bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of S1PR3 gene signature involved in survival of sepsis patients
Authors: Feng Anlin , Ma Wenli , Faraj Reem , Kelly Gabriel T. , Black Stephen M. , Fallon Michael B. , Wang Ting 
Published: February 2021

Abstract
Background
Sepsis is a life-threatening complication of infection that rapidly triggers tissue damage in multiple organ systems and leads to multi-organ deterioration. Up to date, prognostic biomarkers still have limitations in predicting the survival of patients with sepsis. We need to discover more prognostic biomarkers to improve the sensitivity and specificity of the prognosis of sepsis patients. Sphingosine-1-phosphate (S1P) receptor 3 (S1PR3), as one of the S1P receptors, is a prospective prognostic biomarker regulating sepsis-relevant events, including compromised vascular integrity, antigen presentation, and cytokine secretion. Until now, no S1PR3-related prognostic gene signatures for sepsis patients have been found.

Methods
This study intends to obtain an S1PR3-associated gene signature from whole blood samples to be utilized as a probable prognostic tool for patients with sepsis.

Results
We obtained an 18-gene S1PR3-related molecular signature (S3MS) from the intersection of S1PR3-associated genes and survival-associated genes. Numerous important immunity pathways that regulate the progression of sepsis are enriched among our 18 genes. Significantly, S3MS functions greatly in both the discovery and validation cohort. Furthermore, we demonstrated that S3MS obtains significantly better classification performance than random 18-gene signatures.

Conclusions
Our results confirm the key role of S1PR3-associated genes in the development of sepsis, which will be a potential prognostic biomarker for patients with sepsis. Our results also focus on the classification performance of our S3MS as biomarkers for sepsis, which could also provide an early warning system for patients with sepsis.
Rapid ethnographic assessment for potential anti-malarial mass drug administration in an outbreak area of Santo Domingo, Dominican Republic
Authors: Keys Hunter , Ureña Keyla , Reyes Jhefres , Bardosh Kevin , Pell Christopher , Puello Jose , Blount Stephen , Noland Gregory S. 
Published: February 2021

Abstract
Background
In the Dominican Republic, a recent outbreak of malaria in the capital, Santo Domingo, threatens efforts to eliminate the disease. Mass drug administration (MDA) has been proposed as one strategy to reduce transmission. The success of MDA is contingent upon high levels of acceptance among the target population. To inform the design of future MDA campaigns, this rapid ethnographic assessment examined malaria-related knowledge and attitudes toward malaria MDA among residents of a transmission focus in Santo Domingo.

Methods
In October 2019, a rapid ethnographic assessment was conducted in the Los Tres Brazos transmission focus, which had not previously received MDA. National malaria programme staff conducted 61 structured interviews with key informants, recorded observations, and held 72 informal conversations. Using a grounded theory approach, data were analysed during three workshop sessions with research team members.

Results
Among those who had heard of malaria in the structured interviews (n = 39/61; 64%), understanding of the disease was largely based on personal experience from past outbreaks or through word-of-mouth. Community health workers (promotores) were trusted for health information and malaria diagnosis more so than professional clinicians. No participant (0%) was familiar with malaria MDA. After learning about MDA, almost all study participants (92%) said that they would participate, seeing it as a way to care for their community. Reasons for not participating in future MDA included not trusting drug administrators, feeling reluctant to take unprescribed medicine, and fear of missing work. Additional identified challenges to MDA included reaching specific demographic groups, disseminating effective MDA campaign messages, and managing misinformation and political influence.

Conclusion
Residents appear accepting of MDA despite a lack of prior familiarity. Successful MDA will depend on several factors: fostering relationships among community-based health workers, clinicians, community leaders, and others; developing clear health messages that use local terms and spreading them through a variety of media and social networks; and contextualizing MDA as part of a broader effort to promote community health.
Low prevalence of highly sulfadoxine‐resistant dihydropteroate synthase alleles in Plasmodium falciparum isolates in Benin
Authors: Svigel Samaly Souza , Adeothy Adicath , Kpemasse Augustin , Houngbo Ernest , Sianou Antoine , Saliou Ramani , Patton Monica E. , Dagnon Fortune , Halsey Eric S. , Tchevoede Alexis , Udhayakumar Venkatachalam , Lucchi Naomi W. 
Published: February 2021

