bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence and Transmission of Drug-/Multidrug-resistant Mycobacterium leprae in a Former Leprosy Colony in the Brazilian Amazon
Authors: Rosa Patrícia S , D’Espindula Helena R S , Melo Ana C L , Fontes Amanda N B , Finardi Amanda J , Belone Andréa F F , Sartori Beatriz G C , Pires Carla A A , Soares Cleverson T , Marques Flávio B , Branco Francisco J D , Baptista Ida M F D , Trino Lázara M , Fachin Luciana R V , Xavier Marília B , Floriano Marcos C , Ura Somei , Diório Suzana M , Delanina Wladimir F B , Moraes Milton O , Virmond Marcos C L , Suffys Philip N , Mira Marcelo T 
Published: June 2019

AbstractBackgroundLeprosy has been treated with multidrug therapy, which has been distributed for free across the globe and regarded as highly efficient. However, the impossibility of growing Mycobacterium leprae in axenic media has historically impaired assessments of M. leprae resistance, a parameter only recently detectable through molecular methods.MethodsA systematic, population-based search for M. leprae resistance in suspected leprosy relapse cases and contacts was performed in Prata Village, an isolated, hyperendemic, former leprosy colony located in the Brazilian Amazon. Results led to an extended active search involving the entire Prata population. Confirmed leprosy cases were investigated for bacterial resistance using a combination of in vivo testing and direct sequencing of resistance genes folP1, rpoB, and gyrA. A molecular epidemiology analysis was performed using data from 17 variable number tandem repeats (VNTR).ResultsMycobacterium leprae was obtained from biopsies of 37 leprosy cases (18 relapses and 19 new cases): 16 (43.24%) displayed drug-resistance variants. Multidrug resistance to rifampicin and dapsone was observed in 8 relapses and 4 new cases. Single resistance to rifampicin was detected in 1 new case. Resistance to dapsone was present in 2 relapses and 1 new case. Combined molecular resistance and VNTR data revealed evidence of intra-familial primary transmission of resistant M. leprae.ConclusionsA comprehensive, population-based systematic approach to investigate M. leprae resistance in a unique population revealed an alarming scenario of the emergence and transmission of resistant strains. These findings may be used for the development of new strategies for surveillance of drug resistance in other populations.
A Tentative Tamdy Orthonairovirus Related to Febrile Illness in Northwestern China
Authors: Liu Xiafei , Zhang Xu , Wang Zedong , Dong Zhihui , Xie Songsong , Jiang Mengmeng , Song Ruixia , Ma Jun , Chen Shouyi , Chen Kuncai , Zhang Haoji , Si Xingkui , Li Chang , Jin Ningyi , Wang Yuanzhi , Liu Quan 
Published: June 2019

Abstract

Background
Many novel tick-borne viruses have been discovered by deep-sequencing technology in recent years; however, their medical significance is unknown.

Methods
We obtained clinical data of a patient from Xinjiang, China. Possible pathogens were detected by metagenomic analysis; the causative pathogen Tacheng tick virus 1 (TcTV-1) was found and further confirmed by reverse transcriptase–polymerase chain reaction, viral culture, and sequence analyses. Epidemiological investigation was conducted in the local human population, domestic animals, and ticks by serological/molecular methods.

Results
A 62-year-old woman with a history of tick bite in Qinghe, Xinjiang, presented with fever and rashes. These symptoms were relieved after clinical treatment. TcTV-1 (strain QH1) was isolated from the patient’s cerebrospinal fluid, throat swabs, and urine on day 47 after illness onset. Although the blood and urine showed viral RNA positive on day 73 after illness onset, the virus was only isolated from urine. Serological detection revealed a virus neutralizing antibody titer of 1:40 and 1:80 on day 47 and 73 after illness onset, respectively. No coinfection with other pathogens was detected, suggesting TcTV-1 may be the potential causative pathogen. We detected anti–TcTV-1 antibodies (immunoglobulin G: 10.1%; immunoglobulin M: 4.8%) in the local human population. The viral RNA was also found in cattle (4.9%), sheep (9.2%), and ticks, including Dermacentor marginatus (14.3%), Dermacentor silvarum (11.8%), Dermacentor nuttalli (6.7%), and Hyalomma asiaticum (4.8%).

