bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host preference and network properties in biotrophic plant–fungal associations
Authors: Põlme Sergei , Bahram Mohammad , Jacquemyn Hans , Kennedy Peter , Kohout Petr , Moora Mari , Oja Jane , Öpik Maarja , Pecoraro Lorenzo , Tedersoo Leho 
Published: November 2017

Summary

Analytical methods can offer insights into the structure of biological networks, but mechanisms that determine the structure of these networks remain unclear. We conducted a synthesis based on 111 previously published datasets to assess a range of ecological and evolutionary mechanisms that may influence the plant‐associated fungal interaction networks.

We calculated the relative host effect on fungal community composition and compared nestedness and modularity among different mycorrhizal types and endophytic fungal guilds. We also assessed how plant–fungal network structure was related to host phylogeny, environmental and sampling properties.

Orchid mycorrhizal fungal communities responded most strongly to host identity, but the effect of host was similar among all other fungal guilds. Community nestedness, which did not differ among fungal guilds, declined significantly with increasing mean annual precipitation on a global scale. Orchid and ericoid mycorrhizal fungal communities were more modular than ectomycorrhizal and root endophytic communities, with arbuscular mycorrhizal fungi in an intermediate position.

Network properties among a broad suite of plant‐associated fungi were largely comparable and generally unrelated to phylogenetic distance among hosts. Instead, network metrics were predominantly affected by sampling and matrix properties, indicating the importance of study design in properly inferring ecological patterns.
Impact of Ultraviolet Radiation on Expression of Transforming Growth Factor β, Smad2, Metalloproteinases‐1, ‐3, ‐8, ‐9, Cathepsin K and Progerin
Authors: Ciążyńska Magdalena , Bednarski Igor A. , Wódz Karolina , Narbutt Joanna , Sobjanek Michał , Woźniacka Anna , Lesiak Aleksandra 
Published: November 2017

AbstractUltraviolet radiation (UVR) is one of the most important environmental factors involved in photoaging. Exposure to UVR leads to dysregulation of expression of cell cycle‐related proteins which play key role in skin photodegradation that pretends to develop carcinogenesis. This study examines the role of various UVB doses on the expression of transforming growth factor beta (TGF‐β), Smad2, cathepsin K, progerin and matrix metalloproteinases (MMPs)‐1,‐3,‐8,‐9. A group consisting of 63 healthy individuals underwent one of the following treatments: (1) whole body exposed to UVB irradiation on each of 10 consecutive days with 0.7 MED, or (2) whole‐body irradiation as described followed by a single erythemal UVB dose on a small body area, or (3) irradiated only with a single erythemal UVB dose on small body area, or (4) were not irradiated at all (control group). When we compared all irradiated groups to the control group, there was significantly higher expression of TGF‐β, MMP‐1,‐3,‐9 and cathepsin K proteins evaluated by Western blot method. The results suggest the role of UVB in impairment of proteins expression that is involved in cell cycle's regulation. Changes in the protein expression involved by acute and chronic UVR confirm its essential role in skin photodestruction. Moreover, obtained result indicates the tendency to occurrence of photoadaptation phenomenon.
More Reasons Why Jurisprudence Is Not Legal Philosophy
Authors: Robertson Michael 
Published: November 2017

AbstractIt is generally assumed, without argument, that legal theory, legal philosophy, philosophy of law, and jurisprudence all mean the same thing. This paper rejects that assumption, and in particular the assumption that jurisprudence is the same thing as legal philosophy. This assumption has recently been challenged by Roger Cotterrell in his article “Why Jurisprudence Is Not Legal Philosophy,” and I seek to build on his arguments by adding insights found in the work of Stanley Fish.
Asymptotic Approximations for Radial Spheroidal Wavefunctions with Complex Size Parameter
Authors: Martin P. A. 
Published: November 2017

