bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of the particle agglutination/particle agglutination-inhibition test for antigenic analysis of SARS-CoV-2
Authors: Kobayashi Jun , Matsuyama Shutoku , Shirakura Masayuki , Arita Tomoko , Suzuki Yasushi , Asanuma Hideki , Watanabe Shinji , Hasegawa Hideki , Nakamura Kazuya 
Published: September 2022

AbstractThe antigenicity of SARS-CoV-2 is a critical issue for the effectiveness of the vaccine, and thus it should be phenotypically evaluated by serological assays as new field isolates emerge. The hemagglutination/hemagglutination-inhibition (HA/HI) tests are well-known as a representative method for antigenic analysis of influenza viruses, but SARS-CoV-2 is unlikely to agglutinate to human or guinea pig red blood cells. Therefore, the antigenic analysis requires complicated enzyme-linked immunosorbent assay (ELISA) or cell-based assays such as the microneutralization assay. In this study, we developed the particle agglutination/particle agglutination-inhibition (PA/PAI) test to easily and rapidly quantify the virus and antibody using human angiotensin-converting enzyme 2 (hACE2)-bound latex beads. The PA titer was positively correlated with the plaque-forming units. The PAI titer using post-infection Syrian hamster antisera clearly revealed the antigenic difference between the omicron and previous variants. The results show the PAI test is useful for easy and rapid antigenic analysis of SARS-CoV-2.
Comparative analysis of macroalgae supplementation on the rumen microbial community: Asparagopsis taxiformis inhibits major ruminal methanogenic, fibrolytic, and volatile fatty acid-producing microbes in vitro
Authors: O’Hara E , Moote P , Terry S , Beauchemin KA , McAllister TA , Abbott DW , Gruninger RJ 
Published: September 2022

1.AbstractSeaweeds have received a great deal of attention recently for their potential as methane-suppressing feed additives in ruminants. To date, Asparagopsis taxiformis has proven a potent enteric methane inhibitor, but it is a priority to identify local seaweed varieties that may hold similar properties. It is essential that any methane inhibitor does not compromise the function of the rumen microbiome. In this study, we conducted an in vitro experiment using the RUSITEC system to evaluate the impact of A. taxiformis, Palmaria mollis, and Mazzaella japonica on rumen prokaryotic communities. 16S rRNA sequencing showed that A. taxiformis had a profound effect on the microbiome, particularly on methanogens. Weighted Unifrac distances showed significant separation of A. taxiformis samples from the control and other seaweeds (P<0.05). Neither P. mollis nor M. japonica had a substantial effect on the microbiome (P>0.05). A. taxiformis reduced the abundance of all major archaeal species (P<0.05), leading to an almost total disappearance of the methanogens. Prominent fibre-degrading and volatile fatty acid (VFA)-producing bacteria including Fibrobacter and Ruminococcus were also inhibited by A. taxiformis (P<0.05), as were other genera involved in propionate production. However, the abundance of many other major bacteria (e.g. Prevotella) was increased by A. taxiformis suggesting the rumen microbiome adapted to an initial perturbation. Our study provides baseline knowledge of microbial dynamics in response to seaweed feeding over an extended period and suggests that feeding A. taxiformis to cattle to reduce methane may directly or indirectly inhibit important fibre-degrading and VFA-producing bacteria.
Oral health literacy, oral health behavior, and oral health status among dental patients and associated factors
Authors: An Ran , Li Qianqian , Luo Yuan , Chen Wenfeng , Sohaib Muhammad , Liu Meizi , Wu Zitong 
Published: September 2022

