bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do alien free-ranging birds affect human health? A global summary of known zoonoses.
Authors: Mori E. , Meini S. , Strubbe D. , Ancillotto L. , Sposimo P. , Menchetti M. 
Published: July 2018

Abstract

Non-native birds are prominent among alien taxa, with at least 415 species established outside their natural distribution ranges. Impacts of introduced birds on human health have received little attention up to now, despite previous works suggesting that disease transmission is a major impact exerted by introduced bird species. Our synthesis reveals that at least 42 species of introduced birds may represent a hazard to human well-being. Among those, most are Psittaciformes, Columbiformes and Anseriformes, species that frequently occur in urban areas, partly because of their popularity as pets and ornamental species. The main zoonoses potentially brought by these birds include psittacosis, cryptococcosis, listeriosis and salmonellosis, transmitted by direct contact or via arthropod vectors (fleas, lice, ticks and mites). Many Galliformes introduced for hunting purposes can lead to salmonellosis and other gastroenteric diseases in humans. Non-native birds can threaten human health through bird-strikes around airports and through noise pollution by species sharing colonial roosts. While we found that alien birds can theoretically transmit several diseases to humans, empirical case studies of disease outbreaks linked to alien birds are rare or non-existent. The synergistic impacts of ongoing species introductions and global climate change may increase the risk of health hazards in the future. Therefore, sanitary monitoring of traded birds, mainly of the most synanthropic and game species released for human consumption would be prudent. Strict attention should be paid to alien bird populations already established within urban areas, to verify their role in affecting human health and well-being.
Morphologies of co-depositing W layer formed during He plasma irradiation
Authors: Kajita Shin , Kawaguchi Shota , Yoshida Naoaki , Ohno Noriyasu , Tanaka Hirohiko 
Published: July 2018

Abstract
Tungsten (W) samples were exposed to helium (He) plasmas with precipitation of W particles. It was shown that visible large-scale fiberform nanostructures (LFNs) were formed on the surface. The height of the LFN increased exponentially with the irradiation time in the initial phase of the growth. The growth rate was totally different from that of the conventional W nanostructure (fuzz) growth by He plasma irradiation, where the thickness increased in proportion to the square root of time. The LFNs growth had a directionality in a millimeter global scale; the direction was always  ∼45–60 degree rotated in clockwise direction from the magnetic field. The plasma flow measured spectroscopically near the sample was found to significantly increase when inserting a negatively biased sample, and the growth direction of the LFN was consistent with the direction of the plasma flow. Moreover, highly porous fiberform nanostructures or cauliflower-like structures comprised the deposition layer even when the He incident ion energy was lower than the threshold energy of fuzz growth (20–30 eV).
Longitudinal Assessment of Aesthetic Plastic Surgery Training in the United States: The Effect of Increased ACGME Case Log Minimum Requirements
Authors: Kraft Casey T , Harake Mazen S , Janis Jeffrey E 
Published: July 2018

Abstract

Background
In 2014, the Accreditation Council for Graduate Medical Education (ACGME) increased the minimum required aesthetic surgery cases for graduation from plastic surgery residency from 50 to 150. To date, there has been no research into how this has impacted resident aesthetic surgery training focusing on the resident perception.

Objectives
We sought to evaluate resident perception and satisfaction with their aesthetic surgery training before and after the ACGME case log requirement increase to assess its impact on training and comfort level.

Methods
A survey was administered to all graduating senior residents attending the Senior Residents Conference of the ASPS Annual Meeting in 2014 and 2017. The survey evaluated senior resident aesthetic surgery experience and their confidence and satisfaction with their training.

Results
The response rate was 70% in 2014 and 45% in 2017. There was an increase in the number of programs with resident-run cosmetic clinics (14% increase) and designated aesthetic rotations (33% increase) during that time. Resident-run cosmetic clinics were consistently considered the most valuable form of aesthetic training for residents. There also was a substantial increase in the percentage of residents feeling prepared to incorporate aesthetic surgery into their practice after graduation, increasing from 36% to 59% in 2017. The majority of responding residents felt that the ACGME case log requirement increase in 2014 was beneficial for their aesthetic surgery training (68%).

