bluuebunny/crossref_metadata_2025_split huggingface dataset:
The EpiQuant Framework for Computing Epidemiological Concordance of Microbial Subtyping Data
Authors: Hetman Benjamin M. , Mutschall Steven K. , Thomas James E. , Gannon Victor P. J. , Clark Clifford G. , Pollari Frank , Taboada Eduardo N. 
Published: February 2017

ABSTRACT

A fundamental assumption in the use and interpretation of microbial subtyping results for public health investigations is that isolates that appear to be related based on molecular subtyping data are expected to share commonalities with respect to their origin, history, and distribution. Critically, there is currently no approach for systematically assessing the underlying epidemiology of subtyping results. Our aim was to develop a method for directly quantifying the similarity between bacterial isolates using basic sampling metadata and to develop a framework for computing the epidemiological concordance of microbial typing results. We have developed an analytical model that summarizes the similarity of bacterial isolates using basic parameters typically provided in sampling records, using a novel framework (EpiQuant) developed in the R environment for statistical computing. We have applied the EpiQuant framework to a data set comprising 654 isolates of the enteric pathogen
Campylobacter jejuni
from Canadian surveillance data in order to examine the epidemiological concordance of clusters obtained by using two leading
C. jejuni
subtyping methods. The EpiQuant framework can be used to directly quantify the similarity of bacterial isolates based on basic sample metadata. These results can then be used to assess the concordance between microbial epidemiological and molecular data, facilitating the objective assessment of subtyping method performance and paving the way for the improved application of molecular subtyping data in investigations of infectious disease.
Multilaboratory Survey To Evaluate Salmonella Prevalence in Diarrheic and Nondiarrheic Dogs and Cats in the United States between 2012 and 2014
Authors: Reimschuessel Renate , Grabenstein Michael , Guag Jake , Nemser Sarah M. , Song Kyunghee , Qiu Junshan , Clothier Kristin A. , Byrne Barbara A. , Marks Stanley L. , Cadmus Kyran , Pabilonia Kristy , Sanchez Susan , Rajeev Sreekumari , Ensley Steve , Frana Timothy S. , Jergens Albert E. , Chappell Kimberly H. , Thakur Siddhartha , Byrum Beverly , Cui Jing , Zhang Yan , Erdman Matthew M. , Rankin Shelley C. , Daly Russell , Das Seema , Ruesch Laura , Lawhon Sara D. , Zhang Shuping , Baszler Timothy , Diaz-Campos Dubraska , Hartmann Faye , Okwumabua Ogi 
Published: February 2017

ABSTRACTEleven laboratories collaborated to determine the periodic prevalence ofSalmonellain a population of dogs and cats in the United States visiting veterinary clinics. Fecal samples (2,965) solicited from 11 geographically dispersed veterinary testing laboratories were collected in 36 states between January 2012 and April 2014 and tested using a harmonized method. The overall study prevalence ofSalmonellain cats (3 of 542) was <1%. The prevalence in dogs (60 of 2,422) was 2.5%. Diarrhea was present in only 55% of positive dogs; however, 3.8% of the all diarrheic dogs were positive, compared with 1.8% of the nondiarrheic dogs.Salmonella-positive dogs were significantly more likely to have consumed raw food (P= 0.01), to have consumed probiotics (P= 0.002), or to have been given antibiotics (P= 0.01). Rural dogs were also more likely to beSalmonellapositive than urban (P= 0.002) or suburban (P= 0.001) dogs. In the 67 isolates, 27 unique serovars were identified, with three dogs having two serovars present. Antimicrobial susceptibility testing of 66 isolates revealed that only four of the isolates were resistant to one or more antibiotics. Additional characterization of the 66 isolates was done using pulsed-field gel electrophoresis and whole-genome sequencing (WGS). Sequence data compared well to resistance phenotypic data and were submitted to the National Center for Biotechnology Information (NCBI). This study suggests an overall decline in prevalence ofSalmonella-positive dogs and cats over the last decades and identifies consumption of raw food as a major risk factor forSalmonellainfection. Of note is that almost half of theSalmonella-positive animals were clinically nondiarrheic.
The New Aptima HBV Quant Real-Time TMA Assay Accurately Quantifies Hepatitis B Virus DNA from Genotypes A to F
Authors: Chevaliez Stéphane , Dauvillier Claude , Dubernet Fabienne , Poveda Jean-Dominique , Laperche Syria , Hézode Christophe , Pawlotsky Jean-Michel 
Published: February 2017

