bluuebunny/crossref_metadata_2025_split huggingface dataset:
LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins
Authors: Saba James A. , Huang Zixuan , Schole Kate L. , Ye Xianwen , Bhatt Shrey D. , Li Yi , Timp Winston , Cheng Jingdong , Green Rachel 
Published: November 2023

AbstractTerminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies implicate LARP1 in 40S- or 80S-ribosome complexes that repress and stabilize TOPs. However, a mechanistic understanding of how LARP1 and TOPs interact with these complexes to coordinate TOP outcomes is lacking. Here, we show that LARP1 senses the cellular supply of ribosomes by directly binding non-translating ribosomal subunits. Cryo-EM structures reveal a previously uncharacterized domain of LARP1 bound to and occluding the 40S mRNA channel. Free cytosolic ribosomes induce sequestration of TOPs in repressed 80S-LARP1-TOP complexes independent of alterations in mTOR signaling. Together, this work demonstrates a general ribosome-sensing function of LARP1 that allows it to tune ribosome protein synthesis to cellular demand.One-Sentence SummaryLARP1 directly binds free ribosomal subunits to repress TOP mRNAs
Serum Antibody Fingerprinting for SARS-CoV-2 Variants in Infected and Vaccinated Subjects by Label-Free Microarray Biosensor
Authors: Carzaniga Thomas , Casiraghi Luca , Nava Giovanni , Zanchetta Giuliano , Inzani Tommaso , Chiari Marcella , Bollati Valentina , Epis Sara , Bandi Claudio , Lai Alessia , Zehender Gianguglielmo , Bellini Tommaso , Buscaglia Marco 
Published: November 2023

ABSTRACTBoth viral infection and vaccination affect the antibody repertoire of a person. Here we demonstrate that the analysis of serum antibodies carries information not only on the virus type that caused the infection, but also on the specific virus variant. We developed a rapid multiplex assay providing a fingerprint of serum antibodies against five different SARS-CoV-2 variants, based on a microarray of virus antigens immobilized on the surface of a label-free reflectometric biosensor. We analyzed serum from plasma of convalescent subjects and vaccinated volunteers and extracted individual antibody profiles of both total immunoglobulin Ig and IgA fraction. We found that Ig level profiles were strongly correlated with the specific variant of infection or vaccination and that vaccinated subjects displayed larger quantity of total Ig and lower fraction of IgA relative to the population of convalescent unvaccinated subjects.
Newborn DNA methylation age differentiates long-term weight trajectory: The Boston Birth Cohort
Authors: Meir Anat Yaskolka , Wang Guoying , Hong Xiumei , Wang Xiaobin , Liang Liming 
Published: November 2023

AbstractBackgroundGestational age (GEAA) estimated by newborn DNA methylation (GAmAge) is associated with maternal prenatal exposures and immediate birth outcomes. However, the association of GAmAge with long-term overweight or obesity (OWO) trajectories is yet to be determined.MethodsGAmAge was calculated for 831 children from a US predominantly urban, low-income, multi-ethnic birth cohort using Illumina EPIC array and cord-blood DNA samples. Repeated anthropometric measurements aligned with pediatric primary care schedule allowed us to calculate body-mass-index percentiles (BMIPCT) at specific age and to define long-term weight trajectories from birth to 18 years.ResultsFour BMIPCT trajectory groups described the long-term weight trajectories: stable (consistent OWO: “early OWO”; constant normal weight: “NW”) or non-stable (OWO by year 1 of follow-up: “late OWO”; OWO by year 6 of follow-up: “NW to very late OWO”) BMIPCT. were used GAmAge was a predictor of long-term obesity, differentiating between group with consistently high BMIPCT and group with normal BMIPCT patterns and groups with late OWO development. Such differentiation can be observed in the age periods of birth to 1year, 3years, 6years, 10years, and 14years (p<0.05 for all; multivariate models adjusted for GEAA, maternal smoking, delivery method, and child’s sex). Birth weight was a mediator for the GAmAge effect on OWO status for specific groups at multiple age periods.ConclusionsGAmAge is associated with BMI trajectories from birth to age 18 years, independent of GEAA and birth weight. If further confirmed, GAmAge may serve as an early biomarker for future OWO risk.
Understanding Reach, Effectiveness, Adoption, Implementation, and Maintenance of home-based comprehensive sexual health care: a Realist Review
Authors: Goense Cornelia J.D. , Doan Thuan-Huong P. , Kpokiri Eneyi E. , Evers Ymke J. , Estcourt Claudia S. , Crutzen Rik , Klausner Jeffrey D. , Tang Weiming , Baraitser Paula , Hoebe Christian J.P.A. , Dukers-Muijrers Nicole H.T.M. 
Published: November 2023

