bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracting central places from the link structure in Wikipedia
Authors: Keßler Carsten 
Published: June 2017

AbstractExplicit information about places is captured in an increasing number of geospatial datasets. This article presents evidence that relationships between places can also be captured implicitly. It demonstrates that the hierarchy of central places in Germany is reflected in the link structure of the German language edition of Wikipedia. The official upper and middle centers declared, based on German spatial laws, are used as a reference dataset. The characteristics of the link structure around their Wikipedia pages, which link to each other or mention each other, and how often, are used to develop a bottom‐up method for extracting central places from Wikipedia. The method relies solely on the structure and number of links and mentions between the corresponding Wikipedia pages; no spatial information is used in the extraction process. The output of this method shows significant overlap with the official central place structure, especially for the upper centers. The results indicate that real‐world relationships are in fact reflected in the link structure on the web in the case of Wikipedia.
Extracting urban functional regions from points of interest and human activities on location‐based social networks
Authors: Gao Song , Janowicz Krzysztof , Couclelis Helen 
Published: June 2017

AbstractData about points of interest (POI) have been widely used in studying urban land use types and for sensing human behavior. However, it is difficult to quantify the correct mix or the spatial relations among different POI types indicative of specific urban functions. In this research, we develop a statistical framework to help discover semantically meaningful topics and functional regions based on the co‐occurrence patterns of POI types. The framework applies the latent Dirichlet allocation (LDA) topic modeling technique and incorporates user check‐in activities on location‐based social networks. Using a large corpus of about 100,000 Foursquare venues and user check‐in behavior in the 10 most populated urban areas of the US, we demonstrate the effectiveness of our proposed methodology by identifying distinctive types of latent topics and, further, by extracting urban functional regions using K‐means clustering and Delaunay triangulation spatial constraints clustering. We show that a region can support multiple functions but with different probabilities, while the same type of functional region can span multiple geographically non‐adjacent locations. Since each region can be modeled as a vector consisting of multinomial topic distributions, similar regions with regard to their thematic topic signatures can be identified. Compared with remote sensing images which mainly uncover the physical landscape of urban environments, our popularity‐based POI topic modeling approach can be seen as a complementary social sensing view on urban space based on human activities.
The redox‐sensitive module of cyclophilin 20‐3, 2‐cysteine peroxiredoxin and cysteine synthase integrates sulfur metabolism and oxylipin signaling in the high light acclimation response
Authors: Müller Sara M. , Wang Shanshan , Telman Wilena , Liebthal Michael , Schnitzer Helena , Viehhauser Andrea , Sticht Carsten , Delatorre Carolina , Wirtz Markus , Hell Rüdiger , Dietz Karl‐Josef 
Published: June 2017

SummaryThe integration of redox‐ and reactive oxygen species‐dependent signaling and metabolic activities is fundamental to plant acclimation to biotic and abiotic stresses. Previous data suggest the existence of a dynamically interacting module in the chloroplast stroma consisting of cyclophilin 20‐3 (Cyp20‐3), O‐acetylserine(thiol)lyase B (OASTL‐B), 2‐cysteine peroxiredoxins A/B (2‐CysPrx) and serine acetyltransferase 2;1 (SERAT2;1). The functionality of this COPS module is influenced by redox stimuli and oxophytodienoic acid (OPDA), which is the precursor for jasmonic acid. The concept of an integrating function of these proteins in stress signaling was challenged by combining transcriptome and biochemical analyses in Arabidopsis mutants devoid of oastlB, serat2;1, cyp20‐3 and 2‐cysprxA/B, and wild‐type (WT). Leaf transcriptomes were analyzed 6 h after transfer to light intensity 10‐fold in excess of growth light or under growth light. The survey of KEGG‐based gene ontology groups showed common upregulation of translation‐ and protein homeostasis‐associated transcripts under control conditions in all mutants compared with WT. The results revealed that the interference of the module was accompanied with disturbance of carbohydrate, sulfur and nitrogen metabolism, and also citric acid cycle intermediates. Apart from common regulation, specific responses at the transcriptome and metabolite level linked Cyp20‐3 to cell wall‐bound carbohydrates and oxylipin signaling, and 2‐CysPrx to photosynthesis, sugar and amino acid metabolism. Deletion of either OASTL‐B or SERAT2;1 frequently induced antagonistic changes in biochemical or molecular features. Enhanced sensitivity of mutant seedlings to OPDA and leaf discs to NaHS‐administration confirmed the presumed functional interference of the COPS module in redox and oxylipin signaling.
Iowa Model of Evidence‐Based Practice: Revisions and Validation
Authors:   Iowa Model Collaborative, Buckwalter Kathleen C. , Cullen Laura , Hanrahan Kirsten , Kleiber Charmaine , McCarthy Ann Marie , Rakel Barbara , Steelman Victoria , Tripp‐Reimer Toni , Tucker Sharon ,   Authored on behalf of the Iowa Model Collaborative
Published: June 2017

