bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering the diversity of heterotrophic culturable bacteria within the gut of bay scallopArgopecten purpuratus(Lamarck, 1819) from two geographically distant natural banks
Authors: Serrano Wilbert , Tarazona-Janampa Ulrike I. , Olaechea Raul M. , Valle Sonia 
Published: December 2023

ABSTRACTWe study the bacterial diversity within the gut of the peruvian bay scallopArgopecten purpuratus(Lamarck, 1819) (Mollusca: Pectinidae) collected from two shellfish growing areas in Independence Bay (IB) and Sechura Bay (SB) in Peru. This work aimed to identify isolates of culturable gut-associated microbiota ofA. purpuratusthrough repetitive sequence-based PCR (rep-PCR) and 16S rRNA gene sequences comparison. A total of 20 healthy adult scallops were collected from each location twice, in spring and autumn, 2015 and 2016, respectively.Fecal pellets from the distal intestinal tract of each individual were extracted, and after pooling, samples were cultivated on general and selective media following standard culture conditions. In order to prevent duplicate sequencing of the ribosomal 16S rRNA gene sequences of the isolates, a pre-screened step by (rep-PCR) amplification utilizing BOXA1R primer was performed, then isolates showing different banding profiles were selected for further sequencing.Taxonomic distribution based on the 16S rRNA gene comparison of selected strains placed isolates from IB and SB into 29 and 27 different genera, representing 50 and 42 species, respectively. The major proportions of bacterial species found in IB corresponded to the division Firmicutes (46%), whereas the Proteobacteria and Firmicutes were almost equally distributed in (SB) with 38 and 43% respectively. Remarkable, (IB) showed a high number (28%) and diversity of species within the division Actinobacteria compared to (SB); while the speciesSalinimicrobiumsp. of the division Flavobacteria was isolated only in (SB).Common species in both areas are mainly related to the genusBacillus,while strains of speciesVibrio alginolyticusandV. parahaemoliticuswere common representatives of the Proteobacteria. The intestinal tract ofA. purpuratusmay represent an uninvestigated niche for analyzing the structure of new complex microbial communities. This study showed that the diversity of culturable microbiota within the gut of two populations ofA. purpuratusis significantly different at each location.
FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Datasets Built on FragPipe
Authors: Manriquez-Sandoval Edgar , Brewer Joy , Lule Gabriela , Lopez Samanta , Fried Stephen D. 
Published: December 2023

AbstractHere, we present FLiPPR, or FragPipe LiP (limited proteolysis) Processor, a tool that facilitates the analysis of data from limited proteolysis mass spectrometry (LiP-MS) experiments following primary search and quantification in FragPipe. LiP-MS has emerged as a method that can provide proteome-wide information on protein structure and has been applied to a range of biological and biophysical questions. Although LiP- MS can be carried out with standard laboratory reagents and mass spectrometers, analyzing the data can be slow and poses unique challenges compared to typical quantitative proteomics workflows. To address this, we leverage the fast, sensitive, and accurate search and label-free quantification algorithms in FragPipe and then process its output in FLiPPR. FLiPPR formalizes a specific data imputation heuristic that carefully uses missing data in LiP-MS experiments to report on the most significant structural changes. Moreover, FLiPPR introduces a new data merging scheme (from ions to cut-sites) and a protein-centric multiple hypothesis correction scheme, collectively enabling processed LiP-MS datasets to be more robust and less redundant. These improvements substantially strengthen statistical trends when previously published data are reanalyzed with the FragPipe/FLiPPR workflow. As a final feature, FLiPPR facilitates the collection of structural metadata to identify correlations between experiments and structural features. We hope that FLiPPR will lower the barrier for more users to adopt LiP-MS, standardize statistical procedures for LiP-MS data analysis, and systematize output to facilitate eventual larger-scale integration of LiP-MS data.
COVID-19 vaccination uptake among healthcare workers in Ghana: A comprehensive analysis of knowledge, attitude, perceived vaccine effectiveness, and health belief model constructs
Authors: Mbele Whiteson , Dako-Gyeke Phyllis , Frans Andreas Ndapewa 
Published: December 2023

