bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic Review with Meta-analysis: The Impact of Co-occurring Immune-mediated Inflammatory Diseases on the Disease Course of Inflammatory Bowel Diseases
Authors: Attauabi Mohamed , Zhao Mirabella , Bendtsen Flemming , Burisch Johan 
Published: July 2020

Abstract

Background and Aims
Patients with inflammatory bowel diseases (IBDs) are at risk of developing a variety of other immune-mediated inflammatory diseases (IMIDs). The influence of co-occurring IMIDs on the disease course of IBD remains unknown. The aim of this study was therefore to conduct a systematic review and meta-analysis of the impact of IMIDs on phenotypic presentation and outcome in patients with IBD.

Methods
PubMed and Embase were searched from their earliest records through December 2018 and updated in October 2019 for studies reporting proportions or ratios of IBD-related disease outcomes in patients with and without co-occurring IMIDs. Meta-analyses were performed to estimate summary proportions and risks of the main outcomes. PRISMA guidelines were used, and study quality was assessed according to the Newcastle-Ottawa Scale.

Results
A total of 93 studies were identified, comprising 16,064 IBD patients with co-occurring IMIDs and 3,451,414 IBD patients without IMIDs. Patients with IBD and co-occurring IMIDs were at increased risk of having extensive colitis or pancolitis (risk ratio, 1.38; 95% Cl, 1.25–1.52; P &lt; 0.01, I2 = 86%) and receiving IBD-related surgeries (risk ratio, 1.17; 95% Cl, 1.01–1.36; P = 0.03; I2 = 85%) compared with patients without IMIDs. Co-occurrence of IMIDs other than primary sclerosing cholangitis in patients with IBD was associated with an increased risk of receiving immunomodulators (risk ratio, 1.15; 95% Cl, 1.06–1.24; P &lt; 0.01; I2 = 60%) and biologic therapies (risk ratio, 1.19; 95% Cl, 1.08–1.32; P &lt; 0.01; I2 = 53%).

Conclusion
This meta-analysis found that the presence of co-occurring IMIDs influences the disease course of IBD, including an increased risk of surgery and its phenotypical expression.
Networks of export markets and export market diversification
Authors: Guo Qi , Zhu Shengjun , Boschma Ron 
Published: July 2020

Abstract
In the era of globalization, policy makers in both developing and developed countries have sought to expand their export destinations, with the expectation that export market diversification can boost export upgrading and economic development. Although extant literature has confirmed that exporters search for new markets in two distinct ways: direct search underpinned by the gravity effect and remote search driven by the extended gravity effect, it has not advanced very far due to the lack of adequate measures of those effects. This article presents a technique that uses available export data to develop measures of those two effects that capture a larger range of factors and thus allow us to more easily predict export market diversification. Our new indicator also simplifies the prediction by combining gravity and extended gravity effects. Empirical results show that the explanatory and predictive power of our new method is better than that of the traditional one based on gravity and extended gravity models.
Local spillovers from high-growth businesses: do gazelles cannibalize or promote employment growth?
Authors: Crown Daniel , Wojan Timothy , Rupasingha Anil 
Published: July 2020

AbstractThis article estimates the employment spillover effect of high-growth businesses on establishment-level employment growth. We assess whether the impact depends on the rurality of the region, and whether nearby establishments are high-growth businesses themselves. We also estimate the within-industry impact of high-growth establishments (HGEs). The findings show no impact of HGEs on net employment growth, due to equal gross job creation and job destruction on average. However, we find that within the same industry, HGEs contribute to positive net employment growth, with large and nearly equal impacts on existing HGEs across both Metropolitan Statistical Areas regions and non-metro counties.
Feedback control based on discrete-time state observations for stabilization of coupled regime-switching jump diffusion with Markov switching topologies
Authors: Wu Yongbao , Pi Haotian , Li Wenxue 
Published: July 2020

