bluuebunny/crossref_metadata_2025_split huggingface dataset:
CRISPR-MVLST subtyping of Salmonella enterica subsp. entericaserovars Typhimurium and Heidelberg and application in identifying outbreak isolates
Authors: Shariat Nikki , Sandt Carol H , DiMarzio Michael J , Barrangou Rodolphe , Dudley Edward G 
Published: November 2013

AbstractBackgroundSalmonella entericasubsp.entericaserovars Typhimurium (S. Typhimurium) and Heidelberg (S.Heidelberg) are major causes of foodborne salmonellosis, accounting for a fifth of all annual salmonellosis cases in the United States. Rapid, efficient and accurate methods for identification are required for routine surveillance and to track specific strains during outbreaks. We used Pulsed-field Gel Electrophoresis (PFGE) and a recently developed molecular subtyping approach termed CRISPR-MVLST that exploits the hypervariable nature of virulence genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) to subtype clinicalS. Typhimurium andS. Heidelberg isolates.ResultsWe analyzed a broad set of 175S.Heidelberg andS.Typhimurium isolates collected over a five-year period. We identified 21 Heidelberg Sequence Types (HSTs) and 37 Typhimurium STs (TSTs) that were represented by 27 and 45 PFGE pulsotypes, respectively, and determined the discriminatory power of each method.ConclusionsForS.Heidelberg, our data shows that combined typing by both CRISPR-MVLST and PFGE provided a discriminatory power of 0.9213. Importantly, CRISPR-MVLST was able to separate common PFGE patterns such as JF6X01.0022 into distinct STs, thus providing significantly greater discriminatory power. Conversely, we show that subtyping by either CRISPR-MVLST or PFGE independently provides a sufficient discriminatory power (0.9345 and 0.9456, respectively) forS.Typhimurium. Additionally, using isolates from twoS.Typhimurium outbreaks, we demonstrate that CRISPR-MVLST provides excellent epidemiologic concordance.
Type A personality, hostility, time urgency and unintentional injuries among Chinese undergraduates: a matched case–control study
Authors: Shi Hongying , Yang Xinjun , Wang Jingjing , Xi Haiyang , Huang Chenping , He Jincai , Chu Maoping , Zhuang Guihua 
Published: November 2013

Abstract

Background
Associations between type A behaviour pattern (TABP) and injuries are inconsistent. These inconsistencies may be due to different effects of various components of TABP, namely time urgency/impatience, hostility and competitive drive. It is important to examine the relationship between the global TABP, its two components, and unintentional injuries, among undergraduates in China.

Methods
On the basis of a previous cross-sectional study, we conducted a matched case–control study. 253 cases and an equal number of age-, gender-, and major-matched controls were included. The questionnaire solicited socio-demographic information, the experience of injuries, the scale of TABP, and other potential confounding factors. Besides the correlation between the global TABP and injuries, the influences of the two components of TABP on injuries were also evaluated. Conditional logistic regression was used to determine the crude odds ratios (ORs) and adjusted ORs of injury events.

Results
A dose–response relationship was apparent among students who rated themselves higher on the TABP scale (P-value for trend, 0.002), with a crude OR of 2.93 (95% CI: 0.93–9.19) for injuries comparing those with TABP to those with type B behaviour pattern (TBBP). After adjustment for potential confounding factors, TABP remained statistically significant, and the adjusted OR was 5.52 (95% CI: 1.43–21.27); from a comparison of students with TABP to those with TBBP. A dose–response relationship was also apparent between the hostility component and nonfatal injuries, both in crude analysis and after adjusting for other confounders. The relationship between time-hurry and injuries was not statistically significant, based on univariate and multivariate analyses.

Conclusions
Both the global TABP and the hostility component were associated with a dose response increase in the risk of non-fatal unintentional injuries among Chinese undergraduates. Further studies need to be conducted to confirm or reject this correlation.
The interaction of marine fouling organisms with topography of varied scale and geometry: a review
Authors: Myan Felicia Wong Yen , Walker James , Paramor Odette 
Published: November 2013