Conclusions
The recent ACGME case log requirement increase for aesthetic surgery training has had a positive effect on resident comfort with aesthetic procedures and their ability to incorporate them into future practice.
If you build it, they may not come: modifiable barriers to patient portal use among pre- and post-kidney transplant patients
Authors: Lockwood Mark B , Dunn-Lopez Karen , Pauls Heather , Burke Larisa , Shah Sachin D , Saunders Milda A 
Published: July 2018

Abstract

Background
Patient access to health information using electronic patient portals is increasingly common. Portal use has the potential to improve patients’ engagement with their health and is particularly important for patients with chronic illness; however, patients’ abilities, attitudes, and use of portals are poorly understood.

Methods
A single-center, cross-sectional survey was conducted of 240 consecutive pre- and post-kidney transplant patients of all levels of technological proficiency who presented to an urban transplant center in the United States. The investigator-developed Patient Information and Technology Assessment-Patient Portal was used to assess patients’ attitudes towards the use of patient portals.

Results
Most patients surveyed did not use the patient portal (n = 176, 73%). Patients were more likely to use the patient portal if they were White, highly educated, in the post-transplant period, more comfortable with technology, and reported being a frequent internet user (P &lt; .05). The most common reasons for not using the patient portal included: (1) preference for traditional communication, (2) not being aware of the portal, (3) low technological proficiency, and (4) poor interoperability between the portal at the transplant center and the patient’s primary care center.

Conclusions
We identified several modifiable barriers to patient portal use. Some barriers can be addressed by patient education and training on portal use, and federal initiatives are underway to improve interoperability; however, a preference for traditional communications represents the most prominent barrier. Additional strategies are needed to improve portal adoption by encouraging acceptance of technologies as a way of clinical communication.
Incidence, prevalence, mortality and chronic renal damage of anti-neutrophil cytoplasmic antibody-associated glomerulonephritis in a 20-year population-based cohort
Authors: Berti Alvise , Cornec-Le Gall Emilie , Cornec Divi , Casal Moura Marta , Matteson Eric L , Crowson Cynthia S , Ravindran Aishwarya , Sethi Sanjeev , Fervenza Fernando C , Specks Ulrich 
Published: July 2018

Abstract

Background
True population-based clinical and outcomes data are lacking for anti-neutrophil cytoplasmic autoantibody (ANCA)-associated glomerulonephritis (AAGN). Therefore we aimed to estimate the incidence, prevalence and mortality of AAGN, as well as the relationship between the grade of chronic renal damage at presentation and renal and non-renal outcomes.

Methods
Patients with AAGN were identified among a population-based incident cohort of 57 Olmsted County residents diagnosed with ANCA-associated vasculitis (AAV) in 1996–2015. Incidence rates were age and sex adjusted to the 2010 US white population. Age- and sex-adjusted prevalence was calculated for 1 January 2015. Survival rates were compared with expected rates in the Minnesota population. Chronic renal damage was assessed by chronicity score (CS) on biopsies performed at diagnosis.

Results
Thirty-four (60%) patients had AAGN. Of these, 65% had microscopic polyangiitis (MPA) and 74% were myeloperoxidase (MPO)-ANCA positive. The annual incidence of AAGN was 2.0/100 000 population [95% confidence interval (CI) 1.3–2.7] and the overall prevalence was 35/100 000 (95% CI 24–47). Mortality for AAGN was increased (P &lt; 0.001), whereas mortality for AAV without glomerulonephritis did not differ from the general population. Minimal to mild CS predicted recovery of renal function at 1 year; clinical diagnosis (granulomatosis with polyangiitis versus MPA) and ANCA specificity (proteinase 3 versus MPO) did not. This observation was replicated in an independent cohort of 38 newly diagnosed AAGN patients seen at our centre over the 1999–2014 period.

