bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sleep deprivation alters pubertal timing in humans and rats: the role of the gut microbiome
Authors: Gunawan Shirley Priscilla , Huang Shih-Yi , Wang Chun-Chi , Huynh Linh Ba Phuong , Nguyen Nam Nhat , Hsu Shih-Yuan , Chen Yang-Ching 
Published: December 2023

Abstract

Study Objectives
Evidence implied that sleeping duration is associated with the timing of puberty and that sleep deprivation triggers early pubertal onset in adolescents. Sleep deprivation can affect metabolic changes and gut microbiota composition. This study investigated the effects of sleep deprivation on pubertal onset and gut microbiota composition in animal models and a human cohort.

Methods
This study comprised 459 boys and 959 girls from the Taiwan Pubertal Longitudinal Study. Sleep duration was evaluated using the self-report Pittsburgh Sleep Quality Index questionnaire. Early sexual maturation was defined by pediatric endocrinologist assessments. Mediation analyses were done to examine the association between sleep parameters, obesity, and early sexual maturation. Besides, Sprague Dawley juvenile rats were exposed to 4 weeks of chronic sleep deprivation. Vaginal opening (VO) and preputial separation (PS) were observed every morning to determine pubertal onset in female and male rats.

Results
The sleep-deprived juvenile rats in the sleep-deprived-female (SDF) and sleep-deprived-male (SDM) groups experienced delayed VO (mean VO days: 33 days in control; 35 days in SDF; p-value &lt; 0.05) and PS (mean PS days: 42 days in control; 45 days in SDM; p-value &lt; 0.05), respectively. Relative to their non-sleep-deprived counterparts, the sleep-deprived juvenile rats exhibited lower body weight and body fat percentage. Significant differences in relative bacterial abundance at genus levels and decreased fecal short-chain-fatty-acid levels were identified in both the SDF and SDM groups. In the human cohort, insufficient sleep increased the risk of early sexual maturation, particularly in girls (OR, 1.44; 95% CI: 1.09 to 1.89; p-value &lt; 0.01). Insufficient sleep also indirectly affected early sexual maturation in girls, with obesity serving as the mediator.

Conclusions
Overall, sleep deprivation altered the timing of puberty in both animal and human models but in different directions. In the rat model, sleep deprivation delayed the pubertal onset in juvenile rats through gut dysbiosis and metabolic changes, leading to a low body weight and body fat percentage. In the human model, sleep deprivation led to fat accumulation, causing obesity in girls, which increased the risk of early puberty.
Digital Platforms and the Maintenance of the Urban Order
Authors: Lara-Millán Armando , Guzman-Garcia Melissa 
Published: December 2023

Abstract
Neighborhood digital platforms – such as Nextdoor, Citizen, Neighbors, anti-crime Facebook groups, Ring surveillance technology, and 311 see-click-fix applications – are recent entrants into urban life. Existing accounts suggest they help build intra-community relationships, but that they also amplify paranoia, racism, and carceral impulses of American homeowners. We ask: how is the new technology increasing solidarity and exclusionary impulses, and what role does it play in the changing American urban landscape? Using offline and online ethnography of one community’s year-long contestation over public space, we find that three effects of the platforms help explain the maintenance of urban order in this case. First, the platforms push residents to see disparate instances of urban disorder as a linked manifestation of organized crime. Second, the platforms help to turn fleeting and uncorroborated accounts into durable events that foster community efficacy. Third, by increasing perceptions of urban disorder and greater community efficacy, the platforms facilitate the accrual of offline material resources. We suggest that in highly contested areas of American cities – areas where wealthy residents vie with a largely Brown and Black working-class for use of space – neighborhood digital platforms help to funnel services that support property value into smaller sections of otherwise disinvested neighborhoods.
Assessing the market viability of a packaged intensive health behavior and lifestyle treatment
Authors: Persaud Alicia , Smith Natalie Riva , Lindros Jeanne , Salmon Jeremiah , Ventura Giustina , Perkins Meghan , Taveras Elsie M , Fiechtner Lauren , Simione Meg 
Published: December 2023