Many studies have examined the effects of surface topography on the settlement behaviour of marine organisms and this article reviews these investigations with more emphasis on the effects of topography scale. It has been observed that macro topographies (1-100 mm) are generally favoured by marine fouling taxa and are unsuitable for antifouling applications. This is because macro topographies are usually large enough to fit fouling organisms and provide refuge from dangers in the marine environment. Micro topographies had only limited success at reducing fouling from a wide range of marine taxa. The antifouling performance of micro topographies (1 to ≤1000 μm) is dependent on the properties of topography features in terms of symmetry, isotropy, width, length, height/depth, separation distance and average roughness. In terms of the antifouling performance of micro topography, topography geometry may only be of secondary importance in comparison to the size of features itself. It is also noted that hydrodynamic stresses also contribute to the settlement trends of foulers on textured surfaces. Future studies on antifouling topographies should be directed to hierarchical topographies because the mixed topography scales might potentially reduce fouling by both micro and macro organisms. Patterned nano-topographies (1- ≤1000 nm) should also be explored because the antifouling mechanisms of these topographies are not yet clear.
Low-dose aspirin-associated upper gastric and duodenal ulcers in Japanese patients with no previous history of peptic ulcers
Authors: Kawamura Naohiko , Ito Yoshitsugu , Sasaki Makoto , Iida Akihito , Mizuno Mari , Ogasawara Naotaka , Funaki Yasushi , Kasugai Kunio 
Published: November 2013

AbstractBackgroundLong-term administration of low-dose aspirin (LDA) is associated with a greater risk of adverse events, including gastroduodenal ulcers. The purpose of this study was to identify the risk factors for and assess the role of medication use in the development of peptic ulcer disease in Japanese patients with no history of peptic ulcers.MethodsConsecutive outpatients receiving LDA (75 mg/day) who underwent esophagogastroduodenoscopy between January and December 2010 were enrolled. Clinical parameters, peptic ulcer history, concomitant drugs, the presence ofHelicobacter pyloriinfection, reason for endoscopy, and endoscopic findings were analysed.ResultsOf 226 total patients, 14 (6.2%) were endoscopically diagnosed with peptic ulcer. Age, sex, current smoking status, current alcohol consumption, endoscopic gastric mucosal atrophy, and abdominal symptoms were not significantly associated with peptic ulcers. Diabetes mellitus was more frequent (42.9% vs. 16.5%;P = 0.024) in patients with peptic ulcers than in those without peptic ulcers. Using multiple logistic regression analysis, co-treatment with anticoagulants or proton pump inhibitors (PPIs) was significantly associated with increased and decreased risk for peptic ulcer, respectively (odds ratio [OR], 5.88; 95% confidence interval [CI], 1.19 − 28.99;P = 0.03 and OR, 0.13; 95% CI, 0.02 − 0.73;P = 0.02, respectively). Co-treatment with additional antiplatelet agents, H2-receptor antagonists, angiotensin II Type 1 receptor blockers, angiotensin-converting enzyme inhibitor, 3-hydroxy-3-methylglutaryl-CoA reductase inhibitor, or nonsteroidal anti-inflammatory drugs was not associated with peptic ulcer development.ConclusionThe use of PPIs reduces the risk of developing gastric or duodenal ulcers in Japanese patients taking LDA without pre-existing gastroduodenal ulcers. However, this risk is significantly increased in both patients ingesting anticoagulants and patients with diabetes. These results may help identify patients who require intensive prophylaxis against aspirin-induced peptic ulcers.
Identification of three new Alu Yb subfamilies by source tracking of recently integrated Alu Yb elements
Authors: Ahmed Musaddeque , Li Wen , Liang Ping 
Published: November 2013

Abstract

Background

Alu elements are the most abundant mobile elements in the human genome, with over 1 million copies and constituting more than 10% of the genome. The majority of these Alu elements were inserted into the primate genome 35 to 60 million years ago, but certain subfamilies of Alu elements are relatively very new and suspected to be still evolving. We attempted to trace the source/master copies of all human-specific members of the Alu Yb lineage using a computational approach by clustering similar Yb elements and constructing an evolutionary relation among the members of a cluster.

Results
We discovered that one copy of Yb8 at 10p14 is the source of several active Yb8 copies, which retrotransposed to generate 712 copies or 54% of all human-specific Yb8 elements. We detected eight other Yb8 elements that had generated ten or more copies, potentially acting as 'stealth drivers’. One Yb8 element at 14q32.31 seemed to act as the source copy for all Yb9 elements tested, having producing 13 active Yb9 elements, and subsequently generated a total of 131 full-length copies. We identified and characterized three new subclasses of Yb elements: Yb8a1, Yb10 and Yb11. Their copy numbers in the reference genome are 75, 8 and 16. We analysed personal genome data from the 1000 Genome Project and detected an additional 6 Yb8a1, 3 Yb10 and 15 Yb11 copies outside the reference genome. Our analysis indicates that the Yb8a1 subfamily has a similar age to Yb9 (1.93 million years and 2.15 million years, respectively), while Yb10 and Yb11 evolved only 1.4 and 0.71 million years ago, suggesting a linear evolutionary path from Yb8a1 to Yb10 and then to Yb11. Our preliminary data indicate that members in Yb10 and Yb11 are mostly polymorphic, indicating their young age.