ABSTRACTBackgroundTesting forhuman immunodeficiency virus(HIV) and sexually transmitted infections (STI) is increasingly offered outside a clinic-based setting. Among key populations barriers to accessing testing and sexual health care may could be lowered due to home-based testing and care services. This review identifies which elements of home-based comprehensive sexual health care (home-based CSH) impacted which key populations, under which circumstances.MethodsA realist review of studies focused on home-based CSH with at least self-sampling or self-testing HIV and additional sexual health care (e.g., treatment, counselling). PubMed, Embase, Cochrane Register of Controlled Trials, and PsycINFO databases were searched. Peer-reviewed quantitative and qualitative literature published between February 2012 and February 2023 was examined. The RE-AIM framework was used to systematically assess the (R) reach of key populations, (E) effectiveness of the intervention, and (AIM) effects on the adoption, implementation, and maintenance within routine sexual health care.ResultsOf 730 uniquely identified records, 92 were selected for extraction. Of these studies, 59% (54/92) reported actual interventions and 41% (38/92) described the acceptability and feasibility. Studies were mainly based in Europe or North America and were mostly targeted to MSM (59%; 55/92) (R). Overall, self-sampling or self-testing was highly acceptable across key populations. The effectiveness (E) of most studies was (expected) increased HIV testing. Adoption (A) of the home-based CSH was acceptable for care providers if linkage to care was available, even though a minority of studies reported adoption by care providers and implementation fidelity (I) of the intervention. In terms of maintenance (M), home-based CSH should be institutionalised and complementary to clinic-based sexual health care.ConclusionsFive key findings were identified which may enhance implementation of home-based CSH. When providing the individual with a choice of testing, clear instructions, and tailored dissemination successful uptake of HIV testing may increase. For implementers perceived care and treatment benefits for clients may increase their willingness to implement home-based CSH. Therefore, home-based CSH may determine more accessible sexual health care and increased uptake of HIV testing among key populations.
Incidence and Predictors of In-stent Restenosis Following Intervention for Pulmonary Vein Stenosis due to Fibrosing Mediastinitis
Authors: Jia Mengfei , Su Hongling , Jiang Kaiyu , Wang Aqian , Guo Zhaoxia , Zhu Hai , Zhang Fu , Xin Pan , Cao Yunshan 
Published: November 2023

AbstractBackgroundPercutaneous transluminal pulmonary venoplasty (PTPV) is an emerging treatment for pulmonary vein stenosis (PVS) caused by fibrosing mediastinitis (FM). However, the incidence and predictors of in-stent restenosis (ISR) are elusive. We sought to identify the predictors of ISR in patients with PVS caused by extraluminal compression due to FM.MethodsWe retrospectively enrolled patients with PVS-FM who underwent PTPV between July 1, 2018, and December 31, 2022. According to ISR status, patients were divided into two groups: the ISR group and the non-ISR group. Baseline characteristics (demographics and lesions) and procedure-related information were abstracted from patient records and analyzed. Univariate and multivariate analyses were performed to determine the predictors of ISR.ResultsA total of 142 stents were implanted in 134 PVs of 65 patients with PVS-FM. Over a median follow-up of 6.6 (3.4-15.7) months, 61 of 134 PVs suffered from ISR. Multivariate analysis demonstrated a significantly lower risk of ISR in PVs with a larger reference vessel diameter (RVD) (odds ratio (OR): 0.79; 95% confidence interval [CI]: 0.64 to 0.98;P=0.032), and stenosis of the corresponding pulmonary artery (Cor-PA) independently increased the risk of restenosis (OR: 3.41; 95% CI: 1.31 to 8.86;P=0.012). The cumulative ISR was 6.3%, 21.4%, and 39.2% at the 3-, 6-, and 12-month follow-ups, respectively.ConclusionISR is very high in PVS-FM, which is independently associated with RVD and Cor-PA stenosis.Central illustrationBased on the constructed prediction model, the RVD and stenosis of Cor-PA were found to be independently associated with ISR, and their sensitivity and optimal cutoff values for the prediction of restenosis are shown in (a) and (b), respectively. The risk of ISR significantly increased when PA stenosis occurred; the risk of restenosis decreased significantly when the RVD was larger than 8.4 mm.
Identification of novel tail-anchored membrane proteins integrated by the bacterial twin-arginine translocase
Authors: Gallego-Parrilla José Jesús , Severi Emmanuele , Chandra Govind , Palmer Tracy 
Published: November 2023

