bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ability of near-infrared spectroscopy and chemometrics to predict the age of mosquitoes reared under different conditions
Authors: Ong Oselyne , Kho Elise , Esperança Pedro , Freebairn Chris , Dowell Floyd , Devine Gregor , Churcher Thomas 
Published: December 2019

Abstract
Background: Practical, field-ready age-grading tools for mosquito vectors of disease are urgently needed because of the impact that daily survival has on vectorial capacity. Previous studies have shown that near-infrared spectroscopy (NIRS), in combination with chemometrics and predictive modeling, can forecast the age of laboratory-reared mosquitoes with moderate to high accuracy. However, it remains it is unclear whether the technique has utility for identifying shifts in the age structure of wild-caught mosquitoes or whether models derived from the laboratory or semi-field mosquitoes can be applied to mosquitoes reared under different environments. Methods: NIRS spectral data from adult female Aedes albopictus mosquitoes reared in the laboratory (2, 5, 8, 12 and 15 days old) and in semi-field cages populated by wild-caught pupae (resulting in adults of 1, 7 and 14 days old). Spectral data collected from mosquitoes were used to determine if models derived from laboratory material using partial least squares (PLS) regression for the development of predictive models could be effectively applied to mosquitoes from more natural semi-field environments. Results: Models trained on spectra from laboratory-reared material were able to predict the age of other laboratory-reared mosquitoes with moderate accuracy and successfully differentiated all day 2 and 15 mosquitoes. Models derived with laboratory mosquitoes could not differentiate between semi-field age groups, with age predictions relatively indistinguishable for day 1-14. Pre-processing of spectral data and improving the PLS regression framework to avoid overfitting can increase accuracy, but predictions of mosquitoes reared in different environments remained poor. Principle component analysis confirms substantial spectral variations between laboratory and semi-field mosquitoes despite both being derived from the same island population. Conclusions: Model trained on laboratory mosquitoes were able to predict ages of laboratory mosquitoes with good sensitivity and specificity, however it was unable to predict age class of semi-field mosquitoes. This study suggests that laboratory-reared mosquitoes do not capture enough environmental variation to accurately predict the age of the same species reared under different conditions. Further research is needed to explore alternative pre-processing methods and machine learning techniques, and to understand factors that affect absorbance in mosquitoes before field application using NIRS.
Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites
Authors: Gage Hunter L. , Merrick Catherine J. 
Published: December 2019

Abstract
Background:
The Plasmodium genus of malaria parasites encodes several families of antigen-encoding genes. These genes tend to be hyper-variable, highly recombinogenic and variantly expressed. The best-characterized family is the var genes, exclusively found in the Laveranian subgenus of malaria parasites infecting humans and great apes. Var genes encode major virulence factors involved in immune evasion and the maintenance of chronic infections. In the human parasite P. falciparum, var gene recombination and diversification appear to be promoted by G-quadruplex (G4) DNA motifs, which are strongly associated with var genes in P. falciparum. Here, we investigated how this association might have evolved across Plasmodium species – both Laverania and also more distantly related species which lack vars but encode other, more ancient variant gene families.
Results:
The association between var genes and G4-forming motifs was conserved across Laverania, spanning ~1 million years of evolutionary time, with suggestive evidence for evolution of the association occurring within this subgenus. In rodent malaria species, G4-forming motifs were somewhat associated with pir genes, but this was not conserved in the Laverania, nor did we find a strong association of these motifs with any gene family in a second outgroup of avian malaria parasites. Secondly, we compared two different G4 prediction algorithms in their performance on extremely A/T-rich Plasmodium genomes, and also compared these predictions with experimental data from G4-seq, a DNA sequencing method for identifying G4-forming motifs. We found a surprising lack of concordance between the two algorithms and also between the algorithms and G4-seq data.
Conclusions:
G4-forming motifs are uniquely strongly associated with Plasmodium var genes, suggesting a particular role for G4s in recombination and diversification of these genes. Secondly, in the A/T-rich genomes of Plasmodium species, the choice of prediction algorithm may be particularly influential when studying G4s in these important protozoan pathogens.
Management of Constipation in Long-term Care Hospitals and its Ward Manager and Organization Factors
Authors: Takaoka Manami , Igarashi Ayumi , Futami Asako , Yamamoto-Mitani Noriko 
Published: December 2019

