bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping of yaws endemicity in Ghana; Lessons to strengthen the planning and implementation of yaws eradication
Authors: Basing Laud Anthony Wihibeturo , Djan Moses , Simpson Shirley Victoria , Adu-Sarkodie Yaw 
Published: February 2020

AbstractIntroductionYaws caused by Treponema pallidum subsp pertenue is a disease of poverty and affects communities where basic socio-economic amenities are lacking. With results showing that single dose azithromycin is effective in the treatment of yaws, the World Health Organisation introduced the Morges strategy with the intent to eradicate yaws by 2020. Ghana is one of the countries with the most yaws cases globally, and the National Yaws Eradication Program in Ghana intends to conduct Mass Drug Administration (MDA) of endemic communities in line with the Total Community Treatment plan of the Morges strategy. It is therefore important to map out endemic communities to ensure that MDA is both effective and financially efficient.MethodsChildren with suspected yaws lesions were actively selected from the recruitment sites (schools and communities). A full medical history, study site information including GPS coordinates, demographic data including communities of residence and clinical assessment were taken. Each of the clinically diagnosed children were screened using the DPP® Syphilis Screen & Confirm Assay (DPP). Samples for PCR were collected by swabbing ulcerative lesions of participants and tested for Treponema pallidum subsp pertenue and Haemophilus ducreyi DNAResultsIn all, 625 children with a median age of 10 years were recruited into the study. While 401(64.2%) were DPP positive, only 141 of them had Treponema pallidum subsp pertenue DNA (TPE_DNA) accounting for 22.6% of those who were clinically diagnosed. Based on the DPP results, yaws was endemic in all the 4 study sites with participants from 88 communities in 13 districts in 4 regions in Ghana. There was no statistically significant difference between the various districts in terms of DPP results (x2=0.9364, p= 0.817) and 154 (24.6%) of those clinically diagnosed as yaws were positive for Haemophilus ducreyi i DNA.ConclusionOur study shows that communities endemic for yaws are also endemic for Haemophilus ducreyi i. Most yaws endemic communities were found at the border of other districts and regions. It is recommended that MDA should not only target endemic communities, it should target entire endemic districts as well as neighbouring districts in order to be effective.
Artificial neural networks in neurorehabilitation: A scoping review
Authors: Moon Sanghee , Ahmadnezhad Pedram , Song Hyun-Je , Thompson Jeffrey , Kipp Kristof , Akinwuntan Abiodun E , Devos Hannes 
Published: February 2020

AbstractBACKGROUNDAdvances in medical technology produce highly complex datasets in neurorehabilitation clinics and research laboratories. Artificial neural networks (ANNs) have been utilized to analyze big and complex datasets in various fields, but the use of ANNs in neurorehabilitation is limited. OBJECTIVE: To explore the current use of ANNs in neurorehabilitation. METHODS: PubMed, CINAHL, and Web of Science were used for literature search. Studies in the scoping review (1) utilized ANNs, (2) examined populations with neurological conditions, and (3) focused rehabilitation outcomes. The initial search identified 1,136 articles. A total of 19 articles were included. RESULTS: ANNs were used for prediction of functional outcomes and mortality (n = 11) and classification of motor symptoms and cognitive status (n = 8). Most ANN-based models outperformed regression or other machine learning models (n = 11) and showed accurate performance (n = 6; no comparison with other models) in predicting clinical outcomes and accurately classifying different neurological impairments.CONCLUSIONSThis scoping review provides encouraging evidence to use ANNs for clinical decision-making of complex datasets in neurorehabilitation. However, more research is needed to establish the clinical utility of ANNs in diagnosing, monitoring, and rehabilitation of individuals with neurological conditions.
Estimating the Asymptomatic Proportion of 2019 Novel Coronavirus onboard the Princess Cruises Ship, 2020
Authors: Mizumoto Kenji , Kagaya Katsushi , Zarebski Alexander , Chowell Gerardo 
Published: February 2020