Conclusions
TcTV-1 may be associated with a febrile illness syndrome, and epidemiological data of the virus in humans and animals necessitate disease surveillance of TcTV-1 infection in China.
Infection With Chlamydia trachomatis Increases the Risk of High-grade Anal Intraepithelial Neoplasia in People Living With Human Immunodeficiency Virus
Authors: Masiá Mar , Fernández-González Marta , García José A , Padilla Sergio , García-Payá Elena , Gutiérrez Ana , Ortiz de la Tabla Victoria , García-Abellán Javier , Agulló Vanesa , Gutiérrez Félix 
Published: July 2019

Abstract

Background
We aimed to assess the relationship between sexually transmitted infections (STIs)—including a large panel of human papillomavirus (HPV) genotypes—and high-grade anal intraepithelial neoplasia (HGAIN) in men who have sex with men (MSM) who were living with human immunodeficiency virus (HIV).

Methods
In a prospective study in an HIV cohort, participants underwent high-resolution anoscopy (HRA) for anorectal swabs collection to investigate STIs and for anal biopsy. Multiplex real-time polymerase chain reactions were performed, detecting several STIs and 28 HPV genotypes. Univariate and multivariate generalized linear models were used to analyze the relationships of variables of interest with HGAIN.

Results
There were 145 participants included; in 49, 2 HRAs were performed. Ureaplasma urealyticum (UU) was detected in 25 (17.2%) participants, Chlamydia trachomatis (CT) in 13 (9.0%), Mycoplasma genitalium (MG) in 4 (2.8%), HPV16 in 38 (26.2%), HPV52 in 29 (20%), and HPV53 and HPV42 in 28 (19.3%) participants each. There were 35 (24.1%) subjects diagnosed with HGAIN. In the univariate analysis, HGAIN was associated with CT, UU, MG, HPV16, HPV53, HPV68, and HPV70, and significant interactions were found between CT and HPV16 (odds ratio [OR] 31.0 95% confidence interval [CI] 4.3–221.7) and between UU and HPV16 (OR 8.8, 95% CI 2.1–37.5). In the adjusted model, CT, HPV16, HPV53, HPV70, the CD4+/CD8+ ratio, and the interaction between CT and HPV16 remained independent predictors of HGAIN. HPV16, HPV53, and HPV70 persisted in the second HRA in all the participants with recurrent HGAIN.

Conclusions
Coinfection with CT may potentiate the oncogenic capability of HPV16 and increase the risk of HGAIN in people with HIV. HPV53 and HPV70 should be considered among the genotypes associated with HGAIN.
Genome-Wide Single-Nucleotide Polymorphism Data Unveil Admixture of Chinese Indigenous Chicken Breeds with Commercial Breeds
Authors: Nie Changsheng , Almeida Pedro , Jia Yaxiong , Bao Haigang , Ning Zhonghua , Qu Lujiang 
Published: June 2019

Abstract
The conservation and development of chicken have received considerable attention, but the admixture history of chicken breeds, especially Chinese indigenous breeds, has been poorly demonstrated. In this study, we aimed to evaluate the genetic diversity and population structure of eight chicken breeds (including conserved chicken breeds) from different geographic origin and to identify admixture within these breeds using a 600-K single-nucleotide polymorphism panel for genotyping. Using the genotype of 580,961 single-nucleotide polymorphism markers scored in 1,200 animals, we evaluated the genetic diversity (heterozygosity and proportion of polymorphic markers), linkage disequilibrium decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (FST and genetic distance), and migration events (TreeMix and f-statistics) of the eight domesticated chicken breeds. The results of population analytical methods revealed patterns of hybridization that occurred after divergence in Tibetan chicken. We argue that chicken migration and admixture, followed by trade, have been important forces in shaping the genomic variation in modern Chinese chicken. Moreover, isolation by distance might play a critical role in shaping the genomic variation within Eurasia continent chicken breeds. Moreover, genetic information provided in this study is valuable resources for production applications (genomic prediction, and breeding strategy) and scientific research (genetic basis detection, studying evolution, or domestication).
Sex Differences in Depression as a Risk Factor for Alzheimer’s Disease: A Systematic Review
Authors: Underwood Emily A , Davidson Heather P , Azam Amber B , Tierney Mary C 
Published: June 2019

Abstract

Background and Objectives
Depression is an important risk factor for Alzheimer’s disease (AD) but little is known about the mechanisms of this association. Given sex differences in both AD and depression, we sought to conduct a systematic review and meta-analysis to examine whether there are sex differences in their association, as this may improve understanding of underlying mechanisms.