Abstract
Background: Studies examining organizational factors that may influence constipation management in long-term care (LTC) hospitals are lacking. This study aimed to clarify the practice of constipation management in LTC hospitals and to explore its factors, including ward manager’s perception, organizational climate, and constipation assessment.Methods: In this cross-sectional questionnaire survey of ward managers and staff nurses working in LTC wards, we determined daily assessment and practices regarding constipation management. We also conducted multivariate analyses to examine factors related to constipation management.Results: There was a 20% response rate to the questionnaire. Nearly all LTC wards routinely assessed bowel movement frequency; other assessments were infrequent. Laxatives were used, but the use of dietary fiber and probiotic products was implemented in only 20%–30% of wards. The implementation of non-pharmacological management and adequate use of stimulant laxatives were positively associated with the ward manager’s belief and knowledge, organizational climate, the existence of nursing records for constipation assessment, planned nursing care for constipation, and organized conferences and in-hospital study sessions on constipation management.Conclusion: Areas to improve constipation management in LTC hospitals include altering the ward manager’s perception, improving hospital’s organizational climate, and introducing standardized assessment/care planning systems.
Molecular surveillance of antimalarial drug resistance in Democratic Republic of Congo: high variability of chloroquinoresistance and lack of amodiaquinoresistance
Authors: Yobi Doudou Malekita , Kayiba Nadine Kalenda , Mvumbi Dieudonné Makaba , Boreux Raphael , Kabututu Pius Zakayi , Situakibanza Hippolyte Nani-Tuma , Likwela Joris Losimba , De Mol Patrick , Okitolonda Emile Wemakoy , Speybroeck Niko , Mvumbi Georges Lelo , Hayette Marie-Pierre 
Published: December 2019

Abstract
Background The loss of chloroquine (CQ) effectiveness has led to its withdrawal from national policies as first-line treatment for uncomplicated malaria in several endemic countries such as in the Democratic Republic of Congo (DRC). The K76T mutation on the pfcrt gene has been identified as a marker of CQ resistance and the SVMNT haplotype in codons 72–76 on the same gene has been associated with resistance to amodiaquine (AQ). In DRC, the prevalence of K76T has decreased from 100% in 2000 to 63.9% in 2014. The purpose of the study was to determine the prevalence of K76T mutations in P. falciparum circulating strains, sixteen years after CQ withdrawal in DRC and to investigate the presence of SVMNT haplotype. Methods In 2017, ten geographical sites across DRC were selected. Dried blood samples were collected from patients attending health centers. Malaria was first detected by rapid diagnostic test (RDT) available on site (SD Bioline malaria Ag Pf or CareStart Malaria Pf) or thick blood smear and then confirmed by a P. falciparum species-specific real-time PCR assay. A pfcrt gene segment containing a fragment that encodes amino acids at positions 72-76 was amplified by conventional PCR before sequencing. Results A total of 1070 patients were enrolled. Of the 806 PCR-confirmed P. falciparum positive samples, 764 were successfully sequenced. The K76T mutation was detected in 218 (28.5%; IC95%: 25.4% – 31.9%) samples, mainly (96%) with the CVIET haplotype. The CQ resistance prevalence was unequally distributed across the country ranging from 1.5% in Fungurume to 89.5% in Katana. The SVMNT haplotype, related to AQ resistance, was not detected. Conclusion Overall, the P. falciparum CQ resistance rate has decreased significantly and no resistance marker to AQ was detected in DRC in 2017. However, the between regions variability of CQ resistance remains high in the country. Further studies are needed for a continuous monitoring of the CQ resistance level for a prospective re-use in malaria management. The absence of AQ resistance is in line with the use of this drug in the current DRC malaria treatment policy.
Genome wide association analysis on semen volume and milk yield using different strategies of imputation to whole genome sequence in French dairy goats
Authors: Talouarn Estelle , Bardou Philippe , Palhière Isabelle , Oget Claire , Clément Virginie , Tosser-Klopp Gwenola , Rupp Rachel , Robert-Granié Christèle 
Published: December 2019

