bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is the period of austerity in the UK associated with increased rates of adverse birth outcomes?
Authors: Watson Rachael , Walsh David , Scott Sonya , Carruthers Jade , Fenton Lynda , McCartney Gerry , Moore Emily 
Published: November 2024

Abstract
Hugely concerning changes to health outcomes have been observed in the UK since the early 2010s, including reductions in life expectancy and widening of inequalities. These have been attributed to UK Government ‘austerity’ policies which have profoundly affected poorer populations. Studies in mainland Europe have shown associations between austerity and increases in adverse birth outcomes such as low birthweight (LBW). The aim here was to establish whether the period of UK austerity was also associated with higher risks of such outcomes. We analysed all live births in Scotland between 1981 and 2019 (n = 2.3 million), examining outcomes of LBW, preterm birth (PB) and small-for-gestational-age (SGA). Descriptive trend analyses, segmented regression (to identify changes in trends) and logistic regression modelling (to compare risk of outcomes between time periods) were undertaken, stratified by infant sex and quintiles of socioeconomic deprivation. There were marked increases in LBW and PB rates in the austerity period, particularly in the most deprived areas. However, rates of SGA decreased, suggesting prematurity as the main driver of LBW rather than intrauterine growth restriction. The regression analyses confirmed these results: trends in LBW and PB changed within 1–3 years of the period in which austerity was first implemented, and that period was associated with higher risk of such outcomes in adjusted models. The results add to the European evidence base of worsening birth outcomes associated with austerity-related economic adversity. The newly elected UK government needs to understand the causes of these changes, and the future implications for child and adult health.
Ecological processes shaping highly connected bacterial communities along strong environmental gradients
Authors: Wu Wenxue , Hsieh Chih-hao , Logares Ramiro , Lennon Jay T , Liu Hongbin 
Published: October 2024

Abstract
Along the river–sea continuum, microorganisms are directionally dispersed by water flow while being exposed to strong environmental gradients. To compare the two assembly mechanisms that may strongly and differently influence metacommunity dynamics, namely homogenizing dispersal and heterogeneous selection, we characterized the total (16S rRNA gene) and putatively active (16S rRNA transcript) bacterial communities in the Pearl River–South China Sea Continuum, during the wet (summer) and dry (winter) seasons using high-throughput sequencing. Moreover, well-defined sampling was conducted by including freshwater, oligohaline, mesohaline, polyhaline, and marine habitats. We found that heterogeneous selection exceeded homogenizing dispersal in both the total and active fractions of bacterial communities in two seasons. However, homogeneous selection was prevalent (the dominant except in active bacterial communities during summer), which was primarily due to the bacterial communities’ tremendous diversity (associated with high rarity) and our specific sampling design. In either summer or winter seasons, homogeneous and heterogeneous selection showed higher relative importance in total and active communities, respectively, implying that the active bacteria were more responsive to environmental gradients than were the total bacteria. In summary, our findings provide insight into the assembly of bacterial communities in natural ecosystems with high spatial connectivity and environmental heterogeneity.
Thousands of trait-specific KASP markers designed for diverse breeding applications in rice (Oryza sativa)
Authors: Steele Katherine , Quinton-Tulloch Mark , Vyas Darshna , Witcombe John 
Published: November 2024

Abstract
This study aimed to broaden applicability of KASP for Oryza sativa across diverse genotypes through incorporation of ambiguous (degenerate) bases into their primer designs and to validate 4,000 of them for genotyping applications. A bioinformatics pipeline was used to compare 129 rice genomes from 89 countries with the indica reference genome R498 and generate ∼1.6 million KASP designs for the more common variants between R498 and the other genomes. Of the designs, 98,238 were for predicted functional markers. Up to 5 KASP each for 1,024 breeder-selected loci were assayed in a panel of 178 diverse rice varieties, generating 3,366 validated KASP. The 84% success rate was within the normal range for KASP demonstrating that the ambiguous bases do not compromise efficacy. The 3,366-trait-specific marker panel was applied for population structure analysis in the diversity panel and resolved them into 4 expected groups. Target variations in 13 genomes used for designs were compared with the corresponding KASP genotypes in different accessions of the same 13 varieties in the diversity panel. There was agreement for 79% or more markers in 12 varieties; 10 having agreement &gt;88%. One variety, a selection from a landrace, had only 46.5% marker agreement. Breeders can search for the validated KASP and more than a million so-far untested designs in three reference genomes (including Niponbare MSU7) with a search tool, that includes designs in proximity to previously published microsatellite markers, and retrieve target variations for 129 rice genomes plus their genomic locations with ±25 bp flanking sequences.
Commercial inpatient hospital price growth driven by system affiliation and nonprofit-status hospitals
Authors: Chang Jessica Y , Martin Kathryn 
Published: November 2024