AbstractThe novel Coronavirus Disease 19 (COVID-19) caused devastating effects globally, and healthcare workers were among the most affected by the pandemic. To mitigate this impact, healthcare workers were prioritized in COVID-19 vaccination globally and in Ghana. However, hesitancy by healthcare workers to receive the vaccination resulted in delayed control of the pandemic. In Ghana, vaccine acceptance rate among healthcare workers was estimated to be 39.3% in the pre-vaccine rollout period. Consequently, this study assessed uptake of COVID-19 vaccination and associated factors among healthcare workers in Ghana in the post-vaccine roll-out period.This was an analytical cross-sectional study that used a semi-structured questionnaire to collect data on COVID-19 vaccination uptake and influencing factors from randomly selected 256 healthcare workers in Ayawaso West Municipality, Ghana. Bivariable and Multivariable logistic regression was performed using IBM SPSS version 22 to identify predictors of vaccine uptake and a statistical significance was declared at p<0.05.More than three-fourths of participants 220 (85.9%) had received at least one dose of the COVID-19 vaccination, while 36 (14.9%) were hesitant. More than half 139 (54.3%) had adequate knowledge about COVID-19 vaccination and the majority 188 (73.4%) had positive perceptions about its effectiveness. Moreover, 218 (85.2%) of HCWs had a positive attitude towards COVID-19 vaccination. Positive attitude towards COVID-19 vaccination (AOR = 4.3; 95% CI: 1.4, 13.0) and high cues to action (AOR = 5.7; 95% CI: 2.2, 14.8) were the factors that significantly predicted uptake of COVID-19 vaccination among healthcare workers.COVID-19 vaccination among HCWs in Ghana is promising. However, hesitancy to receive the vaccination among a significant proportion of HCWs raises concerns. To ensure vaccination of all healthcare workers, interventions to promote vaccination should target key determinants of vaccination uptake, such as attitude towards the vaccination and cues to action.
Breast and cervical cancer screening among women at reproductive age in Cambodia: A Secondary Analysis of Cambodia Demographic and Health Survey 2022
Authors: Um Samnang , Sopheab Heng 
Published: December 2023

AbstractBreast and cervical cancers are the most prevalent diagnosed in women worldwide, significantly contributing to maternal morbidity and mortality. We examined socio-demographic and behavioral factors associated with breast and cervical cancer screening among Cambodian women aged 15-49 years old. We analyzed women’s data from the 2022 Cambodia Demographic and Health Survey (CDHS). In total, 19,496 women were interviewed. Multiple logistic regression was performed using STATA V17 to examine factors associated with breast and cervical cancer screening. The proportion of breast and cervical cancer screenings was 10.6% and 15.3%, respectively. After being adjusted, factors independently associated with breast cancer screening included age group 20-29 years [AOR=2.51; 95% CI: 1.55-4.06], 30-39 years [AOR=4.34; 95% CI: 2.66-7.09], and 40-49 years [AOR=4.66; 95% CI: 2.81-7.71], higher education [AOR=1.92; 95% CI: 1.26-2.93], exposure media [AOR=1.66; 95% CI: 1.32-2.10], and rich wealth quintile [AOR=1.50; 95% CI: 1.25-1.80]. Similarly, the odds of having cervical cancer screening were age group 20-29 years [AOR=2.88; 95% CI: 1.76-4.71], 30-39 years [AOR=5.94; 95% CI: 3.58-9.83], and 40-49 years [AOR=7.61; 95% CI: 4.55-12.73], higher education [AOR=1.55; 95% CI: 1.55-2.73], exposure media [AOR=1.62; 95% CI: 1.35,1.95], and rich wealth quintile [AOR=2.14; 95% CI: 1.78-2.58]. In conclusion, this study shows the low screening proportion for both breast and cervical cancers, and it also highlights that socio-economic factors are significantly important in determining the health care seeking for these two main cancer screening services among women aged 15-49 years in Cambodia. Therefore, increase of exposure media with health education focusing on these cancer screenings should be made better accessible to women, particularly those of low socio-economic status.
Determinants of timely administration of the birth dose of hepatitis B vaccine in Senegal in 2019: Secondary analysis of the demographic and health survey
Authors: Bassoum Oumar , Ba Mouhamadou Faly , Sougou Ndeye Mareme , Sow Adama , Seck Ibrahima 
Published: December 2023