AbstractRadial spheroidal wavefunctions are functions of four variables, usually denoted by m, n, x, and γ, the last of which is known as the size parameter. This parameter becomes complex when the problem of scattering of a sound pulse by a spheroid is treated using a Laplace transform with respect to time together with the method of separation of variables. Several asymptotic approximations, involving modified Bessel functions, are developed and analyzed.
The TCP4 transcription factor regulates trichome cell differentiation by directly activating GLABROUS INFLORESCENCE STEMS in Arabidopsis thaliana
Authors: Vadde Batthula Vijaya Lakshmi , Challa Krishna Reddy , Nath Utpal 
Published: November 2017

SummaryTrichomes are the first cell type to be differentiated during the morphogenesis of leaf epidermis and serve as an ideal model to study cellular differentiation. Many genes involved in the patterning and differentiation of trichome cells have been studied over the past decades, and the majority of these genes encode transcription factors that specifically regulate epidermal cell development. However, the upstream regulators of these genes that link early leaf morphogenesis with cell type differentiation are less studied. The TCP proteins are the plant‐specific transcription factors involved in regulating diverse aspects of plant development including lateral organ morphogenesis by modulating cell proliferation and differentiation. Here, we show that the miR319‐regulated class II TCP proteins, notably TCP4, suppress trichome branching in Arabidopsis leaves and inflorescence stem by direct transcriptional activation of GLABROUS INFLORESCENCE STEMS (GIS), a known negative regulator of trichome branching. The trichome branch number is increased in plants with reduced TCP activity and decreased in the gain‐of‐function lines of TCP4. Biochemical analyses show that TCP4 binds to the upstream regulatory region of GIS and activates its expression. Detailed genetic analyses show that GIS and TCP4 work in same pathway and GIS function is required for TCP4‐mediated regulation of trichome differentiation. Taken together, these results identify a role for the class II TCP genes in trichome differentiation, thus providing a connection between organ morphogenesis and cellular differentiation.
Candida auris: an Emerging Fungal Pathogen
Authors: Spivak Emily S. , Hanson Kimberly E. 
Published: November 2017

ABSTRACT

Candida auris
has emerged globally as a multidrug-resistant health care-associated fungal pathogen. Recent reports highlight ongoing challenges due to organism misidentification, high rates of antifungal drug resistance, and significant patient mortality. The predilection for transmission within and between health care facilities possibly promoted by virulence factors that facilitate skin colonization and environmental persistence is unique among
Candida
species. This minireview details the global emergence of
C. auris
and discusses issues relevant to clinical microbiology laboratories, hospital infection control, and antimicrobial stewardship efforts.
Insight into the Roles of E3 Ubiquitin Ligase c-Cbl, ESCRT Machinery, and Host Cell Signaling in Kaposi's Sarcoma-Associated Herpesvirus Entry and Trafficking
Authors: Kumar Binod , Roy Arunava , Veettil Mohanan Valiya , Chandran Bala 
Published: November 2017

ABSTRACT

Kaposi's sarcoma-associated herpesvirus (KSHV)
in vitro
infection of dermal endothelial cells begins with its binding to host cell surface receptor molecules such as heparan sulfate (HS), integrins (α3β1, αVβ3, and αVβ5), xCT, and EphA2 receptor tyrosine kinase (EphA2R). These initial events initiate dynamic host protein-protein interactions involving a multimolecular complex of receptors, signal molecules (focal adhesion kinase [FAK], Src, phosphatidylinositol 3-kinase [PI3-K], and RhoA-GTPase), adaptors (c-Cbl, CIB1, Crk, p130Cas, and GEF-C3G), actin, and myosin II light chain that lead to virus entry via macropinocytosis. Here we discuss how KSHV hijacks c-Cbl, an E3 ubiquitin ligase, to monoubiquitinate the receptors and actin, which acts like a marker for trafficking (similar to zip codes), resulting in the recruitment of the members of the host endosomal sorting complexes required for transport (ESCRT) Hrs, Tsg101, EAP45, and the CHMP5 and -6 proteins (zip code readers) recognizing the ubiquitinated protein and adaptor machinery to traffic through the different endosomal compartments in the cytoplasm to initiate the macropinocytic process and infection.
Persistence of an Oncogenic Papillomavirus Genome Requires
cis
Elements from the Viral Transcriptional Enhancer
Authors: Van Doorslaer Koenraad , Chen Dan , Chapman Sandra , Khan Jameela , McBride Alison A. 
Published: November 2017

