bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of Pseudomonas hussainii Strain MB3, a Denitrifying Aerobic Bacterium Isolated from the Rhizospheric Region of Mangrove Trees in the Andaman Islands, India
Authors: Jaiswal Shubham K. , Saxena Rituja , Mittal Parul , Gupta Ankit , Sharma Vineet K. 
Published: February 2017

ABSTRACT

The genome sequence of
Pseudomonas hussainii
MB3, isolated from the rhizospheric region of mangroves in the Andaman Islands, is comprised of 3,644,788 bp and 3,159 protein coding genes. Draft genome analysis indicates that MB3 is an aerobic bacterium capable of performing assimilatory sulfate reduction, dissimilatory nitrate reduction, and denitrification.
Draft Genome Sequence of Pseudonocardia autotrophica Strain DSM 43083, an Efficient Producer of Peroxidases for Lignin Modification
Authors: Grumaz Christian , Rais Dominik , Kirstahler Philipp , Vainshtein Yevhen , Rupp Steffen , Zibek Susanne , Sohn Kai 
Published: February 2017

ABSTRACT

Pseudonocardia autotrophica
strain DSM 43083 is a filamentous actinobacterium and was described to degrade or modify lignin. Here, we present its draft genome sequence, with a size of 5.8 Mb, to unravel the gene set coding for promising monooxygenases, dioxygenases, and DyP-type peroxidases associated with aromatic metabolism and lignin modification.
Complete Genome Sequence of Thermus thermophilus TMY, Isolated from a Geothermal Power Plant
Authors: Fujino Yasuhiro , Nagayoshi Yuko , Ohshima Toshihisa , Ogata Seiya , Doi Katsumi 
Published: February 2017

ABSTRACT

Thermus thermophilus
TMY (JCM 10668) was isolated from silica scale formed at a geothermal power plant in Japan. Here, we report the complete genome sequence for this strain, which contains a chromosomal DNA of 2,121,526 bp with 2,500 predicted genes and a pTMY plasmid of 19,139 bp, with 28 predicted genes.
Crisis-Affected Populations and Tuberculosis
Authors: Zenner Dominik 
Published: February 2017

ABSTRACT
By definition, humanitarian crises can severely affect human health, directly through violence or indirectly through breakdown of infrastructure or lack of provision for basic human needs, such as safe shelter, food, clean water, and suitable clothing. After the initial phase, these indirect effects are the most important determinants of morbidity and mortality in humanitarian emergencies, and infectious diseases are among the most significant causes of ill health. Tuberculosis (TB) incidence in humanitarian emergencies varies depending on a number of factors, including the country background epidemiology, but will be elevated compared with precrisis levels. TB morbidity and mortality are associated with access to appropriate care and medications, and will also be elevated due to barriers to access to diagnosis and appropriate treatment, including robust TB drug supplies. While reestablishment of TB control is challenging in the early phases, successful treatment programs have been previously established, and the WHO has issued guidance on establishing such successful programs. Such programs should be closely linked to other health programs and established in close collaboration with the country’s national treatment program. Individuals who flee the emergency also have a higher TB risk and can face difficulties accessing care en route to or upon arrival in host countries. These barriers, often associated with treatment delays and worse outcomes, can be the result of uncertainties around legal status, other practical challenges, or lack of health care worker awareness. It is important to recognize and mitigate these barriers with an increasing number of tools now available and described.
The use of rituximab in newly diagnosed patients with systemic lupus erythematosus: long-term steroid saving capacity and clinical effectiveness
Authors: Gracia-Tello Borja , Ezeonyeji Amara , Isenberg David 
Published: February 2017