ABSTRACTThe twin arginine protein transport (Tat) system exports folded proteins across the cytoplasmic membranes of prokaryotes and the energy transducing membranes of plant thylakoids and mitochondria. Proteins are targeted to the Tat machinery by N-terminal signal peptides with a conserved twin arginine motif, and some substrates are exported as heterodimers where the signal peptide is present on one of the partner proteins. A subset of Tat substrates is found in the membrane. Tat-dependent membrane proteins usually have large globular domains and a single transmembrane helix present at the N- or C-terminus. Five Tat substrates that have C-terminal transmembrane helices have previously been characterised in the model bacteriumEscherichia coli. Each of these is an iron-sulphur cluster-containing protein involved in electron transfer from hydrogen or formate. Here we have undertaken a bioinformatic search to identify further tail-anchored Tat substrates encoded in bacterial genomes. Our analysis has revealed additional tail-anchored iron-sulphur proteins associated in modules with either ab-type cytochrome or a quinol oxidase. We also identified further candidate tail-anchored Tat substrates, particularly among members of the actinobacterial genus, that are not predicted to contain cofactors. Using reporter assays we show experimentally that six of these have both N-terminal Tat signal peptides and C-terminal transmembrane helices. The newly-identified proteins include a carboxypeptidase and a predicted protease, and four sortase substrates for which membrane integration is a pre-requisite for covalent attachment to the cell wall.
Association cortical areas in the mouse contain a large population of fast-spiking GABAergic neurons that do not express parvalbumin
Authors: Courcelles Erik Justin , Kjelsberg Kasper , Convertino Laura , Nair Rajeevkumar Raveendran , Witter Menno P. , Nigro Maximiliano José 
Published: November 2023

AbstractGABAergic neurons represent 10-15% of the neuronal population of the cortex but exert a powerful control over information flow in cortical circuits. The largest GABAergic class in the neocortex is represented by the parvalbumin-expressing (PV-INs) fast-spiking neurons, which provide powerful somatic inhibition to their postsynaptic targets. Recently, the density of PV-INs has been shown to be lower in associative areas of the mouse cortex as compared to sensory and motor areas. Modeling work based on these quantifications linked the low-density of PV-INs with specific computations of associative cortices. However, it is still unknown whether the total GABAergic population of association cortices is smaller or whether another GABAergic type can compensate for the low density of PV-INs. In the present study we investigated these hypotheses using a combination of neuroanatomy, mouse genetics and neurophysiology. We found that the GABAergic population of association areas is comparable to that of primary sensory areas, and it is enriched of fast-spiking neurons that do not express PV and were not accounted for by previous quantifications. We developed an intersectional viral strategy to demonstrate that the synaptic output of fast-spiking neurons is comparable across cortical regions. Our results provide quantifications of the density and output strength of fast-spiking GABAergic neurons and offers new biological constrains to refine current models of cortical computations.
Apobec-Mediated Retroviral HypermutationIn Vivois Dependent on Mouse Strain
Authors: Byun Hyewon , Singh Gurvani B. , Xu Wendy Kaichun , Das Poulami , Reyes Alejandro , Battenhouse Anna , Wylie Dennis C. , Lozano Mary M. , Dudley Jaquelin P. 
Published: November 2023

