bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors associated with the health and cognition of 6‐year‐old to 8‐year‐old children in KwaZulu‐Natal, South Africa
Authors: Ajayi Oluwakemi R. , Matthews Glenda , Taylor Myra , Kvalsvig Jane , Davidson Leslie L. , Kauchali Shuaib , Mellins Claude A. 
Published: March 2017

AbstractObjectiveTo investigate 6‐year‐old to 8‐year‐old children's health, nutritional status and cognitive development in a predominantly rural area of KwaZulu‐Natal, South Africa.MethodsCohort study of 1383 children investigating the association of demographic variables (area of residence, sex, pre‐school education, HIV status, height for age and haemoglobin level) and family variables (socioeconomic status, maternal and paternal level of education), with children's cognitive performance. The latter was measured using the Grover‐Counter Scale of Cognitive Development and subtests of the Kaufman Assessment Battery for Children, second edition (KABC‐II). General linear models were used to determine the effect of these predictors.ResultsArea of residence and height‐for‐age were the statistically significant factors affecting cognitive test scores, regardless of attending pre‐school. Paternal level of education was also significantly associated with the cognitive test scores of the children for all three cognitive test results, whereas HIV status, sex and their socioeconomic status were not.ConclusionChildren with low cognitive scores tended to be stunted (low height‐for‐age scores), lacked pre‐school education and were younger. Area of residence and their parents’ educational level also influenced their cognition.
Picard curves over with good reduction away from 3
Authors: Malmskog Beth , Rasmussen Christopher 
Published: March 2017

Inspired by methods of N. P. Smart, we describe an algorithm to determine all Picard curves over $\mathbb{Q}$ with good reduction away from 3, up to $\mathbb{Q}$-isomorphism. A correspondence between the isomorphism classes of such curves and certain quintic binary forms possessing a rational linear factor is established. An exhaustive list of integral models is determined and an application to a question of Ihara is discussed.
Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples
Authors: Votintseva Antonina A. , Bradley Phelim , Pankhurst Louise , del Ojo Elias Carlos , Loose Matthew , Nilgiriwala Kayzad , Chatterjee Anirvan , Smith E. Grace , Sanderson Nicolas , Walker Timothy M. , Morgan Marcus R. , Wyllie David H. , Walker A. Sarah , Peto Tim E. A. , Crook Derrick W. , Iqbal Zamin 
Published: March 2017

ABSTRACT

Routine full characterization of
Mycobacterium tuberculosis
is culture based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatment, augmented with strain information for global surveillance; such data could be transformative if provided at or near the point of care. We demonstrate a low-cost method of DNA extraction directly from patient samples for
M. tuberculosis
WGS. We initially evaluated the method by using the Illumina MiSeq sequencer (40 smear-positive respiratory samples obtained after routine clinical testing and 27 matched liquid cultures).
M. tuberculosis
was identified in all 39 samples from which DNA was successfully extracted. Sufficient data for antibiotic susceptibility prediction were obtained from 24 (62%) samples; all results were concordant with reference laboratory phenotypes. Phylogenetic placement was concordant between direct and cultured samples. With Illumina MiSeq/MiniSeq, the workflow from patient sample to results can be completed in 44/16 h at a reagent cost of £96/£198 per sample. We then employed a nonspecific PCR-based library preparation method for sequencing on an Oxford Nanopore Technologies MinION sequencer. We applied this to cultured
Mycobacterium bovis
strain BCG DNA and to combined culture-negative sputum DNA and BCG DNA. For flow cell version R9.4, the estimated turnaround time from patient to identification of BCG, detection of pyrazinamide resistance, and phylogenetic placement was 7.5 h, with full susceptibility results 5 h later. Antibiotic susceptibility predictions were fully concordant. A critical advantage of MinION is the ability to continue sequencing until sufficient coverage is obtained, providing a potential solution to the problem of variable amounts of
M. tuberculosis
DNA in direct samples.
RNA-Associated Early-Stage Antiviral Factor Is a Major Component of Lv2 Restriction
Authors: Marno Kelly M. , O'Sullivan Eithne , Jones Christopher E. , Díaz-Delfín Julieta , Pardieu Claire , Sloan Richard D. , McKnight Áine 
Published: March 2017