BackgroundPrevious reports indicate that treating patients with lupus (SLE) at or close to the time of diagnosis successfully without using any, or minimal, corticosteroids by using B-cell depletion (BCD) is possible in the short-term. It is not however known whether using BCD is as effective or reduces corticosteroid use in the long-term. We report the long-term (up to 7 years) use of BCD with respect to its steroid-saving capacity and clinical effectiveness in newly diagnosed SLE.MethodsSixteen female patients with SLE were treated at, or shortly after diagnosis, with BCD therapy (BCDT) minimising the routine use of oral steroids. Post-treatment, most patients were given hydroxychloroquine (n=14) and azathioprine (n=10). The British Isles Lupus Assessment Group (BILAG) disease activity index was used for clinical assessment. Serum antidouble-stranded DNA (dsDNA) antibodies, complement (C3), erythrocyte sedimentation rate (ESR), circulating B lymphocytes (CD19+) and total inmmunoglobulins were tested every 2–6 months (average of 4.5 years) (SD 2) post-treatment. Disease activity and steroid requirement were compared with three patients with SLE treated conventionally, each matched for ethnicity, sex, age, clinical features, disease duration at diagnosis and follow-up period.ResultsAll patients given rituximab achieved BCD. The mean number of flares during follow-up (new BILAG A or B) was 2.63 (SD 3) in the BCDT group and 4 (SD 3.6) in the controls (NS, p=0.14). Post-BCDT, mean anti-dsDNA antibody level fell from 1114 U/mL (SD 1699.3) to 194 (SD 346.7) at 18 months (p=0.043), mean serum ESR fell by >70% at 6 months maintained during follow-up and serum C3 level normalised in 8 patients. The mean cumulative prednisolone dose at 60 months for the patients who underwent BCDT (n=11) was 4745.67 mg (SD 6090 mg) vs 12 553.92 mg (SD 12 672 mg) for the controls (p=0.01).ConclusionsEarly treatment of patients with SLE with BCDT is safe, effective and enables a reduction in steroid use.
Involvement of gut microbiota in association between GLP-1/GLP-1 receptor expression and gastrointestinal motility
Authors: Yang Mo , Fukui Hirokazu , Eda Hirotsugu , Xu Xin , Kitayama Yoshitaka , Hara Ken , Kodani Mio , Tomita Toshihiko , Oshima Tadayuki , Watari Jiro , Miwa Hiroto 
Published: February 2017

The microbiota in the gut is known to play a pivotal role in host physiology by interacting with the immune and neuroendocrine systems in gastrointestinal (GI) tissues. Glucagon-like peptide 1 (GLP-1), a gut hormone, is involved in metabolism as well as GI motility. We examined how gut microbiota affects the link between GLP-1/GLP-1 receptor (GLP-1R) expression and motility of the GI tract. Germ-free (GF) mice (6 wk old) were orally administered a fecal bacterial suspension prepared from specific pathogen-free (SPF) mice, and then after fecal transplantation (FT) GI tissues were obtained from the GF mice at various time points. The expression of GLP-1 and its receptor was examined by immunohistochemistry, and gastrointestinal transit time (GITT) was measured by administration of carmine red solution. GLP-1 was expressed in endocrine cells in the colonic mucosa, and GLP-1R was expressed in myenteric neural cells throughout the GI wall. GLP-1R-positive cells throughout the GI wall were significantly fewer in GF mice with FT than in GF mice without gut microbiota reconstitution. GITT was significantly shorter in GF mice with FT than in control GF mice without FT and correlated with the number of GLP-1R-positive cells throughout the GI wall. GITT was significantly longer in GF control mice than in SPF mice. When those mice were treated with GLP-1 agonist extendin4, GITT was significantly longer in the GF mice. The gut microbiota may accelerate or at least modify GI motility while suppressing GLP-1R expression in myenteric neural cells throughout the GI tract. NEW & NOTEWORTHY The gut microbiota has been intensively studied, because it plays a pivotal role in various aspects of host physiology. On the other hand, glucagon-like peptide 1 (GLP-1) plays important roles in metabolism as well as gastrointestinal motility. In the present study, we have suggested that the gut microbiota accelerates gastrointestinal motility while suppressing the expression of GLP-1 receptor in myenteric neural cells throughout the gastrointestinal tract. We believe that this article is very timely and suggestive work.
Impact of Social and Built Environment Factors on Body Size among Breast Cancer Survivors: The Pathways Study
Authors: Shariff-Marco Salma , Von Behren Julie , Reynolds Peggy , Keegan Theresa H.M. , Hertz Andrew , Kwan Marilyn L. , Roh Janise M. , Thomsen Catherine , Kroenke Candyce H. , Ambrosone Christine , Kushi Lawrence H. , Gomez Scarlett Lin 
Published: February 2017