AbstractThe potential infectiousness of asymptomatic COVID-19 cases together with a substantial fraction of asymptomatic infections among all infections, have been highlighted in clinical studies. We conducted statistical modeling analysis to derive the delay-adjusted asymptomatic proportion of the positive COVID-19 infections onboard the Princess Cruises ship along with the timeline of infections. We estimated the asymptomatic proportion at 17.9% (95% CrI: 15.5%–20.2%), with most of the infections occurring before the start of the 2-week quarantine.
Association between proteomic blood biomarkers and DTI/NODDI metrics in adolescent football players
Authors: Kawata Keisuke , Steinfeldt Jesse A. , Huibregtse Megan E. , Nowak Madeleine K. , Macy Jonathan T. , Shin Andrea , Chen Zhongxue , Ejima Keisuke , Kercher Kyle , Newman Sharlene D. , Cheng Hu 
Published: February 2020

ABSTRACTThe objective of the study was to examine the association between diffusion MRI techniques [diffusion tensor imaging (DTI) and neurite orientation/dispersion density imaging (NODDI)] and brain-injury blood biomarker levels [Tau, neurofilament-light (NfL), glial-fibrillary-acidic-protein (GFAP)] in high-school football and cross-country runners at their baseline, aiming to detect cumulative neuronal damage from prior seasons. Twenty-five football players and 8 cross-country runners underwent MRI and blood biomarker measures during preseason data collection. The whole-brain, tract-based spatial statistics was conducted for six diffusion metrics: fractional anisotropy (FA), mean diffusivity (MD), axial/radial diffusivity (AD, RD), neurite density index (NDI), and orientation dispersion index (ODI). Diffusion metrics and blood biomarker levels were compared between groups and associated within each group. The football group showed lower AD and MD than the cross-country group in various axonal tracts of the right hemisphere. Elevated ODI was observed in the football group in the right hemisphere of the corticospinal tract. Blood biomarker levels were consistent between groups except for elevated Tau levels in the cross-country group. Tau level was positively associated with MD and negatively associated with NDI in the corpus callosum of football players, but not in cross-country runners. Our data suggest that football players may develop axonal microstructural abnormality. Levels of MD and NDI in the corpus callosum were associated with serum Tau levels, highlighting the vulnerability of the corpus callosum against cumulative head impacts. Despite observing multimodal associations in some brain areas, neuroimaging and blood biomarkers may not strongly correlate to reflect the severity of brain damage.
Research on the relationship between postoperative D-dimer clearance and trauma infection complications in patients with different degrees of fracture
Authors: Ma Hai-Mei , Pan Yong-wei , Chen Lianxu 
Published: February 2020

AbstractBackgroundOccurrence of thrombotic disease after orthopedic surgery has always been an important issue affecting the prognosis of patients. In this paper, retrospective analysis was used to analyze the D-dimer clearance rate after different degrees of fractures, suggesting that the D-dimer clearance rate can be used as an index to evaluate thrombotic diseases after orthopedic surgery.Material/MethodsSeventy-five patients with orthopedic surgery were randomly selected from March to June 2017. According to the degrees of fractures and complications, they were divided into SF(single fracture), MF(multiple fracture), FCI(Fracture combined with infection)three groups, 25 in each group.D-dimer results of each case on 1 day, 2 days, 3 days, 4 days, 5 days, and 7 days after orthopedic surgery were recorded and counted.The slope of correlation equation of D-dimer value according to time is the D-dimer clearance rate.ResultsThe D-dimer clearance rate in the SF□JMF □FCI group was −0.0490, −0.0502 and −0.0692□The P value is respectively 0.0049, 0.0061 and 0.0163, the difference is significant.ConclusionsAfter traumatic fracture surgery, whether D-dimer clears at a normal rate is closely related to its outcome. Decreasing D-dimer clearance is related to postoperative infections and thrombotic diseases. D-dimer clearance can be used as an important parameter and observation index for judging the clinical outcome of patients with complications such as severe trauma and infection. At the same time, we can further study the cut-off value of D-dimer clearance.
Dose-response relationship between protein intake and muscle mass increase: a systematic review and meta-analysis of randomized controlled trials
Authors: Tagawa Ryoichi , Watanabe Daiki , Ito Kyoko , Ueda Keisuke , Nakayama Kyosuke , Sanbongi Chiaki , Miyachi Motohiko 
Published: February 2020