AbstractIn developing countries, hepatitis B is spread primarily by the perinatal or horizontal route. Thus, the Senegalese government recommends administering the birth dose of the hepatitis B vaccine (HepB0) within 24 hours of birth. The objective was to identify the determinants of timely administration of HepB0 in Senegal in 2019. A secondary analysis of the demographic and health survey was carried out. The study population consisted of children aged 12 to 23 months. A cluster survey, stratified in urban and rural areas, drawn at two stages, was carried out. Individual interviews were conducted. Logistic regression was applied to estimate the adjusted odds ratio (aOR) and their 95% confidence interval. In total, 1130 children were included. Among them, 48.1% were born to mothers aged 25 to 34, 46.8% were male and 82.6% were born in health facilities. The average time between birth and HepB0 administration was 13.1±46.6 days. Among 747 children vaccinated, only 65.2% were vaccinated within 24 hours of birth. The determinants were maternal age of at least 35 years (aOR= 2.03 [1.29 – 3.20]), primary education of the mother (aOR=1.94 [1.13 – 3. 35]), at least four antenatal care (aOR=1.74 [1.12 – 2.69]), belonging to the central (ORa=0.22 [0.11 – 0.44]) and northern regions (aOR= 0.18 [0.08 – 0.40]), and delivery in a health facility (aOR=3.42 [1.90 – 6.15]). Education and keeping girls in school, local postnatal care in hard-to-reach regions, promotion of antenatal acre and delivery in a health facility should improve the timeliness of HepB0 vaccination.
Awareness, Attitude, and Perception of Telemedicine Among Trinidad and Tobago Population
Authors: Ezinne Ngozika Esther , Bhattarai Dipesh , Anyasodor Anayochukwu Edward , Antwi-Adjei Ellen K. , Ekemiri Kingsley Kene , Armitage James Andrew , Osuagwu Uchechukwu Levi 
Published: December 2023

AbstractAimTo assess the awareness, attitude and perception of Trinidad and Tobago population towards telemedicineMethodA cross-sectional study was conducted using a structured questionnaire on patients that visited health centres in the North Central region. A systematic random sampling method was used to select participants. Descriptive statistics including mean and standard deviation were used to calculate categorical and continuous variables. Comparison between the categorical groups of the demographic variables for each of the three main outcome variables were analysed through one-way analysis of variance (ANOVA). Statistical significance was defined as P<0.05.ResultsA total of 528 participated in the study. Most (60%) of them were female, and aged 21 to 40 years (62.1%). Awareness of telemedicine was 34.4%, but the majority (82.5%) had never used telemedicine before. About half (51.3%) acknowledged the necessity of telemedicine but few (36.4%) were satisfied with the services. Most (64%) were willing to try mobile-based healthcare apps. Concerns over lack of familiarity with telemedicine platforms (44.5%) and result accuracy (15.5%) were the major barriers to using telemedicine. Awareness of telemedicine was significantly associated with being female (P < 0.001), a medical profession (P = 0.004), familiarity in use of computers (P = 0.004) and frequent interaction with doctors online (P < 0.001). Positive attitude towards telemedicine was associated with having a diploma, being a medical professional, being computer literate and frequent interaction with doctor online. Positive perception towards telemedicine was associated with marital status (Single or Previously Married) (P = 0.011), one’s ability to use the computer (P = 0.009), their level of competency in computer usage (P = 0.002), and frequency of interacting with doctors online (P < 0.002).ConclusionThe study revealed that although the level of telemedicine awareness is low, the majority of respondents demonstrated positive attitude and perception towards telemedicine. The findings suggest the need to educate the public on the benefits of telemedicine and create awareness of its use in T&T.
Perception of butenolides byBacillus subtilisvia the α/β-hydrolase RsbQ
Authors: Melville Kim T , Kamran Muhammad , Yao Jiaren , Costa Marianne , Holland Madeleine , Taylor Nicolas L , Fritz Georg , Flematti Gavin R , Waters Mark T 
Published: December 2023