Abstract
In the USA, more than 14 million children are impacted by obesity. Despite intensive health behavior and lifestyle treatments being found effective, gaps exist in moving these interventions into widespread use. Focusing on market viability could improve the dissemination and sustainment of interventions. The purpose of this paper is to outline the process and results of our market viability assessment for the Healthy Weight Clinic (HWC), a Centers for Disease Control and Prevention-recognized Family Health Weight Program. We conducted a market viability assessment using the Speeding Research-test INTerventions (SPRINT) program to gain insights into the commercialization and marketplace for the HWC. Through the process of customer discovery, we interviewed 50 stakeholders to test our hypotheses pertaining to our business model. Key takeaways were the need for packaged interventions that offer support and training for providers, and interventions that are multidisciplinary and located within the medical home. We also learned that (i) the intervention goals must align with the healthcare organization’s performance metrics; (ii) services need to be reimbursable; and (iii) the importance of understanding different customer segments (i.e. program users vs. organization decision-makers) and their unique needs. The market viability assessment is a critical step to transforming the HWC into a viable commercial product. The process we have outlined is replicable by others and by encouraging other teams to design for dissemination we can increase the number of evidence-based, packaged IHBLTs available to children with obesity.
Bypassing the brain barriers: upregulation of serum miR-495 and miR-543-3p reflects thyroid-mediated developmental neurotoxicity in the rat
Authors: O’Shaughnessy Katherine L , Sasser Aubrey L , Bell Kiersten S , Riutta Cal , Ford Jermaine L , Grindstaff Rachel D , Gilbert Mary E 
Published: December 2023

Abstract
Evaluating the neurodevelopmental effects of thyroid-disrupting chemicals is challenging. Although some standardized developmental and reproductive toxicity studies recommend serum thyroxine (T4) measures in developing rats, extrapolating between a serum T4 reduction and neurodevelopmental outcomes is not straightforward. Previously, we showed that the blood-brain and blood-cerebrospinal fluid barriers may be affected by developmental hypothyroidism in newborn rats. Here, we hypothesized that if the brain barriers were functionally disturbed by abnormal thyroid action, then small molecules may escape from the brain tissue and into general circulation. These small molecules could then be identified in blood samples, serving as a direct readout of thyroid-mediated developmental neurotoxicity. To address these hypotheses, pregnant rats were exposed to propylthiouracil (PTU, 0 or 3 ppm) to induce thyroid hormone insufficiency, and dams were permitted to give birth. PTU significantly reduced serum T4 in postnatal offspring. Consistent with our hypothesis, we show that tight junctions of the brain barriers were abnormal in PTU-exposed pups, and the blood-brain barrier exhibited increased permeability. Next, we performed serum microRNA Sequencing (miRNA-Seq) to identify noncoding RNAs that may reflect these neurodevelopmental disturbances. Of the differentially expressed miRNAs identified, 7 were upregulated in PTU-exposed pups. Validation by qRT-PCR shows that miR-495 and miR-543-3p were similarly upregulated in males and females. Interestingly, these miRNAs have been linked to cell junction dysfunction in other models, paralleling the identified abnormalities in the rat brain. Taken together, these data show that miR-495 and miR-543-3p may be novel in vivo biomarkers of thyroid-mediated developmental neurotoxicity.
Responses of stomatal density and carbon isotope composition of sugar maple and yellow birch foliage to N, P and CaSiO3 fertilization
Authors: Zukswert Jenna M , Vadeboncoeur Matthew A , Yanai Ruth D 
Published: December 2023

Abstract
Stomatal density, stomatal length and carbon isotope composition can all provide insights into environmental controls on photosynthesis and transpiration. Stomatal measurements can be time-consuming; it is therefore wise to consider efficient sampling schemes. Knowing the variance partitioning at different measurement levels (i.e., among stands, plots, trees, leaves and within leaves) can aid in making informed decisions around where to focus sampling effort. In this study, we explored the effects of nitrogen (N), phosphorus (P) and calcium silicate (CaSiO3) addition on stomatal density, length and carbon isotope composition (δ13C) of sugar maple (Acer saccharum Marsh.) and yellow birch (Betula alleghaniensis Britton). We observed a positive but small (8%) increase in stomatal density with P addition and an increase in δ13C with N and CaSiO3 addition in sugar maple, but we did not observe effects of nutrient addition on these characteristics in yellow birch. Variability was highest within leaves and among trees for stomatal density and highest among stomata for stomatal length. To reduce variability and increase chances of detecting treatment differences in stomatal density and length, future protocols should consider pretreatment and repeated measurements of trees over time or measure more trees per plot, increase the number of leaf impressions or standardize their locations, measure more stomata per image and ensure consistent light availability.
Species delimitation and phylogenetic analyses of a New Guinean frog genus (Microhylidae: Hylophorbus) reveal many undescribed species and a complex diversification history driven by late Miocene events
Authors: Ferreira Flavien , Kraus Fred , Richards Stephen , Oliver Paul , Günther Rainer , Trilaksono Wahyu , Arida Evy Ayu , Hamidy Amir , Riyanto Awal , Tjaturadi Burhan , Thébaud Christophe , Gaucher Philippe , Fouquet Antoine 
Published: December 2023