AbstractBackgroundOral health plays an important role in overall health. Little is known about oral health literacy, oral health behavior, and oral health status in dental patients.PurposeThis study aimed to assess oral health literacy (OHL), oral health behavior, oral health status, and associated factors in dental patients.MethodsThis cross-sectional study was conducted between June,13, 2022 and July, 26, 2022 in a tertiary general hospital, in Hebei, China. A total of 184 patients participated in the study. OHL was assessed by the Chinese version of the Health Literacy Dental Scale (HeLD-14). Trained interviewers performed face-to-face interviews for oral health-related behavior information. Data were analyzed using SPSS version 24. Mann–Whitney U-tests, chi-square tests, and binary logistic regression analysis were performed.ResultsParticipants were 184 dental patients which consisted of 78.3% men and a mean age of 28.36 ± 10.72 years old. The mean oral health literacy score was 43.07±9.920 (out of 56). There were significant associations between inadequate OHL and economic burden (odds ratio [OR]=2.636, P = 0.003), mouthwash (OR=2.433, P = 0.006), gum bleeding (OR=3.798, P = 0.030), and dental visiting (OR=1.885, P = 0.049).ConclusionThe oral health literacy of dental patients is at a medium level overall. Patients with inadequate OHL had a higher frequency of bleeding gums and less frequent dental visiting. Health care providers should consider improving oral health literacy among dental patients.
Distinct and joint effects of low and high levels of Aβ and tau deposition on cortical thickness
Authors: Hojjati Seyed Hani , Butler Tracy A. , Chiang Gloria C. , Habeck Christian , RoyChoudhury Arindam , Feiz Farnia , Shteingart Jacob , Nayak Siddharth , Ozoria Sindy , Fernández Antonio , Stern Yaakov , Luchsinger José A. , Devanand Davangere P. , Razlighi Qolamreza R. 
Published: September 2022

AbstractAlzheimer’s disease (AD) is defined by the presence of Amyloid-β (Aβ), tau, and neurodegeneration (ATN framework) in the human cerebral cortex. Prior studies have suggested that Aβ deposition can be associated with both cortical thinning and thickening. These contradictory results may be due to small sample sizes, the presence versus absence of tau, and limited detectability in the earliest phase of protein deposition, which may begin in young adulthood and cannot be captured in studies enrolling only older subjects. In this study, we aimed to find the distinct and joint effects of Aβ and tau on neurodegeneration during the progression from normal to abnormal stages of pathologies that remain incompletely understood. We used 18F-MK6240 and 18F-Florbetaben/18F-Florbetapir positron emission tomography (PET) and magnetic resonance imaging (MRI) to quantify tau, Aβ, and cortical thickness in 529 participants ranging in age from 20 to 90. We applied a novel partial volume correction technique based on the absence of proteinopathy in young controls to optimize spatial resolution. Aβ/tau abnormality was defined at 95th percentile of the normal distribution of global Ab/tau observed in young participants. We performed multiple regression analyses to assess the distinct and joint effects of Aβ and tau on cortical thickness. Using 529 participants (83 young, 394 healthy older, 52 MCI) we showed that normal levels of Aβ deposition were significantly associated with increased cortical thickness regardless of the amount of tau (e.g., left entorhinal cortex with t>3.241). The relationship between tau deposition and neurodegeneration was more complex: abnormal levels of tau were associated with cortical thinning in several regions of the brain (e.g., left entorhinal with t<-2.80 and left insula with t<-3.202), as expected based on prior neuroimaging and neuropathological studies. Surprisingly, however, normal levels of tau were found to be associated with cortical thickening. Moreover, at abnormal levels of Aβ and tau, the resonance between them, defined as their correlation throughout the cortex, was associated strongly with cortical thinning when controlling for their additive effect. We confirm prior findings of an association between Aβ deposition and cortical thickening and suggest this may also be the case in the earliest stages of deposition in normal aging. We discuss potential pathophysiologic processes underlying this effect such as inflammation and hyperactivation (excitotoxicity). We also illustrate that resonance between high levels of Aβ and tau uptake is strongly associated with cortical thinning, emphasizing the effects of Aβ/tau synergy in AD pathogenesis.
Using Lambda phages as a proxy for pathogen transmission in hospitals
Authors: Burke Kylie B. , Berryhill Brandon A. , Garcia Rodrigo , Goldberg David A. , Manuel Joshua A. , Gannon Paige , Levin Bruce R. , Kraft Colleen S. , Mumma Joel 
Published: September 2022

