bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the Survival of Multiple Salmonella enterica Serovars
In Vivo
via Massively Parallel Whole-Genome Sequencing To Predict Zoonotic Risk
Authors: Vohra Prerna , Bugarel Marie , Turner Frances , Loneragan Guy H. , Hope Jayne C. , Hopkins John , Stevens Mark P. 
Published: November 2017

ABSTRACT

Salmonella enterica
is an animal and zoonotic pathogen of worldwide importance.
Salmonella
serovars that differ in their host and tissue tropisms exist. Cattle are an important reservoir of human nontyphoidal salmonellosis, and contaminated bovine peripheral lymph nodes enter the food chain via ground beef. The relative abilities of different serovars to survive within the bovine lymphatic system are poorly understood and constrain the development of control strategies. This problem was addressed by developing a massively parallel whole-genome sequencing method to study mixed-serovar infections
in vivo
.
Salmonella
serovars differ genetically by naturally occurring single nucleotide polymorphisms (SNPs) in certain genes. It was hypothesized that these SNPs could be used as markers to simultaneously identify serovars in mixed populations and quantify the abundance of each member in a population. The performance of the method was validated
in vitro
using simulated pools containing up to 11 serovars in various proportions. It was then applied to study serovar survival
in vivo
in cattle challenged orally with the same 11 serovars. All the serovars successfully colonized the bovine lymphatic system, including the peripheral lymph nodes, and thus pose similar risks of zoonosis. This method enables the fates of multiple genetically unmodified strains to be evaluated simultaneously in a single animal. It could be useful in reducing the number of animals required to study mixed-strain infections and in testing the cross-protective efficacy of vaccines and treatments. It also has the potential to be applied to diverse bacterial species which possess shared but polymorphic alleles.

IMPORTANCE
While some
Salmonella
serovars are more frequently isolated from lymph nodes rather than the feces and environment of cattle, the relative abilities of serovars to survive within the lymphatic system of cattle remain ill defined. A sequencing-based method which used available information from sequenced
Salmonella
genomes to study the dynamics of mixed-serovar infections
in vivo
was developed. The main advantages of the method include the simultaneous identification and quantification of multiple strains without any genetic modification and minimal animal use. This approach could be used in vaccination trials or in epidemiological surveys where an understanding of the dynamics of closely related strains of a pathogen in mixed populations could inform the prediction of zoonotic risk and the development of intervention strategies.
Referrers’ point of view on the referral process to neurosurgery and opinions on neurosurgeons: a large-scale regional survey in the UK
Authors: Amarouche Meriem , Neville Jonathan J , Deacon Simon , Kalyal Nida , Adams Nikita , Cheserem Beverly , Curley Daniel , DeSouza Ruth-Mary , Hafiz Fehmi , Jayawardena Tanya , Khetani Nishi , Matthews Diana , Mustoe Sophie , Okafor Sabrina , Padfield Olivia , Rao Ishani , Samir Reem , Tahir Hyder , Varghese Benjamin , Tolias Christos Michael 
Published: November 2017

ObjectivesThere is an increased reliance on online referral systems (ORS) within neurosurgical departments across the UK. Opinions of neurosurgeons on ORS are extensively reported but those of referrers have hardly been sought. Our study aims at ascertaining our referring colleagues’ views on our ORS and its impact on patient care, their opinions on neurosurgeons and how to improve our referral process.Setting14 district general hospitals and one teaching hospital.Participants641 healthcare professionals across a range of medical and surgical specialties including doctors of all grades, nurses and physiotherapists. Survey responses were obtained by medical students using a smartphone application.ResultsAlthough 92% of respondents were aware of the ORS, 74% would routinely phone the on-call registrar either before or after making referrals online. The majority (44%) believed their call to relate to a life-threatening emergency. 62% of referrers considered the ORS helpful in informing patients’ care and 48% had a positive opinion of their interaction with neurosurgical registrars. On ways to improve the ORS, 50% selected email/text confirmation of response sent to referrers and 16% to referring consultants.ConclusionOur results confirm that referrers feel that using our ORS positively impacts patient care but that it remains in need of improvement in order to better suit our colleagues’ needs when it comes to managing neurosurgical patients. We feel that the promotion of neurosurgical education and mitigation of the effects of adverse workplace human factors are likely to achieve the common goal of neurosurgeons and referrers alike: a high standard in patient care.
A cross-sectional study examining associations between substance use frequency, problematic use and STIs among youth living with HIV
Authors: Gamarel Kristi E , Nichols Sharon , Kahler Christopher W , Westfall Andrew O , Lally Michelle A , Wilson Craig M 
Published: November 2017