AbstractIn this paper, the stabilization of coupled regime-switching jump diffusion with Markov switching topologies (CRJDM) is discussed. Particularly, we remove the restrictions that each of the switching subnetwork topologies is strongly connected or contains a directed spanning tree. Furthermore, a feedback control based on discrete-time state observations is proposed to make the CRJDM asymptotically stable. In most existing literature, feedback control only depends on discrete-time observations of state processes, while switching processes are observed continuously. Different from previous literature, feedback control depends on discrete-time observations of state processes as well as switching processes in this paper. Meanwhile, based on graph theory, stationary distribution of switching processes and Lyapunov method, some sufficient conditions are deduced to ensure the asymptotic stability of CRJDM. By applying the theoretical results to second-order oscillators with Markov switching topologies, a stability criterion is obtained. Finally, the effectiveness of the results is illustrated by a numerical example.
The Emerging Role for CTL Epitope Specificity in HIV Cure Efforts
Authors: Kaseke Clarety , Tano-Menka Rhoda , Senjobe Fernando , Gaiha Gaurav D 
Published: July 2020

AbstractThe development of an effective human immunodeficiency virus (HIV) cure is a critical global health priority. A major obstacle to this effort is the establishment of a latent reservoir of HIV infected cells, which necessitates lifelong therapy, causing both logistical and adherence burdens for infected individuals. However, in a subset of these individuals, cytotoxic T lymphocytes (CTLs) can durably suppress viral outgrowth in the absence of therapy, providing a path towards a viable HIV cure. In this review, we discuss the emerging role that CTLs have in HIV cure efforts, with particular emphasis on epitope specificity. Recent studies have demonstrated that successful in vivo containment of the virus is rooted in the specific targeting of fitness-constrained, mutation-resistant regions of the HIV proteome. We highlight these new insights, providing context with previous observations in HIV and other models of viral control, and delineate their translation into a therapeutic vaccine.
Direct Observation of Repeated Infections With Endemic Coronaviruses
Authors: Galanti Marta , Shaman Jeffrey 
Published: July 2020

Abstract

Background
Although the mechanisms of adaptive immunity to pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63, and OC43 provide a useful reference for understanding repeat infection risk.

Methods
Here we used data from proactive sampling carried out in New York City from fall 2016 to spring 2018. We combined weekly nasal swab collection with self-reports of respiratory symptoms from 191 participants to investigate the profile of recurring infections with endemic coronaviruses.

Results
During the study, 12 individuals tested positive multiple times for the same coronavirus. We found no significant difference between the probability of testing positive at least once and the probability of a recurrence for the betacoronaviruses HKU1 and OC43 at 34 weeks after enrollment/first infection. We also found no significant association between repeat infections and symptom severity, but found strong association between symptom severity and belonging to the same family.

Conclusions
This study provides evidence that reinfections with the same endemic coronavirus are not atypical in a time window shorter than 1 year and that the genetic basis of innate immune response may be a greater determinant of infection severity than immune memory acquired after a previous infection.
Sociodemographic, Ecological, and Spatiotemporal Factors Associated with Human Immunodeficiency Virus Drug Resistance in Florida: A Retrospective Analysis
Authors: Rich Shannan N , Poschman Karalee , Hu Hui , Mavian Carla , Cook Robert L , Salemi Marco , Spencer Emma C , Prosperi Mattia 
Published: July 2020

Abstract

Background
Persons living with human immunodeficiency virus (HIV) with resistance to antiretroviral therapy are vulnerable to adverse HIV-related health outcomes and can contribute to transmission of HIV drug resistance (HIVDR) when nonvirally suppressed. The degree to which HIVDR contributes to disease burden in Florida—the US state with the highest HIV incidence– is unknown.

Methods
We explored sociodemographic, ecological, and spatiotemporal associations of HIVDR. HIV-1 sequences (n = 34 447) collected during 2012–2017 were obtained from the Florida Department of Health. HIVDR was categorized by resistance class, including resistance to nucleoside reverse-transcriptase , nonnucleoside reverse-transcriptase , protease , and integrase inhibitors. Multidrug resistance and transmitted drug resistance were also evaluated. Multivariable fixed-effects logistic regression models were fitted to associate individual- and county-level sociodemographic and ecological health indicators with HIVDR.

Results
The HIVDR prevalence was 19.2% (nucleoside reverse-transcriptase inhibitor resistance), 29.7% (nonnucleoside reverse-transcriptase inhibitor resistance), 6.6% (protease inhibitor resistance), 23.5% (transmitted drug resistance), 13.2% (multidrug resistance), and 8.2% (integrase strand transfer inhibitor resistance), with significant variation by Florida county. Individuals who were older, black, or acquired HIV through mother-to-child transmission had significantly higher odds of HIVDR. HIVDR was linked to counties with lower socioeconomic status, higher rates of unemployment, and poor mental health.