ABSTRACT

Sensitive and accurate hepatitis B virus (HBV) DNA detection and quantification are essential to diagnose HBV infection, establish the prognosis of HBV-related liver disease, and guide the decision to treat and monitor the virological response to antiviral treatment and the emergence of resistance. Currently available HBV DNA platforms and assays are generally designed for batching multiple specimens within an individual run and require at least one full day of work to complete the analyses. The aim of this study was to evaluate the ability of the newly developed, fully automated, one-step Aptima HBV Quant assay to accurately detect and quantify HBV DNA in a large series of patients infected with different HBV genotypes. The limit of detection of the assay was estimated to be 4.5 IU/ml. The specificity of the assay was 100%. Intra-assay and interassay coefficients of variation ranged from 0.29% to 5.07% and 4.90% to 6.85%, respectively. HBV DNA levels from patients infected with HBV genotypes A to F measured with the Aptima HBV Quant assay strongly correlated with those measured by two commercial real-time PCR comparators (Cobas AmpliPrep/Cobas TaqMan HBV test, version 2.0, and Abbott RealTi
m
e HBV test). In conclusion, the Aptima HBV Quant assay is sensitive, specific, and reproducible and accurately quantifies HBV DNA in plasma samples from patients with chronic HBV infections of all genotypes, including patients on antiviral treatment with nucleoside or nucleotide analogues. The Aptima HBV Quant assay can thus confidently be used to detect and quantify HBV DNA in both clinical trials with new anti-HBV drugs and clinical practice.
Evaluation of Genotypic and Phenotypic Protease Virulence Tests for Dichelobacter nodosus Infection in Sheep
Authors: McPherson Andrew S. , Dhungyel Om P. , Whittington Richard J. 
Published: February 2017

ABSTRACTDichelobacter nodosusis a fastidious, strictly anaerobic bacterium, an obligate parasite of the ruminant hoof, and the essential causative agent of virulent ovine footrot. The clinical disease results from a complex interplay between the pathogen, the environment, and the host. Sheep flocks diagnosed with virulent but not benign footrot in Australia may be quarantined and required to undergo a compulsory eradication program, with costs met by the farmer. Virulence ofD. nodosusat least partially depends on the elaboration of a protease encoded byaprV2and manifests as elastase activity. Laboratory virulence tests are used to assist diagnosis because clinical differentiation of virulent and benign footrot can be challenging during the early stages of disease or when the disease is not fully expressed due to unfavorable pasture conditions. Using samples collected from foot lesions from 960 sheep from 40 flocks in four different geographic regions, we evaluated the analytical characteristics of qPCR tests for the protease gene allelesaprV2andaprB2, and compared these with results from phenotypic protease (elastase and gelatin gel) tests. There was a low level of agreement between clinical diagnosis and quantitative PCR (qPCR) test outcomes at both the flock and sample levels and poor agreement between qPCR test outcomes and the results of phenotypic virulence tests. The diagnostic specificity of the qPCR test was low at both the flock and individual swab levels (31.3% and 18.8%, respectively). By contrast, agreement between the elastase test and clinical diagnosis was high at both the flock level (diagnostic sensitivity [DSe], 100%; diagnostic specificity [DSp], 78.6%) and the isolate level (DSe, 69.5%; DSp, 80.5%).
Careers in Virology: Working at the Centers for Disease Control and Prevention
Authors: Konopka-Anstadt Jennifer L. , Burns Cara C. 
Published: February 2017

ABSTRACT
As nonacademic careers in science have become less and less “alternative,” one field that has consistently attracted early-career virologists is public health research. The desire to make tangible contributions to public health needs and better protect the public from infectious disease often motivates the transition. In this career-related Gem, two academically trained virologists offer insights into pursuing a research career in public health at the Centers for Disease Control and Prevention.
How to build a low-cost underwater camera housing for aquatic research
Authors: Bergshoeff Jonathan A. , Zargarpour Nicola , Legge George , Favaro Brett 
Published: February 2017