Abstract
Goats were domesticated 10,500 years ago to supply humans with useful resources. Since then, specialized breeds that are adapted to their local environment have been developed and display specific genetic profiles. The VarGoats project is a 1,000 genomes resequencing program designed to cover the genetic diversity of the Capra genus. In this study, our main objective was to assess the use of sequence data to detect genomic regions associated with traits of interest in French Alpine and Saanen breeds. Sequence variants were assessed using indicators of quality, depth, minor allele frequency (MAF) and position.
Direct imputation from the GoatSNP50 BeadChip genotypes to sequence level was investigated in these breeds using FImpute and different reference panels: within-breed, all Capra hircus sequenced individuals, European goats and French mainland goats. The best results were obtained with the French goat panel with allele and genotype concordance rates reaching 0.86 and 0.75 in the Alpine and 0.86 and 0.73 in the Saanen breed respectively. Mean correlations tended to be low in both breeds due to the high proportion of variants with low MAF profiles.
For association analysis, imputation was performed using FImpute for 1,129 French Alpine and Saanen males using within-breed and French panels on the 23,338,436 filtered variants. Association analysis was carried out using polygenic models with GCTA. The association results of both imputation scenarios were then compared. In Saanen goats, a large region on chromosome 19 was significantly linked to semen volume and milk yield in both scenarios. Significant variants for milk yield were annotated for 91 genes on chromosome 19 in Saanen goats. For semen volume, the annotated genes include YBOX2 which is related to azoospermia or oligospermia in other species. New signals for milk yield were detected on chromosome 2 in Alpine goats and on chromosome 5 in Saanen goats when using a multi-breed panel. GWAS on imputed sequences confirmed the existence of QTLs and identified new regions of interest in dairy goats. Adding identified candidates to a genotyping array and sequencing more individuals might corroborate the involvement of these regions in functional and production traits while removing potential imputation errors.
Competitive endogenous RNA network reveals that miR-1343 play key regulatory roles in longissimus dorsi muscle between Saba and Yorkshire pigs
Authors: Hu Wei , Chen Qiang , Wang Xiaoyi , Dong Xinxing , Li Mingli , Lan Guoxiang , Yan Dawei , Yang Yu , Lu Shaoxiong 
Published: December 2019

Abstract
Background Pork quality is an important economic trait in pig industry, and increasing data shows that Chinese indigenous and Western commercial pig breeds have significant differences in pork quality. However, the molecular regulatory mechanism of pork quality formation is still unclear. The aim of this study was to explore the transcriptional regulation mechanism of pork quality formation of Chinese Saba pig (SS) and Western Yorkshire pig (YY) breeds.
Results A total of 31 DEmiRNAs, 902 DEmRNAs, 47 DElncRNAs and 198 DEcircRNAs were identified in longissimus dorsi muscles between SSs and YYs. On the basis of differentially expressed RNAs, two ceRNA networks including lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA were established, and two ceRNA networks showed that miR-1343 had the most links in two ceRNA networks, which demonstrated that miR-1343 might play key regulatory roles in longissimus dorsi muscle formation between SS and YY breeds.
Conclusions The present study identified miR-1343 as key regulatory factor in pig longissimus dorsi muscle formation by ceRNA networks, which provides novel insights into molecular regulatory mechanism of pork quality formation between fat-type and lean-type pig breeds.
The role of residents in medical students’ neurology education: current status and future perspectives
Authors: Keser Zafer , Rodriguez Yvo A , Tremont Jennifer , Hsieh Peggy H , McCullough Louise D. , Sandrone Stefano , Stimming Erin F 
Published: December 2019