Conclusions
Our findings indicate that HIVDR prevalence is higher in Florida than aggregate North American estimates with significant geographic and socioecological heterogeneity.
Phexpo: a package for bidirectional enrichment analysis of phenotypes and chemicals
Authors: Hawthorne Christopher , Simpson David A , Devereux Barry , López-Campos Guillermo 
Published: July 2020

Abstract
Phenotypes are the result of the complex interplay between environmental and genetic factors. To better understand the interactions between chemical compounds and human phenotypes, and further exposome research we have developed “phexpo,” a tool to perform and explore bidirectional chemical and phenotype interactions using enrichment analyses. Phexpo utilizes gene annotations from 2 curated public repositories, the Comparative Toxicogenomics Database and the Human Phenotype Ontology. We have applied phexpo in 3 case studies linking: (1) individual chemicals (a drug, warfarin, and an industrial chemical, chloroform) with phenotypes, (2) individual phenotypes (left ventricular dysfunction) with chemicals, and (3) multiple phenotypes (covering polycystic ovary syndrome) with chemicals. The results of these analyses demonstrated successful identification of relevant chemicals or phenotypes supported by bibliographic references. The phexpo R package (https://github.com/GHLCLab/phexpo) provides a new bidirectional analyses approach covering relationships from chemicals to phenotypes and from phenotypes to chemicals.
Genetic dissection of Ragulator structure and function in amino acid-dependent regulation of mTORC1
Authors: Nada Shigeyuki , Okada Masato 
Published: July 2020

Abstract
Ragulator is a heteropentameric protein complex consisting of two roadblock heterodimers wrapped by the membrane anchor p18/Lamtor1. The Ragulator complex functions as a lysosomal membrane scaffold for Rag GTPases to recruit and activate mechanistic target of rapamycin complex 1 (mTORC1). However, the roles of Ragulator structure in the regulation of mTORC1 function remain elusive. In this study, we disrupted Ragulator structure by directly anchoring RagC to lysosomes and monitored the effect on amino acid-dependent mTORC1 activation. Expression of lysosome-anchored RagC in p18-deficient cells resulted in constitutive lysosomal localization and amino acid-independent activation of mTORC1. Co-expression of Ragulator in this system restored the amino acid dependency of mTORC1 activation. Furthermore, ablation of Gator1, a suppressor of Rag GTPases, induced amino acid-independent activation of mTORC1 even in the presence of Ragulator. These results demonstrate that Ragulator structure is essential for amino acid-dependent regulation of Rag GTPases via Gator1. In addition, our genetic analyses revealed new roles of amino acids in the regulation of mTORC1 as follows: amino acids could activate a fraction of mTORC1 in a Rheb-independent manner, and could also drive negative-feedback regulation of mTORC1 signalling via protein phosphatases. These intriguing findings contribute to our overall understanding of the regulatory mechanisms of mTORC1 signalling.
Indigenous Peoples and Litigation: Strategies for Legal Empowerment
Authors: Gilbert* Jérémie 
Published: July 2020

AbstractAcross the globe indigenous peoples are increasingly using litigation to seek remedies for violation of their fundamental human rights. The rise of litigation is to be placed in the larger context of increased land grabbing, exploitation of natural resources, and the general lack of recognition of indigenous peoples’ rights at the national level. This lack of legal rights is usually coupled with a lack of political will to address the issues faced by indigenous peoples, often leading to serious human rights violations, leaving indigenous advocates with few options but to turn to courts as a last resort to seek remedies. This article examines some of the issues faced by indigenous peoples and their advocates when engaging in human rights litigation. The goal is to offer a practice-based reflection on the encounter between courts and indigenous peoples with a specific focus on analysing strategies to support indigenous peoples’ legal empowerment. This is particularly important knowing the technicalities, externalities and complexities of the process of litigation, and the fact that many decisions do not get implemented. In this context this article explores how the process of litigation in itself can support legal empowerment and the wider fight for justice.
History in International Criminal Trials
Authors: Zammit Borda Aldo 
Published: July 2020