Conclusions
The annual incidence and prevalence of AAGN in Minnesota are 2.0/100 000 and 35/100 000, respectively. Mortality is worse compared with AAV patients without glomerulonephritis. More advanced renal damage at diagnosis predicts less renal recovery.
Endothelial sphingosine-1-phosphate receptor 1 deficiency exacerbates brain injury and blood brain barrier dysfunction upon subarachnoid hemorrhage in mice
Authors: Ito Akira , Uchida Hiroki , Kim Gab Seok , Faraco Giuseppe , Proia Richard , Niizuma Kuniyasu , Tominaga Teiji , Anrather Josef , Iadecola Costantino , Kluk Michael J , Sanchez Teresa 
Published: July 2018

ABSTRACTBlood brain barrier (BBB) dysfunction upon ischemia and hypoxia has been implicated in the exacerbation of neuronal injury in stroke. Despite the therapeutic potential of the cerebrovascular endothelium, the limited understanding of the endothelial signaling pathways governing BBB function restricts progress towards developing novel therapeutic approaches specifically targeting the endothelium. Sphingosine-1-phosphate (S1P) is a potent modulator of endothelial function via its receptors (S1PR). Recent human and mouse studies indicate that vasoprotective endothelial S1P signaling via S1PR1 may be impaired in cardiovascular and inflammatory diseases. Herein, we investigated the expression of S1PR1 in the mouse and human cerebrovascular endothelium and the role of endothelial-specific S1PR1 signaling in brain injury in a mouse model of aneurysmal subarachnoid hemorrhage (SAH), the most devastating type of stroke. We found that S1PR1 is the most abundant S1PR transcript in the mouse brain and in mouse and human brain endothelial cells (20-100 mRNA copies per cell). S1PR1 transcripts were significantly enriched (~6 fold) in mouse cortical microvessels compared to total brain. Using the S1PR1-eGFP knock in mouse, we found that S1PR1-eGFP is abundantly expressed in the cerebrovascular endothelium in the mouse brain. A similar pattern of expression was observed in human brain samples. Endothelial specific deletion of S1PR1 in adult mice (S1pr1flox/floxxCdh5-CreERT2, referred to asS1pr1iECKO), resulted in exacerbation of brain edema, neuronal injury and worsened neurological outcomes upon SAH compared toS1pr1flox/floxlittermates. No differences in the subarachnoid blood, hemostasis or cerebral blood flow changes during and after SAH were found between groups. Mechanistically,S1pr1iECKOexhibited aggravated BBB dysfunction and increased phosphorylation of myosin light chain (MLC) in isolated cortical microvessels, a downstream effector of the Rho-ROCK pathway implicated in endothelial inflammation and barrier dysfunction. Taken together, our data indicate that S1PR1 is an endogenous protective signaling pathway in the endothelium, critical to maintain BBB function and to mitigate neuronal injury in pathological conditions. Thus, the therapeutic and diagnostic potential of the endothelial sphingosine-1-phosphate pathway in stroke deserves further study.
An integrative systems biology and experimental approach identifies convergence of epithelial plasticity, metabolism, and autophagy to promote chemoresistance
Authors: Xu Shengnan , Ware Kathryn E. , Ding Yuantong , Kim So Young , Sheth Maya , Rao Sneha , Chan Wesley , Armstrong Andrew J. , Eward William C. , Jolly Mohit K. , Somarelli Jason A. 
Published: July 2018

AbstractThe evolution of therapeutic resistance is a major cause of death for patients with solid tumors. The development of therapy resistance is shaped by the ecological dynamics within the tumor microenvironment and the selective pressure induced by the host immune system. These ecological and selective forces often lead to evolutionary convergence on one or more pathways or hallmarks that drive progression. These hallmarks are, in turn, intimately linked to each other through gene expression networks. Thus, a deeper understanding of the evolutionary convergences that occur at the gene expression level could reveal vulnerabilities that could be targeted to treat therapy-resistant cancer. To this end, we used a combination of phylogenetic clustering, systems biology analyses, and wet-bench molecular experimentation to identify convergences in gene expression data onto common signaling pathways. We applied these methods to derive new insights about the networks at play during TGF-β-mediated epithelial-mesenchymal transition in a lung cancer model system. Phylogenetics analyses of gene expression data from TGF-β treated cells revealed evolutionary convergence of cells toward amine-metabolic pathways and autophagy during TGF-β treatment. Using high-throughput drug screens, we found that knockdown of the autophagy regulatory, ATG16L1, re-sensitized lung cancer cells to cancer therapies following TGF-β-induced resistance, implicating autophagy as a TGF-β-mediated chemoresistance mechanism. Analysis of publicly-available clinical data sets validated the adverse prognostic importance of ATG16L expression in multiple cancer types including kidney, lung, and colon cancer patients. These analyses reveal the usefulness of combining evolutionary and systems biology methods with experimental validation to illuminate new therapeutic vulnerabilities.
Intentional gestures predict complex sociality in wild chimpanzee
Authors: Roberts Anna Ilona , Roberts Sam George Bradley 
Published: July 2018

