C 
Published: March 2024

Since screening for cystic fibrosis (CF) was incorporated into the newborn screening program, the number of recognised variants in theCF transmembrane conductance regulator (CFTR) gene has significantly increased. This has led to the discovery of combinations of gene variants with an uncertain prognosis. One outcome is the designation of ‘cystic fibrosis screen positive inconclusive diagnosis’ (CFSPID). While the majority of these children are expected to be unaffected by theirCFTRvariants, a small proportion have been seen to develop symptoms or increasing sweat chloride levels over time, which may reflect dysfunction of the CFTR protein.As the number of children with CFSPID increases, paediatricians and those working in primary care are more likely to encounter them in their practice. It is important that professionals have an understanding of CFSPID: what it is and, importantly, what it is not (ie, they do not have CF). In this article, we hope to explore this using some example cases, illustrating the ways in which these children may present symptomatically and how to manage them.
Longitudinal changes in diet quality and food intake before and after diabetes awareness in American adults: the Coronary Artery Risk Development in Young Adults (CARDIA) study
Authors: Cha EunSeok , Choi Yuni , Bancks Michael , Faulkner Melissa Spezia , Dunbar Sandra B , Umpierrez Guillermo E , Reis Jared , Carnethon Mercedes R , Shikany James M , Yan Fengxia , Jacobs David R 
Published: March 2024

IntroductionLimited longitudinal research is available examining how American adults make dietary changes after learning they have diabetes. We examined the associations between diabetes awareness and changes in dietary quality and food intake in a prospective cohort from the Coronary Artery Risk Development in Young Adults (CARDIA) study.Research design and methodsA nested case-control design was used. In the original CARDIA study, black and white participants were recruited from four US urban areas and partitioned into one control group (no diabetes over 30-year follow-up) and three case groups (early-onset, intermediate-onset, later-onset diabetes groups) based on timing of diagnosis and first awareness of diabetes. Estimated meanA Priori Diet Quality Score(APDQS), and food subgroup intake were examined at three CARDIA examinations (year (Y)0, Y7, and Y20). The mean APDQS with 95% CIs and food intake (servings/day) were compared across the one control group and three case groups using exam-specific and repeated measures linear regression.ResultsAmong 4576 participants (mean age: 25±4 years; 55% female; 49% black race), 653 incident cases (14.3%) of diabetes were observed over 30 years. APDQS was lowest at Y0 when the diabetes-free participants were aged 18–30 years (61.5–62.8), but increased over 20 years with advancing age across all groups (64.6–73.3). Lower APDQS in young adulthood was associated with a higher incidence of diabetes later in life. Diabetes awareness was associated with a net increase of 2.95 points in APDQS. The greatest increase of APDQS was when people learned of their diabetes for the first time (an increase of 5.71 in early-onset and 6.64 in intermediate-onset diabetes groups, respectively).ConclusionsAdvancing age and diabetes awareness were associated with more favorable dietary changes leading to improved diet quality. Optimal diet quality and healthy food intake in young adulthood seem important to prevent diabetes later in life.
Prepublication abstract-only reports compared with full-text manuscripts for randomised controlled trials in inflammatory bowel disease: a systematic review
Authors: Sinopoulou Vassiliki , Gordon Morris , Moran Gordon William , Egiz Abdullah Mohammed Abousaleh ma , Phlananthachai Sanjana , Rane Aditi , Al-Tameemi Ahmed Hussein Ali 
Published: March 2024