SummaryOne major concern in hospitalized patients is infections with pathogens borne on surfaces, patients, and healthcare workers. Fundamental to controlling nosocomial infections is identifying the sources of pathogens, monitoring the processes responsible for their transmission, and evaluating the efficacy of the procedures employed for restricting their transmission. Here we present a method using the bacteriophage Lambda (λ) to achieve these ends. Defined densities of multiple genetically marked λ phages were inoculated at known hotspots for contamination on high-fidelity mannequins. Healthcare workers (HCWs) then entered a pre-sanitized simulated hospital room and performed a series of patient care tasks on the mannequins. Sampling occurred on the scrubs and hands of the HCWs, as well as previously defined high-touch surfaces in hospital rooms. Following sampling, the rooms were decontaminated using procedures designed and demonstrated to be effective. Following the conclusion of the simulation, the samples were tested for the presence, identity, and densities of these Lambda phages.The data generated enabled the determination of the sources and magnitude of contamination caused by the breakdown of established infection prevention practices by HCW. This technique enabled the standardized tracking of multiple contaminants during a single episode of patient care. While our application of these methods focused on nosocomial infections and the role of HCW behaviors in their spread, these methods could be employed for identifying the sources and sites of microbial contamination in other settings.
Estimating the cost-effectiveness of maternal vaccination and monoclonal antibodies for respiratory syncytial virus in Kenya and South Africa
Authors: Koltai Mihaly , Moyes Jocelyn , Nyawanda Bryan , Nyiro Joyce , Munywoki Patrick , Tempia Stefano , Li Xiao , Antillon Marina , Bilcke Joke , Flasche Stefan , Beutels Philippe , Nokes D. James , Cohen Cheryl , Jit Mark 
Published: September 2022

AbstractBackgroundRespiratory syncytial virus (RSV) causes a substantial burden of acute lower respiratory infection in children under 5 years, particularly in low- and middle-income countries (LMICs). Maternal vaccine (MV) and next-generation monoclonal antibody (mAb) candidates have been shown to reduce RSV disease in infants in phase III clinical trials. The cost-effectiveness of these biologics has been estimated using disease burden data from global meta-analyses, but these are sensitive to the detailed age breakdown of paediatric RSV disease, for which there have previously been limited data.MethodsWe use original hospital-based incidence data from South Africa and Kenya collected between 2010 and 2018 of RSV-associated acute respiratory infection (ARI), influenza-like illness (ILI), severe acute respiratory infection (SARI) as well as deaths with monthly age-stratification, supplemented with data on healthcare-seeking behaviour and costs to the healthcare system and households. We estimated the incremental cost per DALY averted (incremental cost-effectiveness ratio or ICER) of public health interventions by MV or mAb for a plausible range of prices (3-30 USD for vaccines and 6-60 USD for monoclonals), using an adapted version of a previously published health economic model (McMarcel) of RSV immunisation.ResultsOur data show higher disease incidence for infants younger than 6 months of age in the case of Kenya and South Africa than suggested by earlier projections from community incidence-based meta-analyses of LMIC data. Since MV and mAb provide protection for these youngest age groups, this leads to a substantially larger reduction of disease burden and therefore, more favourable cost-effectiveness of both interventions in both countries. Specifically, using published efficacy data, our mean estimate for reducing RSV-associated deaths in children under 5 years of age is 9% for MV and 28% for mAb in Kenya. In South Africa, the reduction is larger, with the mean estimate of 14% for MV and 48% for mAb.In the case of the lowest dose prices (3 USD for MV and 6 USD for mAb), the healthcare system perspective ICERs per DALY averted drop to 144 USD (mAb) and 397 USD (MV) in Kenya, whereas it is net cost-saving from the perspective of the South African healthcare system. At the highest assumed dose prices of 30 USD for MV and 60 USD for mAb, the median estimates for the ICER are 4528 USD for MV and 2748 USD for mAb in Kenya, while in South Africa, it is 4694 USD for MV and 2566 USD for mAb.ConclusionInterventions against RSV disease may be more cost-effective than previously estimated following the incorporation of new data indicating that the disease burden is highly concentrated in the first 6 months of life in two African settings.
HexSE: Simulating evolution in overlapping reading frames
Authors: Muñoz-Baena Laura , Wade Kaitlyn E. , Poon Art F. Y. 
Published: September 2022