ABSTRACT

Human papillomavirus (HPV) genomes are replicated and maintained as extrachromosomal plasmids during persistent infection. The viral E2 proteins are thought to promote stable maintenance replication by tethering the viral DNA to host chromatin. However, this has been very difficult to prove genetically, as the E2 protein is involved in transcriptional regulation and initiation of replication, as well as its assumed role in genome maintenance. This makes mutational analysis of viral
trans
factors and
cis
elements in the background of the viral genome problematic and difficult to interpret. To circumvent this problem, we have developed a complementation assay in which the complete wild-type HPV18 genome is transfected into primary human keratinocytes along with subgenomic or mutated replicons that contain the minimal replication origin. The wild-type genome provides the E1 and E2 proteins in
trans
, allowing us to determine additional
cis
elements that are required for long-term replication and partitioning of the replicon. We found that, in addition to the core replication origin (and the three E2 binding sites located therein), additional sequences from the transcriptional enhancer portion of the URR (upstream regulatory region) are required in
cis
for long-term genome replication.

IMPORTANCE
Human papillomaviruses infect cutaneous and mucosal epithelial cells of the host, and this results in very-long-lived, persistent infection. The viral genomes are small, circular, double-stranded DNA molecules that replicate extrachromosomally in concert with cellular DNA. This replication strategy requires that the virus has a robust mechanism to partition and retain the viral genomes in dividing cells. This has been difficult to study, because viral transcription, replication, and partitioning are regulated by the same viral proteins and involve overlapping elements in the viral genome. We developed a complementation assay that allows us to separate these functions and define the elements required for long-term replication and stable maintenance replication of the HPV genome. This has important implications, as disruption of viral maintenance replication can eliminate viral genomes from infected cells, thus curing persistent HPV infection.
Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers
Authors: Nguyen Sophie , Baker Kristi , Padman Benjamin S. , Patwa Ruzeen , Dunstan Rhys A. , Weston Thomas A. , Schlosser Kyle , Bailey Barbara , Lithgow Trevor , Lazarou Michael , Luque Antoni , Rohwer Forest , Blumberg Richard S. , Barr Jeremy J. 
Published: November 2017

ABSTRACT

Bacterial viruses are among the most numerous biological entities within the human body. These viruses are found within regions of the body that have conventionally been considered sterile, including the blood, lymph, and organs. However, the primary mechanism that bacterial viruses use to bypass epithelial cell layers and access the body remains unknown. Here, we used
in vitro
studies to demonstrate the rapid and directional transcytosis of diverse bacteriophages across confluent cell layers originating from the gut, lung, liver, kidney, and brain. Bacteriophage transcytosis across cell layers had a significant preferential directionality for apical-to-basolateral transport, with approximately 0.1% of total bacteriophages applied being transcytosed over a 2-h period. Bacteriophages were capable of crossing the epithelial cell layer within 10 min with transport not significantly affected by the presence of bacterial endotoxins. Microscopy and cellular assays revealed that bacteriophages accessed both the vesicular and cytosolic compartments of the eukaryotic cell, with phage transcytosis suggested to traffic through the Golgi apparatus via the endomembrane system. Extrapolating from these results, we estimated that 31 billion bacteriophage particles are transcytosed across the epithelial cell layers of the gut into the average human body each day. The transcytosis of bacteriophages is a natural and ubiquitous process that provides a mechanistic explanation for the occurrence of phages within the body.