IntroductionRandomised controlled trials (RCTs) of key therapies in inflammatory bowel disease (IBD) are often presented and available as abstracts for significant periods of time prior to full publication, often being employed to make strategic and clinical prescribing decisions. We compared the concordance of prepublication abstract-only reports and their respective full-text manuscripts.MethodsPairs of full-text manuscripts and their respective prepublication abstract-only reports for the same RCT outcomes, at the same time point of analysis were included. The RCTs were on treatments for IBD with full-text manuscripts published between 2010 and 2023.ResultsWe found 77 pairs of full-text manuscripts and their prepublication abstract-only reports. There were significant mismatches in the reporting of stated planned outcomes (65/77 matched, p<0.001) and primary outcomes reported in their results sections (67/77, p<0.001); trial registrations (34/65, p<0.001); the number of randomised participants (49/77, p=0.18); participants reaching end of study (21/71, p<0.001) and primary outcome data (40/73, p<0.001). Authors conclusions matched (75/77, p=0.157). Authors did not provide explicit or implied justifications for the absence or non-concordance for any of the above items.ConclusionsAbstract-only reports have consistent issues with both limited reporting of key information and significant differences in data when compared with their later full-text publications. These are not related to further recruitment of patients or word count limitations and are never explained. As abstracts are often used in guidelines, reviews and stakeholder decision-making on prescribing, caution in their use is strongly suggested. Further work is needed to enhance minimum reporting standards in abstract-only works and ensure consistency with final published papers.
All cause and cause specific mortality associated with transition to daylight saving time in US: nationwide, time series, observational study
Authors: Zhao Shi , Cao Wangnan , Liao Gengze , Guo Zihao , Xu Lufei , Shen Chen , Chang Chun , Liang Xiao , Wang Kai , He Daihai , Sun Shengzhi , Chen Rui , Dominici Francesca 
Published: March 2024

ObjectivesTo estimate the association between the transition to daylight saving time and the risks of all cause and cause specific mortality in the US.DesignNationwide time series observational study based on weekly data.SettingUS state level mortality data from the National Center for Health Statistics, with death counts from 50 US states and the District of Columbia, from the start of 2015 to the end of 2019.Population13 912 837 reported deaths in the US.Main outcome measuresWeekly counts of mortality for any cause, and for Alzheimer's disease, dementia, circulatory diseases, malignant neoplasms, and respiratory diseases.ResultsDuring the study period, 13 912 837 deaths were reported. The analysis found no evidence of an association between the transition to spring daylight saving time (when clocks are set forward by one hour on the second Sunday of March) and the risk of all cause mortality during the first eight weeks after the transition (rate ratio 1.003, 95% confidence interval 0.987 to 1.020). Autumn daylight saving time is defined in this study as the time when the clocks are set back by one hour (ie, return to standard time) on the first Sunday of November. Evidence indicating a substantial decrease in the risk of all cause mortality during the first eight weeks after the transition to autumn daylight saving time (0.974, 0.958 to 0.990). Overall, when considering the transition to both spring and autumn daylight saving time, no evidence of any effect of daylight saving time on all cause mortality was found (0.988, 0.972 to 1.005). These patterns of changes in mortality rates associated with transition to daylight saving time were consistent for Alzheimer's disease, dementia, circulatory diseases, malignant neoplasms, and respiratory diseases. The protective effect of the transition to autumn daylight saving time on the risk of mortality was more pronounced in elderly people aged ≥75 years, in the non-Hispanic white population, and in those residing in the eastern time zone.ConclusionsIn this study, transition to daylight saving time was found to affect mortality patterns in the US, but an association with additional deaths overall was not found. These findings might inform the ongoing debate on the policy of shifting daylight saving time.
Mezagitamab in systemic lupus erythematosus: clinical and mechanistic findings of CD38 inhibition in an autoimmune disease
Authors: McDonnell Scott R P , Nguyen Van Anh , Walton Noah M , Merkwirth Carsten , Hong Feng , Berg Deborah , Muensterman Elena Tomaselli , Furie Richard A 
Published: March 2024