ABSTRACTMotivationGene overlap occurs when two or more genes are encoded by the same nucleotides. This phenomenon is found in all taxonomic domains, but is particularly common in viruses, where it may provide a mechanism to increase the information content of compact genomes. The presence of overlapping reading frames (OvRFs) can skew estimates of selection based on the rates of non-synonymous and synonymous substitutions, since a substitution that is synonymous in one reading frame may be non-synonymous in another, and vice versa.ResultsTo understand the impact of OvRFs on molecular evolution, we implemented a versatile simulation model of nucleotide sequence evolution along a phylogeny with any distribution of open reading frames in linear or circular genomes. We use a custom data structure to track the substitution rates at every nucleotide site, which is determined by the stationary nucleotide frequencies, transition bias, and the distribution of selection biases (dN/dS) in the respective reading frames.Availability and implementationOur simulation model is implemented in the Python scripting language. All source code is released under the GNU General Public License (GPL) version 3, and is available at https://github.com/PoonLab/HexSE.
Molecular mechanism of substrate recognition by folate transporter SLC19A1
Authors: Dang Yu , Zhou Dong , Du Xiaojuan , Zhao Hongtu , Lee Chia-Hsueh , Yang Jing , Wang Yijie , Qin Changdong , Guo Zhenxi , Zhang Zhe 
Published: September 2022

AbstractFolate (vitamin B9) is the coenzyme involved in one-carbon transfer biochemical reactions essential for cell survival and proliferation, with its inadequacy causing developmental defects or severe diseases. Notably, mammalian cells lack the ability tode novosynthesize folate but instead rely on its intake from extracellular sources via specific transporters or receptors, among which SLC19A1 is the ubiquitously expressed one in tissues. However, the mechanism of substrate recognition by SLC19A1 has been unclear. Here we report the cryo-EM structures of human SLC19A1 and its complex with 5-methyltetrahydrofolate at 3.5-3.6 Å resolution and elucidate the critical residues for substrate recognition. In particular, we reveal that two variant residues among SLC19 subfamily members would designate the specificity for folate. Moreover, we identify intracellular thiamine pyrophosphate as the favorite coupled substrate for folate transport by SLC19A1. Together, this work has established the molecular basis of substrate recognition by this central folate transporter.
Your turn, my turn. Neural synchrony in mother-infant proto-conversation
Authors: Nguyen Trinh , Zimmer Lucie , Hoehl Stefanie 
Published: September 2022

SummaryEven before infants utter their first words, they engage in highly coordinated vocal exchanges with their caregivers. During these so-called proto-conversations, caregiver-infant dyads use a presumably universal communication structure - turn-taking, which has been linked to favourable developmental outcomes. However, little is known about potential mechanisms involved in early turn-taking. Previous research pointed to interpersonal synchronisation of brain activity between adults and preschool-aged children during turn-taking. Here, we assessed caregivers and infants at 4-6 months of age (N=55) during a face-to-face interaction. We used functional-near infrared spectroscopy hyperscanning to measure dyads’ brain activity and microcoded their turn-taking. We also measured infants’ inter-hemispheric connectivity as an index for brain maturity and later vocabulary size and attachment security as developmental outcomes potentially linked to turn-taking. The results showed that more frequent turn-taking was related to interpersonal neural synchrony, but the strength of the relation decreased over the course of the proto-conversation. Importantly, turn-taking was positively associated with infant brain maturity and later vocabulary size, but not with later attachment security. Taken together, these findings shed light on mechanisms facilitating preverbal turn-taking and stress the importance of emerging turn-taking for child brain and language development.
In-silico comparative modeling and interaction studies of PRSV proteins - Accelerated towards dissection of structure based evolutionary divergence and functional interaction of virus within the host
Authors: Saleem Anam , Ali Zahid , Naseem Saadia 
Published: September 2022