AbstractReplication of the complex retrovirus mouse mammary tumor virus (MMTV) is antagonized by murine Apobec3 (mA3), a member of the Apobec family of cytidine deaminases. We have shown that MMTV-encoded Rem protein inhibits proviral mutagenesis by the Apobec enzyme, activation-induced cytidine deaminase (AID) during viral replication in BALB/c mice. To further study the role of Remin vivo, we have infected C57BL/6 (B6) mice with a superantigen-independent lymphomagenic strain of MMTV (TBLV-WT) or a mutant strain (TBLV-SD) that is defective in Rem and its cleavage product Rem-CT. Unlike MMTV, TBLV induced T-cell tumors in µMT mice, indicating that mature B cells, which express the highest AID levels, are not required for TBLV replication. Compared to BALB/c, B6 mice were more susceptible to TBLV infection and tumorigenesis. The lack of Rem expression accelerated B6 tumorigenesis at limiting doses compared to TBLV-WT in either wild-type B6 or AID-deficient mice. However, unlike proviruses from BALB/c mice, high-throughput sequencing indicated that proviral G-to-A or C-to-T changes did not significantly differ in the presence and absence of Rem expression.Ex vivostimulation showed higher levels of mA3 relative to AID in B6 compared to BALB/c splenocytes, but effects of agonists differed in the two strains. RNA-Seq revealed increased transcripts related to growth factor and cytokine signaling in TBLV-SD-induced tumors relative to those from TBLV-WT, consistent with a third Rem function. Thus, Rem-mediated effects on tumorigenesis in B6 mice are independent of Apobec-mediated proviral hypermutation.
A Novel Tiled-Amplicon Sequencing Assay Targeting theTomato Brown Rugose Fruit Virus(ToBRFV) Genome Reveals Widespread Distribution in Municipal Wastewater Treatment Systems in the Province of Ontario, Canada
Authors: Nash Delaney , Ellmen Isaac , Knapp Jennifer J. , Menon Ria , Overton Alyssa K. , Cheng Jiujun , Lynch Michael D.J. , Nissimov Jozef I. , Charles Trevor C. 
Published: November 2023

AbstractTomato Brown Rugose Fruit Virus(ToBRFV) is a plant pathogen that infects importantSolanaceaecrop species and can dramatically reduce tomato crop yields. TheToBRFVhas rapidly spread around the globe due to its ability to escape detection by antiviral host genes, most notablyTm-22, which are used to confer resistance to otherTobamovirusesin tomato plants. Development of robust and reproducible methods for detecting viruses in the environment aids in the tracking and reduction of pathogen transmission. We detectedToBRFVin municipal wastewater influent (WWI) samples, likely due to its presence in human waste, demonstrating a widespread distribution ofToBRFVin WWI throughout Ontario, Canada. To aid in globalToBRFVsurveillance efforts, we developed a tiled-amplicon approach to sequence and track the evolution ofToBRFVgenomes in municipal WWI. Our assay recovers 97.5% of the 6393 bpToBRFVRefSeq genome, omitting the terminal 5’ and 3’ ends. We demonstrate that our sequencing assay is a robust, sensitive, and highly specific method for recoveringToBRFVgenomes. OurToBRFVassay was developed using existing ARTIC Network resources, which includes genome specific primer design, sequencing library prep, and read analysis. Additionally, we adapted our lineage abundance estimation tool, Alcov, to estimate the abundance ofToBRFVclades in samples.
Obtaining Actigraphy Sleep Report Using Garmin Wearable Devices and Labfront App
Authors: Hsu Chang Francis , Huang Han-Ping , Peng Chris , Masys Jordan , Ahn Andrew C. 
Published: November 2023

AbstractIn a collaborative effort between Labfront and Garmin, an actigraphy-based sleep analysis report has been developed for Garmin’s consumer-grade wearable devices, accessible via the Labfront application. Comparative analyses against established medical-grade actigraphic devices, namely Actiwatch-2 and Motionlogger, demonstrate notable concordance in key performance indicators. Specifically, the Garmin device yielded a sensitivity of over 95% for sleep detection, a specificity of over 80% for wake detection, and an overall accuracy exceeding 95%.The study introduces a transparent methodology for deriving sleep metrics from acceleration data, thereby addressing a current gap in the literature regarding consumer-grade actigraphy solutions. Additionally, the system allows for individual customization of sleep/wake detection parameters, offering adaptability to specific user conditions. These findings suggest that consumer-grade wearable devices may serve as viable alternatives to medical-grade actigraphs for sleep analysis, without sacrificing analytical rigor.
Neutron crystallographic refinement with REFMAC5 from the CCP4 suite
Authors: Catapano Lucrezia , Long Fei , Yamashita Keitaro , Nicholls Robert A. , Steiner Roberto A. , Murshudov Garib N. 
Published: November 2023