Abstract
New Guinea is the largest tropical island in the world and hosts immense endemic biodiversity. However, our understanding of how the gradual emergence of the terrestrial ecosystems of the island over the last 40 Myr has generated this biological richness is hampered by poorly documented species diversity and distributions. Here, we address both these issues through an integrative taxonomy and biogeographical approach using Hylophorbus, a New Guinea-endemic genus of frogs with 12 recognized species. We delimited candidate species by integrating mitochondrial DNA, nuclear DNA, and bioacoustics, then investigated their evolutionary history. Our results suggest that the current taxonomy of the genus misses true species diversity by ≥3.5-fold. Nevertheless, most candidate species (27) remain unconfirmed because of missing data, whereas five were identified unambiguously as undescribed (we describe three of these formally). Time-calibrated phylogenetic analyses suggest that Hylophorbus diversification began ~9 Mya in the northern or eastern portion of New Guinea. It would appear that lineages dispersed to new terrestrial habitats in the west, notably uplifted by the central range orogeny, until eventually reaching the Bird’s Head during the Mio-Pliocene (7–5 Mya). Conversely, a past barrier appears to have prevented north–south dispersal. These data suggest that new habitat availability has primarily driven the diversification of Hylophorbus.
Geometric morphometry enables species hypotheses testing and the assignment of historical type specimens in the genus Callirhinus Blanchard (Coleoptera: Scarabaeidae: Anomalini)
Authors: Ponce Andrés Ramírez , Caballero Santiago Zaragoza , Seidel Matthias 
Published: December 2023

Abstract
Assignation of old type specimens is important for nomenclatural stability, but when it comes to ancient specimens, the use of certain techniques is sometimes not appropriate, due to the condition or age of the specimen. In this study, the supposedly polymorphic and monotypic genus Callirhinus Blanchard was analysed with geometric morphometric techniques and photographs of the pronotum, with the purpose of identifying the locality of the old type specimen (19th century) and to test a priori defined hypothetical species by cumulation of evidence within an integrative taxonomic protocol using geometric morphometry, complemented by morphology and geographical discontinuity. Five morphotypes were defined a priori, and principal component, canonical variates analysis, and distances tests for the assignment of the type specimen based on canonical scores and Procrustes distances between means of groups were carried out. Statistical significance was found in four axes validating the species hypotheses, discovering that the type specimen belongs to the morphotype from Jalisco state. Additionally, a taxonomic treatment, the description of four new species, C. choperi Ramírez-Ponce & Zaragoza sp. nov., C. nanduRamírez-Ponce & Zaragoza sp. nov., C. huiinisRamírez-Ponce & Zaragoza sp. nov., and C. veemeRamírez-Ponce & Zaragoza sp. nov. , keys for the species determination, new distributional records, and a map are provided. The present work demonstrates that Geometric Morphometry is an adequate analytical tool that supports taxonomic identification at low cost and without damaging historical specimens.
Characterization of metabolic phenotypes and distinctive genes in mice with low‐weight gain
Authors: Nemoto Shino , Kubota Tetsuya , Ishikura Tomoyuki , Nakayama Manabu , Kobayashi Atsuo , Yazaki Junshi , Uchida Kazuyo , Matsuda Masashi , Kondo Takashi , Ohara Osamu , Koseki Haruhiko , Koyasu Shigeo , Ohno Hiroshi 
Published: December 2023