Abstract
Background: As social and built environment factors have been shown to be associated with physical activity, dietary patterns, and obesity in the general population, they likely also influence these health behaviors among cancer survivors and thereby impact survivorship outcomes.
Methods: Enhancing the rich, individual-level survey and medical record data from 4,505 breast cancer survivors in the Pathways Study, a prospective cohort drawn from Kaiser Permanente Northern California, we geocoded baseline residential addresses and appended social and built environment data. With multinomial logistic models, we examined associations between neighborhood characteristics and body mass index and whether neighborhood factors explained racial/ethnic/nativity disparities in overweight/obesity.
Results: Low neighborhood socioeconomic status, high minority composition, high traffic density, high prevalence of commuting by car, and a higher number of fast food restaurants were independently associated with higher odds of overweight or obesity. The higher odds of overweight among African Americans, U.S.-born Asian Americans/Pacific Islanders, and foreign-born Hispanics and the higher odds of obesity among African Americans and U.S.-born Hispanics, compared with non-Hispanic whites, remained significant, although somewhat attenuated, when accounting for social and built environment features.
Conclusions: Addressing aspects of neighborhood environments may help breast cancer survivors maintain a healthy body weight.
Impact: Further research in this area, such as incorporating data on individuals' perceptions and use of their neighborhood environments, is needed to ultimately inform multilevel interventions that would ameliorate such disparities and improve outcomes for breast cancer survivors, regardless of their social status (e.g., race/ethnicity, socioeconomic status, nativity). Cancer Epidemiol Biomarkers Prev; 26(4); 505–15. ©2017 AACR.
See all the articles in this CEBP Focus section, “Geospatial Approaches to Cancer Control and Population Sciences.”
Sudden Cardiac Death in Patients With Ischemic Heart Failure Undergoing Coronary Artery Bypass Grafting
Authors: Rao Meena P. , Al-Khatib Sana M. , Pokorney Sean D. , She Lilin , Romanov Alexander , Nicolau Jose C. , Lee Kerry L. , Carson Peter , Selzman Craig H. , Stepinska Janina , Cleland John G.F. , Tungsubutra Wiwun , Desvigne-Nickens Patrice M. , Sueta Carla A. , Siepe Matthias , Lang Irene , Feldman Arthur M. , Yii Michael , Rouleau Jean L. , Velazquez Eric J. 
Published: February 2017

Background:
The risk of sudden cardiac death (SCD) in patients with heart failure after coronary artery bypass graft surgery (CABG) has not been examined in a contemporary clinical trial of surgical revascularization. This analysis describes the incidence, timing, and clinical predictors of SCD after CABG.

Methods:
Patients enrolled in the STICH trial (Surgical Treatment of Ischemic Heart Failure) who underwent CABG with or without surgical ventricular reconstruction were included. We excluded patients with prior implantable cardioverter-defibrillator and those randomized only to medical therapy. The primary outcome was SCD as adjudicated by a blinded committee. A Cox model was used to examine and identify predictors of SCD. The Fine and Gray method was used to estimate the incidence of SCD accounting for the competing risk of other deaths.

Results:
Over a median follow-up of 46 months, 113 of 1411 patients who received CABG without (n = 934) or with (n = 477) surgical ventricular reconstruction had SCD; 311 died of other causes. The mean left ventricular ejection fraction at enrollment was 28±9%. The 5-year cumulative incidence of SCD was 8.5%. Patients who had SCD and those who did not die were younger and had fewer comorbid conditions than did those who died of causes other than SCD. In the first 30 days after CABG, SCD (n=5) accounted for 7% of all deaths. The numerically greatest monthly rate of SCD was in the 31- to 90-day time period. In a multivariable analysis including baseline demographics, risk factors, coronary anatomy, and left ventricular function, end-systolic volume index and B-type natriuretic peptide were most strongly associated with SCD.

Conclusions:
The monthly risk of SCD shortly after CABG among patients with a low left ventricular ejection fraction is highest between the first and third months, suggesting that risk stratification for SCD should occur early in the postoperative period, particularly in patients with increased preoperative end-systolic volume index or B-type natriuretic peptide.

Clinical Trial Registration:

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT0002359.
Heritability of Vascular Structure and Function: A Parent–Child Study
Authors: Ryder Justin R. , Pankratz Nathan D. , Dengel Donald R. , Pankow James S. , Jacobs David R. , Sinaiko Alan R. , Gooty Vasu , Steinberger Julia 
Published: February 2017

Background
Understanding the heritable contribution of vascular measures, from parent to offspring, may aid in risk stratification and atherosclerosis prevention efforts. We hypothesized that measures of vascular structure and function would be heritable in this cohort of parents and their adolescent offspring.