ObjectivesThis study sought to examine the prevalence of STIs and whether substance use frequency and/or problematic use—specifically alcohol, marijuana and other drugs—was associated with having an STI diagnosis among youth living with HIV (YLWH)MethodsA sample of 823 YLWH were recruited at 14 adolescent HIV clinics through the Adolescent Medicine Trials Network for HIV Interventions. Study staff abstracted STI data from medical records for up to 26 weeks prior to participants’ completing a cross-sectional survey including the ASSIST (Alcohol, Smoking and Substance Involvement Screening Test), which measures substance use frequency and consequences.ResultsAlmost one-third of youth had been diagnosed with an STI (30.5%) at the time of their baseline assessment. In multivariable analyses, those who engaged in weekly or greater marijuana use (adjusted OR (AOR)=10.66, 95% CI: 4.39 to 25.87, P<0.001) had an increased odds of being diagnosed with an STI. Additionally, youth who met alcohol use criteria for moderate (AOR=5.23, 95% CI: 2.50 to 10.93, P<0.001) and high risk (AOR=6.53, 95% CI: 1.20 to 35.68, P<0.05) alcohol use had an increased odds of being diagnosed with an STI compared with low-risk alcohol users.ConclusionsStudy findings underscore the need to investigate the role of greater frequency of marijuana use and problematic alcohol use in STI incidence among YLWH. Given the associations between both substance use frequency and problematic use in STI diagnoses among YLWH seen in HIV care settings, clinicians should use validated substance use screening tools which capture both frequencies and consequences in order to identify YLWH who may need further evaluation and treatment.
The structure and interaction mechanisms of C10H16@(13, 0)SWCNT under high pressure
Authors: Yao Zhen , Liu Chun-Jian , Lv Hang 
Published: November 2017

The high-pressure deformation and polymerization of peapod structure (C[Formula: see text]H[Formula: see text] filled into (13, 0) single-walled carbon nanotube) is studied by using density function theory. The guest–host interaction mechanism under pressure is analyzed by combining the van der Waals (vdW) potential with the electron localization function (ELF). Our studies show that the cross-section of the filled single-walled carbon nanotube changes from a circle into an ellipse shape, and then into a walnut shape with the transition pressures of 3 GPa and 10 GPa, respectively. The intertubular bonding of adjacent tubes occurs at 17 GPa, 30 GPa, 32 GPa, 82 GPa and 152 GPa. The attractive and repulsive guest–host interactions are exhibited for the pressures lower and higher than 10 GPa, respectively. Except for the ambient pressure structure, six stable high pressure structures, which can hold their structures when the pressure is released, are identified by combining the systematic binding energy with geometry optimization.
New Mechanisms of Resistance to MEK Inhibitors in Melanoma Revealed by Intravital Imaging
Authors: Brighton Hailey E. , Angus Steven P. , Bo Tao , Roques Jose , Tagliatela Alicia C. , Darr David B. , Karagoz Kubra , Sciaky Noah , Gatza Michael L. , Sharpless Norman E. , Johnson Gary L. , Bear James E. 
Published: November 2017