Abstract
Background
In 2004, in response to high levels of treatment failure associated with sulfadoxine-pyrimethamine (SP) resistance, Benin changed its first-line malaria treatment from SP to artemisinin-based combination therapy for treatment of uncomplicated Plasmodium falciparum malaria. Resistance to SP is conferred by accumulation of single nucleotide polymorphisms (SNPs) in P. falciparum genes involved in folate metabolism, dihydrofolate reductase (Pfdhfr) and dihydropteroate synthase (Pfdhps), targeted by pyrimethamine and sulfadoxine, respectively. Because SP is still used for intermittent preventive treatment in pregnant women (IPTp) and seasonal malaria chemoprevention (SMCP) in Benin, the prevalence of Pfdhfr and Pfdhps SNPs in P. falciparum isolates collected in 2017 were investigated.

Methods
This study was carried out in two sites where the transmission of P. falciparum malaria is hyper-endemic: Klouékanmey and Djougou. Blood samples were collected from 178 febrile children 6–59 months old with confirmed uncomplicated P. falciparum malaria and were genotyped for SNPs associated with SP resistance.

Results
The Pfdhfr triple mutant IRN (N51I, C59R, and S108N) was the most prevalent (84.6%) haplotype and was commonly found with the Pfdhps single mutant A437G (50.5%) or with the Pfdhps double mutant S436A and A437G (33.7%). The quintuple mutant, PfdhfrIRN/PfdhpsGE (A437G and K540E), was rarely observed (0.8%). The A581G and A613S mutant alleles were found in 2.6 and 3.9% of isolates, respectively. Six isolates (3.9%) were shown to harbour a mutation at codon I431V, recently identified in West African parasites.

Conclusions
This study showed that Pfdhfr triple IRN mutants are near fixation in this population and that the highly sulfadoxine-resistant Pfdhps alleles are not widespread in Benin. These data support the continued use of SP for chemoprevention in these study sites, which should be complemented by periodic nationwide molecular surveillance to detect emergence of resistant genotypes.
Four decades of measuring stillbirths and neonatal deaths in Demographic and Health Surveys: historical review
Authors: Akuze Joseph , Cousens Simon , Lawn Joy E. , Waiswa Peter , Gordeev Vladimir Sergeevich , Arnold Fred , Croft Trevor , Baschieri Angela , Blencowe Hannah 
Published: February 2021

AbstractBackgroundWorldwide, an estimated 5.1 million stillbirths and neonatal deaths occur annually, 98% in low- and middle-income countries. Limited coverage of civil and vital registration systems necessitates reliance on women’s retrospective reporting in household surveys for data on these deaths. The predominant platform, Demographic and Health Surveys (DHS), has evolved over the last 35 years and differs by country, yet no previous study has described these differences and the effects of these changes on stillbirth and neonatal death measurement.MethodsWe undertook a review of DHS model questionnaires, protocols and methodological reports from DHS-I to DHS-VII, focusing on the collection of information on stillbirth and neonatal deaths describing differences in approaches, questionnaires and geographic reach up to December 9, 2019. We analysed the resultant data, applied previously used data quality criteria including ratios of stillbirth rate (SBR) to neonatal mortality rate (NMR) and early NMR (ENMR) to NMR, comparing by country, over time and by DHS module.ResultsDHS has conducted >320 surveys in 90 countries since 1984. Two types of maternity history have been used: full birth history (FBH) and full pregnancy history (FPH). A FBH collecting information only on live births has been included in all model questionnaires to date, with data on stillbirths collected through a reproductive calendar (DHS II-VI) or using additional questions on non-live births (DHS-VII). FPH collecting information on all pregnancies including live births, miscarriages, abortions and stillbirths has been used in 17 countries. We found no evidence of variation in stillbirth data quality assessed by SBR:NMR over time for FBH surveys with reproductive calendar, some variation for surveys with FBH in DHS-VII and most variation among the surveys conducted with a FPH. ENMR:NMR ratio increased over time, which may reflect changes in data quality or real epidemiological change.ConclusionDHS remains the major data source for pregnancy outcomes worldwide. Although the DHS model questionnaire has evolved over the last three and half decades, more robust evidence is required concerning optimal methods to obtain accurate data on stillbirths and neonatal deaths through household surveys and also to develop and test standardised data quality criteria.
Termination of pregnancy data completeness and feasibility in population-based surveys: EN-INDEPTH study
Authors:   the Every Newborn-INDEPTH Study Collaborative Group, Enuameh Yeetey Akpe Kwesi , Dzabeng Francis , Blencowe Hannah , Thysen Sanne M. , Abebe Solomon Mekonnen , Asante Kwaku Poku , Tawiah Charlotte , Gordeev Vladimir Sergeevich , Adeapena Wisdom , Kwesiga Doris , Kasasa Simon , Zandoh Charles , Imam Md. Ali , Amenga-Etego Seeba , Newton Sam K. , Owusu-Agyei Seth , Lawn Joy E. , Waiswa Peter , Cresswell Jenny A. 
Published: February 2021

