bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of two POC technologies for CD4 count in Morocco
Authors: Elharti Elmir , Abbadi Halima , Bensghir Rajae , Filali Kamal Marhoum El , Elmrabet Hajar , Oumzil Hicham 
Published: June 2020

Abstract
Background : In the era of “test and treat strategy”, CD4 testing remains an important tool for monitoring HIV-infected individuals. Since conventional methods of CD4 count measurement are costly and cumbersome, POC CD4 counting technique are more affordable and practical for countries with limited resources. Before introducing such methods in Morocco, we decided to assess their reliability. Methods : In this study 92 blood samples from HIV-infected patients, were tested by PIMA and FACSPresto to derive CD4 count. Flow cytometry using FacsCalibur, was used as reference method for CD4 count comparison. Linear regression, Bland-Altman analysis were performed to assess correlation and agreement between these POC methods and the reference method. In addition, sensitivity and specificity, positive predictive value (PPV), negative predictive value (NPV) and misclassification percentage at 350 and 200 CD4 count thresholds; were also determined. Finally, because FACSPresto can also measure hemoglobin (Hb) concentration, 52 samples were used to compare FACSPresto against an automated hematology analyzer. Results : The coefficient of determination R 2 was 0.93 for both methods. Bland-Altman analysis displayed a mean bias of -32.3 and -8.1 cells/µl for PIMA and FACSPresto, respectively. Moreover, with a threshold of 350 CD4 count, PIMA displayed a sensitivity, specificity, PPV, NPV, were 88.57%, 94.12%, 91.18%, 92.31%; respectively. FACSPresto showed 88.23%, 96.23%,93.75% and 92.73%; respectively. Furthermore, the upward misclassification percentage was 8.57 and 5.88%, for PIMA and FACSPresto, respectively; whereas the downward misclassification percentage was 7.84% and 7.54%; respectively. With 200 cells/µl threshold, PIMA had a sensitivity, specificity, PPV and NPV of 83.33%, 98.53%, 93.75% and 95.71%, respectively. Regarding FACSPresto, sensitivity, specificity, PPV and NPV was 82.35%, 98.57%, 88.57% and 95.83%; respectively. Upward misclassification percentage was 5.56% and 5.88%, for PIMA and FACSPresto, respectively; whereas downward misclassification percentage was 4.41% and 4.29%; respectively. Finally, the hemoglobin measurement evaluation displayed an R 2 of 0.80 and a mean bias of-0.12 with a LOA between -1.75 and 1.51. Conclusion : When compared to the reference method, PIMA and FACSPresto have shown good performance, for CD4 counting. The introduction of such POC technology will speed up the uptake of patients in the continuum of HIV care, in our country.
Distinct evolutionary trajectories of V1R clades across mouse species
Authors: Miller Caitlin H , Campbell Polly , Sheehan Michael J 
Published: June 2020

Abstract
Background Many animals rely heavily on olfaction to navigate their environment. Among rodents, olfaction is crucial for a wide range of social behaviors. The vomeronasal olfactory system in particular plays an important role in mediating social communication, including the detection of pheromones and recognition signals. In this study we examine patterns of vomeronasal type-1 receptor (V1R) evolution in the house mouse and related species within the genus Mus . We report the extent of gene repertoire turnover and conservation among species and clades, as well as the prevalence of positive selection on gene sequences across the V1R tree. By exploring the evolution of these receptors, we provide insight into the functional roles of receptor subtypes as well as the dynamics of gene family evolution. Results We generated transcriptomes from the vomeronasal organs of 5 Mus species, and produced high quality V1R repertoires for each species. We find that V1R clades in the house mouse and relatives exhibit distinct evolutionary trajectories. Some clades are highly conserved, while others reveal patterns of rapid evolutionary change. We identify putative species-specific gene expansions, including a large clade D expansion in the house mouse. While gene gains are abundant, we detect very few gene losses. We describe a novel V1R clade and highlight candidate receptors for future study. We find evidence for different clades experiencing distinct evolutionary processes, from large scale turnover to highly conserved repertoires. Patterns of positive selection are similarly variable across clades, some clades reveal abundant positive selection across branches and orthologs while others display high gene sequence conservation. Based on clade-level evolutionary patterns, we identify receptor families that are strong candidates for detecting social signals and predator cues. Our results reveal that clades with receptors detecting female reproductive status are among the most conserved across species, suggesting an important role in V1R chemosensation. Conclusion Analysis of clade-level evolution is critical for understanding species’ chemosensory adaptations. This study provides clear evidence that V1R clades are characterized by distinct evolutionary trajectories. As receptor evolution is shaped by ligand identity, these results provide a framework for examining the functional roles of different receptors.
Malaria in children and women of childbearing age: prevalence and knowledge in the province of Nyanga, Gabon
Authors: IMBOUMY-LIMOUKOU Roméo Karl , MAGHENDJI-NZONDO Sydney , SIR-ONDO-ENGUIER Pater Noster , Niemczura Julie , TEGOMO Nathalie Pernelle TSAFACK , Buekens Julie Julie , OKOUGA Alain Prince , ONDEME Augustin MOUINGA , NOLNA Sylvie KWEDY , LEKANA-DOUKI Jean Bernard 
Published: June 2020