IMPORTANCE
Bacteriophages (phages) are viruses that infect bacteria. They cannot infect eukaryotic cells but can penetrate epithelial cell layers and spread throughout sterile regions of our bodies, including the blood, lymph, organs, and even the brain. Yet how phages cross these eukaryotic cell layers and gain access to the body remains unknown. In this work, epithelial cells were observed to take up and transport phages across the cell, releasing active phages on the opposite cell surface. Based on these results, we posit that the human body is continually absorbing phages from the gut and transporting them throughout the cell structure and subsequently the body. These results reveal that phages interact directly with the cells and organs of our bodies, likely contributing to human health and immunity.
The association between gastro-oesophageal reflux disease and subsequent rheumatoid arthritis occurrence: a nested case–control study from Taiwan
Authors: Lin Herng-Ching , Xirasagar Sudha , Lee Cha-Ze , Huang Chung-Chien , Chen Chao-Hung 
Published: November 2017

ObjectiveGastro-oesophageal reflux disease (GORD) is a common comorbidity among patients with rheumatoid arthritis (RA). While GORD has been attributed to the antirheumatic medications, no studies of human cohorts have investigated a link between GORD and RA. This study investigates whether GORD is associated with a subsequent RA diagnosis over a 5-year follow-up using a population-based dataset.SettingTaiwanParticipantsWe used data from the Taiwan Longitudinal Health Insurance Database. The study group consisted of 13 645 patients with an ambulatory claim showing a GORD diagnosis. We used propensity score matching to select 13 645 comparison patients (one per study patient with GORD).InterventionWe tracked each patient’s claims over a 5-year period to identify those who subsequently received a diagnosis of RA. Cox proportional hazard (PH) regression modelling was used for analysis.ResultsOver 5-year follow-up, RA incidence rate per 1000 person-years was 2.81 among patients with GORD and 0.84 among the comparison group. Cox PH modelling showed that GORD was independently associated with a 2.84-fold increased risk of RA (95% CI 2.09 to 3.85) over 5-year follow-up, after adjusting for the number of ambulatory care visits within the year following the index date (to mitigate surveillance bias).ConclusionsWe observed that GORD might associate with subsequent RA occurrence. Because current treatment guidelines for RA emphasise early diagnosis and prompt treatment, the observed association between GORD and RA may help acquaint clinicians to patients with GORD with higher RA risk and facilitate early diagnosis and treatment.
Prevalence of health services usage and associated factors in the Amazon region of Brazil: a population-based cross-sectional study
Authors: Araujo Maria Elizete A , Silva Marcus T , Galvao Tais F , Pereira Mauricio G 
Published: November 2017

ObjectivesTo estimate the prevalence of healthcare use and associated factors in the Manaus metropolitan region and to describe the reasons for lack of access.DesignCross-sectional population-based study.SettingA survey conducted between May and August of 2015 in eight cities from Manaus metropolitan region, Amazonas, Brazil.Participants4001 adults ≥18 years of age.Primary outcomes measuresPhysician visits, dentist visits and hospitalisations in the last 12 months were the primary outcomes. Associated factors were investigated through the calculation of prevalence ratio (PR) obtained by hierarchical Poisson regression modelling.Results4001 adults were included in the study, 53% of whom were women. The self-reported prevalence of medical visits was 77% (95% CI 75% to 77%); dentist visits, 36% (95% CI 34% to 37%) and hospital admission, 7% (95% CI 6% to 7%). Physician visits were higher in women PR=1.18 (95% CI 1.14 to 1.23), the elderly PR=1.18 (95% CI 1.10 to 1.26) and people with health insurance PR=1.14 (95% CI 1.10 to 1.19). Dentist visits declined with older age PR=0.38 (95% CI 0.30 to 0.49), lower education level PR=0.62 (95% CI 0.51 to 0.74) and lower economic class PR=0.65 (95% CI 0.57 to 0.75). Hospitalisations were found to be twice as frequent for women than for men and three times as frequent among those who reported very poor health status. Among the individuals who did not receive medical attention in the previous 2 weeks, 58% reported lack of facilities or appointment unavailable and 14% reported lack of doctors.ConclusionWhile more than half visited the doctor in the last year, a lower proportion of people with socioeconomic inequities visited the dentist. Organisational and service policies are needed to increase equity in health services in the region.
Exploring the effects of transfers and readmissions on trends in population counts of hospital admissions for coronary heart disease: a Western Australian data linkage study
Authors: Lopez Derrick , Nedkoff Lee , Knuiman Matthew , Hobbs Michael S T , Briffa Thomas G , Preen David B , Hung Joseph , Beilby John , Mathur Sushma , Reynolds Anna , Sanfilippo Frank M 
Published: November 2017