AbstractBackgroundLean body mass (LBM) is essential for health; however, consensus regarding the effectiveness of protein interventions in increasing LBM is lacking.ObjectiveEvaluate the dose-response relationship of the effects of protein on LBM.Data SourcesPubMed and Ichushi-Web databases were searched. A manual search of the references of the literature included here and in other meta-analyses was conducted.Study SelectionRandomized controlled trials evaluating the effect of protein intake on LBM were included.Data ExtractionTwo researchers independently screened the abstracts; five reviewed the full-texts.Results5402 subjects from 105 articles were included. In the multivariate-spline model, the mean and corresponding 95% confidence intervals (CIs) for LBM increase for 0.1 g/kg body weight (BW)/day increment was 0.39 [95% CI, 0.36–0.41] kg and 0.12 [0.11–0.14] kg below and above total protein intake 1.3 g/kg BW/day, respectively.ConclusionsOur findings suggest that slightly increasing current protein intake for several months by 0.1 g/kg BW/day may increase or maintain LBM in a dose-response manner from 0.5 to 3.5 g/kg BW/day.
Genetic association of FMRP targets with psychiatric disorders
Authors: Clifton Nicholas E , Rees Elliott , Holmans Peter A , Pardiñas Antonio F. , Harwood Janet C , Di Florio Arianna , Kirov George , Walters James TR , O’Donovan Michael C , Owen Michael J , Hall Jeremy , Pocklington Andrew J 
Published: February 2020

AbstractGenes encoding the mRNA targets of Fragile X mental retardation protein (FMRP) are enriched for genetic association with psychiatric disorders. However, many FMRP targets possess functions that are themselves genetically associated with psychiatric disorders, including synaptic transmission and plasticity, making it unclear whether the genetic risk is truly related to binding by FMRP or is alternatively mediated by the sampling of genes better characterised by another trait or functional annotation. Using published common variant, rare coding variant and copy number variant data, we examined the relationship between FMRP binding and genetic association with schizophrenia, major depressive disorder and bipolar disorder. We then explored the partitioning of genetic association between overrepresented functional categories. High-confidence targets of FMRP were enriched for common schizophrenia risk alleles, as well as rare loss-of-function andde novononsynonymous variants in cases. Similarly, through common variation, FMRP targets were associated with major depressive disorder, and we present novel evidence of association with bipolar disorder. These relationships could not be explained by membership of other functional annotations known to be associated with psychiatric disorders, including those related to synaptic structure and function. This study reinforces the evidence that targeting by FMRP captures a subpopulation of genes enriched for genetic association with a range of psychiatric disorders, across traditional diagnostic boundaries.
Combining rational design and continuous evolution on minimalist proteins that target DNA
Authors: Inamoto Ichiro , Sheoran Inder , Popa Serban C. , Hussain Montdher , Shin Jumi A. 
Published: February 2020

ABSTRACTWe designedMEFto mimic the basic region/helix-loop-helix/leucine zipper (bHLHZ) domain of transcription factors Max and Myc, which bind with high DNA sequence specificity and affinity to the E-box motif (enhancer box, CACGTG). To makeMEF, we started with our rationally designed ME47, a hybrid of the Max basic region and E47 HLH, that effectively inhibited tumor growth in a mouse model of breast cancer. ME47, however, displays propensity for instability and misfolding. We therefore sought to improve ME47’s structural and functional features. We used phage-assisted continuous evolution (PACE) to uncover “nonrational” changes to complement our rational design. PACE mutated Arg12 that contacts the DNA phosphodiester backbone. We would not have rationally made such a change, but this mutation improved ME47’s stability with little change in DNA-binding function. We mutated Cys29 to Ser and Ala in ME47’s HLH to eliminate undesired disulfide formation; these mutations reduced E-box binding activity. To compensate, we fused the designed FosW leucine zipper to ME47 to increase the dimerization interface and improve protein stability and E-box targeting activity. This “franken-protein”MEFcomprises the Max basic region, E47 HLH, and FosW leucine zipper—plus mutations that arose during PACE and rational design—and is a tractable, reliable proteinin vivoandin vitro.Compared with ME47,MEFgives three-fold stronger binding to E-box with four-fold increased specificity for E-box over nonspecific DNA. Generation ofMEFdemonstrates that combining rational design and continuous evolution can be a powerful tool for designing proteins with robust structure and strong DNA-binding function.
Networks of HIV-1 envelope glycans maintain antibody epitopes in the face of glycan additions and deletions
Authors: Seabright Gemma E. , Cottrell Christopher A. , van Gils Marit J. , D’addabbo Alessio , Harvey David J. , Behrens Anna-Janina , Allen Joel D. , Watanabe Yasunori , Maker Allison , Vasiljevic Snezana , de Val Natalia , Sanders Rogier W. , Ward Andrew B. , Crispin Max 
Published: February 2020