ABSTRACT
Human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) replication in human cells is restricted at early postentry steps by host inhibitory factors. We previously described and characterized an early-phase restriction of HIV-1 and -2 replication in human cell lines, primary macrophages, and peripheral blood mononuclear cells. The restriction was termed lentiviral restriction 2 (Lv2). The viral determinants of Lv2 susceptibility mapped to the HIV-2 envelope (Env) and capsid (CA). We subsequently reported a whole-genome small interfering RNA screening for factors involved in HIV that identified RNA-associated early-stage antiviral factor (REAF). Using HIV-2 chimeras of susceptible and nonsusceptible viruses, we show here that REAF is a major component of the previously described Lv2 restriction. Further studies of the viral CA demonstrate that the CA mutation I73V (previously called I207V), a potent determinant for HIV-2, is a weak determinant of susceptibility for HIV-1. More potent CA determinants for HIV-1 REAF restriction were identified at P38A, N74D, G89V, and G94D. These results firmly establish that in HIV-1, CA is a strong determinant of susceptibility to Lv2/REAF. Similar to HIV-2, HIV-1 Env can rescue sensitive CAs from restriction. We conclude that REAF is a major component of the previously described Lv2 restriction.

IMPORTANCE
Measures taken by the host cell to combat infection drive the evolution of pathogens to counteract or sidestep them. The study of such virus-host conflicts can point to possible weaknesses in the arsenal of viruses and may lead to the rational design of antiviral agents. Here we describe our discovery that the host restriction factor REAF fulfills the same criteria previously used to describe lentiviral restriction (Lv2). We show that, like the HIV-2 CA, the CA of HIV-1 is a strong determinant of Lv2/REAF susceptibility. We illustrate how HIV counteracts Lv2/REAF by using an envelope with alternative routes of entry into cells.
Mutating the CX3C Motif in the G Protein Should Make a Live Respiratory Syncytial Virus Vaccine Safer and More Effective
Authors: Boyoglu-Barnum S. , Todd S. O. , Meng J. , Barnum T. R. , Chirkova T. , Haynes L. M. , Jadhao S. J. , Tripp R. A. , Oomens A. G. , Moore M. L. , Anderson L. J. 
Published: March 2017

ABSTRACT

Respiratory syncytial virus (RSV) belongs to the family
Paramyxoviridae
and is the single most important cause of serious lower respiratory tract infections in young children, yet no highly effective treatment or vaccine is available. Through a CX3C chemokine motif (
182
CWAIC
186
) in the G protein, RSV binds to the corresponding chemokine receptor, CX3CR1. Since RSV binding to CX3CR1 contributes to disease pathogenesis, we investigated whether a mutation in the CX3C motif by insertion of an alanine, A
186
, within the CX3C motif, mutating it to CX4C (
182
CWAIAC
187
), which is known to block binding to CX3CR1, might decrease disease. We studied the effect of the CX4C mutation in two strains of RSV (A2 and r19F) in a mouse challenge model. We included RSV r19F because it induces mucus production and airway resistance, two manifestations of RSV infection in humans, in mice. Compared to wild-type (wt) virus, mice infected with CX4C had a 0.7 to 1.2 log
10
-fold lower virus titer in the lung at 5 days postinfection (p.i.) and had markedly reduced weight loss, pulmonary inflammatory cell infiltration, mucus production, and airway resistance after challenge. This decrease in disease was not dependent on decrease in virus replication but did correspond to a decrease in pulmonary Th2 and inflammatory cytokines. Mice infected with CX4C viruses also had higher antibody titers and a Th1-biased T cell memory response at 75 days p.i. These results suggest that the CX4C mutation in the G protein could improve the safety and efficacy of a live attenuated RSV vaccine.