Abstract
As policymakers continue to grapple with rising health care costs and prices, understanding trends and variations in inpatient prices among hospital characteristics is an important benchmark to allow policymakers to craft targeted policies. In this study, we provide descriptive trends on variation in inpatient prices paid by commercial health plans stratified by hospital characteristics using data from Health Care Cost Institute's employer-sponsored insured claims data. Our analyses found evidence of considerable variation among inpatient price levels and growth among system affiliation and profitability. Prices among system-affiliated hospitals grew from $14 281.74 in 2012 to $20 731.95 in 2021, corresponding to a 45.2% increase during this period. On the other hand, prices among independent hospitals grew more slowly, from $13 460.50 in 2012 to $18 196.90 in 2021, corresponding to a 35.2% increase. We did not observe a similar trend in growth rates among case mix index by hospital characteristics, implying that differential inpatient price growth is not driven by changes in case mix by hospital characteristics. Heterogeneity in hospital prices and price growth by type of hospital suggests that public and private policymakers aiming to rein in health spending should consider policies that address this variation.
The long-term effects of cash transfer programmes on young adults’ mental health: a quasi-experimental study of Colombia, Mexico, and South Africa
Authors: Zimmerman Annie , Avendano Mauricio , Lund Crick , Araya Ricardo , Diaz Yadira , Sanchez-Ariza Juliana , Hessel Philipp , Garman Emily , Evans-Lacko Sara 
Published: November 2024

Abstract
Poverty is associated with poorer mental health in early adulthood. Cash transfers (CTs) have been shown to improve child health and education outcomes, but it is unclear whether these effects may translate into better mental health outcomes as children reach young adulthood. Using a quasi-experimental approach that exploits variation across countries in the timing of national CT programme introduction, we examine whether longer exposure to CTs during childhood (0–17 years) reduces depressive symptoms in early adulthood (18–30 years). Based on harmonized data from Colombia, Mexico, and South Africa (N = 14 431), we applied logistic regression models with country and birth-cohort fixed effects to estimate the impact of cumulative years of CT exposure on mental health, educational attainment, and employment outcomes. Our findings indicate that each additional year of CT exposure during childhood is associated with a 4% reduction in the odds of serious depressive symptoms in early adulthood [odds ratio (OR) = 0.96, 95% confidence intervals (CIs): 0.93, 0.98]. We find no consistent effect of years of exposure on completion of secondary school (OR = 1.01, 95% CIs: 0.99, 1.03) and a negative effect on the probability of employment in early adulthood (OR = 0.90, 95% CIs: 0.88, 0.91). These results suggest that longer exposure to CTs may contribute to modest but meaningful reductions in population-level depressive symptoms during early adulthood.
Genome-wide analysis of non-coding RNA reveals the role of a novel miR319c for tuber dormancy release process in potato
Authors: Liu Shengyan , Yang Jiangwei , Zhang Ning , Si Huaijun 
Published: October 2024

Abstract
Tuber dormancy and sprouting are significant for potato cultivation, storage, and processing. Although the substantial role of microRNAs (miRNAs) in some biological processes has been recognized, the critical role of miRNA in breaking potato tuber dormancy is not well understood to date. In this investigation, we expand research on miRNA-mediated gene regulation in tuber dormancy release. In this work, 204 known and 192 novel miRNAs were identified. One hundred thirty-six differentially expressed miRNAs (DE-miRNAs) were also screened out, of which 56 DE-miRNAs were regulated by temperature during tuber dormancy release. Additionally, degradome sequencing revealed that 821 target genes for 202 miRNAs were discovered. Among them, 63 target genes and 48 miRNAs were predicted to be involved in plant hormone signaling pathways. This study used degradome sequencing, tobacco cotransformation system, and β-glucuronidase (GUS) staining technology to confirm that stu-miR319c can target StTCP26 and StTCP27 and effectively suppress their expression. The transgenic approach exhibited that stu-miR319c overexpressed tubers sprouted in advance, while silent expression of stu-miR319c showed delayed sprouting. Treatment of wild-type tubers with exogenous MeJA revealed that 1 mg/L MeJA significantly broke dormancy and enhanced potato sprouting ability. Furthermore, transgenic tubers revealed variance in jasmonic acid (JA) content and relative expression of genes associated with the JA synthesis pathway, including StAOC, StLOX2, and StLOX4, suggesting that the miR319c may participate in the JA pathway to regulate tuber dormancy release. In summary, our research offers evidence that miRNA regulates potato dormancy release and supports the idea that stu-miR319c is a unique epigenetic regulator for dormancy-sprouting transition in potatoes.
The evolution of soft balancing in informal institutions: the case of BRICS
Authors: Papa Mihaela , Han Zhen 
Published: October 2024