Abstract
While the question of whether international criminal courts and tribunals (ICTs) ought to write historical narratives of armed conflicts is an old one, it has gained renewed relevance in the context of the recent turn to history in international criminal law and the minimal attention paid to historical context in the first judgment of the International Criminal Court. The ‘proper’ place of history-writing in international criminal adjudication remains controversial, and even though some judges have preferred to de-emphasize it, the fact remains that ICTs are epistemic engines, systematically and inevitably producing knowledge about the conflicts that come before them. This article develops a framework for analysing the historical knowledge generated by ICTs, namely, the ‘crime-driven lens’. It argues that this lens is characterized by two important constraints, one qualitative, relating to interpretation and the other quantitative, relating to scope, both of which may give rise to blind spots. In the final analysis, while the important contributions of ICTs to deepening understanding of the histories of armed conflicts should not be underestimated, the constraints of the ‘crime-driven lens’ and its blind spots have to be taken into account when assessing their historical legacies.
Long-term ureteroscopic management of upper tract urothelial carcinoma: 28-year single-centre experience
Authors: Maruyama Yuki , Araki Motoo , Wada Koichiro , Yoshinaga Kasumi , Mitsui Yosuke , Sadahira Takuya , Nishimura Shingo , Edamura Kohei , Kobayashi Yasuyuki , Watanabe Masami , Watanabe Toyohiko , Monga Manoj , Nasu Yasutomo , Kumon Hiromi 
Published: July 2020

Abstract

Background
Long-term survival outcomes of patients who undergo endoscopic management of non-invasive upper tract urothelial carcinoma remain uncertain. The longest mean follow-up period in previous studies was 6.1 years. This study reports the long-term outcomes of patients with upper tract urothelial carcinoma who underwent ureteroscopic ablation at a single institution over a 28-year period.

Methods
We identified all patients who underwent ureteroscopic management of upper tract urothelial carcinoma as their primary treatment at our institution between January 1991 and April 2011. Survival outcomes, including overall survival, cancer-specific survival, upper-tract recurrence-free survival and renal unit survival, were estimated using Kaplan−Meier methodology.

Results
A total of 15 patients underwent endoscopic management, with a mean age at diagnosis of 66 years. All patients underwent ureteroscopy, and biopsy-confirmed pathology was obtained. Median (range; mean) follow-up was 11.7 (2.3–20.9, 11.9) years. Upper tract recurrence occurred in 87% (n = 13) of patients. Twenty percent (n = 3) of patients proceeded to nephroureterectomy. The estimated cancer-specific survival rate was 93% at 5, 10, 15 and 20 years. Estimated overall survival rates were 86, 80, 54 and 20% at 5, 10, 15 and 20 years. Only one patient experienced cancer-specific mortality. The estimated mean and median overall survival times were 14.5 and 16.6 years, respectively. The estimated mean cancer-specific survival time was not reached.

Conclusions
Although upper tract recurrence is common, endoscopic management of non-invasive upper tract urothelial carcinoma provides a 90% cancer-specific survival rate at 20 years in selected patients.
High day and night temperatures distinctively disrupt fatty acid and jasmonic acid metabolism, inducing male sterility in cotton
Authors: Khan Aamir Hamid , Min Ling , Ma Yizan , Wu Yuanlong , Ding Yuanhao , Li Yanlong , Xie Sai , Ullah Abid , Shaban Muhammad , Manghwar Hakim , Shahid Muhammad , Zhao Yunlong , Wang Chaozhi , Zhang Xianlong 
Published: July 2020

Abstract
High temperature stress is an inevitable environmental factor in certain geographical regions. To study the effect of day and night high temperature stress on male reproduction, the heat-sensitive cotton line H05 was subjected to high temperature stress. High day/normal night (HN) and normal day/high night (NH) temperature treatments were compared with normal day/normal night (NN) temperature as a control. At the anther dehiscence stage, significant differences were observed, with a reduction in flower size and filament length, and sterility in pollen, seen in NH more than in HN. A total of 36 806 differentially expressed genes were screened, which were mainly associated with fatty acid and jasmonic acid (JA) metabolic pathways. Fatty acid and JA contents were reduced more in NH than HN. Under NH, ACYL-COA OXIDASE 2 (ACO2), a JA biosynthesis gene, was down-regulated. Interestingly, aco2 CRISPR-Cas9 mutants showed male sterility under the NN condition. The exogenous application of methyl jasmonate to early-stage buds of mutants rescued the sterile pollen and indehiscent anther phenotypes at the late stage. These data show that high temperature at night may affect fatty acid and JA metabolism in anthers by suppressing GhACO2 and generate male sterility more strongly than high day temperature.
The matrix revolutions: towards the decoding of the plant chromatin three-dimensional reality
Authors: Huang Ying , Rodriguez-Granados Natalia Yaneth , Latrasse David , Raynaud Cecile , Benhamed Moussa , Ramirez-Prado Juan Sebastian 
Published: July 2020