ABSTRACTBackgroundThe Iowa Model is a widely used framework for the implementation of evidence‐based practice (EBP). Changes in health care (e.g., emergence of implementation science, emphasis on patient engagement) prompted the re‐evaluation, revision, and validation of the model.MethodsA systematic multi‐step process was used capturing information from the literature and user feedback via an electronic survey and live work groups. The Iowa Model Collaborative critically assessed and synthesized information and recommendations before revising the model.ResultsSurvey participants (n = 431) had requested access to the Model between years 2001 and 2013. Eighty‐eight percent (n = 379) of participants reported using the Iowa Model and identified the most problematic steps as: topic priority, critique, pilot, and institute change. Users provided 587 comments with rich contextual rationale and insightful suggestions. The revised model was then evaluated by participants (n = 299) of the 22nd National EBP Conference in 2015. They validated the model as a practical tool for the EBP process across diverse settings. Specific changes in the model are discussed.ConclusionThis user driven revision differs from other frameworks in that it links practice changes within the system. Major model changes are expansion of piloting, implementation, patient engagement, and sustaining change.Linking Evidence to ActionThe Iowa Model‐Revised remains an application‐oriented guide for the EBP process. Intended users are point of care clinicians who ask questions and seek a systematic, EBP approach to promote excellence in health care.
Complete Genome Sequence of Staphylococcus lutrae ATCC 700373, a Potential Pathogen Isolated from Deceased Otters
Authors: Veseli Iva A. , Tang Chenling , Pombert Jean-François 
Published: June 2017

ABSTRACT

Despite their relevance to human health, not all staphylococcal species have been characterized. As such, the potential zoonotic threats posed by uninvestigated species and their contribution to the staphylococcal pangenome are unclear. Here, we report the complete genome sequence of
Staphylococcus lutrae
ATCC 700373, a coagulase-positive species isolated from deceased otters.
Complete Genome Sequence of Bacillus paralicheniformis MDJK30, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity
Authors: Wang Yun , Liu Hu , Liu Kai , Wang Chengqiang , Ma Hailin , Li Yuhuan , Hou Qihui , Liu Fangchun , Zhang Tongrui , Wang Haide , Wang Beibei , Ma Jinjin , Ge Ruofei , Xu Baochao , Yao Gan , Xu Wenfeng , Fan Lingchao , Ding Yanqin , Du Binghai 
Published: June 2017

ABSTRACT

Bacillus paralicheniformis
MDJK30 was isolated from the rhizosphere of a peony. It could control the pathogen of peony root rot. Here, we report the complete genome sequence of
B. paralicheniformis
MDJK30. Eleven secondary metabolism gene clusters were predicted.
Lung Microbiota and Its Impact on the Mucosal Immune Phenotype
Authors: Wu Benjamin G. , Segal Leopoldo N. 
Published: June 2017