Remote cameras are an increasingly important tool in field-based biological research. Terrestrial researchers can purchase inexpensive off-the-shelf cameras, but aquatic researchers face challenges in adopting similar systems for underwater science. Although technology allows researchers to deploy cameras in any aquatic environment, high procurement costs are often a barrier, particularly for studies that require the collection of lengthy videos. In this note, we provide a detailed guide explaining how to assemble an underwater camera system for less than $425 USD. We focus especially on the construction of the underwater housing, which is typically the most expensive component of an underwater camera system. As described, this system can record 13 h full high-definition videos in depths up to 100 m. It can be constructed and assembled with limited technical background using tools available in most workshops. The guide includes a general overview of the system, a full list of components, detailed instructions on constructing the camera housing, and suggestions on how to mount and use the camera in fieldwork. Our goal for this note is to promote the wider use of remote underwater cameras in aquatic research by making them accessible to those with limited financial means.
A Rare Type of Upper Extremity Injury: Penetrating Injuries Caused by Blunt-edged Items
Authors: Şirinoğlu Hakan , Certel Furkan , Yeşïloğlu Nebil , Temïz Gökhan , Kalafatlar Kübra Ece , Sarici Murat , Çelebïler Özhan 
Published: February 2017

Background: Penetrating upper extremity injury is a common encountered cause of significant loss of labor force and it is generally caused by sharp items. This article presents five rare cases of penetrating hand and forearm injury caused by blunt-edged items in conjunction with a detailed discussion of the mechanism and management of the injury. Methods: Five patients with a mean age of 37.6 were treated for upper extremity trauma caused by “blunt-edged items” such as corrugated iron fence, garden wires, iron stick or iron safety fence between 2009 to 2014. All patients were operated under general anesthesia after performing detailed physical examination and x-ray imaging. Results: The explorative surgery of the affected limbs revealed no nervous or vascular injury. In two patients, partial tear of the muscles bellies of intrinsic hand muscles (opponens pollicis and adductor pollicis); in two patients, partial extensor digitorum communis tendon laceration and in the remaining patient, partial tear of the third annular pulley were the only encountered injuries. The physical examinations performed in the last visit of each patient revealed, complete healing of the affected limb without any functional, vascular or sensorial deficiency in a mean follow-up period of 19.2 months. Conclusions: Despite their initial horrible appearance, injuries caused by “blunt-edged items” are quite harmless to the affected limb because they follow weak anatomic spaces of the extremity and cause minimal tissue damage leaving all vascular and nervous structures intact.
Arthrodesis of Little Finger Distal Interphalangeal Joint in Flexion to Regain Sporting Ability
Authors: Beecher S.M. , O’Briain D.E. , Ng J.P. , Murphy E. , O’Sullivan M.E. 
Published: February 2017

Background: Finger injuries are common in the sport of hurling. Injury to the little finger distal interphalangeal joint (DIPJ) often occurs when a high dropping ball impacts on the outstretched finger. The little finger contributes to approximately 15% of grip strength. Injury therefore results in reduced grip strength and may impair the ability of players to grip or catch a ball.Methods: Six elite hurlers with post-traumatic arthritis of their non-dominant little finger DIPJ underwent arthrodesis in 30 degrees of flexion. Kirchner wires were inserted for up to 8 weeks to achieve fusion of the joint. Patients were evaluated after recovery using a dynamometer to assess grip strength, the DASH questionnaire and a sport specific questionnaire.Results: All arthrodeses achieved bony union without complication. All patients reported a resolution of their pain and recovery in their ability to catch & retain a ball. Measurements of grip strengths were comparable between hands. DASH scores improved by up to 47 points. All scores were less than 5 at final follow-up.Conclusions: Grip strength decreases when fingers are immobilized in full extension. In sports that require catching or gripping a ball or a bat, arthrodesis of the DIP joint in flexion can improve grip strength and hand function. Fusion in 30 degrees of flexion for hurlers results in restoration of function and resolution of pain. Little finger DIPJ arthrodesis is a valid method of treating posttraumatic arthritis in ball and bat sports.
Treating the Storage Stack Like a Network
Authors: Stefanovici Ioan , Schroeder Bianca , O'Shea Greg , Thereska Eno 
Published: February 2017

In a data center, an IO from an application to distributed storage traverses not only the network but also several software stages with diverse functionality. This set of ordered stages is known as the storage or IO stack. Stages include caches, hypervisors, IO schedulers, file systems, and device drivers. Indeed, in a typical data center, the number of these stages is often larger than the number of network hops to the destination. Yet, while packet routing is fundamental to networks, no notion of IO routing exists on the storage stack. The path of an IO to an endpoint is predetermined and hard coded. This forces IO with different needs (e.g., requiring different caching or replica selection) to flow through a one-size-fits-all IO stack structure, resulting in an ossified IO stack.
This article proposes sRoute, an architecture that provides a routing abstraction for the storage stack. sRoute comprises a centralized control plane and “sSwitches” on the data plane. The control plane sets the forwarding rules in each sSwitch to route IO requests at runtime based on application-specific policies. A key strength of our architecture is that it works with unmodified applications and Virtual Machines (VMs). This article shows significant benefits of customized IO routing to data center tenants: for example, a factor of 10 for tail IO latency, more than 60% better throughput for a customized replication protocol, a factor of 2 in throughput for customized caching, and enabling live performance debugging in a running system.
Cancer Stem Cells Regulate Cancer-Associated Fibroblasts via Activation of Hedgehog Signaling in Mammary Gland Tumors
Authors: Valenti Giovanni , Quinn Hazel M. , Heynen Guus J.J.E. , Lan Linxiang , Holland Jane D. , Vogel Regina , Wulf-Goldenberg Annika , Birchmeier Walter 
Published: February 2017