AbstractBeing overweight exacerbates various metabolic diseases, necessitating the identification of target molecules for obesity control. In the current study, we investigated common physiological features related to metabolism in mice with low weight gain: (1) G protein‐coupled receptor, family C, group 5, member B‐knockout; (2) gastric inhibitory polypeptide receptor‐knockout; and (3) Iroquois‐related homeobox 3‐knockout. Moreover, we explored genes involved in metabolism by analyzing differentially expressed genes (DEGs) between low‐weight gain mice and the respective wild‐type control mice. The common characteristics of the low‐weight gain mice were low inguinal white adipose tissue (iWAT) and liver weight despite similar food intake along with lower blood leptin levels and high energy expenditure. The DEGs of iWAT, epididymal (gonadal) WAT, brown adipose tissue, muscle, liver, hypothalamus, and hippocampus common to these low‐weight gain mice were designated as candidate genes associated with metabolism. One such gene tetraspanin 7 (Tspan7) from the iWAT was validated using knockout and overexpressing mouse models. Mice with low Tspan7 expression gained more weight, while those with high Tspan7 expression gained less weight, confirming the involvement of the Tspan7 gene in weight regulation. Collectively, these findings suggest that the candidate gene list generated in this study contains potential target molecules for obesity regulation. Further validation and additional data from low‐weight gain mice will aid in understanding the molecular mechanisms associated with obesity.
P-GRe : an efficient pipeline to maximised pseudogene prediction in plants/eucaryotes
Authors: Cabanac Sébastien , Dunand Christophe , Mathé Catherine 
Published: December 2023

ABSTRACTFormerly considered as part of “junk DNA”, pseudogenes are nowadays known for their role in the post-transcriptional regulation of functional genes. In addition, their identification allows a better understanding of gene evolution in the frame of multigenic families. Despite this, there is, to our knowledge, no fully automatic user-friendly software allowing the annotation of pseudogenes on a whole genome. Here, we present Pseudo-Gene Retriever (P-GRe), a fully automated pseudogene prediction software requiring only a genome sequence and its corresponding GFF annotation file. P-GRe detects the sequences of the pseudogenes on a whole genome and returns to the user all their genomic sequences and their pseudo-coding sequences. The ability of P-GRe to finely reconstruct the structure of pseudogenes also allow to obtain a set of proteins virtually encoded by the predicted pseudogenes. We show here that in 70% of the cases, virtual proteins constructed by P-GRe fromArabidopsis thalianaproteome and genome aligned better to their parent protein than their annotated counterpart.
Repeated Activation of Gαq by neurotransmitters causes age-dependent accumulation of stress granules inC.elegans
Authors: Rennie Madison , Scarlata Suzanne 
Published: December 2023

ABSTRACTGαq proteins mediate signals from neurotransmitters to transduce calcium signals. In PC12 cells, we have shown that Gαq stimulation results in retraction of neurites and induces the formation of stress granules that sequester two specific mRNAs,ChbgbandATP5f1b. Here, we show that repeated activation of Gαq inC. elegansadversely reduces lifespan potentially through accumulation of stress granules and inefficient recovery from neurite retraction. In the absence of stimulation, we could not detect significant changes in number of stress granules from Day 1-15 worms. Single Gαq activation increases stress granule size through the enlargement of pre-formed particles with younger worms (Day 1-4) being more responsive than older (Day 8). Repeated Gαq stimulation impacts the number of particles through the assembly of nascent particles. Additionally, we a systematic rise in the number of AGL-1 stress granules with repeated Gαq stimulation suggesting that stress granules accumulate in neurons and sequester mRNAs. This idea is supported by immunofluorescence studies of ATP5f1b as well as changes in peristaltic speed. In addition to stress granule accumulation, we find that repeated Gαq activation results in age-dependent morphological defects in mechanosensory neurons. Taken together, studies show that repeated Gαq activation negatively influences the health ofC.elegans.
Conserved N-terminal Regulation of the ACA8 Calcium Pump with Two Calmodulin Binding Sites
Authors: Larsen Sigrid Thirup , Dannersø Josephine Karlsen , Nielsen Christine Juul Fælled , Poulsen Lisbeth Rosager , Palmgren Michael , Nissen Poul 
Published: December 2023