AbstractA key challenge for primates is coordinating behavior with conspecifics in large, complex social groups. Gestures play a key role in this process and chimpanzees show considerable flexibility communicating through single gestures, sequences of gestures interspersed with periods of response waiting (persistence) and rapid sequences where gestures are made in quick succession, too rapid for the response waiting to have occurred. Previous studies examined behavioral reactions to single gestures and sequences, but whether this complexity is associated with more complex sociality at the level of the dyad partner and the group as a whole is not well understood. We used social network analysis to examine how the production of single gestures and sequences of gestures was related to the duration of time spent in proximity and individual differences in proximity in wild East African chimpanzees (Pan troglodytes schweinfurthii). Pairs of chimpanzees that spent a longer duration of time in proximity had higher rates of persistence, but not a higher rate of single gesture or rapid sequences. Central individuals in the social network received higher rates of persistence, but not rapid sequence or single gesture. Intentional gestural communication plays an important role in regulating social interactions in complex primate societies.
CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning
Authors: Oomen Marlies E. , Hansen Anders S. , Liu Yu , Darzacq Xavier , Dekker Job 
Published: July 2018

AbstractCTCF plays a key role in formation of topologically associating domains (TADs) and loops in interphase. During mitosis TADs are absent, but how TAD formation is dynamically controlled during the cell cycle is not known. Several contradicting observations have been made regarding CTCF binding to mitotic chromatin using both genomics and microscopy-based techniques. Here we have used 4 different assays to address this debate. First, using 5C we confirmed that TADs and CTCF loops are readily detected in interphase, but absent during prometaphase. Second, ATAC-seq analysis showed that CTCF sites display greatly reduced accessibility and lose the CTCF footprint in prometaphase, suggesting loss of CTCF binding and rearrangement of the nucleosomal array around the binding motif. In contrast, transcription start sites remain accessible in prometaphase, although adjacent nucleosomes can also become repositioned and occupy at least a subset of start sites during mitosis. Third, loss of site-specific CTCF binding was directly demonstrated using CUT&RUN. Histone modifications and histone variants are maintained in mitosis, suggesting a role in bookmarking of active CTCF sites. Finally, live-cell imaging, fluorescence recovery after photobleaching and single molecule tracking showed that almost all CTCF chromatin binding is lost in prometaphase. Combined, our results demonstrate loss of CTCF binding to CTCF sites during prometaphase and rearrangement of the chromatin landscape around CTCF motifs. This contributes to loss of TADs and CTCF loops during mitosis, and reveals that CTCF sites, a key architectural cis-element of the genome, display cell cycle stage-dependent dynamics in factor binding and nucleosome positioning.
Analysis of Local Variability and Allostery in Macromolecular Assemblies using Cryo-EM and Focused Classification
Authors: Zhang Cheng , Cantara William , Jeon Youngmin , Musier-Forsyth Karin , Grigorieff Nikolaus , Lyumkis Dmitry 
Published: July 2018