Abstract
The concept of soft balancing emerged in 2005 to analyse how states engage in non-military balancing against the United States. By 2025, soft balancing has become extensively discussed in the context of BRICS, which has evolved from a loose grouping of diverse powers into an active, complex and rapidly growing entity. However, scholars remain divided on the nature and drivers of soft balancing within BRICS. How has BRICS developed into a robust soft balancing coalition? This article uses insights from compensatory layering—a process where transformative change occurs through sequential bargains over institutional design—to demonstrate how BRICS builds soft balancing collaborations, selectively institutionalizes some cooperative activities, and expands its scope to include both soft balancing and non-soft balancing elements. It clarifies balancing and non-balancing behaviours within BRICS, providing new insights into soft balancing in contemporary power dynamics. The study shows how states centre their cooperation around a specific informal institution, enabling effective soft balancing outcomes.
Immunometabolic Contributions of Atopobiaceae Family Members in Human Papillomavirus Infection, Cervical Dysplasia, and Cancer
Authors: Jimenez Nicole R , Mancilla Vianney , Łaniewski Paweł , Herbst-Kralovetz Melissa M 
Published: November 2024

Abstract

Background
In the cervicovaginal environment, human papillomavirus (HPV) acquisition and cervical cancer progression are linked to non-Lactobacillus dominance, of which Atopobiaceae are key taxa. We hypothesize that Atopobiaceae modulates the cervicovaginal microenvironment to promote HPV persistence and progression to cancer. However, the extent to which Atopobiaceae impact the immunometabolic microenvironment is poorly understood.

Methods
We investigated Atopobiaceae in a cohort of primarily Hispanic and non-Hispanic White women who were HPV-negative (n = 20), HPV-positive (n = 31) without dysplasia, diagnosed with cervical dysplasia (n = 38), or newly diagnosed with invasive cervical carcinoma (n = 9). Microbiome data were integrated with clinical and demographic surveys, immunoproteomics, and metabolomics data.

Results
Atopobiaceae identified were Fannyhessea vaginae, Fannyhessea massiliense, Fannyhessea species type 2, Lancefieldella deltae, and an unclassified species. A higher prevalence of Atopobiaceae was observed in women who were Hispanic and had higher gravidity and parity. F. species type 2 and F. vaginae were observed with infections of high-risk HPV genotypes 31 and 52. Atopobiaceae were negatively correlated with Lactobacillus and positively correlated to Sneathia, Dialister, Anaerococcus, Prevotella, and Bifidobacterium/Gardnerella. Proinflammatory cytokines (IL-1α, IL-1β, IL-12, TNF-α), immune checkpoint proteins (PD-L1, LAG3), and cancer biomarkers (CEA, MIF, TRAIL) were positively associated with Atopobiaceae-rich profiles. Prooncogenic metabolites, including 4-hydroxybutyrate and sphingosine, were also elevated in women colonized by Atopobiaceae.

Conclusions
Our data implicate Atopobiaceae in lipid modulation, oxidative stress, inflammatory responses, and immune evasion, which may contribute to cancer. This study highlights a key family of pathogenic cervicovaginal bacteria that could be exploited to monitor HPV persistence and/or targeted to prevent HPV-mediated cancer.
Clinical Characteristics and In-hospital Outcomes Associated With Respiratory Syncytial Virus vs Other Viral Acute Lower Respiratory Infections in Hospitalized Children Younger Than 2 Years
Authors: Ozturk Acacia , Chan Mei , Khan Jahid Rahman , Hu Nan , McMullan Brendan , Britton Philip N , Bartlett Adam , Kandasamy Rama , Saravanos Gemma L , Prentice Bernadette , Shi Ting , Jaffe Adam , Owens Louisa , Homaira Nusrat 
Published: November 2024

Abstract

Background
Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory infection (ALRI)–associated hospitalizations in children. It is unclear if hospitalized RSV-positive ALRI is clinically different from other viral ALRIs. We aimed to compare the disease impact of hospitalized RSV with other viral ALRI in children aged &lt;2 years.