Conclusions
Our findings suggest that the Yb lineage is still evolving with new subfamilies being formed. Due to their very young age and the high rate of being polymorphic, insertions from these young subfamilies are very useful genetic markers for studying human population genetics and migration patterns, and the trend for mobile element insertions in the human genome.
MicroRNA-10b overexpression promotes non-small cell lung cancer cell proliferation and invasion
Authors: Liu Yi , Li Minghui , Zhang Guoqing , Pang Zuoliang 
Published: November 2013

Abstract

Background
miRNAs are a class of small non-coding RNA molecules that play an important role in the pathogenesis of human diseases through negative regulation of gene expression. Although miRNA-10b (miR-10b) has been implicated in other tumors, its role in non-small cell lung cancer (NSCLC) is still unknown. The aim of the present study was to investigate the role of miR-10b in NSCLC.

Methods
Expression of miR-10b was analyzed in NSCLC cell line A549 by qRT-PCR. Cell viability was evaluated using Cell Counting Kit (CCK)-8. Cell migration and invasion were evaluated by wound healing assay and transwell assays. Cell cycle and apoptosis analyses were performed. Western blotting was used to predicate the target of miR-10b.

Results
The A549 cell line transfected with the miR-10b exhibited significantly increased proliferation, migration, and invasion capacities when compared with the control cells (P < 0.05). Krüppel-like factor 4 (KLF4) may be indirectly targeted by miR-10b during the proliferation increasing of A549 cells.

Conclusion
In this study, we found that miR-10b is a tumor enhancer in NSCLC. Thus, miR-10b may represent a potential therapeutic target for NSCLC intervention.
“Breaking news” from spermatids
Authors: Gouraud Anne , Brazeau Marc-André , Grégoire Marie-Chantal , Simard Olivier , Massonneau Julien , Arguin Mélina , Boissonneault Guylain 
Published: November 2013

Abstract
During the haploid phase of spermatogenesis, spermatids undergo a complex remodeling of the paternal genome involving the finely orchestrated replacement of histones by the highly-basic protamines. The associated striking change in DNA topology is characterized by a transient surge of both single- and double-stranded DNA breaks in the whole population of spermatids which are repaired before spermiation. These transient DNA breaks are now considered part of the normal differentiation program of these cells. Despite an increasing interest in the study of spermiogenesis in the last decade and the potential threat to the haploid genome, the origin of these DNA breaks still remains elusive. This review briefly outlines the current hypotheses regarding possible mechanisms that may lead to such transient DNA fragmentation including torsional stress, enzyme-induced breaks, apoptosis-like processes or oxidative stress. A better understanding of the origin of these DNA breaks will lead to further investigations on the genetic instability and mutagenic potential induced by the chromatin remodeling.
Study on the TOC concentration in raw water and HAAs in Tehran’s water treatment plant outlet
Authors: Ghoochani Mahboobeh , Rastkari Noushin , Nabizadeh Nodehi Ramin , Mahvi Amir Hossein , Nasseri Simin , Nazmara Shahrokh 
Published: November 2013

Abstract
A sampling has been undertaken to investigate the variation of haloacetic acids formation and nature organic matter through 81 samples were collected from three water treatment plant and three major rivers of Tehran Iran. Changes in the total organic matter (TOC), ultraviolet absorbance (UV254), specific ultraviolet absorbance (SUVA) were measured in raw water samples. Haloacetic acids concentrations were monitored using a new static headspace GC-ECD method without a manual pre-concentration in three water treatment plants. The average concentration of TOC and HAAs in three rivers and three water treatment plants in spring, summer and fall, were 4, 2.41 and 4.03 mg/L and 48.75, 43.79 and 51.07 μg/L respectively. Seasonal variation indicated that HAAs levels were much higher in spring and fall.
Analysis of 10 km swimming performance of elite male and female open-water swimmers
Authors: Vogt Pascale , Rüst Christoph Alexander , Rosemann Thomas , Lepers Romuald , Knechtle Beat 
Published: November 2013