Hydrogen (H) atoms are abundant in macromolecules and often play critical roles in enzyme catalysis, ligand-recognition processes and protein–protein interactions. However, their direct visualization by diffraction techniques is challenging. Macromolecular X-ray crystallography affords the localization of only the most ordered H atoms at (sub-)atomic resolution (around 1.2 Å or higher). However, many H atoms of biochemical significance remain undetectable by this method. In contrast, neutron diffraction methods enable the visualization of most H atoms, typically in the form of deuterium (2H) atoms, at much more common resolution values (better than 2.5 Å). Thus, neutron crystallography, although technically demanding, is often the method of choice when direct information on protonation states is sought. REFMAC5 from the Collaborative Computational Project No. 4 (CCP4) is a program for the refinement of macromolecular models against X-ray crystallographic and cryo-EM data. This contribution describes its extension to include the refinement of structural models obtained from neutron crystallographic data. Stereochemical restraints with accurate bond distances between H atoms and their parent atom nuclei are now part of the CCP4 Monomer Library, the source of prior chemical information used in the refinement. One new feature for neutron data analysis in REFMAC5 is refinement of the protium/deuterium (1H/2H) fraction. This parameter describes the relative 1H/2H contribution to neutron scattering for hydrogen isotopes. The newly developed REFMAC5 algorithms were tested by performing the (re-)refinement of several entries available in the PDB and of one novel structure (FutA) using either (i) neutron data only or (ii) neutron data supplemented by external restraints to a reference X-ray crystallographic structure. Re-refinement with REFMAC5 afforded models characterized by R-factor values that are consistent with, and in some cases better than, the originally deposited values. The use of external reference structure restraints during refinement has been observed to be a valuable strategy, especially for structures at medium–low resolution.
Foreign bank presence and inclusive growth in Africa: the moderating role of financial development
Authors: Iddrisu Khadijah , Abor Joshua Yindenaba , Banyen Thadious Kannyiri 
Published: November 2023

PurposeThe purpose of this study is to assess the extent to which the nexus between foreign bank presence (FBP) and inclusive growth is being impacted by the financial development.Design/methodology/approachThe study used a two-stage system generalized method of moment (GMM), using 28 African countries from the period 2000 to 2018.FindingsThe study found a positive effect of FBP on inclusive growth. While financial development magnifies the positive effect of FBP, inclusive growth nexus, it has a direct effect on inclusive growth.Practical implicationsFor Africa to ascertain the positive effect of FBP on inclusive growth, financial system must be developed to reduce the cream-skim behavior of foreign banks.Originality/valueThis paper assess the extent to which developing economy's developed financial system form synergies with FBP to further enhance the inclusiveness of growth.
Social housing development: a case study in Bac Ninh province, Vietnam
Authors: Dinh Trung Nguyen , Phuong Nam Pham 
Published: November 2023

Purpose
This paper aims to assess the overall social housing development, point out factors affecting it and propose some policy implications for social housing development.

Design/methodology/approach
The research investigated investors, credit institutions and officials involved in social housing development. Bac Ninh province currently has 51 social housing projects that have been and are being implemented. The hypothetical regression model has seven latent variables and is tested by the criteria through the SPSS25.0 software.

Findings
There are 29 factors belonging to seven groups affecting housing development. Their impact rates range from 3.47% to 30.25%.

Research limitations/implications
The study has only identified the factors affecting social housing development but has not undertaken an in-depth assessment of its development status and forecast for the future. Therefore, this gap needs to be further studied. The proposed research method could also be applied when researching social housing developments in other countries around the world.

Practical implications
To develop social housing to meet the needs of the real estate market, it is necessary to improve the policies that have the strongest impact first. Then, it is necessary to improve the factors with a smaller impact.

Social implications
The study proposes policy implications for faster housing development for low-income people that improve their living standards.

Originality/value
To the best of the authors’ knowledge, the paper has studied for the first time social housing development and the factors affecting it. The paper also shows the level of their impact so that priority policies can be applied to each factor.