AbstractBackgroundTermination of pregnancy (TOP) is a common cause of maternal morbidity and mortality in low- and middle-income countries. Population-based surveys are the major data source for TOP data in LMICs but are known to have shortcomings that require improving. The EN-INDEPTH multi-country survey employed a full pregnancy history approach with roster and new questions on TOP and Menstrual Restoration. This mixed methods paper assesses the completeness of responses to questions eliciting TOP information from respondents and reports on practices, barriers, and facilitators to TOP reporting.MethodsThe EN-INDEPTH study was a population-based cross-sectional study. The Full Pregnancy History arm of the study surveyed 34,371 women of reproductive age between 2017 and 2018 in five Health and Demographic Surveillance System (HDSS) sites of the INDEPTH network: Bandim, Guinea-Bissau; Dabat, Ethiopia; IgangaMayuge, Uganda; Kintampo, Ghana; and Matlab, Bangladesh. Completeness and time spent in answering TOP questions were evaluated using simple tabulations and summary statistics. Exact binomial 95% confidence intervals were computed for TOP rates and ratios. Twenty-eight (28) focus group discussions were undertaken and analysed thematically.ResultsCompleteness of responses regarding TOP was between 90.3 and 100.0% for all question types. The new questions elicited between 2.0% (1.0–3.4), 15.5% (13.9–17.3), and 11.5% (8.8–14.7) lifetime TOP cases over the roster questions from Dabat, Ethiopia; Matlab, Bangladesh; and Kintampo, Ghana, respectively. The median response time on the roster TOP questions was below 1.3 minutes in all sites. Qualitative results revealed that TOP was frequently stigmatised and perceived as immoral, inhumane, and shameful. Hence, it was kept secret rendering it difficult and uncomfortable to report. Miscarriages were perceived to be natural, being easier to report than TOP. Interviewer techniques, which were perceived to facilitate TOP disclosure, included cultural competence, knowledge of contextually appropriate terms for TOP, adaptation to interviewee’s individual circumstances, being non-judgmental, speaking a common language, and providing detailed informed consent.ConclusionsSurvey roster questions may under-represent true TOP rates, since the new questions elicited responses from women who had not disclosed TOP in the roster questions. Further research is recommended particularly into standardised training and approaches to improving interview context and techniques to facilitate TOP reporting in surveys.
Stillbirth outcome capture and classification in population-based surveys: EN-INDEPTH study
Authors:   the Every Newborn-INDEPTH Study Collaborative Group, Blencowe Hannah , Bottecchia Matteo , Kwesiga Doris , Akuze Joseph , Haider M. Moinuddin , Galiwango Edward , Dzabeng Francis , Fisker Ane B. , Enuameh Yeetey Akpe Kwesi , Geremew Bisrat Misganaw , Nareeba Tryphena , Woodd Susannah , Beedle Alexandra , Peven Kimberly , Cousens Simon , Waiswa Peter , Lawn Joy E. 
Published: February 2021