Abstract
Background: There is little information on the social perception of malaria and the use of preventative measures in Gabon, especially in rural areas. Adequate knowledge of malaria prevention and control can help in reducing the burden of malaria among vulnerable groups, particularly pregnant women and children aged under 5 years old living in malaria endemic settings. This study was designed to assess the prevalence of malaria and the knowledge and attitude towards this disease in households in the Nyanga Province. Methods: A cross-sectional study was conducted to assess malaria knowledge, prevention practices and prevalence of the infection in five departments of the Nyanga Province. Malaria infection was confirmed using rapid diagnostic tests. A questionnaire was administered randomly to 535 households during a two weeks period in March 2018. Overall, the respondents’ socio-demographic characteristics, knowledge on malaria, malaria prevention practices and malaria prevalence were evaluated and compared across the five departments. Results: Data was collected on 1,307 participants were included in this study, 631 women of childbearing age (including 61 pregnant women) and 676 children. Practically the entire (97.7%) interviewed population had already heard about malaria and attributed the cause of malaria to a mosquito bite (95.7%). This survey revealed that the bed net coverage rate was 73.3%. The study observed an average malaria parasite prevalence of 13.9%. All departments of Nyanga province had significant level of malaria infection except for the Mayumba department where no plasmodial infection was found. The overall prevalence of the plasmodial infection was significantly higher in children and pregnant women compared to adults in the cities of Tchibanga and Moabi. Conclusion: Malaria is highly prevalent in the province of Nyanga. Our findings show that children under five and pregnant women are more vulnerable to malaria in this area of the country. This study reveals that respondents have a high knowledge of mode of transmission, malaria symptoms and preventive measures. Despite this high level of knowledge of the disease and its preventive measures, the incidence of malaria remains relatively high in this rural community highlighting the need for continuous strategic interventions particularly health awareness and educational programs
Is a Differentiated Care Model needed for Patients with TB? A cohort analysis of risk factors contributing to unfavourable outcomes among TB patients in two states in south India.
Authors: Washington Reynold , Potty RAJARAM Subramanian , Rajesham A , Seenappa T , Singarajipura Anil , Swamickan Reuben , Shah Amar , Prakash KH , Kar Arin , Kumaraswamy Karthikeyan , BS Prarthana , Maryala Bala Krishna , Sushma J , Dasari Ramesh , Shetty Bharath , Panibatla Vikas , Mohan HL , Becker Marissa 
Published: June 2020