Abstract
This study investigated trends in performance and sex difference in swimming speed of elite open-water swimmers at FINA 10 km competitions (i.e. World Cup races, European Championships, World Championships and Olympic Games). Swimming speed and sex difference in swimming speed of the fastest and the top ten women and men per event competing at 10 km open-water races between 2008 and 2012 were analysed using single and multi-level regression analyses. A total of 2,591 swimmers (i.e. 1,120 women and 1,471 men) finished 47 races. Swimming speed of the fastest women (1.35 ± 0.9 m/s) and men (1.45 ± 0.10 m/s) showed no changes across years. The mean sex difference in swimming speed for the fastest swimmers was 6.8 ± 2.5%. Swimming speed of the top ten female swimmers per event was 1.34 ± 0.09 m/s and remained stable across the years. The top ten male swimmers per event showed a significant decrease in swimming speed over time, even though swimming speed in the first race (i.e. January 2008, 1.40 ± 0.0 m/s) was slower than the swimming speed in the last race (i.e. October 2012, 1.50 ± 0.0 m/s) (P < 0.05). To summarize, swimming performances remained stable for the fastest elite open-water swimmers at 10 km FINA competitions between 2008 and 2012, while performances of the top ten men tended to decrease. The sex difference in swimming speed in elite ultra-swimmers (~7%) appeared smaller compared to other ultra-distance disciplines such as running. Further studies should examine how body shape and physiology of elite open-water ultra-distance swimmers influence performances.
Porphyromonas gingivalis oral infection exacerbates the development and severity of collagen-induced arthritis
Authors: Marchesan Julie Teresa , Gerow Elizabeth Ann , Schaff Riley , Taut Andrei Dan , Shin Seung-Yun , Sugai James , Brand David , Burberry Aaron , Jorns Julie , Lundy Steven Karl , Nuñez Gabriel , Fox David A , Giannobile William V 
Published: November 2013

Abstract
Introduction
Clinical studies suggest a direct influence of periodontal disease (PD) on serum inflammatory markers and disease assessment of patients with established rheumatoid arthritis (RA). However, the influence of PD on arthritis development remains unclear. This investigation was undertaken to determine the contribution of chronic PD to immune activation and development of joint inflammation using the collagen-induced arthritis (CIA) model.

Methods
DBA1/J mice orally infected with Porphyromonas gingivalis were administered with collagen II (CII) emulsified in complete Freund’s adjuvant (CFA) or incomplete Freund’s adjuvant (IFA) to induce arthritis. Arthritis development was assessed by visual scoring of paw swelling, caliper measurement of the paws, mRNA expression, paw micro-computed tomography (micro-CT) analysis, histology, and tartrate resistant acid phosphatase for osteoclast detection (TRAP)-positive immunohistochemistry. Serum and reactivated splenocytes were evaluated for cytokine expression.

Results
Mice induced for PD and/or arthritis developed periodontal disease, shown by decreased alveolar bone and alteration of mRNA expression in gingival tissues and submandibular lymph nodes compared to vehicle. P. gingivalis oral infection increased paw swelling and osteoclast numbers in mice immunized with CFA/CII. Arthritis incidence and severity were increased by P. gingivalis in mice that received IFA/CII immunizations. Increased synovitis, bone erosions, and osteoclast numbers in the paws were observed following IFA/CII immunizations in mice infected with P gingivalis. Furthermore, cytokine analysis showed a trend toward increased serum Th17/Th1 ratios when P. gingivalis infection was present in mice receiving either CFA/CII or IFA/CII immunizations. Significant cytokine increases induced by P. gingivalis oral infection were mostly associated to Th17-related cytokines of reactivated splenic cells, including IL-1β, IL-6, and IL-22 in the CFA/CII group and IL-1β, tumor necrosis factor-α, transforming growth factor-β, IL-6 and IL-23 in the IFA/CII group.

Conclusions
Chronic P. gingivalis oral infection prior to arthritis induction increases the immune system activation favoring Th17 cell responses, and ultimately accelerating arthritis development. These results suggest that chronic oral infection may influence RA development mainly through activation of Th17-related pathways.
The Adverse Health Consequences of the Use of Multiple Performance-Enhancing Substances—A Deadly Cocktail
Authors: Perera Nimalie J. , Steinbeck Katherine S. , Shackel Nicholas 
Published: November 2013

Context:
The harmful consequences of abuse of performance-enhancing substances (PESs), stimulants, and masking agents among athletes, recreational weight lifters, and physical trainers are common. However, the adverse health outcomes with severe unexpected and dramatic consequences are unrecognized or under-reported at the expense of short-term glory or body-image effects, especially in elite sports.