IMPORTANCE
RSV binds to the corresponding chemokine receptor, CX3CR1, through a CX3C chemokine motif (
182
CWAIC
186
) in the G protein. RSV binding to CX3CR1 contributes to disease pathogenesis; therefore, we investigated whether a mutation in the CX3C motif by insertion of an alanine, A
186
, within the CX3C motif, mutating it to CX4C (
182
CWAIAC
187
), known to block binding to CX3CR1, might decrease disease. The effect of this mutation and treatment with the F(ab′)
2
form of the anti-RSV G 131-2G monoclonal antibody (MAb) show that mutating the CX3C motif to CX4C blocks much of the disease and immune modulation associated with the G protein and should improve the safety and efficacy of a live attenuated RSV vaccine.
Vaccinia Virus A6 Is a Two-Domain Protein Requiring a Cognate N-Terminal Domain for Full Viral Membrane Assembly Activity
Authors: Meng Xiangzhi , Rose Lloyd , Han Yue , Deng Junpeng , Xiang Yan 
Published: March 2017

ABSTRACT
Poxvirus virion biogenesis is a complex, multistep process, starting with the formation of crescent-shaped viral membranes, followed by their enclosure of the viral core to form spherical immature virions. Crescent formation requires a group of proteins that are highly conserved among poxviruses, including A6 and A11 of vaccinia virus (VACV). To gain a better understanding of the molecular function of A6, we established a HeLa cell line that inducibly expressed VACV-A6, which allowed us to construct VACV mutants with an A6 deletion or mutation. As expected, the A6 deletion mutant of VACV failed to replicate in noncomplementing cell lines with defects in crescent formation and A11 localization. Surprisingly, a VACV mutant that had A6 replaced with a close ortholog from the Yaba-like disease virus YLDV-97 also failed to replicate. This mutant, however, developed crescents and had normal A11 localization despite failing to form immature virions. Limited proteolysis of the recombinant A6 protein identified an N domain and a C domain of approximately 121 and 251 residues, respectively. Various chimeras of VACV-A6 and YLDV-97 were constructed, but only one that precisely combined the N domain of VACV-A6 and the C domain of YLDV-97 supported VACV replication albeit at a reduced efficiency. Our results show that VACV-A6 has a two-domain architecture and functions in both crescent formation and its enclosure to form immature virions. While a cognate N domain is not required for crescent formation, it is required for virion formation, suggesting that interactions of the N domain with cognate viral proteins may be critical for virion assembly.

IMPORTANCE
Poxviruses are unique among enveloped viruses in that they acquire their primary envelope not through budding from cellular membranes but by forming and extending crescent membranes. The crescents are highly unusual, open-ended membranes, and their origin and biogenesis have perplexed virologists for decades. A group of five viral proteins were recently identified as being essential for crescent formation, including the A6 protein of vaccinia virus. It is thus important to understand the structure and function of A6 in order to solve the long-standing mystery of poxvirus membrane biogenesis. Here, we established an experimental system that allowed the genetic manipulation of the essential A6L gene. By studying A6 mutant viruses, we found that A6 plays an essential role not only in the formation of crescents but also in their subsequent enclosure to form immature virions. We defined the domain architecture of A6 and suggested that one of its two domains cooperates with cognate viral proteins.
Association between highly active antiretroviral therapy and selected cardiovascular disease risk factors in sub-Saharan Africa: a systematic review and meta-analysis protocol
Authors: Dimala Christian Akem , Blencowe Hannah 
Published: March 2017