Abstract
Background: Neurophobia, a well-described fear of Neurology affecting medical students worldwide, may be one of the causes of the decreased interest in neurology, which is leading to a shortage of neurologists in the United States. Within educational systems, residents play a key role in education of students, although often underrecognized. Here we formally investigate the impact of resident teaching on medical students’ neurologic educational experience, analyze how this relates to students’ confidence and interest in neurology. Methods: Third year medical students (n=234) of UTHealth’s McGovern Medical School rotating at Neurology as their core rotation completed two surveys regarding their rotation experiences; before and after their rotation in an anonymous manner to measure their interest and confidence in neurology and the impact of their interactions with the neurology residents on their rotation experience. Also residents underwent a workshop on small group teaching to improve their teaching effectiveness. Non-parametrical comparison and ordinal regression analyses were utilized for data analyses. Results: Rotating medical students felt significantly more confident in managing neurological conditions more interested in pursuing neurology residency after their rotation. There was a significant association between the medical students’ overall rotation experience and the residents’ teaching effectiveness. Their overall rotation experience was also associated with their interest and confidence in neurology. There was a trend of increase in residents’ teaching effectiveness and students’ rotation experience after the workshop. Conclusion: This study shows that resident led teaching efforts are important in improving the medical students’ neurologic education. We also discuss future strategies to exploit “near-peer” teaching in a sustainable fashion to increase the medical students educational experience and competencies and how these could potentially mitigate neurophobia.
Dealing with patient expectations regarding the prescription of antibiotics in ambulatory care in Germany: A qualitative analysis
Authors: Stuermlinger Anna , Poss-Doering Regina , Glassen Katharina , Wensing Michel , Kamradt Martina 
Published: December 2019

Abstract
Background Antibiotics prescription rates are relatively high in primary care in Germany. Patients’ expectations have frequently been mentioned as reason for high prescription rates. The extent to which patients’ expectations play a role and the strategies that physicians use to deal with these expectations and prevent non-indicated prescriptions in acute, uncomplicated infections are the subject of this paper.Methods In this qualitative study, twenty-seven semi-structured interviews with physicians were conducted in 2018. Data were audiotaped, pseudonymized and transcribed verbatim. The analysis was based on a framework analysis according to the Tailored Implementation in Chronic Diseases (TICD) checklist, and was expanded for deeper analysis and completed with the Behavior Change Techniques (BCT) taxonomy. Results The data revealed that patients’ expectations regarding the prescription of antibiotics can play an important role, although they may be ignored by physicians. If physicians respond to patients’ expectations, they use various strategies to deal and communicate with patients. Successful communication is more often achieved, if the physician takes sufficient time with the patient and if this results in a cooperative conversation. Thus, patients get informed about antibiotics and antimicrobial resistance, and it is possible to discuss alternative treatments. Seven strategies from the BCT taxonomy were mentioned by physicians in this study.Conclusion Constructive physician-patient communication was key to reducing antibiotic prescribing. The range of behavior change techniques mentioned by physicians was relatively limited and the use of a wider range of strategies could be the focus of future implementation strategies. Trial registration: ISRCTN, ISRCTN58150046. Registered 24 August 2017. Keywords Antibiotics prescription, patient expectations, physician-patient communication, patient education, communication strategies, behavior change technique, qualitative research
Dried blood spot versus venous blood sampling for phenylalanine and tyrosine: a large difference?
Authors: Vliet Kimber van , Ginkel Wiggert G. van , Dam Esther van , de Blaauw Pim , Koehorst Martijn , Kingma Hermi A. , Spronsen Francjan J. van , Heiner-Fokkema M. Rebecca 
Published: December 2019