Abstract
Targeted therapeutics that are initially effective in cancer patients nearly invariably engender resistance at some stage, an inherent challenge in the use of any molecular-targeted drug in cancer settings. In this study, we evaluated resistance mechanisms arising in metastatic melanoma to MAPK pathway kinase inhibitors as a strategy to identify candidate strategies to limit risks of resistance. To investigate longitudinal responses, we developed an intravital serial imaging approach that can directly visualize drug response in an inducible RAF-driven, autochthonous murine model of melanoma incorporating a fluorescent reporter allele (tdTomatoLSL). Using this system, we visualized formation and progression of tumors in situ, starting from the single-cell level longitudinally over time. Reliable reporting of the status of primary murine tumors treated with the selective MEK1/2 inhibitor (MEKi) trametinib illustrated a time-course of initial drug response and persistence, followed by the development of drug resistance. We found that tumor cells adjacent to bundled collagen had a preferential persistence in response to MEKi. Unbiased transcriptional and kinome reprogramming analyses from selected treatment time points suggested increased c-Kit and PI3K/AKT pathway activation in resistant tumors, along with enhanced expression of epithelial genes and epithelial-mesenchymal transition downregulation signatures with development of MEKi resistance. Similar trends were observed following simultaneous treatment with BRAF and MEK inhibitors aligned to standard-of-care combination therapy, suggesting these reprogramming events were not specific to MEKi alone. Overall, our results illuminate the integration of tumor–stroma dynamics with tissue plasticity in melanoma progression and provide new insights into the basis for drug response, persistence, and resistance.
Significance: A longitudinal study tracks the course of MEKi treatment in an autochthonous imageable murine model of melanoma from initial response to therapeutic resistance, offering new insights into the basis for drug response, persistence, and resistance. Cancer Res; 78(2); 542–57. ©2017 AACR.
t-Darpp Activates IGF-1R Signaling to Regulate Glucose Metabolism in Trastuzumab-Resistant Breast Cancer Cells
Authors: Lenz Gal , Hamilton Angelica , Geng Shuhui , Hong Teresa , Kalkum Markus , Momand Jamil , Kane Susan E. , Huss Janice M. 
Published: November 2017

Abstract
Purpose: Increased glycolysis and glucose dependence is a hallmark of malignancy that enables tumors to maximize cell proliferation. In HER2+ cancers, an increase in glycolytic capacity is associated with trastuzumab resistance. IGF-1R activation and t-Darpp overexpression both confer trastuzumab resistance in breast cancer. We therefore investigated a role for IGF-1R and t-Darpp in regulating glycolytic capacity in HER2+ breast cancers.
Experimental Design: We examined the relationship between t-Darpp and IGF-1R expression in breast tumors and their respective relationships with patient survival. To assess t-Darpp's metabolic effects, we used the Seahorse flux analyzer to measure glucose metabolism in trastuzumab-resistant SK-BR-3 cells (SK.HerR) that have high endogenous t-Darpp levels and SK.tDrp cells that stably overexpress exogenous t-Darpp. To investigate t-Darpp's mechanism of action, we evaluated t-Darpp:IGF-1R complexes by coimmunoprecipitation and proximity ligation assays. We used pathway-specific inhibitors to study the dependence of t-Darpp effects on IGF-1R signaling. We used siRNA knockdown to determine whether glucose reliance in SK.HerR cells was mediated by t-Darpp.
Results: In breast tumors, PPP1R1B mRNA levels were inversely correlated with IGF-1R mRNA levels and directly associated with shorter overall survival. t-Darpp overexpression was sufficient to increase glucose metabolism in SK.tDrp cells and essential for the glycolytic phenotype of SK.HerR cells. Recombinant t-Darpp stimulated glucose uptake, glycolysis, and IGF-1R–Akt signaling in SK-BR-3 cells. Finally, t-Darpp stimulated IGF-1R heterodimerization with ErbB receptors and required IGF-1R signaling to confer its metabolic effects.
Conclusions: t-Darpp activates IGF-1R signaling through heterodimerization with EGFR and HER2 to stimulate glycolysis and confer trastuzumab resistance. Clin Cancer Res; 24(5); 1216–26. ©2017 AACR.
Registro e análise de estruturas relacionadas com a tectônica extensional do rifteamento Macaúbas na Serra Central, norte de Minas Gerais
Authors: Bersan Samuel Moreira , Danderfer Filho André 
Published: November 2017