Methods
We conducted a retrospective study using the electronic medical records of children aged &lt;2 years who were hospitalized with ALRIs at Sydney Children's Hospital Network from 2020 to 2022. We compared demographics and clinical features between RSV-positive cases and RSV-negative ones (ie, positive for other viruses). Poisson quasi-likelihood regression was used to estimate adjusted prevalence ratios for 3 in-hospital outcomes: length of stay, need for respiratory support, and intensive care.

Results
We examined 330 children aged &lt;2 years hospitalized with RSV-positive ALRIs and 330 with RSV-negative ALRIs (positive for other viruses). RSV-positive cases were older (12 vs 8 months, P &lt; .001) and more often presented with cough (99% vs 92%), fever (80% vs 58%), crackles (89% vs 76%), hypoxia (50% vs 36%), and lethargy (36% vs 20%). They were also more likely to undergo chest radiographs (74% vs 49%) and receive antibiotics (65% vs 35%). Adjusted analysis showed that children who were RSV positive had a higher likelihood of an extended length of stay (&gt;2 days; adjusted prevalence ratio, 1.95; 95% CI, 1.14–3.36). However, there were no differences in the need for intensive care or respiratory support.

Conclusions
Children with RSV-positive ALRI exhibited more severe symptoms, received more antibiotics, and had longer hospital stays as compared with those with other viral ALRIs, underscoring the need for effective prevention and treatment strategies for RSV.
Cyanorhodopsin-II represents a yellow-absorbing proton-pumping rhodopsin clade within cyanobacteria
Authors: Hasegawa-Takano Masumi , Hosaka Toshiaki , Kojima Keiichi , Nishimura Yosuke , Kurihara Marie , Nakajima Yu , Ishizuka-Katsura Yoshiko , Kimura-Someya Tomomi , Shirouzu Mikako , Sudo Yuki , Yoshizawa Susumu 
Published: November 2024

Abstract
Microbial rhodopsins are prevalent in many cyanobacterial groups as a light-energy-harvesting system in addition to the photosynthetic system. It has been suggested that this dual system allows efficient capture of sunlight energy using complementary ranges of absorption wavelengths. However, the diversity of cyanobacterial rhodopsins, particularly in accumulated metagenomic data, remains underexplored. Here, we used a metagenomic mining approach, which led to the identification of a novel rhodopsin clade unique to cyanobacteria, cyanorhodopsin-II (CyR-II). CyR-IIs function as light-driven outward H+ pumps. CyR-IIs, together with previously identified cyanorhodopsins (CyRs) and cyanobacterial halorhodopsins (CyHRs), constitute cyanobacterial ion-pumping rhodopsins (CyipRs), a phylogenetically distinct family of rhodopsins. The CyR-II clade is further divided into two subclades, YCyR-II and GCyR-II, based on their specific absorption wavelength. YCyR-II absorbed yellow light (λmax = 570 nm), whereas GCyR-II absorbed green light (λmax = 550 nm). X-ray crystallography and mutational analysis revealed that the difference in absorption wavelengths is attributable to slight changes in the side chain structure near the retinal chromophore. The evolutionary trajectory of cyanobacterial rhodopsins suggests that the function and light-absorbing range of these rhodopsins have been adapted to a wide range of habitats with variable light and environmental conditions. Collectively, these findings shed light on the importance of rhodopsins in the evolution and environmental adaptation of cyanobacteria.
Restricted feeding of weight control diets induces weight loss and affects body composition, voluntary physical activity, blood metabolites, hormones, and oxidative stress markers, and fecal metabolites and microbiota of obese cats
Authors: Opetz Danielle L , Oba Patricia M , Lin Ching-Yen , Ren Ping , Swanson Kelly S 
Published: November 2024