Methods and Results

High‐resolution ultrasound scans of the brachial and carotid arteries were obtained in parents (n=558) and their offspring (n=369). Lumen diameter and flow‐mediated dilation were measured in the brachial artery. Intima‐media thickness, lumen diameter, incremental elastic modulus, diameter distensibility, and cross‐sectional distensibility were measured, and carotid cross‐sectional compliance was measured in the carotid artery. Carotid–radial pulse wave velocity was obtained using SphygmoCor
®
. Heritability analysis (h
2
, expressed as %) using Sequential Oligogenic Linkage Analysis Routines was performed on the entire cohort and adjusted for age, sex, race, body–mass index, smoking, and mean arterial pressure. Data are presented as mean±
SE
. Measures of brachial artery diameter (h
2
=25±9%,
P
=0.001), lumen diameter (h
2
=55±9%,
P
<0.001), intima‐media thickness (h
2
=29±13%,
P
=0.014), diameter distensibility (h
2
=28±7%,
P
<0.001), cross‐sectional distensibility (h
2
=27±7%,
P
<0.001), and pulse wave velocity (h
2
=26±9%,
P
<0.001) were significantly heritable. Flow‐mediated dilation and incremental elastic modulus were not significantly heritable. Similar associations were observed in analysis restricted to siblings and complete Trios (mother, father, and child).

Conclusions
These data show that the majority of noninvasive measures of vascular structure and function are heritable, suggesting that measurement of these subclinical risk factors in parents may be helpful in assessing childhood risk for future cardiovascular disease.
Two new species in the Ficinia indica complex (Cyperaceae, tribe Cypereae) from South Africa
Authors: TSHIILA ALUWANI A. , CHIMPHANGO SAMSON B.M. , VILJOEN JAN-ADRIAAN , MUASYA A. MUTHAMA 
Published: February 2017

Unclear boundaries between species hinder identification in the field and in herbaria, especially in species groups that can only be distinguished on the basis of subtle morphological and ecological features. One such taxon is Ficinia indica, widespread in the Greater Cape Floristic Region, growing on deep sandy soils between sea level and 1000 m elevation. Within its range, several phylogenetically related and morphologically similar species co-occur or occupy distinct habitats. Studies in herbaria show species in the Ficinia indica complex to be largely misidentified based on the use of qualitative information. Here, we investigate whether the six taxa recognized, based on one or a few characters, are supported as distinct species based on multivariate analysis of macro-morphological data. Two of the taxa were mostly separated whereas the other four taxa overlapped in multivariate space, but all the taxa could be distinguished using a single or a combination of morphological and ecological characters. We uphold the four previously recognized taxa (Ficinia argyropus, F. elatior, F. indica, F. laevis) as species, describe two new species (F. arnoldii and F. montana), and provide a dichotomous key for their identification.
A critical role of spinal Shank2 proteins in NMDA-induced pain hypersensitivity
Authors: Yoon Seo-Yeon , Kwon Soon-Gu , Kim Yong Ho , Yeo Ji-Hee , Ko Hyoung-Gon , Roh Dae-Hyun , Kaang Bong-Kiun , Beitz Alvin J , Lee Jang-Hern , Oh Seog Bae 
Published: February 2017

Background Self-injurious behaviors (SIBs) are devastating traits in autism spectrum disorder (ASD). Although deficits in pain sensation might be one of the contributing factors underlying the development of SIBs, the mechanisms have yet to be addressed. Recently, the Shank2 synaptic protein has been considered to be a key component in ASD, and mutations of SHANK2 gene induce the dysfunction of N-methyl-D-aspartate (NMDA) receptors, suggesting a link between Shank2 and NMDA receptors in ASD. Given that spinal NMDA receptors play a pivotal role in pain hypersensitivity, we investigated the possible role of Shank2 in nociceptive hypersensitivity by examining changes in spontaneous pain following intrathecal NMDA injection in S hank2−/− ( Shank2 knock-out, KO) mice. Results Intrathecal NMDA injection evoked spontaneous nociceptive behaviors. These NMDA-induced nociceptive responses were significantly reduced in Shank2 KO mice. We also observed a significant decrease of NMDA currents in the spinal dorsal horn of Shank2 KO mice. Subsequently, we examined whether mitogen-activated protein kinase or AKT signaling is involved in this reduced pain behavior in Shank2 KO mice because the NMDA receptor is closely related to these signaling molecules. Western blotting and immunohistochemistry revealed that spinally administered NMDA increased the expression of a phosphorylated form of extracellular signal-regulated kinase (p-ERK) which was significantly reduced in Shank2 KO mice. However, p38, JNK, or AKT were not changed by NMDA administration. The ERK inhibitor, PD98059, decreased NMDA-induced spontaneous pain behaviors in a dose-dependent manner in wild-type mice. Moreover, it was found that the NMDA-induced increase in p-ERK was primarily colocalized with Shank2 proteins in the spinal cord dorsal horn. Conclusion Shank2 protein is involved in spinal NMDA receptor-mediated pain, and mutations of Shank2 may suppress NMDA-ERK signaling in spinal pain transmission. This study provides new clues into the mechanisms underlying pain deficits associated with SIB and deserves further study in patients with ASD.
Effect of Mirrored Views on Endoscopic and Arthroscopic Skill Performance
Authors: Benninger Emanuel , Meier Christoph , Wirth Stefan , Koch Peter Philipp , Meyer Dominik 
Published: February 2017