Abstract
BACKGROUND: To investigate agreement between various dried blood spot (DBS) and venous blood sample measurements of phenylalanine and tyrosine concentrations in Phenylketonuria (PKU) and Tyrosinemia type 1 (TT1) patients. STUDY DESIGN: Phenylalanine and tyrosine concentrations were studied in 45 PKU/TT1 patients in plasma from venous blood in lithium heparin (LH) and EDTA tubes; venous blood from LH and EDTA tubes on a DBS card; venous blood directly on a DBS card; and capillary blood on a DBS card. Plasma was analyzed with an amino acid analyzer and DBS were analyzed with liquid chromatography-mass spectrometry. Agreement between different methods was assessed using Passing and Bablok fit and Bland Altman analyses. RESULTS: In general, phenylalanine concentrations in LH plasma were comparable to capillary DBS, whereas tyrosine concentrations were slightly higher in LH plasma (constant bias of 6.4 µmol/L). However, in the low phenylalanine range, most samples had higher phenylalanine concentrations in DBS compared to LH plasma. Remarkably, phenylalanine and tyrosine in EDTA plasma were higher compared to all other samples (slopes ranging from 7-12%). No differences were observed when comparing capillary DBS to other DBS. CONCLUSIONS: Overall agreement between plasma and DBS is good. However, bias is specimen- (LH vs EDTA), and possibly concentration- (low phenylalanine) dependent. Because of the overall good agreement, we recommend the use of a DBS-plasma correction factor for DBS measurement. Each laboratory should determine their own factor dependent on filter card type, extraction and calibration protocols taking the LH plasma values as gold standard.
Transcript, protein, metabolite and cellular studies in skin fibroblasts demonstrate variable pathogenic impacts of NPC1 mutations.
Authors: Musalkova Dita , Majer Filip , Kuchar Ladislav , Luksan Ondrej , Asfaw Befekadu , Vlaskova Hana , Storkanova Gabriela , Reboun Martin , Poupetova Helena , Jahnova Helena , Hulkova Helena , Ledvinova Jana , Dvorakova Lenka , Sikora Jakub , Jirsa Milan , Vanier Marie Therese , Hrebicek Martin 
Published: December 2019

Abstract
Background:F Niemann-Pick type C (NP-C) is a rare neurovisceral genetic disorder caused by mutations in the NPC1 or the NPC2 gene. NPC1 is a multipass-transmembrane protein essential for egress of cholesterol from late endosomes/lysosomes. To evaluate impacts of NPC1 mutations, we examined fibroblast cultures from 26 NP-C1 patients with clinical phenotypes ranging from infantile to adult neurologic onset forms. The cells were tested with multiple assays including NPC1 mRNA expression levels and allele expression ratios, assessment of NPC1 promoter haplotypes, NPC1 protein levels, cellular cholesterol staining, localization of the mutant NPC1 proteins to lysosomes, and cholesterol/cholesteryl ester ratios. These results were correlated with phenotypes of the individual patients. Results: Overall we identified 5 variant promoter haplotypes. Three of them showed reporter activity decreased down to 70% of the control sequence. None of the haplotypes were consistently associated with more severe clinical presentation of NP-C. Levels of transcripts carrying null NPC1 alleles were profoundly lower than levels of the missense variants. Low levels of the mutant NPC1 protein were identified in most samples. The protein localised to lysosomes in cultures expressing medium to normal NPC1 levels. Fibroblasts from patients with severe infantile phenotypes had higher cholesterol levels and higher cholesterol/cholesteryl ester ratios. On the contrary, cell lines from patients with juvenile and adolescent/adult phenotypes showed values comparable to controls. Conclusion: No single assay fully correlated with the disease severity. However, low residual levels of NPC1 protein and high cholesterol/cholesteryl ester ratios associated with severe disease. The results suggest not only low NPC1 expression due to non-sense mediated decay or low mutant protein stability, but also dysfunction of the stable mutant NPC1 as contributors to the intracellular lipid transport defect.