ObjectiveTo evaluate safety and mechanism of action of mezagitamab (TAK-079), an anti-CD38 monoclonal antibody, in patients with moderate to severe systemic lupus erythematosus (SLE).MethodsA phase 1b double-blind, placebo-controlled, multicentre study was conducted in patients with SLE receiving standard background therapy. Eligible patients were adults who met the 2012 SLICC or ACR criteria for diagnosis, had a baseline SLE Disease Activity Index 2000 (SLEDAI-2K) score of ≥6 and were positive for anti-double-stranded DNA antibodies and/or anti-extractable nuclear antigens antibodies. Patients received 45 mg, 90 mg or 135 mg of mezagitamab or placebo every 3 weeks over 12 weeks. Primary endpoints were safety and tolerability. Secondary endpoints included pharmacokinetics and pharmacodynamics. Exploratory assessments included disease activity scales, deep immune profiling and interferon pathway analysis.Results22 patients received at least one dose of either mezagitamab or placebo. In patients exposed to mezagitamab (n=17), drug was well tolerated. Adverse event (AEs) were balanced across treatment groups, with no treatment emergent AEs exceeding grade 2. Responder analyses for Cutaneous Lupus Erythematosus Disease Area and Severity Index (CLASI) and SLEDAI-2K did not reveal any observable differences across treatment groups. However, there was a trend for more profound skin responses among patients with higher CLASI scores (>10) at baseline. Pharmacodynamic analysis showed median CD38 receptor occupancy up to 88.4% on CD38+ natural killer cells with concurrent depletion of these cells up to 90% in the 135 mg group. Mean reductions in IgG and autoantibodies were less than 20% in all dose groups. Cytometry by time of flight and type 1 interferon gene analysis revealed unique fingerprints that are indicative of a broad immune landscape shift following CD38 targeting.ConclusionsMezagitamab had a favourable safety profile in patients with moderate to severe SLE and elicited a pharmacodynamic effect consistent with CD38+ cell depletion. These findings reveal novel insights into the drug’s mechanism of action and support the continued investigation of mezagitamab in autoimmune diseases.
Hyperactivation and altered selection of B cells in patients with paediatric Sjogren’s syndrome
Authors: Boni Alessandra , Nicolai Rebecca , Caiello Ivan , Marinaro Francesca , Farina Luciapia , Pires Marafon Denise , Carsetti Rita , De Benedetti Fabrizio , Bracaglia Claudia , Marasco Emiliano 
Published: March 2024

ObjectivesPaediatric Sjögren’s syndrome (pSS) is a rare chronic autoimmune disorder, characterised by inflammation of exocrine glands. B cell hyperactivation plays a central role in adult-onset Sjogren. This study was designed to analyse B cell and T cell phenotype, levels of BAFF, and selection of autoreactive B cells in patients with pSS.MethodsA total of 17 patients diagnosed with pSS and 13 healthy donors (controls) comparable for age were enrolled in the study. B cell and T cell subsets and frequency of autoreactive B cells in peripheral blood were analysed by flow cytometry. Levels of BAFF were analysed by ELISA.ResultsThe relative frequency of total B cells, transitional, naïve and switched memory B cells was similar between pSS patients and controls. In patients with pSS, we observed a reduction in the frequency of unswitched memory B cells, an increased frequency of atypical memory B cells and an expansion of PD1hiCXCR5−T peripheral helper cells. Levels of BAFF were higher in patients with pSS compared with controls and correlated with serum levels of total IgG and titres of anti-Ro antibodies. The frequency of autoreactive B cells in the transitional, unswitched memory and plasmablast compartment was significantly higher in pSS patients than in controls.ConclusionsOur results point to a hyperactivation of B cells in pSS. Current therapies do not seem to affect B cell abnormalities, suggesting that novel therapies targeting specifically B cell hyperactivation need to be implemented for paediatric patients.
Sports drinks do not increase acute kidney injury risk in males during industrial work in the heat when euhydration is maintained, a randomized crossover trial
Authors: Atkins Whitley C. , McKenna Zachary J. , McDermott Brendon P. 
Published: March 2024