Research Design and Methods
MEDLINE, PsycINFO, and Cochrane Reviews were searched for observational studies including both sexes and examining the association between history of depression and AD.

Results
Forty studies, including 62,729 women and 47,342 men, were identified. Meta-analysis was not possible because only 3 studies provided sufficient data. Seven studies provided information about the influence of sex for a qualitative synthesis. Two found an association in men only, 2 in women only, and 3 reported no sex differences. The 2 studies finding an association in women only were unique in that they had the shortest follow-up periods, and were the only clinic-based studies.

Discussion and Implications
The findings of our systematic review show that there are important methodological differences among the few studies providing data on the influence of sex on depression as a risk factor for AD. Had all 40 studies provided sex-segregated data, these methodological differences and their impact on sex effects could have been examined quantitatively. We encourage researchers to report these data, as well as potential moderating factors, so that the role of sex differences can be better understood.
Seismic activity during the 2013–2015 intereruptive phase at Lascar volcano, Chile
Authors: Gaete Ayleen , Cesca Simone , Franco Luis , San Martin Juan , Cartes Cristian , Walter Thomas R 
Published: June 2019

SUMMARYIn addition to enabling the physical processes of volcanic systems to be better understood, seismology has been also used to infer the complexity of magma pathways and plumbing systems in steep-sided andesitic and stratovolcanoes. However, in these volcanic environments, the application of seismic location methods is particularly challenging and systematic comparisons of common methods are lacking. Furthermore, little is known about the characteristic seismicity and deep structure of Lascar volcano, one of the most historically active volcanoes in northern Chile known to produce VEI-4 eruptions. To better understand the inner processes and deep structure of Lascar, the local broad-band seismic monitoring network was densified during a temporal installation in 2014–2015. Herein, we focus on the local seismicity during the 2014–2015 unrest episode, during which we recorded numerous seismic events mainly classified as long-period (LP) type, but also denote volcano-tectonic (VT) activity. Specifically, a long-lasting phase of LP activity is observed over a period of ∼14 months that starts in tandem with a pulse of VT activity. The LP rate and amplitude are modulated over time; they are lower in the initial phase, rise during the intermediate period from October 2014 to July 2015, and finally slowly decay while approaching the eruption time. The location of LPs is challenging due to the typical lack of clear seismic onsets. We thus encompass this problem by comparing a broad range of different standard and novel location techniques to map the source region of LPs by fitting the amplitude decay, polarization patterns, coherence of characteristic functions and cross-correlation differential times. As a result, we principally constrain LP locations within the first 5 km depth below the summit extending downward along a narrow, conduit-like path. We identify different regions of complexity: VTs dominate at depth, both VTs and LPs cluster in an intermediate depth region (down to 1.5 km), suggesting a change in the plumbing system geometry, and LPs dominate the shallowest region. Based on these results, we infer the presence of a subvertical conduit extending down to a depth of ∼5 km, and a region of path divergence, possibly accommodating a magma plumbing system, at a depth of ∼3 km beneath the volcano summit. Identifying the locations of complexities in the magma pathways at Lascar may help identify future unrest. The results are compared with independent observations, demonstrating the strength of the location method used herein that will be tested at volcanoes elsewhere.
Motor neuron loss in SMA is not associated with somal stress-activated JNK/c-Jun signaling
Authors: Pilato Celeste M , Park Jae Hong , Kong Lingling , d’Ydewalle Constantin , Valdivia David , Chen Karen S , Griswold-Prenner Irene , Sumner Charlotte J 
Published: June 2019