SummaryThe regulation of behavioural and developmental decisions by small molecules is common to all domains of life. In plants, strigolactones and karrikins are butenolide growth regulators that influence several aspects of plant growth and development, as well as interactions with symbiotic fungi1–3. DWARF14 (D14) and KARRIKIN INSENSITIVE2 (KAI2) are homologous receptors that perceive strigolactones and karrikins, respectively, and that hydrolyse their ligands to effect signal transduction4–7. RsbQ, a homologue of D14 and KAI2 from the Gram-positive bacteriumBacillus subtilis, regulates growth responses to nutritional stress via the alternative transcription factor SigmaB (σB)8,9. However, the molecular function of RsbQ is unknown. Here we show that RsbQ perceives butenolide compounds that are bioactive in plants. RsbQ is thermally destabilised by the synthetic strigolactone GR24 and its desmethyl butenolide equivalent dGR24. We show that, like D14 and KAI2, RsbQ is a functional butenolide hydrolase that undergoes covalent modification of the catalytic histidine residue. Exogenous application of both GR24 and dGR24 inhibited the endogenous signalling function of RsbQin vivo, with dGR24 being 10-fold more potent. Application of dGR24 toB. subtilisphenocopied loss-of-functionrsbQmutations and led to a significant down-regulation of σB-regulated transcripts. We also discovered that exogenous butenolides promoted the transition from planktonic to biofilm growth. Our results suggest that butenolides may serve as inter-kingdom signalling compounds between plants and bacteria to help shape rhizosphere communities.
Control of asparagine homeostasis inBacillus subtilis: Identification of promiscuous amino acid importers and exporters
Authors: Meißner Janek , Königshof Manuel , Wrede Katrin , Warneke Robert , Mardoukhi Mohammad Saba Yousef , Commichau Fabian M. , Stülke Jörg 
Published: December 2023

ABSTRACTAmino acids are the main building block for proteins. The Gram-positive model bacteriumB. subtilisis able to import all proteinogenic amino acids from the environment as well as to synthesize them. However, the players involved in the acquisition of asparagine have not yet been identified for this bacterium. In this work, we used D-asparagine as a toxic analog of L-asparagine to identify asparagine transporters. This revealed that D-but not L-asparagine is taken up by the malate/lactate antiporter MleN. Specific strains that are sensitive to the presence of L-asparagine due to the lack of the second messenger cyclic di-AMP or due to the intracellular accumulation of this amino acid were used to isolate and characterize suppressor mutants that were resistant to the presence of otherwise growth-inhibiting concentrations of L-asparagine. These screens identified the broad-spectrum amino acid importers AimA and BcaP as responsible for the acquisition of L-asparagine. The amino acid exporter AzlCD allows detoxification of L-asparagine in addition to 4-azaleucine and histidine. This work supports the idea that amino acids are often transported by promiscuous importers and exporters. However, our work also shows that even stereo-enantiomeric amino acids do not necessarily use the same transport systems.IMPORTANCETransport of amino acid is a poorly studied function in many bacteria, including the model organismBacillus subtilis. The identification of transporters is hampered by the redundancy of transport systems for most amino acids as well as by the poor specificity of the transporters. Here, we apply several strategies to use the growth-inhibitive effect of many amino acids under defined conditions to isolate suppressor mutants that exhibit either reduced uptake or enhanced export of asparagine, resulting in the identification of uptake and export systems for L-asparagine. The approaches used here may be useful for the identification of transporters for other amino acids both inB. subtilisand other bacteria as well.
Excess fermentation and lactic acidosis as detrimental functions of the gut microbes in treatment-naive TB patients
Authors: Yunusbaeva Milyausha , Borodina Liliya , Terentyeva Darya , Bogdanova Anna , Zakirova Aigul , Bulatov Shamil , Altinbaev Radick , Bilalov Fanil , Yunusbayev Bayazit 
Published: December 2023

AbstractGut microbiota link to host immunity motivated numerous studies of the gut microbiome in tuberculosis (TB) patients. However, these studies did not explore the metabolic capacity of the gut community, which is a key axis of impact on the host’s immunity. We used deep sequencing of fecal samples from 23 treatment-naive TB patients and 48 healthy donors to reconstruct the metabolic capacity and strain/species-level content of the gut microbiome. We show that the strong taxonomic divergence of the gut community in TB patients is explained by the systematic depletion of the commensal flora of the large intestine,Bacteroidetes,and an increase inActinobacteria, Firmicutes, andProteobacteriasuch asStreptococcaceae, Erysipelotrichaceae, Lachnospiraceae,andEnterobacteriaceae.The cumulative expansion of diverse disease-associated pathobionts in patients reached 1/4 of the total gut microbiota, suggesting a heavy toll on host immunity along with MTB infection. Reconstruction of metabolic pathways showed that the microbial community in patients shifted toward rapid growth using glycolysis and excess fermentation to produce acetate and lactate. Higher glucose availability in the intestine likely drives fermentation to lactate and growth, causing acidosis and endotoxemia. Excessive fermentation and lactic acidosis are likely characteristics of TB patients’ disturbed gut microbiomes. Since lactic acidosis strongly suppresses the normal gut flora, directly interferes with macrophage function, and is linked to mortality in TB patients, our findings highlight gut lactate acidosis as a novel research focus and a potential host-directed treatment target that can augment traditional TB treatment.
Adenosine Kinase regulates Sleep Timing and the Homeostatic Sleep Response through Distinct Molecular Pathways
Authors: Wakaf Zeinab , Dang Quang , Ru Yining , Taylor Lewis , Kapoor Sejal , Vasudevan idhar , Dallmann Robert , Jagannath Aarti 
Published: December 2023