IntroductionThe increasing highly active antiretroviral therapy (HAART) coverage in sub-Saharan Africa (SSA) has been associated with increasing cardiovascular disease (CVD) incidence. However, the epidemiology of the association between HAART and CVD risk factors in SSA is sparse. We aim to assess the extent to which HAART is associated with selected cardiovascular risk factors (hypertension, diabetes, dyslipidaemia and metabolic syndrome) in SSA.Methods and analysisThis will be a systematic review and meta-analysis of published studies on the association between HAART and CVD risk factors retrieved from Medline, Embase, Popline, Africa-Wide Information, African Index Medicus and the Cochrane library databases. Studies will be screened for eligibility according to the selection criteria by two independent reviewers. Eligible studies will be assessed for the quality of their evidence and risk of bias using the Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies of the National Health Institute and the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach, with respect to the measured outcomes (hypertension, diabetes, dyslipidaemia and metabolic syndrome). A data abstraction form will be produced on Epi info V.7 and data analysis done on STATA V.14 statistical software. Summary estimates of measures of effects for the association between HAART use and the outcomes will be derived. Random effects meta-analyses will be performed and I2statistic used to assess for heterogeneity between studies with respect to measured parameters. Qualitative synthesis will be used where data is insufficient to produce quantitative synthesis.Ethics and disseminationThe protocol has been reviewed by the Research Governance & Integrity Office of the Research Ethics Committee of the London School of Hygiene and Tropical Medicine and confirmed as not requiring ethical approval. The findings of this study will be made widely available especially to national HIV/AIDS committees formulating HIV/AIDS guidelines for their respective settings.Trial registration numberCRD42016042306; Pre-results.
Cabozantinib Eradicates Advanced Murine Prostate Cancer by Activating Antitumor Innate Immunity
Authors: Patnaik Akash , Swanson Kenneth D. , Csizmadia Eva , Solanki Aniruddh , Landon-Brace Natalie , Gehring Marina P. , Helenius Katja , Olson Brian M. , Pyzer Athalia R. , Wang Lily C. , Elemento Olivier , Novak Jesse , Thornley Thomas B. , Asara John M. , Montaser Laleh , Timmons Joshua J. , Morgan Todd M. , Wang Yugang , Levantini Elena , Clohessy John G. , Kelly Kathleen , Pandolfi Pier Paolo , Rosenblatt Jacalyn M. , Avigan David E. , Ye Huihui , Karp Jeffrey M. , Signoretti Sabina , Balk Steven P. , Cantley Lewis C. 
Published: March 2017

Abstract
Several kinase inhibitors that target aberrant signaling pathways in tumor cells have been deployed in cancer therapy. However, their impact on the tumor immune microenvironment remains poorly understood. The tyrosine kinase inhibitor cabozantinib showed striking responses in cancer clinical trial patients across several malignancies. Here, we show that cabozantinib rapidly eradicates invasive, poorly differentiated PTEN/p53-deficient murine prostate cancer. This was associated with enhanced release of neutrophil chemotactic factors from tumor cells, including CXCL12 and HMGB1, resulting in robust infiltration of neutrophils into the tumor. Critically, cabozantinib-induced tumor clearance in mice was abolished by antibody-mediated granulocyte depletion or HMGB1 neutralization or blockade of neutrophil chemotaxis with the CXCR4 inhibitor plerixafor. Collectively, these data demonstrate that cabozantinib triggers a neutrophil-mediated anticancer innate immune response, resulting in tumor clearance.
Significance: This study is the first to demonstrate that a tyrosine kinase inhibitor can activate neutrophil-mediated antitumor innate immunity, resulting in invasive cancer clearance. Cancer Discov; 7(7); 750–65. ©2017 AACR.
This article is highlighted in the In This Issue feature, p. 653
The distribution of some Copepods (Crustacea) in the Southern Ocean and adjacent regions from 40º to 81º W long
Authors: Yamanaka Naoyo 
Published: March 2017