SUMMARYNumerous broadly neutralizing antibodies (bnAbs) have been identified that target the glycans of the HIV-1 envelope spike. Neutralization breadth is notable given that glycan processing can be substantially influenced by the presence or absence of neighboring glycans. Here, using a stabilized recombinant envelope trimer, we investigate the degree to which mutations in the glycan network surrounding an epitope impact the fine glycan processing of antibody targets. Using cryo-electron microscopy and site-specific glycan analysis, we reveal the hierarchy of importance of glycans in the formation of the 2G12 bnAb epitope, and show that the epitope is only subtly impacted by variations in the glycan network. In contrast, we show that the PG9 and PG16 glycan-based epitopes at the trimer apex are dependent on the presence of the highly conserved surrounding glycans. Glycan networks underpin the conservation of bnAb epitopes and are an important parameter in immunogen design.
Probing SWATH-MS as a tool for proteome level quantification in a non-model fish
Authors: Monroe Alison A. , Zhang Huoming , Schunter Celia , Ravasi Timothy 
Published: February 2020

AbstractQuantitative proteomics via mass spectrometry can provide valuable insight into molecular and phenotypic characteristics of a living system. Recent mass spectrometry developments include data-independent acquisition (SWATH/DIA-MS), an accurate, sensitive, and reproducible method for analyzing the whole proteome. The main requirement for this method is the creation of a comprehensive spectral library. New technologies have emerged producing larger and more accurate species-specific libraries leading to a progressive collection of proteome references for multiple molecular model species. Here, for the first time, we set out to compare different spectral library constructions using multiple tissues from a coral reef fish to demonstrate its value and feasibility for non-model organisms. We created a large spectral library composed of 12,553 protein groups from liver and brain tissues. Via identification of differentially expressed proteins (DEPs) under fish exposure to environmental stressors we validated the application and usefulness of these different spectral libraries. Successful identification of significant DEPs from different environmental exposures occurred using the library with a combination of DIA+DDA data as well as both tissue types. Further analysis revealed expected patterns of significantly upregulated heat shock proteins in a dual condition of ocean warming and acidification indicating the biological accuracy and relevance of the method. This study provides the first reference spectral library for a coral reef fish and for a non-model organism. It represents a useful guide for the future building of accurate spectral library references in non-model organisms allowing the discovery of ecologically relevant changes in the proteome.
Improved Parameterization of Protein–DNA Interactions for Molecular Dynamics Simulations of PCNA Diffusion on DNA
Authors: You Sunjoo , Lee Hongeun , Kim Kimoon , Yoo Jejoong 
Published: February 2020

ABSTRACTHere, we quantitatively evaluate the accuracy of the protein–DNA interactions in AMBER and CHARMM force fields by comparing experimental and simulated diffusion coefficients of proliferating cell nuclear antigen (PCNA). We find that both force fields underestimate diffusion coefficients by at least an order of magnitude because the interactions between basic amino acids and DNA phosphate groups are too attractive. Then, we propose Lennard-Jones parameters optimized using the experimental osmotic pressure data of model chemicals, by using which one can reproduce the experimental diffusion coefficients. Newly optimized parameters will have a broad impact on general protein–DNA interactions.
Identification of a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum
Authors: Longman Dasa , Jackson-Jones Kathryn A. , Maslon Magdalena M. , Murphy Laura C. , Young Robert S. , Stoddart Jack J. , Taylor Martin S. , Papadopoulos Dimitrios K. , Cáceres Javier F. 
Published: February 2020