AbstractA pathological hallmark of spinal muscular atrophy (SMA) is severe motor neuron (MN) loss, which results in muscle weakness and often infantile or childhood mortality. Although it is well established that deficient expression of survival motor neuron (SMN) protein causes SMA, the molecular pathways that execute MN cell death are poorly defined. The c-Jun NH2-terminal kinases (JNKs) are stress-activated kinases with multiple substrates including c-Jun, which can be activated during neuronal injury and neurodegenerative disease leading to neuronal apoptosis. Recently, increased JNK-c-Jun signaling was reported in SMA raising the possibility that JNK inhibitors could be a novel treatment for this disease. We examined JNK-c-Jun activity in SMA mouse and human cultured cells and tissues. Anisomycin treatment of human SMA fibroblasts and sciatic nerve ligation in SMA mice provoked robust phosphorylated-c-Jun (p-c-Jun) expression indicating that SMN-deficiency does not prevent activation of the stress-induced JNK-c-Jun signaling pathway. Despite retained capacity to activate JNK-c-Jun, we observed no basal increase of p-c-Jun levels in SMA compared to control cultured cells, human or mouse spinal cord tissues, or mouse MNs during the period of MN loss in severe SMA model mice. In both controls and SMA, ~50% of α-MN nuclei express p-c-Jun with decreasing expression during the early postnatal period. Together these studies reveal no evidence of stress-activated JNK-c-Jun signaling in MNs of SMA mice or human tissues, but do highlight the important role of JNK-c-Jun activity during normal MN development raising caution about JNK antagonism in this pediatric neuromuscular disease.
Sponge Behavior and the Chemical Basis of Responses: A Post-Genomic View
Authors: Leys Sally P , Mah Jasmine L , McGill Paul R , Hamonic Laura , De Leo Fabio C , Kahn Amanda S 
Published: June 2019

AbstractSponges perceive and respond to a range of stimuli. How they do this is still difficult to pin down despite now having transcriptomes and genomes of an array of species. Here we evaluate the current understanding of sponge behavior and present new observations on sponge activity in situ. We also explore biosynthesis pathways available to sponges from data in genomes/transcriptomes of sponges and other non-bilaterians with a focus on exploring the role of chemical signaling pathways mediating sponge behavior and how such chemical signal pathways may have evolved. Sponge larvae respond to light but opsins are not used, nor is there a common photoreceptor molecule or mechanism used across sponge groups. Other cues are gravity and chemicals. In situ recordings of behavior show that both shallow and deep-water sponges move a lot over minutes and hours, and correlation of behavior with temperature, pressure, oxygen, and water movement suggests that at least one sponge responds to changes in atmospheric pressure. The sensors for these cues as far as we know are individual cells and, except in the case of electrical signaling in Hexactinellida, these most likely act as independent effectors, generating a whole-body reaction by the global reach of the stimulus to all parts of the animal. We found no evidence for use of conventional neurotransmitters such as serotonin and dopamine. Intriguingly, some chemicals synthesized by symbiont microbes could mean other more complex signaling occurs, but how that interplay might happen is not understood. Our review suggests chemical signaling pathways found in sponges do not reflect loss of a more complex set.
Scenario-based analyses evaluate potential outcomes of proposed regulatory changes in recreational fishery
Authors: Thomas Alyssa S , Milfont Taciano L , Gavin Michael C 
Published: June 2019

Abstract
Understanding current and predicting future behaviour of fishers is fundamental to designing effective management strategies. The management of most recreational fisheries requires releasing fish not meeting size or daily limits, and assuming the majority survive. In the Marlborough Sounds, New Zealand, a maximum size limit imposed on the blue cod (Parapercis colias) fishery aimed to achieve a more balanced sex ratio for this hermaphroditic species. We tested three alternative size limit scenarios (current, increased, and no maximum size) in a study with recreational fishers (N = 420) to investigate whether regulation change would influence their intentions to discard fish and fishing satisfaction. Increasing or eliminating the maximum size led to lower discard intentions and greater fishing satisfaction, suggesting strategies to achieve both management goals (e.g. more large fish) and increased fisher satisfaction (potentially increasing compliance). More broadly, the results demonstrate the benefits of using scenarios to evaluate potential regulatory changes prior to implementation.
Attaining sustainable high-rise office buildings in warm-summer-cold-winter climates: a case study on Frankfurt
Authors: Hong Yuanda , Deng Wu , Ezeh Collins I , Peng Zhen 
Published: June 2019