AbstractBackgroundHousehold surveys remain important sources of stillbirth data, but omission and misclassification are common. Classifying adverse pregnancy outcomes as stillbirths requires accurate reporting of vital status at birth and gestational age or birthweight for every pregnancy. Further categorisation, e.g. by sex, or timing (intrapartum/antepartum) improves data to understand and prevent stillbirth.MethodsWe undertook a cross-sectional population-based survey of women of reproductive age in five health and demographic surveillance system sites in Bangladesh, Ethiopia, Ghana, Guinea-Bissau and Uganda (2017–2018). All women answered a full birth history with pregnancy loss questions (FBH+) or a full pregnancy history (FPH). A sub-sample across both groups were asked additional stillbirth questions. Questions were evaluated using descriptive measures. Using an interpretative paradigm and phenomenology methodology, focus group discussions with women exploring barriers to reporting birthweight for stillbirths were conducted. Thematic analysis was guided by an a priori codebook.ResultsOverall 69,176 women reported 98,483 livebirths (FBH+) and 102,873 pregnancies (FPH). Additional questions were asked for 1453 stillbirths, 1528 neonatal deaths and 12,620 surviving children born in the 5 years prior to the survey. Completeness was high (> 99%) for existing FBH+/FPH questions on signs of life at birth and gestational age (months). Discordant responses in signs of life at birth between different questions were common; nearly one-quarter classified as stillbirths on FBH+/FPH were reported born alive on additional questions. Availability of information on gestational age (weeks) (58.1%) and birthweight (13.2%) was low amongst stillbirths, and heaping was common. Most women (93.9%) were able to report the sex of their stillborn baby. Response completeness for stillbirth timing (18.3–95.1%) and estimated proportion intrapartum (15.6–90.0%) varied by question and site. Congenital malformations were reported in 3.1% stillbirths. Perceived value in weighing a stillborn baby varied and barriers to weighing at birth a nd knowing birthweight were common.ConclusionsImproving stillbirth data in surveys will require investment in improving the measurement of vital status, gestational age and birthweight by healthcare providers, communication of these with women, and overcoming reporting barriers. Given the large burden and effect on families, improved data must be made available to end preventable stillbirths.
Stillbirth maternity care measurement and associated factors in population-based surveys: EN-INDEPTH study
Authors:   and the Every Newborn-INDEPTH Study Collaborative Group, Di Stefano Lydia , Bottecchia Matteo , Yargawa Judith , Akuze Joseph , Haider M. Moinuddin , Galiwango Edward , Dzabeng Francis , Fisker Ane B. , Geremew Bisrat Misganaw , Cousens Simon , Lawn Joy E. , Blencowe Hannah , Waiswa Peter 
Published: February 2021

AbstractBackgroundHousehold surveys remain important sources of maternal and child health data, but until now, standard surveys such as Demographic and Health Surveys (DHS) have not collected information on maternity care for women who have experienced a stillbirth. Thus, nationally representative data are lacking to inform programmes to address the millions of stillbirths which occur annually.MethodsThe EN-INDEPTH population-based survey of women of reproductive age was undertaken in five Health and Demographic Surveillance System sites in Bangladesh, Ethiopia, Ghana, Guinea-Bissau and Uganda (2017–2018). All women answered a full birth history with additional questions on pregnancy losses (FBH+) or full pregnancy history (FPH). A sub-sample, including all women reporting a recent stillbirth or neonatal death, was asked additional maternity care questions. These were evaluated using descriptive measures. Associations between stillbirth and maternal socio-demographic characteristics, babies’ characteristics and maternity care use were assessed using a weighted logistic regression model for women in the FBH+ group.ResultsA total of 15,591 women reporting a birth since 1 January 2012 answered maternity care questions. Completeness was very high (> 99%), with similar proportions of responses for both live and stillbirths. Amongst the 14,991 births in the FBH+ group, poorer wealth status, higher parity, large perceived baby size-at-birth, preterm or post-term birth, birth in a government hospital compared to other locations and vaginal birth were associated with increased risk of stillbirth after adjusting for potential confounding factors. Regarding association with reported postnatal care, women with a stillbirth were more likely to report hospital stays of > 1 day. However, women with a stillbirth were less likely to report having received a postnatal check compared to those with a live birth.ConclusionsWomen who had experienced stillbirth were able to respond to questions about pregnancy and birth, and we found no reason to omit questions to these women in household surveys. Our analysis identified several potentially modifiable factors associated with stillbirth, adding to the evidence-base for policy and action in low- and middle-income contexts. Including these questions in DHS-8 would lead to increased availability of population-level data to inform action to end preventable stillbirths.
Efficient CRISPR/Cas9 mediated Pooled-sgRNAs assembly accelerates targeting multiple genes related to male sterility in cotton
Authors: Ramadan Mohamed , Alariqi Muna , Ma Yizan , Li Yanlong , Liu Zhenping , Zhang Rui , Jin Shuangxia , Min Ling , Zhang Xianlong 
Published: February 2021