A distribuição zoogeográfica das espécies de copépodos Rhincalanus gigas,R. nasutus, R. cornutus, Pseudeuchirella hirsuta, Valdiviella insigáis, V. brevicornis, Pseudeuchaeta brevicauda, Undeuchaeta major, U. intermedia, Euchaeta longicornis, E. marina, E. tenuis, Paraeuchaeta antárctica, P. aequatorialis, P. barbata, P biloba, P. birostrata, P. bisinuata, P californica, P. confusa, P dubia, P farrani, P. grandiremis, P hanseni, P. malayensis, P. pseudotonsa, P polita, P. rasa, P. sarsi, P. scotti, P- similis, P. tonsa, P weberi foi estudada de 129 amostras coletadas do U.S.N.S. “Eltanin” em águas entre as latitudes 2°34’ N e 67°28’S e longitudes 42°44’ e 81°61’W. Onde possível a distribuição das espécies foi correlacionada com a profundidade, os meses do ano e as massas dágua ocorrentes na região.Um ciclo migratório foi proposto, e as espécies mais freqüentes, assim como asnovas ocorrências, foram registradas.
The functional morphology of Anodontites trapezeus (Spix) and Anodontites trapesialis (Lamarck). (Bivalvia: Mycetopodidae)
Authors: Hebling Nilton José 
Published: March 2017

A anatomia funcional comparada de duas espécies de bivalves límnicos, é analisada. Anodontites trapezeus e Anodontites trapesialis, pertencem à família Mycetopodidae e são comuns no interior do Estado de São Paulo. Vivem no mesmo local e são adaptadas ao ambiente de águas calmas. Foram, pela primeira vez, estudadas sob o ponto de vista da anatomia funcional e, o estudo do estômago contribuiu com valiosas informações, mostrando que, de maneira geral, a estrutura interna é de grande uniformidade nesses animais, tal como ocorre entre os Unionacea, estudados por outros autores.
The reproduction of some Phyllostomidae (Chiroptera) from the Northwestern region of the state of São Paulo
Authors: Taddei Valdir Antonio 
Published: March 2017

A reprodução dos Phyllostomidae foi estudada examinando-se 1558 exemplares,obtidos no período de 1967 a 1972. Não existe uma estação sexual bem definidapara 9 das 16 espécies registradas. Os dados disponíveis para 7 espécies nãopermitiram conclusões a este respeito, porém, uma delas, Chiroderma v. villosum, aparentemente acompanha o padrão das espécies com atividade sexual não limitada a um período curto.Os períodos de aumento ou diminuição da incidência de gestações, sugerema existência de dois ciclos, um principal com gravidez incipiente, em junho-julho e recém-nascidos em outubro-novembro e outro secundário, em continuidade, com nascimentos em fevereiro-março. O maior número de recém-nascidos do ciclo principal ocorre no início da estação chuvosa e quente, de outubro a março, e os nascidos provenientes do ciclo secundário, no final dessa estação.Nos meses mais secos e mais frios, de junho e julho, observou-se ausênciaou uma porcentagem mínima de fêmeas lactantes.Para as espécies estudadas, o tempo de gestação estimado foi superior a trêsmeses e meio. Observou-se sempre um embrião por gestação, apesar de teremsido encontradas condições que poderiam sugerir a existência de mais do que um embrião.
Studies on Paratrigona subnuda (Moure) Hymenoptera, Apidae, Meliponinae - II. Behaviour of the virgin queen
Authors: Imperatriz Fonseca Vera Lúcia 
Published: March 2017