Abstract
Feline obesity puts many cats at risk for comorbidities such as hepatic lipidosis, diabetes mellitus, urinary tract diseases, and others. Restricted feeding of specially formulated diets may improve feline health and safely support weight loss while maintaining lean mass. The objective of this study was to determine the effects of restricted intake of weight control diets on weight loss, body composition, voluntary physical activity, serum metabolic and inflammatory markers, and fecal metabolites and microbiota of obese cats. Twenty-four obese adult domestic shorthair cats [body weight (BW) = 5.51 ± 0.92 kg; body condition score (BCS) = 8.44 ± 0.53] were used. A leading grocery brand diet was fed during a 4-wk baseline to identify intake needed to maintain BW. After baseline (week 0), cats were allotted to one of 2 weight control diets (DRY or CAN) and fed to lose 1.5% BW per week for 18 wk. At baseline and 6, 12, 18 wk after weight loss, dual-energy x-ray absorptiometry scans were performed, blood and fecal samples were collected, and voluntary physical activity was measured. Change from baseline data was analyzed statistically using the Mixed Models procedure of SAS, with P &lt; 0.05 being significant and P &lt; 0.10 being trends. BW was reduced by 1.54 ± 0.51% per week. Restricted feeding of both diets led to BW (P &lt; 0.01) and fat mass loss (P &lt; 0.01), reduced BCS (P &lt; 0.01), reduced leptin (P &lt; 0.01) and insulin (P &lt; 0.01) concentrations, and increased superoxide dismutase (P &lt; 0.01) and active ghrelin (P &lt; 0.01) concentrations. Change from baseline fecal scores was reduced (P &lt; 0.01) with restricted feeding and weight loss, while total short-chain fatty acid, acetate, and propionate concentration reductions were greater (P &lt; 0.05) in cats fed CAN than those fed DRY. Fecal bacterial alpha diversity measures increased (P &lt; 0.01) with restricted feeding and weight loss. Fecal bacterial beta diversity was altered by time in all cats, with week 0 being different (P &lt; 0.05) than weeks 6, 12, and 18. Change from baseline relative abundances of 3 fecal bacterial phyla and over 30 fecal bacterial genera were impacted (P &lt; 0.05) or tended to be impacted (P &lt; 0.10) by dietary treatment. Our data demonstrate that restricted feeding of both weight control diets was an effective means for weight loss in obese adult domestic cats. Some changes were also impacted by diet, highlighting the importance of diet formulation and format, and nutrient composition in weight control diets.
Method for detection of naturally occurring toxins in human urine using liquid chromatography–high-resolution mass spectrometry
Authors: Hettick Bryan E , Saddy Anisha , Krajewski Logan C , Johnson Rudolph C , Hamelin Elizabeth I 
Published: November 2024

Abstract
Natural toxins present an ongoing risk for human exposure that requires a rapid and accurate diagnosis for proper response. In this study, a qualitative liquid chromatography–high-resolution mass spectrometry (LC–HRMS) method was developed and validated for the detection of a large, diverse selection of natural toxins. Data-dependent acquisition was performed to identify compounds with an in-house mass spectral library of 129 hazardous toxins that originate from plants, animals, and fungi. All 129 compounds were spiked into human urine, extracted, and evaluated for spectral library matching. Of these, 92 toxins met the quality criteria and underwent validation in urine matrix based on American National Standards Institute guidelines. A generalized workflow for method expansion was developed and enables the rapid addition of relevant compounds to the established method. This LC–HRMS method achieves efficient detection of natural toxins in urine, and the created workflow can rapidly increase compound coverage via method expansion.
Invasive Lobular Carcinoma in the Screening Setting
Authors: Reig Beatriu , Heacock Laura 
Published: November 2024

Abstract
Invasive lobular carcinoma (ILC) is the second-most common histologic subtype of breast cancer, constituting 5% to 15% of all breast cancers. It is characterized by an infiltrating growth pattern that may decrease detectability on mammography and US. The use of digital breast tomosynthesis (DBT) improves conspicuity of ILC, and sensitivity is 80% to 88% for ILC. Sensitivity of mammography is lower in dense breasts, and breast tomosynthesis has better sensitivity for ILC in dense breasts compared with digital mammography (DM). Screening US identifies additional ILCs even after DBT, with a supplemental cancer detection rate of 0 to 1.2 ILC per 1000 examinations. Thirteen percent of incremental cancers found by screening US are ILCs. Breast MRI has a sensitivity of 93% for ILC. Abbreviated breast MRI also has high sensitivity but may be limited due to delayed enhancement in ILC. Contrast-enhanced mammography has improved sensitivity for ILC compared with DM, with higher specificity than breast MRI. In summary, supplemental screening modalities increase detection of ILC, with MRI demonstrating the highest sensitivity.