Abstract
Background: TB is a preventable and treatable disease. Yet, successful treatment outcomes at desired levels are elusive in many national TB programs, including India. We aim to identify risk factors for unfavourable outcomes to TB treatment, in order to subsequently design a care model that would improve treatment outcomes among these at-risk patients. Methods: We conducted a cohort analysis among TB patients who had been recently initiated on treatment. The study was part of the internal program evaluation of a USAID-THALI project, implemented in select towns/cities of Karnataka and Telangana, south India. Community Health Workers (CHWs) under the project, used a pre-designed tool to assess TB patients for potential risks of an unfavourable outcome. CHWs followed up this cohort of patients until treatment outcomes were declared. We extracted treatment outcomes from patient’s follow-up data and from the Nikshay portal. The specific cohort of patients included in our study were those whose risk was assessed during July and September, 2018, subsequent to conceptualisation, tool finalisation and CHW training. We used bivariate and multivariate logistic regression to assess each of the individual and combined risks against unfavourable outcomes; death alone, or death, lost to follow up and treatment failure, combined as ‘unfavourable outcome’. Results: A significantly higher likelihood of death and experiencing unfavourable outcome was observed for individuals having more than one risk (AOR: 4.19; 95% CI: 2.47-7.11 for death; AOR 2.21; 95% CI: 1.56-3.12 for unfavourable outcome) or only one risk (AOR: 3.28; 95% CI: 2.11-5.10 for death; AOR 1.71; 95% CI: 1.29-2.26 for unfavourable outcome) as compared to TB patients with no identified risk. Male, a lower education status, an initial weight below the national median weight, co-existing HIV, previous history of treatment, drug-resistant TB, and regular alcohol use had significantly higher odds of death and unfavourable outcome, while age >60 was only associated with higher odds of death. Conclusion: A rapid risk assessment at treatment initiation can identify factors that are associated with unfavourable outcomes. TB programs could intensify care and support to these patients, in order to optimise treatment outcomes among TB patients.
Haemato-immunological responses and effectiveness of feed-based bivalent vaccine against Streptococcus iniae and Aeromonas hydrophila infections in hybrid red tilapia (Oreochromis mossambicus × O. niloticus)
Authors: Monir Md. Shirajum , Yusoff Md Sabri bin Mohd , Zulperi Zarirah binti Mohamed , Hassim Hasliza binti Abu , Mohamad Aslah , Sofie Mohd Hafiz Ngoo Muhamad , Ina-Salwany Md Yasin 
Published: June 2020

Abstract
Background Streptococcosis and Motile Aeromonad Septicemia (MAS) are important diseases of tilapia, Oreochromis spp. and causes huge economic losses in aquaculture globally. The feed-based vaccination may be an alternative to minimize major infectious diseases in tilapia. Thus, this study aims to evaluate the haemato-immunological responses and effectiveness of a newly developed feed-based killed bivalent vaccine against Streptococcus iniae and Aeromonas hydrophila in hybrid red tilapia. A total of 495 hybrid red tilapia of 61.23±4.95 g were distributed into 5 groups (each with triplicate). The fish were immunized orally through bivalent (combined S. iniae and A. hydrophila ) spray vaccine (BS group), bivalent formulate vaccine (BF group), monovalent S. iniae vaccine (MS group), monovalent A. hydrophila vaccine (MA group) and unvaccinated as a control group. The vaccine was orally administered on days 0, 14 and 42 applied feed-based bacterin at 5% body weight. The blood and spleen samples were collected from all groups on 7, 21 and 49 days post-vaccination, and also 96 hours post-infection to assess their haemato-immune responses. Results Compared with the unvaccinated group, leukocyte, lymphocytes, monocytes, granulocytes counts in vaccinated groups were significantly ( P < 0.05) increased on 21, 49 days post-vaccination and also 96 hours post-infection, while erythrocytes, haemoglobin and haematocrit in vaccinated groups were significantly ( P < 0.05) enhanced only 96 hours post-infection. Additionally, the lysozyme and phagocytic activity and, serum antibody (IgM) were significantly higher ( P < 0.05) against S. iniae and A. hydrophila in vaccinated groups compared to the unvaccinated group in the pre- and post-infection. Results from the challenge through co-infection with S. iniae and A. hydrophila showed the relative percent survival (RPS) in BF group was 76.37±5.14%, which had the capacity to induce significant protection ( P < 0.05) compared to others groups. Conclusions This study demonstrates the bivalent formulate (BF) group could elicit significant non-specific and specific immunological responses with higher protection in hybrid red tilapia. In addition, this newly developed feed-based bivalent vaccination can be a promising technique for effective and large scale fish immunization in the aquaculture industry.
A high fat diet with a high C18:0/C16:0 ratio induced worse metabolic and transcriptomic profiles in C57BL/6 mice
Authors: Wang Liqiang , Xu Fei , Song Zhenfeng , Han Dan , Zhang jingyi , Chen Linjun , Na Lixin 
Published: June 2020