ABSTRACTThe use of culture-independent techniques has allowed us to appreciate that the upper and lower respiratory tract contain a diverse community of microbes in health and disease. Research has only recently explored the effects of the microbiome on the host immune response. The exposure of the human body to the bacterial environment is an important factor for immunological development; thus, the interaction between the microbiome and its host is critical to understanding the pathogenesis of disease. In this article, we discuss the mechanisms that determine the composition of the airway microbiome and its effects on the host immune response. With the use of ecological principles, we have learned how the lower airways constitute a unique niche subjected to frequent microbial migration (e.g., through aspiration) and constant immunological pressure. The discussion will focus on the possible inflammatory pathways that are up- and downregulated when the immune system is challenged by dysbiosis. Identification of potential markers and microbial targets to address the modulation of inflammation in early disease, when changes may have the most effect, will be critical for future therapies.
The Genomic Basis of Lactobacilli as Health-Promoting Organisms
Authors: Salvetti Elisa , O’Toole Paul W. 
Published: June 2017

ABSTRACT

Lactobacilli occupy a unique position in human culture and scientific history. Like brewer’s and baker’s yeast, lactobacilli have been associated with food production and preservation for thousands of years.
Lactobacillus
species are used in mixed microbial cultures, such as the classical
Lactobacillus bulgaricus
/
Streptococcus thermophilus
inoculum for yogurt fermentation, or combinations of diverse lactobacilli/yeasts in kefir grains. The association of lactobacilli consumption with greater longevity and improved health formed the basis for developing lactobacilli as probiotics, whose market has exploded worldwide in the past 10 years. The decade that followed the determination of the first genome sequence of a food-associated species,
Lactobacillus plantarum
, saw the application to lactobacilli of a full range of functional genomics methods to identify the genes and gene products that govern their distinctive phenotypes and health associations. In this review, we will briefly remind the reader of the range of beneficial effects attributed to lactobacilli, and then explain the phylogenomic basis for the distribution of these traits across the genus. Recognizing the strain specificity of probiotic effects, we review studies of intraspecific genomic variation and their contributions to identifying probiotic traits. Finally we offer a perspective on classification of lactobacilli into new genera in a scheme that will make attributing probiotic properties to clades, taxa, and species more logical and more robust.
Diagnosis and risk stratification of Barrett’s dysplasia by flow cytometric DNA analysis of paraffin-embedded tissue
Authors: Choi Won-Tak , Tsai Jia-Huei , Rabinovitch Peter S , Small Thomas , Huang Danning , Mattis Aras N , Kakar Sanjay 
Published: June 2017

ObjectiveThe diagnosis of dysplasia in Barrett’s oesophagus (BO) can be challenging, and reliable ancillary techniques are not available. This study examines if DNA content abnormality detected by flow cytometry can serve as a diagnostic marker of dysplasia and facilitate risk stratification of low-grade dysplasia (LGD) and indefinite for dysplasia (IND) patients using formalin-fixed paraffin-embedded (FFPE) BO samples with varying degrees of dysplasia.DesignDNA flow cytometry was performed on 80 FFPE BO samples with high-grade dysplasia (HGD), 38 LGD, 21 IND and 14 negative for dysplasia (ND). Three to four 60-micron thick sections were cut from each tissue block, and the area of interest was manually dissected.ResultsDNA content abnormality was identified in 76 HGD (95%), 8 LGD (21.1%), 2 IND (9.5%) and 0 ND samples. As a diagnostic marker of HGD, the estimated sensitivity and specificity of DNA content abnormality were 95% and 85%, respectively. For patients with DNA content abnormality detected at baseline LGD or IND, the univariate HRs for subsequent detection of HGD or oesophageal adenocarcinoma (OAC) were 7.0 and 20.0, respectively (p =<0.001).ConclusionsThis study demonstrates the promise of DNA flow cytometry using FFPE tissue in the diagnosis and risk stratification of dysplasia in BO. The presence of DNA content abnormality correlates with increasing levels of dysplasia, as 95% of HGD samples showed DNA content abnormality. DNA flow cytometry also identifies a subset of patients with LGD and IND who are at higher risk for subsequent detection of HGD or OAC.
Clinical benefit of the FIFA 11 programme for the prevention of hamstring and lateral ankle ligament injuries among amateur soccer players
Authors: Nouni-Garcia Rauf , Carratala-Munuera Concepcion , Orozco-Beltran Domingo , Lopez-Pineda Adriana , Asensio-Garcia María Rosario , Gil-Guillen Vicente F 
Published: June 2017