AbstractFunction based structure analysis of viral proteins reinforce their distinctive and unanticipated role within the host. The interaction dynamics of virus protein and host which is prerequisite for complete infectivity as well as systemic spread of invading virus demands to explore viral proteins in framework of their interacting partners. Papaya ringspot virus strain from Pakistan (PRSV-PK) spreading as atypical variant and causes drastic reduction in papaya production. The in-depth knowledge of the virus variant and effective management is obligatory. The desired objective is achievable once the evolutionary dynamics, molecular characterization and physicochemical structural properties conceived from the 3D protein structures are comprehended. Although the diversity studies on PRSV-PK strain been established but still there is a niche regarding structural based evolutionary dynamics of virus proteins and their probable interaction mode inside the host. The present investigations provided insights into the in-silico analysis of the functionally significant genes Coat protein (CP), Helper component proteinase (HC-Pro) and Nuclear Inclusion b protein (NIb) of PRSV-PK. The protein structure has been modeled using Phyre2, Swiss-Model and i-TASSER. Phyre2 built model showed 100% confidence for 67%, 63% and 20% sequence identity residues for PRSV CP, HC-Pro and NIb proteins respectively. The Swiss model showed identity values of 63.40%, 62.42% and 16.49% for CP, HC-Pro and NIb protein. whereas, i-TASSER server exhibited identity values of 67%, 63% and 19% for CP, HC-Pro and NIb proteins respectively. These structures provided a base line for functional analysis of experimentally derived crystal structures. The predicted models were validated using protein structure checking tools PROCHECK. Further the PRSV-PK-CP structures were compared with the PRSV-CP structures of representative isolates from different geographical regions. Nevertheless, the comparative modeling provides the insight into the evolutionary characteristics and proposed genetic diversity of PRSV based on protein structures. In addition, the conserved functional motifs have been mapped on aligned protein sequences of CP, HC-Pro and NIb, and their critical function within the host has been highlighted. Eventually, the interaction of papaya protein with the invading PRSV-CP has been predicted through in-silico protein-protein docking to elucidate their possible role in virus inhibition. The established structural-functional relation provided a basis to propose probable host-virus interactions in terms of virus infectivity, resultant host adaptability, and host defense response activation to counteract the virus invasion.
Human commensalCandida albicansstrains demonstrate substantial within-host diversity and retained pathogenic potential
Authors: Anderson Faith M , Visser Noelle , Amses Kevin , Hodgins-Davis Andrea , Weber Alexandra M , Metzner Katura M , McFadden Michael J , Mills Ryan E , O’Meara Matthew J , James Timothy Y , O’Meara Teresa R 
Published: September 2022

ABSTRACTCandida albicansis a frequent colonizer of human mucosal surfaces as well as an opportunistic pathogen.C. albicansis remarkably versatile in its ability to colonize diverse host sites with differences in oxygen and nutrient availability, pH, immune responses, and resident microbes, among other cues. It is unclear how the genetic background of a commensal colonizing population can influence the shift to pathogenicity. Therefore, we undertook an examination of commensal isolates from healthy donors with a goal of identifying site-specific phenotypic adaptation and genetic variation associated with these phenotypes. We demonstrate that healthy people are reservoirs for genotypically and phenotypically diverseC. albicansstrains, and that this genetic diversity includes both SNVs and structural rearrangements. Using limited diversity exploitation, we identified a single nucleotide change in the uncharacterizedZMS1transcription factor that was sufficient to drive hyper invasion into agar. However, our commensal strains retained the capacity to cause disease in systemic models of infection, including outcompeting the SC5314 reference strain during systemic competition assays. This study provides a global view of commensal strain variation and within-host strain diversity ofC. albicansand suggests that selection for commensalism in humans does not result in a fitness cost for invasive disease.