AbstractIn recent years, we have witnessed a significant increase in studies addressing the three-dimensional (3D) chromatin organization of the plant nucleus. Important advances in chromatin conformation capture (3C)-derived and related techniques have allowed the exploration of the nuclear topology of plants with large and complex genomes, including various crops. In addition, the increase in their resolution has permitted the depiction of chromatin compartmentalization and interactions at the gene scale. These studies have revealed the highly complex mechanisms governing plant nuclear architecture and the remarkable knowledge gaps in this field. Here we discuss the state-of-the-art in plant chromosome architecture, including our knowledge of the hierarchical organization of the genome in 3D space and regarding other nuclear components. Furthermore, we highlight the existence in plants of topologically associated domain (TAD)-like structures that display striking differences from their mammalian counterparts, proposing the concept of ICONS—intergenic condensed spacers. Similarly, we explore recent advances in the study of chromatin loops and R-loops, and their implication in the regulation of gene activity. Finally, we address the impact that polyploidization has had on the chromatin topology of modern crops, and how this is related to phenomena such as subgenome dominance and biased gene retention in these organisms.
The Relationship Between Severe Visual Acuity Loss, Traumatic Brain Injuries, and Ocular Injuries in American Service Members From 2001 to 2015
Authors: Flanagan Gerald , Velez Tom , Gu Weidong , Singman Eric 
Published: July 2020

ABSTRACT

Introduction
Although traumatic brain injury (TBI) is known to cause many visual problems, the correlation between the extent of severe visual acuity loss (SVAL) and severity of TBI has not been widely explored. In this retrospective analysis, combined information from Department of Defense (DoD)/Veterans Affairs ocular injury and TBI repositories were used to evaluate the relationship between chronic SVAL, TBI, ocular injuries, and associated ocular sequelae for U.S. service members serving between 2001 and 2015.

Materials and Methods
The Defense and Veterans Eye Injury and Vision Registry (DVEIVR) is an initiative led by the DoD and Veterans Affairs that consists of clinical and related data for service members serving in theater since 2001. The Defense and Veterans Brain Injury Center (DVBIC) is the DoD’s office for tracking TBI data in the military and maintains data on active-duty service members with a TBI diagnosis since 2000. Longitudinal data from these 2 resources for encounters between February 2001 and October 2015 were analyzed to understand the relation between SVAL, and TBI while adjusting for ocular covariates such as open globe injury (OGI), disorders of the anterior segment and disorders of the posterior segment in a logistic regression model. TBI cases in DVEIVR were identified using DVBIC data and classified according to International Statistical Classification of Diseases criteria established by DVBIC. Head trauma and other open head wounds (OOHW) were also included. SVAL cases in DVEIVR were identified using both International Statistical Classification of Diseases criteria for blindness and low vision as well as visual acuity test data recorded in DVEIVR.

Results
Data for a total of 25,193 unique patients with 88,996 encounters were recorded in DVEIVR from February, 2001 to November, 2015. Of these, 7,217 TBI and 1,367 low vision cases were identified, with 638 patients experiencing both. In a full logistic model, neither UTBI nor differentiated TBI (DTBI, ie, mild, moderate, severe, penetrating, or unclassified) were significant risk factors for SVAL although ocular injuries (disorders of the anterior segment, disorders of the posterior segment, and OGI) and OOHW were significant.

Conclusion
Any direct injury to the eye or head risks SVAL but the location and severity will modify that risk. After adjusting for OGIs, OOHW and their sequelae, TBI was found to not be a significant risk factor for SVAL in patients recorded in DVEIVR. Further research is needed to explore whether TBI is associated with more moderate levels of vision acuity loss.