ObjectiveTo analyse the relationship between the implementation of ‘the 11’ protocol during the regular season in a men’s amateur soccer team and the rate of hamstring and lateral ankle ligament (LAL) injuries, and to estimate the clinical benefit of the programme according to the type of injury and the position field.MethodsThis cohort study was conducted in two different men’s amateur soccer teams. During two seasons, the exposed group (43 players) performed ‘the 11’ protocol twice a week, and the unexposed group (43 players) performed the regular training programme. All players trained three times per week for 1.5 hours per day. Data collection was performed for every 1000 hours of play.Results18 hamstring injuries (injury rate (IR) of 2.26 injuries/1000 training+competition hours) and 15 LAL injuries (IR of 1.88 injuries/1000) were registered in the exposed group. In the unexposed group, there were 25 LAL injuries (IR of 3.14 injuries/1000) and 35 hamstring injuries (IR of 4.39 injuries/1000). The number needed to treat to prevent one new case was 3.9 in LAL injuries, 3.31 in biceps femoris injuries and 10.7 in recurrent hamstring injuries.Conclusions‘The 11’ programme reduced the incidence of hamstring and LAL injuries in amateur players. According to the field position, the programme was effective for defenders and midfielders. In accordance with the type of injury, the exposed group had a lower risk of LAL, biceps femoris and hamstring injuries compared with those in the unexposed group.
Elliptic curve variants of the least quadratic nonresidue problem and Linnik’s theorem
Authors: Chen Evan , Park Peter S. , Swaminathan Ashvin A. 
Published: June 2017

Let [Formula: see text] and [Formula: see text] be [Formula: see text]-nonisogenous, semistable elliptic curves over [Formula: see text], having respective conductors [Formula: see text] and [Formula: see text] and both without complex multiplication. For each prime [Formula: see text], denote by [Formula: see text] the trace of Frobenius. Assuming the Generalized Riemann Hypothesis (GRH) for the convolved symmetric power [Formula: see text]-functions [Formula: see text] where [Formula: see text], we prove an explicit result that can be stated succinctly as follows: there exists a prime [Formula: see text] such that [Formula: see text] and [Formula: see text] This improves and makes explicit a result of Bucur and Kedlaya. Now, if [Formula: see text] is a subinterval with Sato–Tate measure [Formula: see text] and if the symmetric power [Formula: see text]-functions [Formula: see text] are functorial and satisfy GRH for all [Formula: see text], we employ similar techniques to prove an explicit result that can be stated succinctly as follows: there exists a prime [Formula: see text] such that [Formula: see text] and [Formula: see text]
Heavy mineral assemblage of marine sediments as an indicator of provenance and east antarctic ice sheet fluctuations
Authors: Pandey Mayuri , Pant Naresh C. , Biswas Paromita , Shrivastava Prakash K. , Joshi Sonalika , Nagi Neety 
Published: June 2017

Abstract
Records of fluctuations of the East Antarctic Ice Sheet (EAIS) are best preserved in proximal marine sediments. The examined section is a part of a drillcore at Site U1359 of IODP (Integrated Oceanic Drilling Program) 318 located at the eastern levee of Jussieau submarine channel off the coast of Wilkes Land. Drillcore U1359 from 200 m below seafloor (mbsf) to 600 mbsf represents samples from Mid-Miocene to Late Miocene. Heavy media separation, characterization of heavy minerals and quantification of their population were carried out using scanning electron microscopy and electron microprobe analysis. Relative abundance of various minerals at different depths revealed that amphiboles and pyroxene show antipathic relationship at some depths. Multiple sources for supply of sediments at drillhole Site U1359 have been proposed with both magmatic and metamorphic minerals and rock fragments contributing clastic sediments. Factor analysis was carried out to test this inference. Six factors were obtained out of which the first three explain 76.6% of the variance. Relating variability of the factors to the provenance allows inference of four major ice advance phases during Mid to Late Micene which are largely positively correlatable with the global climate record.
A Novel Single-Domain Antibody Against von Willebrand Factor A1 Domain Resolves Leukocyte Recruitment and Vascular Leakage During Inflammation—Brief Report
Authors: Aymé Gabriel , Adam Frédéric , Legendre Paulette , Bazaa Amine , Proulle Valérie , Denis Cécile V. , Christophe Olivier D. , Lenting Peter J. 
Published: June 2017