AbstractSingle-particle electron cryo-microscopy and computational image classification can be used to analyze structural variability in macromolecules and their assemblies. In some cases, a particle may contain different regions that each display a range of distinct conformations. We have developed strategies, implemented within the Frealign andcisTEM image processing packages, to focus classify on specific regions of a particle and detect potential covariance. The strategies are based on masking the region of interest using either a 2-D mask applied to reference projections and particle images, or a 3-D mask applied to the 3-D volume. We show that focused classification approaches can be used to study structural allostery, a concept that is likely to gain more importance as datasets grow in size, allowing the distinction of more structural states and smaller differences between states. Finally, we apply the approaches to an experimental dataset containing the HIV-1 Transactivation Response (TAR) element RNA fused into the large bacterial ribosomal subunit, to deconvolve structural mobility within localized regions of interest.HighlightsDescription of different image classification strategies in single-particle cryo-EMQuantitative evaluation of two classification methods using simulated dataApplication of the two classification methods to an experimental dataset
Expression estimation and eQTL mapping for HLA genes with a personalized pipeline
Authors: Aguiar Vitor R.C. , Cesar Jonatas E. , Delaneau Olivier , Dermitzakis Emmanouil T. , Meyer Diogo 
Published: July 2018

AbstractThe HLA (Human Leukocyte Antigens) genes are well-documented targets of balancing selection, and variation at these loci is associated with many disease phenotypes. Variation in expression levels also influences disease susceptibility and resistance, but little information exists about the regulation and population-level patterns of expression due to the difficulty in mapping short reads to these highly polymorphic loci, and in accounting for the existence of several paralogues. We developed a computational pipeline to accurately estimate expression for HLA genes based on RNA-seq, improving both locus-level and allele-level estimates. First, reads are aligned to all known HLA sequences in order to infer HLA genotypes, then quantification of expression is carried out using a personalized index. We use simulations to show that expression estimates are not biased due to divergence from the reference genome. We applied our pipeline to GEUVADIS dataset, and compared the quantifications to those obtained with reference transcriptome, and found that a substantial portion of the variation captured by the HLA-personalized index in not captured by the standard index (23%). We describe the impact of the HLA-personalized approach on downstream analyses for seven HLA loci (HLA-A, HLA-B, HLA-C, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1). Although the influence of the HLA-personalized approach is modest for eQTL mapping, the p-values and the causality of the eQTLs obtained are better than when the reference transcriptome is used. Finally, we integrate information on HLA-allele level expression with the eQTL findings to show that the HLA allele is an important layer of variation to understand HLA regulation.
Comprehensive analysis of potential immunotherapy genomic biomarkers in 1,000 Chinese patients with cancer
Authors: Jiao Shunchang , Zang Yuansheng , Dai Chun , Xu Xiaoman , Cai Xin , Wang Guan , Wei Jinwang , Wu Angela , Sun Wending , Xu Qiang 
Published: July 2018

AbstractBackgroundTumor mutation burden (TMB), DNA mismatch repair deficiency (dMMR), microsatellite instability (MSI), and PD-L1 amplification (PD-L1 AMP) may predict the efficacy of PD-1/PD-L1 blockade. In this study, we aimed to characterize the distributions of these biomarkers in over 1,000 Chinese patients with cancer.MethodsTMB, MSI, dMMR, and PD-L1 AMP were determined based on whole-exome sequencing of tumor/blood samples from > 1,000 Chinese patients with cancer.ResultsIncidence rates among 953 Chinese patients with cancer showing high TMB (TMB-H), high MSI (MSI-H), dMMR and PD-L1 AMP were 35%, 4%, 0.53% and 3.79%, respectively. We found higher rates of TMB-H among hepatocellular carcinoma, breast cancer, and esophageal cancer patients than was reported for The Cancer Genome Atlas data. Lung cancer patients withEGFRmutations had significantly lower TMB values than those with wild-typeEGFR, and increased TMB was significantly associated with dMMR in colorectal cancer (CRC). The frequency of tumors with MSI-H was highest in CRC (14%) and gastric cancer (4%). PD-L1 AMP occurred most frequently in lung squamous cell carcinoma (14.3%) and HER2-positive breast cancer (8.8%). Most MSI-H and dMMR cases exhibited TMB-H, but the overlap among the other biomarkers was low.ConclusionWhile MSI and dMMR are associated with higher mutational loads, correlations between TMB-H and other biomarkers, between MSI-H and dMMR, and between PD-L1 AMP and other biomarkers were low, indicating different underlying causes of the four biomarkers. Thus, it is recommended that all four biomarkers be assessed for certain cancers before administration of PD-1/PD-L1 blockade treatment.