Objective:
We report the case of a recreational weight lifter/physical trainer to help summarize the adverse health consequences and outcomes of polypharmacy among athletes and growing subsets in our population engaged in physical/fitness training. We show that in addition to the risk inherent to “stacking” of PESs, the users are predisposed to harmful consequences, including risk of exposure to toxic contaminants.

Design and Setting:
A previously healthy man with chronic use of multiple PESs, stimulants, and masking agents presented to a tertiary-care hospital with jaundice and mild hepatitis with rapid progression into liver and multisystem organ failure. This is followed by a brief overview of the specific toxicity (arsenic) and PESs that contributed to the poor outcome in this case.

Conclusion:
Surreptitiously or self-administered cocktails of potential PESs including anabolic agents, emerging classes of GH-releasing peptides, androgen precursors, stimulants, and masking agents could lead to adverse consequences including early mortality, multisystem pathology, unmask/accelerate malignancy, and expose or predispose users to extreme danger from contaminants. This cautionary case reinforces the need to increase awareness and highlights the challenges that testing agencies, regulators, and clinicians face in the fast-developing licit/illicit trade of these products.
Degradation Properties and pH-responsive Guest-release of Cyclophanes Having Four Ester Side Chains with Terminal Choline Residues
Authors: Hayashida Osamu , Sato Daisuke 
Published: November 2013

Abstract
Water-soluble cationic cyclophane 1 having four ester side chains with terminal choline residues was synthesized as a pH-responsive degradable host. Alkaline hydrolysis of the ester bonds of 1 gave the corresponding tetraanionic cyclophane 2, which exhibited guest-binding affinities that led to release of the entrapped anionic guest molecules into the bulk aqueous phase.
Synthesis of Rh(I) Complexes Bearing N-p-Toluenesulfonyl-substituted N-Heterocyclic Carbenes
Authors: Sato Tetsuo , Yoshioka Daisuke , Hirose Yoichi , Oi Shuichi 
Published: November 2013

Abstract
We have synthesized Rh(I) complexes bearing a 1,2,4-triazol-3-ylidene or imidazol-2-ylidene substituted N-p-toluenesulfonyl (N-Ts) group. Structural characterizations of the Rh(I) complexes revealed that, because of its mesomeric and inductive electron-withdrawing effects, the N-Ts substituent increased π-accepting ability and decreased σ-donating ability of carbenes compared to N-mesityl substituents.
Layer-by-layer Nanoarchitectonics: Invention, Innovation, and Evolution
Authors: Ariga Katsuhiko , Yamauchi Yusuke , Rydzek Gaulthier , Ji Qingmin , Yonamine Yusuke , Wu Kevin C-W , Hill Jonathan P 
Published: November 2013

Abstract
Materials fabrication with nanoscale structural precision based on bottom-up-type self-assembly has become more important in various current disciplines in chemistry including materials chemistry, organic chemistry, physical chemistry, analytical chemistry, biochemistry, colloid and surface chemistry, and supramolecular chemistry. Although the design of new materials based on nanoscale self-assembly is anticipated as a key concept, preparing complete three-dimensional structures at nanoscale precision remains a difficult target using current technologies. Rather, dimension-reduced approaches such as layering of two-dimensional nanostructures into precisely controlled lamellar nanomaterials are currently achievable. In particular, layer-by-layer (LbL) assembly is known as a highly versatile method for fabrication of controlled layered structures from various kinds of component materials using very simple, inexpensive, and rapid procedures. Therefore, fabrication of multilayer films through the LbL deposition process has attracted growing interest from various research communities. The high versatility and flexibility of LbL assembly is continuously creating new concepts, new materials, new procedures, and new applications. In this highlight review, we focus on nanoarchitectonics by LbL assembly. After an initial introduction on the invention and a brief history of the LbL assembly technique, innovations and the evolution of the technique are described based mainly on recent examples, which are categorized into two sections: (i) developments in methodology (technical, material, and phenomenological aspects with expansion of concept) and (ii) progress in applications (physical, chemical/biochemical, and biomedical applications).