Na região norte da faixa Araçuaí, no domínio fisiográfico do Espinhaço Central, existem registros de bacias sedimentares superpostas instaladas sobre o embasamento do cráton São Francisco. Nesse contexto, a morfoestrutura da Serra Central, norte de Minas Gerais, é sustentada por uma sucessão siliciclástica do Supergrupo Espinhaço superposta a oeste por diamictitos da base do Grupo Macaúbas, representando os registros de rifteamento superpostos ao final do Esteniano e do Toniano Superior, respectivamente. No bordo oeste da Serra Central, são descritas estrias de média a alta obliquidade desenvolvidas sobre os planos de acamamento da sucessão do Grupo Sítio Novo, incompatíveis com a tectônica compressional Brasiliana, que afeta essas rochas. Essas estrias são associadas a degraus e definem vetores de deslizamento interestratais indicativos de movimentação normal a normal destral. Associados a essas lineações, ocorrem veios que também apontam para a atuação de um campo de esforço extensional, com componente destral associada. A análise cinemática e dinâmica dessas estruturas permitiu a interpretação de um regime tectônico distensivo de natureza transtrativa destral e, possivelmente, relacionado ao evento de rifteamento Macaúbas. Nesse cenário, o bloco de capa regional do rifte Macaúbas, representado pela sucessão esteniana do Grupo Sítio Novo, foi deformado sob a atuação de um cisalhamento antitético, com desenvolvimento de um rollover associado. No flanco frontal do rollover, as camadas experimentaram significativa magnitude de rotação, revelando elevado mergulho próximo à borda de falha e favorecendo o desenvolvimento do deslizamento interestratal.
Caracterização geoquímica com indícios paleoambientais de folhelhos da Formação Pimenteiras, estado do Tocantins, Bacia do Parnaíba, Brasil
Authors: Zambrano Eileen Rocío Niño , Oliveira Olívia Maria Cordeiro de , Ribeiro Hélio Jorge Portugal Severiano 
Published: November 2017

A descoberta de gás natural em depósitos siliciclásticos da Bacia do Parnaíba impulsionou novas pesquisas no intuito de entender o sistema petrolífero, caracterizar intervalos de rocha com potencial gerador de hidrocarbonetos, bem como melhorar a caracterização paleoambiental. Visto que a deposição da principal rocha geradora na Bacia do Parnaíba, a Formação Pimenteiras, ocorreu durante o Devoniano, associada a um evento anóxico global no Frasniano, amostras de folhelhos devonianos foram coletadas em afloramentos da Formação Pimenteiras e analisadas por meio das técnicas geoquímicas de carbono orgânico total, enxofre total, pirólise Rock Eval e isótopos estáveis de carbono. Os resultados obtidos das análises nas 27 amostras de rocha geradora coletadas indicaram que 67% das amostras possuem o teor de carbono orgânico total mínimo requerido para gerar hidrocarbonetos. Cerca de 77% das amostras apresentaram potencial para gerar gás, enquanto os percentuais restantes são os correspondentes às amostras com potencial de gerar óleo ou gás. A temperatura máxima de pirólise sugere imaturidade termal das amostras. A correlação dos dados geoquímicos permitiu reconhecer indícios das variações no paleoambiente deposicional dos afloramentos estudados, provavelmente por inundações marinhas.
Global Precipitation Trends across Spatial Scales Using Satellite Observations
Authors: Nguyen Phu , Thorstensen Andrea , Sorooshian Soroosh , Hsu Kuolin , Aghakouchak Amir , Ashouri Hamed , Tran Hoang , Braithwaite Dan 
Published: November 2017

AbstractLittle dispute surrounds the observed global temperature changes over the past decades. As a result, there is widespread agreement that a corresponding response in the global hydrologic cycle must exist. However, exactly how such a response manifests remains unsettled. Here we use a unique recently developed long-term satellite-based record to assess changes in precipitation across spatial scales. We show that warm climate regions exhibit decreasing precipitation trends, while arid and polar climate regions show increasing trends. At the country scale, precipitation seems to have increased in 96 countries, and decreased in 104. We also explore precipitation changes over 237 global major basins. Our results show opposing trends at different scales, highlighting the importance of spatial scale in trend analysis. Furthermore, while the increasing global temperature trend is apparent in observations, the same cannot be said for the global precipitation trend according to the high-resolution dataset, PERSIANN-CDR, used in this study.
Variations of the Mid-Pacific Trough and Their Relations to the Asian–Pacific–North American Climate: Roles of Tropical Sea Surface Temperature and Arctic Sea Ice
Authors: Deng Kaiqiang , Yang Song , Ting Mingfang , Hu Chundi , Lu Mengmeng 
Published: November 2017