Abstract
Background: Differential effects of individual saturated fatty acids (SFAs), particularly stearic acid (C18:0) relative to the shorter-chain SFAs have drawn an interest for more accurate nutritional guidelines. But specific biologic and pathologic functions that can be assigned to particular SFAs are very limited. The present study was designed to compare changes in metabolic and transcriptomic profiles in mice caused by high C18:0 diet and high palmitic acid (C16:0) diet.Methods: Male C57BL/6 mice were assigned to a normal fat diet (NFD), a high fat diet with high C18:0 / C16:0 ratio (HSF) or an isocaloric high fat diet with a low C18:0 / C16:0 ratio (LSF) for 10 weeks. Oral glucose tolerance test, 72h-energy expenditure measurement and CT scan of body fat were done before sacrifice. Fasting glucose and lipids were determined by an auto-biochemical analyzer. Blood insulin, tumor necrosis factor-α (TNF-α)，and interleukin-6 (IL-6) were measured by enzyme linked immunosorbent assay methods. Free fatty acids (FFAs) profiles in blood and liver were determined by using Gas Chromatography-Mass Spectrometry. Microarray analysis was applied to investigate changes in transcriptomic profiles in liver. Pathway analysis and Gene Ontology analysis were applied to describe the roles of differentially expressed mRNAs. Results: Compared with NFD group, body weight, body fat ratio, fasting blood glucose, insulin, homeostasis model assessment of insulin resistance (HOMA-IR), triglyceride, IL-6, serum and liver FFAs including total FFAs, C16:0 and C18:0 were increased in both high fat diet groups, which were much higher in HSF group than those in LSF group. Both HSF and LSF mice exhibited distinguishable lncRNA, microRNA and mRNA expression profiles, compared with NFD mice. And more differentially expressed lncRNAs and mRNAs were observed in HSF group than those in LSF group. Some biological functions and pathways, other than energy metabolism regulation, were identified that differentially expressed mRNAs between HSF group and LSF group probably involved in. Conclusion: The high fat diet with a high C18:0/C16:0 ratio induced much severe glucose and lipid metabolic disorders and inflammation, and affected more lncRNAs and mRNAs expression than an isocaloric low C18:0/C16:0 ratio diet in mice. These results provide new insights into the different biological functions and related mechanisms, other than glucose and lipid metabolism, between C16:0 and C18:0.Take home message: A high fat diet with a high C18:0/C16:0 ratio probably leads to more changes in multiple biological processes or signaling pathways at transcriptional level than an isocaloric low C18:0/C16:0 ratio diet. The ratio of C18:0/C16:0 in diets should be taken into account for accurate nutrition and health in future.
Host DNA released by NETosis in neutrophils exposed to seasonal H1N1 and highly pathogenic H5N1 influenza viruses
Authors: Chan Louisa L.Y. , Nicholls John M. , Peiris J.S. Malik , Lau Yu Lung , Chan Michael C.W. , Chan Renee WY 
Published: June 2020

Abstract
Background: Neutrophil is of the most abundant number in human immune system. During acute influenza virus infection, neutrophils are already active in the early phase of inflammation-a time in which clinical biopsy or autopsy material is not readily available. However, the role of neutrophil in virus infection is not well understood. Here, we studied the role of neutrophil in host defense during influenza A virus infection, specifically assessing if it contributes to the differential pathogenesis in H5N1 disease. Methods: Neutrophils were freshly isolated from healthy volunteers and subjected to direct influenza H1N1 and H5N1 virus infection in vitro. The ability of the naïve neutrophils to infiltrate from the basolateral to the apical phase of the influenza virus infected alveolar epithelium was assessed. The viral replication, innate immune responses and Neutrophil extracellular trap (NET) formation of neutrophils upon influenza virus infection were evaluated. Results: Our results demonstrated that influenza virus infected alveolar epithelium allowed more neutrophils transmigration. Significantly more neutrophils migrated across the H5N1 influenza virus infected the epithelium than the counterpart infected by the seasonal influenza H1N1 virus infected. Neutrophils were equally susceptible to H5N1 and H1N1 virus infection with similar viral gene transcription. Productive replication was observed in H5N1 infected neutrophils. H5N1 induced higher cytokine and chemokine gene transcription than H1N1 infected neutrophils, including TNF-α, IFN-β, CXCL10, MIP-1α and IL-8. This inferred a more intense inflammatory response posed by H5N1 than H1N1 virus. Strikingly, NADPH oxidase-independent NET formation was only observed in H1N1 infected neutrophils at 6 hpi while no NET formation was observed upon H5N1 infection.Conclusion: Our data is the first to demonstrate that NET formation is abrogated in H5N1 influenza virus infection and might contribute to the severity of H5N1 disease.
Discriminative Validity of the Core Outcome Set Functional Independence in a Population of Older Adults
Authors: Dockx Yvonne , Molenaar Esther , Barten Di-Janne , Veenhof Cindy 
Published: June 2020