Objective—
von Willebrand factor (VWF) is crucial to hemostasis, but also plays a role in inflammatory processes. Unfortunately, no proper monoclonal antibodies to study VWF function in mice are currently available. We therefore aimed to generate single-domain antibodies (sdAbs) recognizing murine VWF and blocking its function in vivo.

Approach and Results—
Llama-derived sdAbs recognizing both human and murine VWF were isolated via phage display technology. One of them (designated KB-VWF-006) recognized the VWF A1 domain with picomolar affinity. This sdAb avidity was strongly enhanced via dimerization using a triple Ala linker (KB-VWF-006bi). When administered in vivo to wild-type mice, KB-VWF-006bi dose dependently induced bleeding in a tail clip model. In 2 distinct models of inflammation, KB-VWF-006bi efficiently interfered with leukocyte recruitment and vascular leakage.

Conclusions—
KB-VWF-006bi is an sdAb recognizing the A1 domain of human VWF and murine VWF that interferes with VWF–platelet interactions in vivo. By using this sdAb, we now also show that the A1 domain is pertinent to the participation of VWF in the inflammatory response.
Ager
Deletion Enhances Ischemic Muscle Inflammation, Angiogenesis, and Blood Flow Recovery in Diabetic Mice
Authors: López-Díez Raquel , Shen Xiaoping , Daffu Gurdip , Khursheed Md , Hu Jiyuan , Song Fei , Rosario Rosa , Xu Yunlu , Li Qing , Xi Xiangmei , Zou Yu Shan , Li Huilin , Schmidt Ann Marie , Yan Shi Fang 
Published: June 2017

Objective—
Diabetic subjects are at higher risk of ischemic peripheral vascular disease. We tested the hypothesis that advanced glycation end products (AGEs) and their receptor (RAGE) block angiogenesis and blood flow recovery after hindlimb ischemia induced by femoral artery ligation through modulation of immune/inflammatory mechanisms.

Approach and Results—

Wild-type mice rendered diabetic with streptozotocin and subjected to unilateral femoral artery ligation displayed increased accumulation and expression of AGEs and RAGE in ischemic muscle. In diabetic wild-type mice, femoral artery ligation attenuated angiogenesis and impaired blood flow recovery, in parallel with reduced macrophage content in ischemic muscle and suppression of early inflammatory gene expression, including
Ccl2
(chemokine [C-C motif] ligand-2) and
Egr1
(early growth response gene-1) versus nondiabetic mice. Deletion of
Ager
(gene encoding RAGE) or transgenic expression of
Glo1
(reduces AGEs) restored adaptive inflammation, angiogenesis, and blood flow recovery in diabetic mice. In diabetes mellitus, deletion of
Ager
increased circulating Ly6C
hi
monocytes and augmented macrophage infiltration into ischemic muscle tissue after femoral artery ligation. In vitro, macrophages grown in high glucose display inflammation that is skewed to expression of tissue damage versus tissue repair gene expression. Further, macrophages grown in high versus low glucose demonstrate blunted macrophage–endothelial cell interactions. In both settings, these adverse effects of high glucose were reversed by
Ager
deletion in macrophages.

Conclusions—
These findings indicate that RAGE attenuates adaptive inflammation in hindlimb ischemia; underscore microenvironment-specific functions for RAGE in inflammation in tissue repair versus damage; and illustrate that AGE/RAGE antagonism may fill a critical gap in diabetic peripheral vascular disease.