Industrial workers regularly perform physical labor under high heat stress, which may place them at risk for dehydration and acute kidney injury. Current guidelines recommend that workers should consume sports drinks to maintain euhydration during work shifts. However, the impact of fructose sweetened sports drinks on acute kidney injury risk is unknown. The purpose of this study was to investigate the effects of sports drink consumption on markers of acute kidney injury following simulated industrial work in the heat. Twenty males completed two matched 2 h simulated industrial work trial visits in a warm and humid environment (30 °C and 55% relative humidity). During and following the bout of simulated work, participants consumed either a commercially available sports drink or a noncaloric placebo. Urine and blood samples, collected pre-, post-, and 16 h post-work were assayed for markers of hydration (plasma/urine osmolality, and urine specific gravity) and acute kidney injury (KIM-1 and NGAL). There were no differences in physiological or perceptual responses to the bout of work (interaction p > 0.05 for all indices), and markers of hydration were similar between trials (interaction p > 0.05 for all indices). KIM-1 (Placebo: Δ Ln 1.18 ± 1.64; Sports drink: Δ Ln 1.49 ± 1.10 pg/mL; groupwide d = 0.89, p < 0.001) and NGAL (Placebo: Δ Ln 0.44 ± 1.11; Sports drink: Δ Ln 0.67 ± 1.22 pg/mL; groupwide d = 0.39, p = 0.03) were elevated pre- to post-work, but there were no differences between trials (interaction p > 0.05). These data provide no evidence that consumption of fructose sweetened sports drinks increases the risk of acute kidney injury during physical work in the heat.
Dynamics of viable f(R) dark energy models in the presence of curvature–matter interactions
Authors: Chatterjee Anirban , Roy Rahul , Dey Sayantan , Bandyopadhyay Abhijit 
Published: March 2024

AbstractIn this study, we analyze the dynamics of the interaction between dark matter and curvature-driven dark energy in viable f(R) gravity models using the framework of dynamical system analysis. We incorporate this interaction by introducing a source term in their respective continuity equations, given by $$Q = \frac{\kappa ^2 \alpha }{3\,H}\tilde{\rho }_\textrm{m}\rho _\textrm{curv}$$

Q
=

κ
2

α

3

H

ρ
~

m

ρ
curv

, and examine two f(R) gravity models that comply with local gravity constraints and cosmological viability criteria. Our findings reveal subtle modifications to fixed points and their stability criteria when compared to the conventional dynamical analysis of f(R) gravity models without matter-curvature interactions as proposed and examined in prior literature. We determine the parameter limits associated with the stability criteria of critical points of the dynamical system for both the models. Additionally, the introduction of interaction reveals variations in the dynamical aspects of cosmic evolution, contingent on the range of values for the relevant model parameters. These results are consistent with the observed features of cosmic evolution within specific limits of the f(R) models parameters and the coupling parameter $$\alpha $$
α
. We also examine the evolutionary dynamics of the universe in the interacting scenario through cosmological and cosmographic parameters. Our analysis demonstrates that the interacting scenario comprehensively accounts for all the observed phases of the universe’s evolution and also results in a stable late-time cosmic acceleration. Additionally, we’ve studied how the coupling parameter affects evolutionary dynamics, particularly its impact on the matter-to-curvature energy density ratio. Our findings suggest that the chosen form of interaction can also address the cosmic coincidence problem.
The simpliciality of higher-order networks
Authors: Landry Nicholas W. , Young Jean-Gabriel , Eikmeier Nicole 
Published: March 2024

AbstractHigher-order networks are widely used to describe complex systems in which interactions can involve more than two entities at once. In this paper, we focus on inclusion within higher-order networks, referring to situations where specific entities participate in an interaction, and subsets of those entities also interact with each other. Traditional modeling approaches to higher-order networks tend to either not consider inclusion at all (e.g., hypergraph models) or explicitly assume perfect and complete inclusion (e.g., simplicial complex models). To allow for a more nuanced assessment of inclusion in higher-order networks, we introduce the concept of “simpliciality” and several corresponding measures. Contrary to current modeling practice, we show that empirically observed systems rarely lie at either end of the simpliciality spectrum. In addition, we show that generative models fitted to these datasets struggle to capture their inclusion structure. These findings suggest new modeling directions for the field of higher-order network science.