Background: Arthroscopic procedures may be technically challenging because of impaired vision, limited space, and the 2-dimensional vision of a 3-dimensional structure. Spatial orientation may get more complicated when the camera is pointing toward the surgeon. Hypothesis: Spatial orientation and arthroscopic performance may be improved by simply mirroring the image on the monitor in different configurations regarding the position and orientation of camera and instrument. Study Design: Descriptive laboratory study. Methods: Thirty volunteers from an orthopaedic department were divided into 3 equal groups according to their arthroscopic experience (beginners, intermediates, seniors). All subjects were asked to perform a standardized task in a closed box mimicking an endoscopic space. The same task had to be performed in 4 different configurations regarding camera and instrument position and orientation (pointing toward or away from the subject) with either the original or mirrored image on the monitor. Efficiency (time per stick; TPS), precision (successful completion of the task), and difficulty rating using a visual analog scale (VAS) were analyzed. Results: Mirroring the image demonstrated no advantage over the original images in any configuration regarding TPS. Successful completion of the task was significantly better when the image was mirrored in the configuration with the camera pointing toward and the instrument away from the surgeon. There was a positive correlation between TPS and subjective VAS difficulty rating ( r = 0.762, P = .000) and a negative correlation between the successful completion of the task and VAS ( r = −0.515, P = .000). Conclusion: Mirroring the image may have a positive effect on arthroscopic performance of surgeons in certain configurations. A significantly improved performance was seen when the arthroscope was pointing toward and the grasping instrument pointing away from the subject. Mirroring the image may facilitate surgery in such clinical situations. Clinical Relevance: Mirroring the image may facilitate arthroscopic procedures in certain clinical situations.
Comparison of self-report and electronic monitoring of 6MP intake in childhood ALL: a Children’s Oncology Group study
Authors: Landier Wendy , Chen Yanjun , Hageman Lindsey , Kim Heeyoung , Bostrom Bruce C. , Casillas Jacqueline N. , Dickens David S. , Evans William E. , Maloney Kelly W. , Mascarenhas Leo , Ritchey A. Kim , Termuhlen Amanda M. , Carroll William L. , Relling Mary V. , Wong F. Lennie , Bhatia Smita 
Published: February 2017

Key Points
Self-report overestimated electronically monitored 6MP adherence at least some of the time in a large majority of patients (84.4%). Nonadherers were more likely to overreport 6MP intake (47%) compared with adherent patients (8%).
Challenging the foundations of the clinical model of foot function: further evidence that the root model assessments fail to appropriately classify foot function
Authors: Jarvis Hannah L. , Nester Christopher J. , Bowden Peter D. , Jones Richard K. 
Published: February 2017

AbstractBackgroundThe Root model of normal and abnormal foot function remains the basis for clinical foot orthotic practice globally. Our aim was to investigate the relationship between foot deformities and kinematic compensations that are the foundations of the model.MethodsA convenience sample of 140 were screened and 100 symptom free participants aged 18–45 years were invited to participate. The static biomechanical assessment described by the Root model was used to identify five foot deformities. A 6 segment foot model was used to measure foot kinematics during gait. Statistical tests compared foot kinematics between feet with and without foot deformities and correlated the degree of deformity with any compensatory motions.ResultsNone of the deformities proposed by the Root model were associated with distinct differences in foot kinematics during gait when compared to those without deformities or each other. Static and dynamic parameters were not correlated.ConclusionsTaken as part of a wider body of evidence, the results of this study have profound implications for clinical foot health practice. We believe that the assessment protocol advocated by the Root model is no longer a suitable basis for professional practice. We recommend that clinicians stop using sub‐talar neutral position during clinical assessments and stop assessing the non‐weight bearing range of ankle dorsiflexion, first ray position and forefoot alignments and movement as a means of defining the associated foot deformities. The results question the relevance of the Root assessments in the prescription of foot orthoses.