AbstractNonsense-mediated decay (NMD) is a translation-dependent RNA quality control mechanism that occurs in the cytoplasm. However, it is unknown how NMD regulates the stability of RNAs translated at the Endoplasmic Reticulum (ER). Here, we identify a localized NMD pathway dedicated to ER-translated mRNAs. We previously identified NBAS, a component of the Syntaxin 18 complex involved in Golgi-to-ER trafficking, as a novel NMD factor. Here, we show that NBAS fulfils an independent function in NMD. This ER-NMD pathway requires the interaction of NBAS with the core NMD factor UPF1, which is partially localized at the ER in the proximity of the translocon. NBAS and UPF1 co-regulate the stability of ER-associated transcripts, in particular those associated with the cellular stress response. We propose a model where NBAS recruits UPF1 to the membrane of the ER and activates an ER-dedicated NMD pathway, thus providing an ER protective function by ensuring quality control of ER-translated mRNAs.Graphical AbstractHIGHLIGHTSNBAS is an NMD factor that localizes to the membrane of the endoplasmic reticulum (ER)NBAS has dual, independent, roles in Golgi-to-ER retrograde transport and in ER-NMDNBAS recruits the core NMD factor UPF1 to the membrane of the ERThe ER-NMD pathway targets for degradation mRNAs that are translated at the ER
Serum alpha-mannosidase as an additional barrier to eliciting oligomannose-specific HIV-1-neutralizing antibodies
Authors: Bruxelle Jean-François , Kirilenko Tess , Qureshi Quratulain , Lu Naiomi , Trattnig Nino , Kosma Paul , Pantophlet Ralph 
Published: February 2020

ABSTRACTOligomannose-type glycans on HIV-1 gp120 form a patch that is targeted by several broadly neutralizing antibodies (bnAbs) and that therefore is of interest to vaccine design. However, attempts to elicit similar oligomannose-specific bnAbs by immunizing with oligomannosidic glycoconjugates have only been modestly successful so far. A common assumption is that eliciting oligomannose-specific bnAbs is hindered by B cell tolerance, resulting from the presented oligomannosides being sensed as self molecules. Here, we present data, along with existing scientific evidence, supporting an additional, or perhaps alternate, explanation: serum mannosidase trimming of the presented oligomannosidesin vivo. Mannosidase trimming lessens the likelihood of eliciting antibodies with capacity to bind full-sized oligomannose, which typifies the binding mode of existing bnAbs to the oligomannose patch. The rapidity of the observed trimming suggests the need for immunization strategies and/or synthetic glycosides that readily avoid or resist mannosidase trimming upon immunization and can overcome possible tolerance restrictions.
Beyond copper: China and Chile relations
Authors: Serrano Moreno Juan Enrique , Pérez Ceballos Alejandra , De Abreu Negrón María Gabriela 
Published: February 2020

PurposeThis study aims to investigate the Chile–China diplomatic and economic relations in the light of the extension of the bilateral free trade agreement (FTA) and the Chile's accession to the Belt and Road Initiative (BRI) in 2019.Design/methodology/approachThis study takes Chile as a case of study to identify the main upcoming challenges and opportunities for relations between China and Latin American and the Caribbean (LAC) countries. The study examines news and official data on trade, investment and foreign policy.FindingsThe findings are twofold. First, the increasing and diversification of exports from Chile to China. Second, the participation of Chinese companies in public tendering procedures, which is increasing Chinese foreign direct investment (FDI) in the country. The growing volume of trade does not make Chile's economy more dependent on copper exports, and Chinese investment may help solve the structural deficit in infrastructures of the Andean country.Originality/valueThis study presents an overview of Chile as a partner for China and evaluates the relationship's impact on the development of the former. Recently collected data on bilateral trade and investments are analyzed to contribute to the emerging literature on Chinese and Chile relations.