Abstract
Attaining sustainability in high-rise office buildings necessitates determining the major elements and their associating impacts on the energy performance of this building typology. This study investigates the impact of architectural and engineering features on the energy performance of high-rise office buildings within a warm-summer-cold-winter climate. A rectangular building plan form with a 1:1.44 plan ratio, vertical split core position and central atrium presented the best building performance. The plan form, core position and atrium effect accounted for 59, 30 and 11%, respectively, of an estimated 20.6% building energy savings. Furthermore, exploiting passive strategies founded on the climate and building features as defined by `PassivHaus’ standards further reduced the building energy usage.
Legitimation Strategies in International Hierarchies
Authors: MacKay Joseph 
Published: June 2019

AbstractHow do hierarchical cores or metropoles legitimate their influence or rule? How do their approaches to legitimation inform resistance? This theory note rethinks how legitimation operates in hierarchies, with a focus on variation in cores’ legitimation strategies. I argue that varying claims to hierarchical legitimacy shape both action at the core and resistance at the periphery. I develop a four-part typology of legitimation strategies, differentiated along two axes. On the first, cores may be universalist, recognizing no legitimate equals, or competitive, recognizing other cores as peer rivals. On the second, they may chiefly innovate legitimacy claims internally, drawing them from their own political traditions, or externally, borrowing the claims of others. These strategies shape available options for revisionism by rivals and resistance by hierarchical subordinates. I illustrate with historical examples.
Accuracy in the Application of Statistical Matching Methods for Continuous Variables Using Auxiliary Data
Authors: Van Delden Arnout , Du Chatinier Bart J , Scholtus Sander 
Published: June 2019

AbstractStatistical matching is a technique to combine variables in two or more nonoverlapping samples that are drawn from the same population. In the current study, the unobserved joint distribution between two target variables in nonoverlapping samples is estimated using a parametric model. A classical assumption to estimate this joint distribution is that the target variables are independent given the background variables observed in both samples. A problem with the use of this conditional independence assumption is that the estimated joint distribution may be severely biased when the assumption does not hold, which in general will be unacceptable for official statistics. Here, we explored to what extent the accuracy can be improved by the use of two types of auxiliary information: the use of a common administrative variable and the use of a small additional sample from a similar population. This additional sample is included by using the partial correlation of the target variables given the background variables or by using an EM algorithm. In total, four different approaches were compared to estimate the joint distribution of the target variables. Starting with empirical data, we show how the accuracy of the joint distribution is affected by the use of administrative data and by the size of the additional sample included via a partial correlation and through an EM algorithm. The study further shows how this accuracy depends on the strength of the relations among the target and auxiliary variables. We found that including a common administrative variable does not always improve the accuracy of the results. We further found that the EM algorithm nearly always yielded the most accurate results; this effect is largest when the explained variance of the separate target variables by the common background variables is not large.
Effect of turbulent reacceleration on electrons produced by dark matter annihilation in the Coma cluster
Authors: Marchegiani P 
Published: June 2019

ABSTRACT
In this paper, we study the effect of reacceleration provided by turbulences on electrons produced by dark matter (DM) annihilation in the Coma cluster. We use a simplified phenomenological model to describe the effect of the turbulences, and explore a limited subset of three possible DM models for neutralino particles with different mass and annihilation channel. We find that, for values of the annihilation cross-section of the order of the upper limits found with Fermi–LAT measurements in astrophysical objects, and for conservative values of the boosting factor due to DM substructures, the reacceleration due to turbulences can enhance the radio emission produced by DM-originated electrons up to the level of the observed flux of the radio halo in Coma, for moderate reacceleration intensity in relatively short times. Therefore, we conclude that, even if it is not possible to distinguish between the fits obtained in this paper because of the scattering present in the radio flux data, the electrons produced by DM annihilation can be possible seed electrons for the reacceleration, as well as secondary electrons of hadronic origin. A possible discriminant between these two classes of models is the flux produced in the gamma ray band, which in the case of DM-originated electrons should be more than two orders of magnitude smaller than the present Fermi–LAT upper limits, whereas in the hadronic case the expected gamma ray flux should be close to the value of present upper limits.