Abstract
Many tumors display intracellular heterogeneity with subsets of cancer stem cells (CSC) that sustain tumor growth, recurrence, and therapy resistance. Cancer-associated fibroblasts (CAF) have been shown to support and regulate CSC function. Here, we investigate the interactions between CSCs and CAFs in mammary gland tumors driven by combined activation of Wnt/β-catenin and Hgf/Met signaling in mouse mammary epithelial cells. In this setting, CSCs secrete the Hedgehog ligand SHH, which regulate CAFs via paracrine activation of Hedgehog signaling. CAFs subsequently secrete factors that promote expansion and self-renewal of CSCs. In vivo treatment of tumors with the Hedgehog inhibitor vismodegib reduce CAF and CSC expansion, resulting in an overall delay of tumor formation. Our results identify a novel intracellular signaling module that synergistically regulates CAFs and CSCs. Targeting CAFs with Hedgehog inhibitors may offer a novel therapeutic strategy against breast cancer. Cancer Res; 77(8); 2134–47. ©2017 AACR.
Scavenger Receptor A1 Prevents Metastasis of Non–Small Cell Lung Cancer via Suppression of Macrophage Serum Amyloid A1
Authors: Zhang Yan , Wei Yongyue , Jiang Bin , Chen Lili , Bai Hui , Zhu Xudong , Li Xiaoyu , Zhang Hanwen , Yang Qing , Ma Junqing , Xu Yong , Ben Jingjing , Christiani David C. , Chen Qi 
Published: February 2017

Abstract
Mechanisms of cross-talk between tumor cells and tumor-associated macrophages (TAM), which drive metastasis, are not fully understood. Scavenger receptor A1 (SR-A1) expressed primarily in macrophages has been associated with lung tumorigenesis. In this study, we used population genetics, transcriptomics, and functional analyses to uncover how SR-A1 is involved in lung cancer and its prognosis. SR-A1 genetic variants were investigated for possible association with survival of advanced stage NSCLC patients in the Harvard Lung Cancer Study cohort. Two SNPs (rs17484273, rs1484751) in SR-A1 were associated significantly with poor overall survival in this cohort. Data from The Cancer Genome Atlas showed considerable downregulation of SR-A1 in lung tumor tissues. The association of SR-A1 with prognosis was validated in animal models in the context of lung cancer metastasis. Macrophages derived from mice genetically deficient for SR-A1 exhibited accelerated metastasis in a model of lung cancer. On the other hand, tumor cell seeding, migration, and invasion, as well as macrophage accumulation in lung cancer tissue, were enhanced in SR-A1–deficient mice. SR-A1 deletion upregulated serum amyloid A1 (SAA1) in macrophages via MAPK/IκB/NFκB signaling. SAA1 promoted tumor cell invasion and macrophage migration in vitro and in vivo, but these effects were blocked by administration of an anti-SAA1 antibody. Overall, our findings show how SR-A1 suppresses lung cancer metastasis by downregulating SAA1 production in TAMs. Cancer Res; 77(7); 1586–98. ©2017 AACR.
Modeling the Genetic Regulation of Cancer Metabolism: Interplay between Glycolysis and Oxidative Phosphorylation
Authors: Yu Linglin , Lu Mingyang , Jia Dongya , Ma Jianpeng , Ben-Jacob Eshel , Levine Herbert , Kaipparettu Benny Abraham , Onuchic José N. 
Published: February 2017