AbstractSleep behaviour is broadly regulated by two drives, the circadian (Process C), which is orchestrated by the suprachiasmatic nuclei (SCN), and controls sleep timing, and the homeostatic (Process S), which controls sleep amount and the response to sleep deprivation (Borbélyet al., 2016). However, the molecular pathways that mediate their independent effects, and their interactions remain unclear. Adenosine is an important integrator of both processes (Bjorness & Greene, 2009; Jagannathet al., 2021, 2022), such that adenosine levels track and modulate wakefulness, whilst adenosine signalling inhibits the circadian response to light. Therefore, we studied the sleep/circadian behaviour, and cortical and SCN transcriptomic profiles of a mouse model overexpressing Adenosine Kinase (Adk-Tg) (Fedeleet al., 2005), (Palchykovaet al., 2010). We found that overall, the Adk-Tg mouse slept less and showed lower amplitude circadian rhythms with an altered sleep/wake distribution across the 24h day, which correlated with changes in transcription of synaptic signalling genes that would shift the excitatory/inhibitory balance. In addition, the Adk-Tg mouse showed a reduced level of ERK phosphorylation, and attenuation of DNA repair related pathways. After sleep deprivation, however, the Adk-Tg mouse significantly increased relative to wildtype, immediate early gene expression levels including ofArc, but paradoxically reduced ERK phosphorylation. Thus, baseline sleep levels and timing are regulated by ERK signalling, whereas the response to sleep loss is mediated by the alteration of the transcriptomic landscape independently of ERK.
#GotGlycans: Role of N343 Glycosylation on the SARS-CoV-2 S RBD Structure and Co-Receptor Binding Across Variants of Concern
Authors: Ives Callum M. , Nguyen Linh , Fogarty Carl A. , Harbison Aoife M. , Durocher Yves , Klassen John S. , Fadda Elisa 
Published: December 2023

AbstractGlycosylation of the SARS-CoV-2 spike (S) protein represents a key target for viral evolution because it affects both viral evasion and fitness. Successful variations in the glycan shield are difficult to achieve though, as protein glycosylation is also critical to folding and to structural stability. Within this framework, the identification of glycosylation sites that are structurally dispensable can provide insight into the evolutionary mechanisms of the shield and inform immune surveillance. In this work we show through over 45 μs of cumulative sampling from conventional and enhanced molecular dynamics (MD) simulations, how the structure of the immunodominant S receptor binding domain (RBD) is regulated byN-glycosylation at N343 and how this glycan’s structural role changes from WHu-1, alpha (B.1.1.7), and beta (B.1.351), to the delta (B.1.617.2) and omicron (BA.1 and BA.2.86) variants. More specifically, we find that the amphipathic nature of theN-glycan is instrumental to preserve the structural integrity of the RBD hydrophobic core and that loss of glycosylation at N343 triggers a specific and consistent conformational change. We show how this change allosterically regulates the conformation of the receptor binding motif (RBM) in the WHu-1, alpha and beta RBDs, but not in the delta and omicron variants, due to mutations that reinforce the RBD architecture. In support of these findings, we show that the binding of the RBD to monosialylated ganglioside co-receptors is highly dependent on N343 glycosylation in the WHu-1, but not in the delta RBD, and that affinity changes significantly across VoCs. Ultimately, the molecular and functional insight we provide in this work reinforces our understanding of the role of glycosylation in protein structure and function and it also allows us to identify the structural constraints within which the glycosylation site at N343 can become a hotspot for mutations in the SARS-CoV-2 S glycan shield.