AbstractThe autoinhibited plasma membrane calcium ATPase, ACA8 fromA. thalianahas an N-terminal autoinhibitory domain. Calcium-bound calmodulin binding at two sites located at residues 42-62 and 74-96 relieves autoinhibition of ACA8 activity.We investigated N-terminally truncated ACA8 constructs (WT, Δ20, Δ30, Δ35, Δ37, Δ40, Δ74 and Δ100) to explore the role of conserved motifs in the N-terminal segment preceding the calmodulin binding sites. Furthermore, we purified WT, Δ20- and Δ100-ACA8, tested activityin vitroand performed structural studies of purified Δ20-ACA8 stabilized in its native form to explore the mechanism of autoinhibition.Through activity studies and a yeast complementation assay, we show that an N-terminal segment between residues 20 and 35, upstream of the calmodulin binding sites, is important for autoinhibition and the activation by calmodulin, and that a conserved Phe32 is essential for autoinhibition. Cryo-EM structure determination at 3.3 Å resolution of a beryllium fluoride inhibited form shows no autoinhibition, but a low-resolution structure for an E1 state indicates autoinhibitory domain binding consistent with the mutational studies and AlphaFold predicted structures.
Transcriptomic analysis of N-terminal mutatedTrypanosoma cruziUBP1 knockdown underlines the importance of this RNA-binding protein in parasite development
Authors: Sabalette Karina B. , Campo Vanina A. , Sotelo-Silveira José R. , Smircich Pablo , De Gaudenzi Javier G. 
Published: December 2023

ABSTRACTDuring its life cycle, the human pathogen Trypanosoma cruzi must quickly adapt to different environments, in which the variation in the gene expression of the regulatory U-rich RNA-binding protein 1 (TcUBP1) plays a crucial role. We have previously demonstrated that the overexpression of TcUBP1 in insect-dwelling epimastigotes orchestrates an RNA regulon to promote differentiation to infective forms. In an attempt to generate TcUBP1 knockout parasites by using CRISPR-Cas9 technology, in the present study, we obtained a variant transcript that encodes a protein with 95% overall identity and a modified N-terminal sequence. The expression of this mutant protein, named TcUBP1mut, was notably reduced compared to that of the endogenous form found in normal cells. TcUBP1mut-knockdown epimastigotes exhibited normal growth and differentiation into infective metacyclic trypomastigotes and were capable of infecting mammalian cells. We analyzed the RNA-Seq expression profiles of these parasites and identified 276 up- and 426 downregulated genes with respect to the wildtype control sample. RNA-Seq comparison across distinct developmental stages revealed that the transcriptomic profile of these TcUBP1mut-knockdown epimastigotes significantly differs not only from that of epimastigotes in the stationary phase but also from the gene expression landscape characteristic of infective forms. This is both contrary to and consistent with the results of our recent study involving TcUBP1-overexpressing cells. Together, our findings demonstrate that the genes exhibiting opposite changes under overexpression and knockdown conditions unveil key mRNA targets regulated by TcUBP1. These mostly encompass transcripts that encode for trypomastigote-specific surface glycoproteins and ribosomal proteins, supporting a role for TcUBP1 in determining the molecular characteristics of the infective stage.
Assessment of phytoplanktonic community and abiotic parameters of Rana stream in Mandi district, Himachal Pradesh, India
Authors: Bains N. , Banyal H.S. 
Published: December 2023

AbstractThis research paper gives insight into the physico-chemical characteristics of the Rana stream located in the Mandi district of Himachal Pradesh, India, with a particular emphasis on the diversity of diatoms. During the course of this study, eight genera of phytoplankton were identified. Statistical analysis using Pearson correlation unveiled significant associations between the physicochemical parameters and the different groups of diatoms. To assess the diversity of phytoplankton within the stream, several diversity indices were employed. Highest diversity was observed during the month of February. Furthermore, the calculation of water quality indices for the Rana stream yielded values falling within the range of 47.34 to 59.01. This range signifies that the water quality within the Rana stream can be categorized according to the Water Quality Index (WQI) scale, spanning from “good” to “poor.” It is worth noting that the presence of a diverse assembly of pollution-tolerant diatoms such asFragilaria, Navicula, Gomphonema, andCymbella, particularly during the month of March, which coincided with the period of the poorest water quality, is indicative of the eutrophic nature of the stream.