Abstract
Background
Upland cotton (Gossypium hirsutum), harboring a complex allotetraploid genome, consists of A and D sub-genomes. Every gene has multiple copies with high sequence similarity that makes genetic, genomic and functional analyses extremely challenging. The recent accessibility of CRISPR/Cas9 tool provides the ability to modify targeted locus efficiently in various complicated plant genomes. However, current cotton transformation method targeting one gene requires a complicated, long and laborious regeneration process. Hence, optimizing strategy that targeting multiple genes is of great value in cotton functional genomics and genetic engineering.

Results
To target multiple genes in a single experiment, 112 plant development-related genes were knocked out via optimized CRISPR/Cas9 system. We optimized the key steps of pooled sgRNAs assembly method by which 116 sgRNAs pooled together into 4 groups (each group consisted of 29 sgRNAs). Each group of sgRNAs was compiled in one PCR reaction which subsequently went through one round of vector construction, transformation, sgRNAs identification and also one round of genetic transformation. Through the genetic transformation mediated Agrobacterium, we successfully generated more than 800 plants. For mutants identification, Next Generation Sequencing technology has been used and results showed that all generated plants were positive and all targeted genes were covered. Interestingly, among all the transgenic plants, 85% harbored a single sgRNA insertion, 9% two insertions, 3% three different sgRNAs insertions, 2.5% mutated sgRNAs. These plants with different targeted sgRNAs exhibited numerous combinations of phenotypes in plant flowering tissues.

Conclusion
All targeted genes were successfully edited with high specificity. Our pooled sgRNAs assembly offers a simple, fast and efficient method/strategy to target multiple genes in one time and surely accelerated the study of genes function in cotton.
Rapid tannin profiling of tree fodders using untargeted mid-infrared spectroscopy and partial least squares regression
Authors: Ortuño Jordi , Stergiadis Sokratis , Koidis Anastasios , Smith Jo , Humphrey Chris , Whistance Lindsay , Theodoridou Katerina 
Published: February 2021

Abstract
Background
The presence of condensed tannins (CT) in tree fodders entails a series of productive, health and ecological benefits for ruminant nutrition. Current wet analytical methods employed for full CT characterisation are time and resource-consuming, thus limiting its applicability for silvopastoral systems. The development of quick, safe and robust analytical techniques to monitor CT’s full profile is crucial to suitably understand CT variability and biological activity, which would help to develop efficient evidence-based decision-making to maximise CT-derived benefits. The present study investigates the suitability of Fourier-transformed mid-infrared spectroscopy (MIR: 4000–550 cm−1) combined with multivariate analysis to determine CT concentration and structure (mean degree of polymerization—mDP, procyanidins:prodelphidins ratio—PC:PD and cis:trans ratio) in oak, field maple and goat willow foliage, using HCl:Butanol:Acetone:Iron (HBAI) and thiolysis-HPLC as reference methods.

Results
The MIR spectra obtained were explored firstly using Principal Component Analysis, whereas multivariate calibration models were developed based on partial least-squares regression. MIR showed an excellent prediction capacity for the determination of PC:PD [coefficient of determination for prediction (R2P) = 0.96; ratio of prediction to deviation (RPD) = 5.26, range error ratio (RER) = 14.1] and cis:trans ratio (R2P = 0.95; RPD = 4.24; RER = 13.3); modest for CT quantification (HBAI: R2P = 0.92; RPD = 3.71; RER = 13.1; Thiolysis: R2P = 0.88; RPD = 2.80; RER = 11.5); and weak for mDP (R2P = 0.66; RPD = 1.86; RER = 7.16).

Conclusions
MIR combined with chemometrics allowed to characterize the full CT profile of tree foliage rapidly, which would help to assess better plant ecology variability and to improve the nutritional management of ruminant livestock.