ObjectivesTo develop a method for categorising coronary heart disease (CHD) subtype in linked data accounting for different CHD diagnoses across records, and to compare hospital admission numbers and ratios of unlinked versus linked data for each CHD subtype over time, and across age groups and sex.DesignCohort study.Data sourcePerson-linked hospital administrative data covering all admissions for CHD in Western Australia from 1988 to 2013.Main outcomeRatios of (1) unlinked admission counts to contiguous admission (CA) counts (accounting for transfers), and (2) 28-day episode counts (accounting for transfers and readmissions) to CA counts stratified by CHD subtype, sex and age group.ResultsIn all CHD subtypes, the ratios changed in a linear or quadratic fashion over time and the coefficients of the trend term differed across CHD subtypes. Furthermore, for many CHD subtypes the ratios also differed by age group and sex. For example, in women aged 35–54 years, the ratio of unlinked to CA counts for non-ST elevation myocardial infarction admissions in 2000 was 1.10, and this increased in a linear fashion to 1.30 in 2013, representing an annual increase of 0.0148.ConclusionThe use of unlinked counts in epidemiological estimates of CHD hospitalisations overestimates CHD counts. The CA and 28-day episode counts are more aligned with epidemiological studies of CHD. The degree of overestimation of counts using only unlinked counts varies in a complex manner with CHD subtype, time, sex and age group, and it is not possible to apply a simple correction factor to counts obtained from unlinked data.
Association of homocysteine and smoking with cerebral microemboli in patients with mechanical heart valves: a transcranial Doppler study
Authors: Mattia Alicia , Azarpazhooh M Reza , Munoz Claudio , Bogiatzi Chrysi , Quantz Mackenzie A , Spence J David 
Published: November 2017

ObjectivesMicroembolic signals (MES) on transcranial Doppler (TCD) predict stroke and cognitive decline. Plasma levels of total homocysteine (tHcy), a prothrombotic factor, are higher in patients with microemboli in carotid stenosis and in patients with paradoxical embolism. In this study we assessed the association between the level of tHcy and the number of MES in patients with mechanical heart valves (MHVs).MethodsTCD monitoring was performed to detect MES before and after breathing 100% oxygen and repeated every 2–4 weeks up to six times.ResultsTwenty-five patients with MHVs (mean age: 63.60±10.15 years) participated in this study; 15 were men (66.47±7.25 years) and 10 were women (59.30±12.60 years). In total, there were 126 study visits. In multiple regression, higher tHcy was associated with more MES in both preoxygenation (OR 1.34 (95% CI 1.07 to 1.68, P=0.009)) and postoxygenation (OR 1.40 (95% CI 1.07 to 1.83, P=0.01)) phases. Current smoking and the length of time between the operation and monitoring also correlated with a higher number of MES before and after breathing oxygen, particularly in women.ConclusionsHigher tHcy and smoking were associated with a higher MES count in both preoxygenation and postoxygenation phases. Because smoking can be stopped and hyperhomocysteinaemia is treatable, these are clinically important findings.
Probing light bino and higgsinos at the LHC
Authors: Han Chengcheng 
Published: November 2017

Motivated by the naturalness, we study a simplified Minimal Supersymmetric Standard Model (MSSM) scenario where only the bino-like lightest supersymmetric particle (LSP) and higgsino-like next-lightest supersymmetric particle (NLSP) are light. We first scan the parameter space of this scenario, considering the constraints from the Higgs mass, flavor physics, electroweak precision measurements and dark matter experiments. Then in the allowed parameter space, we perform a Monte Carlo simulation for the [Formula: see text] production followed by [Formula: see text] and [Formula: see text]. By examining the presently available trilepton bounds on the wino-like chargino/neutralino, we find that only a narrow region [Formula: see text] and [Formula: see text] on the plane of [Formula: see text] can be excluded. Finally, we explore the potential of trilepton signature in probing such a scenario at 14 TeV Large Hadron Collider (LHC) and find that the region with [Formula: see text] and [Formula: see text] can be covered at [Formula: see text] level with luminosity [Formula: see text].