O comportamento das rainhas virgens de Paratrigona subnuda (Moure) foi observado em cerca de 20 colônias. Verificou-se que elas possuem u m ciclo de atividades definido, constando de: a) eclosão, b) atividade na região dos potes, c) reclusão esporádica em potes e procura de contacto com as operárias, d) estabelecimento na colônia, e) tentativa de substituição da rainha fecundada da colônia, f) saída para u m novo ninho. O comportamento após a substituição da rainha foi relatado. Como acontece em outras espécies de Trigonini, as rainhas virgens de Paratrigona subnuda (Moure) também passam por u m a fase de reclusão, utilizando potes de alimentos vazios. Essa reclusão, porém, é considerada "voluntária”, pois as rainhas virgens saem dos potes e circulam livremente pela colmeia, mantendo contacto com operárias. A rainha virgem tem u m papel decisivo na substituição natural da rainha fecundada da colônia, visto que o processo de substituição é iniciado com a deposição de uma gota de substância mandibular, pela rainha virgem, sobre o corpo da rainha fisogástrica da colônia. Foram discutidas tanto a possibilidade de u m controle feromonal para a manutençâo da rainha poedeira na colonia como a importáncia dos prováveis feromónios nas diversas etapas do ciclo biológico da rainha virgem na colmeia.
Some Enchytraeidae (Oligochaeta) from Serra do Mar, São Paulo
Authors: Christoffersen Martin Lindsey 
Published: March 2017

Os animais foram coletados num pequeno trecho da nossa floresta tropical latifoliada úmida de encosta. Hemienchytraeus (H.) stephensoni (Cognetti, 1927) foi encontrado pela primeira vez no Brasil, sendo redescrito. Discutem-se ainda pequenas diferenças morfológicas de Fridericia bulbosa (Rosa, 1887), F. agricola Moore, 1895 e F bollonsi Benham, 1914, com relação a descrições anterioresdo Estado de São Paulo.
Valor nutritivo de algumas dietas artificiais para Anastrepha obliqua (Diptera, Tephritidae)
Authors: Zucoloto Fernando Sergio , Puschel Suzana , Message Creusa M. 
Published: March 2017

Valor nutritivo de algumas dietas artificias para Anastrepha obliqua (Diptera, Tephritidae). Algumas dietas artificias, em diferentes concentrações, foram testadas e sua eficiência foi calculada a partir do peso das pupas, do tempo para apupar e da porcentagem de empupação. Os melhores resultados foram obtidos com fermento 4,5 g/ 150 ml de dieta; os outros produtos testados foram: germe de trigo, feijão soja, leite em pó e aveia.
On a new planktobenthic Scolecithricid copepod (Calanoida, Crustacea) from the Brazilian continental shelf
Authors: Campaner A. F. 
Published: March 2017

Descreve-se neste trabalho o copépodo planctobentônico “Scolecithricella” pseudoculata sp. n. e sua posição genérica é discutida.
Bivalves e gastrópodes do Saco da Ribeira, Ubatuba - São Paulo. II. Avaliação das alterações ocorridas na taxocenose dos bivalves da Praia do Saco da Ribeira
Authors: Lopes Sônia Godoy Bueno Carvalho , Schaeffer-Novelli Yara 
Published: March 2017

Alterações biológicas que ocorreram durante os anos de 1972 a 1980 na Praia do Saco da Ribeira, Ubatuba, Estado de são Paulo, Brasil (23º30'S e 45°07'W) são discutidas, comparando-se os resultados obtidos no presente estudo, comaqueles obtidos por outros autores para a mesma localidade. A análise dessas alterações foi feita levando-se em consideração apenas a taxocenose dos bivalves. Os resultados obtidos indicam: alteração na associação das espéciesdominantes (Anomalocardia brasiliana e Tellina lineata continuam presentes, enquanto que Macoma cleryana e Iphigenia brasiliensis desapareceram); não houve alteração na densidade de A. brasiliana, enquanto que a de T. lineataquase duplicou; o número de espécies raras aumentou de 6 para 21; a estrutura espacial de A. brasiliana passou de casual para agregada na região de areia branca da praia; houve redução no número de indivíduos de maior tamanho de A. brasiliana; houve redução nos índices de diversidade e de equidade. Os dados indicam que a estrutura da taxocenose de bivalves mudou. Não foi possível associar essa mudança às variáveis ambientais conhecidas para a área em estudo. Essa mudança pode estar relacionada a perturbações ecológicas queestão ocorrendo na área, facilmente observáveis, mas de difícil mensuração.