AbstractThe mid-Pacific trough (MPT), occurring in the upper troposphere during boreal summer, acts as an atmospheric bridge connecting the climate variations over Asia, the Pacific, and North America. The first (second) mode of empirical orthogonal function analysis of the MPT, which accounts for 20.3% (13.4%) of the total variance, reflects a change in its intensity on the southwestern (northeastern) portion of the trough. Both modes are significantly correlated with the variability of tropical Pacific sea surface temperature (SST). Moreover, the first mode is affected by Atlantic SST via planetary waves that originate from the North Atlantic and propagate eastward across the Eurasian continent, and the second mode is influenced by the Arctic sea ice near the Bering Strait by triggering an equatorward wave train over the northeast Pacific.A stronger MPT shown in the first mode is significantly linked to drier and warmer conditions in the Yangtze River basin, southern Japan, and the northern United States and wetter conditions in South Asia and northern China, while a stronger MPT shown in the second mode is associated with a drier and warmer southwestern United States. In addition, an intensified MPT (no matter whether in the southwestern or the northeastern portion) corresponds to more tropical cyclones (TCs) over the western North Pacific (WNP) and fewer TCs over the eastern Pacific (EP) in summer, which is associated with the MPT-induced ascending and descending motions over the WNP and the EP, respectively.
Development of a One-Month-Long, Westward-Propagating Subtropical Low in Boreal Summer
Authors: Molinari John , Vollaro David 
Published: November 2017

Abstract
A strong MJO event produced an upper-tropospheric jet streak in northeast Asia and repeated wave breaking in the jet exit region along 150°E during July 1988. A midlatitude low moved equatorward and intensified in the presence of bandpass-filtered (15–100 day) Q vector forcing for upward motion associated with the wave breaking. This forced ascent helped to moisten the atmosphere enough to increase the column water vapor to above 55 mm. This value was sufficiently large to support a self-sustaining low even after the upper forcing weakened. The horizontal scale of the Q vector forcing was about 1500 km, consistent with the scale of most favorable convective response to quasigeostrophic forcing in the subtropics described by Nie and Sobel. The low lasted one month as it moved southwestward, then westward, while remaining north of 20°N. Maximum precipitation along the track of the low exceeded 700 mm, with an anomaly more than 400 mm. A climatology of long-lasting lows was carried out for the monsoon gyre cases studied previously. During El Niño, long-lasting lows often began near the equator in the central Pacific, and were likely to have a mixed Rossby–gravity wave or equatorial Rossby wave structure. It is speculated that the quasi-biweekly mode, the submonthly oscillation, the 20–25-day mode, and the Pacific–Japan pattern are each variations on this kind of event. During La Niña, long-lasting lows that originated in midlatitudes were more common. It is argued that these lows from midlatitudes represent a unique disturbance type in boreal summer.
Health Care Utilization Following Vagus Nerve Stimulation Therapy in Pediatric Epilepsy Patients From a Pediatric Accountable Care Organization
Authors: Patel Anup , Wang Ling , Gedela Satyanarayana 
Published: November 2017

Background: Vagus nerve stimulation has been a therapy for epilepsy approved by the US Food and Drug Administration (FDA) for patients 4 and older and shown efficacy and safety in younger pediatric patients. Methods: The authors performed a retrospective analysis utilizing Medicaid claims from an accountable care organization to measure the intervention of vagus nerve stimulation therapy in regard to unplanned health care utilization. Thirteen unique patients were included who had vagus nerve stimulation therapy who had at least 6 months of continuous enrollment in a managed Medicaid health plan. Comparison with 12 months of data before and after vagus nerve stimulation implantation was performed. Results: Patients had statistically significant fewer unplanned inpatient visits per patient per enrollment month after vagus nerve stimulation implantation. Conclusion: Utilizing claims data, vagus nerve stimulation implantation demonstrates a reduction in unplanned hospitalizations.