Abstract
Background: Clinicians are currently challenged to support older adults to maintain a certain level of Functional Independence (FI). FI is defined as “functioning physically safely and independent from another person, within one’s own context”. A Core Outcome Set was developed to measure FI. The purpose of this study was to assess discriminative validity of the Core Outcome Set FI (COSFI) in a population of Dutch older adults (³ 65 years) with different levels of FI. Secondary objective was to assess to what extent the underlying domains ‘coping’, ‘empowerment’ and ‘health literacy’ contribute to the COSFI in addition to the domain ‘physical capacity’. Methods: A population of 200 community-dwelling older adults and older adults living in residential care facilities were evaluated by the COSFI. The COSFI contains measurements on the four domains of FI: physical capacity, coping, empowerment and health literacy. In line with the COSMIN Study Design checklist for Patient-reported outcome measurement instruments, predefined hypotheses regarding prediction accuracy and differences between three subgroups of FI were tested. Testing included ordinal logistic regression analysis, with main outcome prediction accuracy of the COSFI on a proxy indicator for FI. Results: Overall, the prediction accuracy of the COSFI was 68%. For older adults living at home and depending on help in (i)ADL, prediction accuracy was 58%. 60% of the preset hypotheses were confirmed. Only physical capacity measured with Short Physical Performance Battery was significantly associated with group membership. Adding health literacy with coping or empowerment to a model with physical capacity improved the model significantly (p<0.01). Conclusions: The current composition of the COSFI, did not yet meet the COSMIN criteria for discriminative validity. However, with some adjustments, the COSFI potentially becomes a valuable instrument for clinical practice. Context-related factors, like the presence of a spouse, also may be a determining factor in this population. It is recommended to include context-related factors in further research on determining FI in subgroups of older people.
The human gut archaeome: identification of diverse haloarchaea in Korean subjects
Authors: Kim Joon Yong , Whon Tae Woong , Lim Mi Young , Kim Yeon Bee , Kim Namhee , Kwon Min-Sung , Kim Juseok , Lee Se Hee , Choi Hak-Jong , Nam In-Hyun , Chung Won-Hyung , Kim Jung-Ha , Bae Jin-Woo , Roh Seong Woon , Nam Young-Do 
Published: June 2020

Abstract
Background: Archaea are one of the least-studied members of the gut-dwelling autochthonous microbiota. Few studies have reported the dominance of methanogens in the archaeal microbiome (archaeome) of the human gut, although limited information regarding the diversity and abundance of other archaeal phylotypes is available.Results: We surveyed the archaeome of faecal samples collected from 897 East Asian subjects living in South Korea. In total, 42.47% faecal samples were positive for archaeal colonisation; these were subsequently subjected to archaeal 16S rRNA gene deep sequencing and real-time quantitative polymerase chain reaction-based abundance estimation. The mean archaeal relative abundance was 10.24% ± 4.58% of the total bacterial and archaeal abundance. We observed extensive colonisation of haloarchaea (95.54%) in the archaea-positive faecal samples, with 9.63% mean relative abundance in archaeal communities. Haloarchaea were relatively more abundant than methanogens in some samples. The presence of haloarchaea was also verified by fluorescence in situ hybridisation analysis. Owing to large inter-individual variations, we categorised the human gut archaeome into four archaeal enterotypes.Conclusions: The study demonstrated that the human gut archaeome is indigenous, responsive, and functional, expanding our understanding of the archaeal signature in the gut of human individuals.