Abstract
Abnormal metabolism is a hallmark of cancer, yet its regulation remains poorly understood. Cancer cells were considered to utilize primarily glycolysis for ATP production, referred to as the Warburg effect. However, recent evidence suggests that oxidative phosphorylation (OXPHOS) plays a crucial role during cancer progression. Here we utilized a systems biology approach to decipher the regulatory principle of glycolysis and OXPHOS. Integrating information from literature, we constructed a regulatory network of genes and metabolites, from which we extracted a core circuit containing HIF-1, AMPK, and ROS. Our circuit analysis showed that while normal cells have an oxidative state and a glycolytic state, cancer cells can access a hybrid state with both metabolic modes coexisting. This was due to higher ROS production and/or oncogene activation, such as RAS, MYC, and c-SRC. Guided by the model, we developed two signatures consisting of AMPK and HIF-1 downstream genes, respectively, to quantify the activity of glycolysis and OXPHOS. By applying the AMPK and HIF-1 signatures to The Cancer Genome Atlas patient transcriptomics data of multiple cancer types and single-cell RNA-seq data of lung adenocarcinoma, we confirmed an anticorrelation between AMPK and HIF-1 activities and the association of metabolic states with oncogenes. We propose that the hybrid phenotype contributes to metabolic plasticity, allowing cancer cells to adapt to various microenvironments. Using model simulations, our theoretical framework of metabolism can serve as a platform to decode cancer metabolic plasticity and design cancer therapies targeting metabolism. Cancer Res; 77(7); 1564–74. ©2017 AACR.
Gut Microbiota Promotes Obesity-Associated Liver Cancer through PGE2-Mediated Suppression of Antitumor Immunity
Authors: Loo Tze Mun , Kamachi Fumitaka , Watanabe Yoshihiro , Yoshimoto Shin , Kanda Hiroaki , Arai Yuriko , Nakajima-Takagi Yaeko , Iwama Atsushi , Koga Tomoaki , Sugimoto Yukihiko , Ozawa Takayuki , Nakamura Masaru , Kumagai Miho , Watashi Koichi , Taketo Makoto M. , Aoki Tomohiro , Narumiya Shuh , Oshima Masanobu , Arita Makoto , Hara Eiji , Ohtani Naoko 
Published: February 2017

Abstract
Obesity increases the risk of cancers, including hepatocellular carcinomas (HCC). However, the precise molecular mechanisms through which obesity promotes HCC development are still unclear. Recent studies have shown that gut microbiota may influence liver diseases by transferring its metabolites and components. Here, we show that the hepatic translocation of obesity-induced lipoteichoic acid (LTA), a Gram-positive gut microbial component, promotes HCC development by creating a tumor-promoting microenvironment. LTA enhances the senescence-associated secretory phenotype (SASP) of hepatic stellate cells (HSC) collaboratively with an obesity-induced gut microbial metabolite, deoxycholic acid, to upregulate the expression of SASP factors and COX2 through Toll-like receptor 2. Interestingly, COX2-mediated prostaglandin E2 (PGE2) production suppresses the antitumor immunity through a PTGER4 receptor, thereby contributing to HCC progression. Moreover, COX2 overexpression and excess PGE2 production were detected in HSCs in human HCCs with noncirrhotic, nonalcoholic steatohepatitis (NASH), indicating that a similar mechanism could function in humans.
Significance: We showed the importance of the gut–liver axis in obesity-associated HCC. The gut microbiota–driven COX2 pathway produced the lipid mediator PGE2 in senescent HSCs in the tumor microenvironment, which plays a pivotal role in suppressing antitumor immunity, suggesting that PGE2 and its receptor may be novel therapeutic targets for noncirrhotic NASH-associated HCC. Cancer Discov; 7(5); 522–38. ©2017 AACR.
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The Prosody of the Czech Discourse Marker ‘Jasně': An Analysis of Forms and Functions
Authors: Volin Jan , Weingartová Lenka , Niebuhr Oliver 
Published: February 2017

AbstractWords like yeah, okay and (al)right are fairly unspecific in their lexical semantics, and not least for this reason there is a general tendency for them to occur with highly varied and expressive prosodic patterns across languages. Here we examine in depth the prosodic forms that express eight pragmatic functions of the Czech discourse marker jasně, including resignation, reassurance, surprise, indifference or impatience. Using a collection of 172 tokens from a corpus of scripted dialogues by 30 native speakers, we performed acoustic analyses, applied classification algorithms and solicited judgments from native listeners in a perceptual experiment. There appeared to be multi-parametric differences between jasně realizations in terms of their F0, timing and intensity patterns, which gave rise to generally consistent form-function mappings. For example, resignation seems to be realized with a falling intonation contour, relatively slow tempo, long wordinitial consonant and a short word-final vowel. Although the most significant prosodic parameters used for clustering analysis involved segment durations, all pragmatic functions were expressed by patterns of multiple features.