bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of Multidrug-Resistant Escherichia coli NIVEDI-P44, Isolated from a Chicken Fecal Sample in Northeast India
Authors: Tewari Rituparna , Das Mitra Susweta , Das Sangita , Jadhao Sudhir , Mishra Gayatri , Ganaie Feroze , Shome Rajeswari , Rahman Habibur , Shome Bibek Ranjan 
Published: April 2018

ABSTRACT

We report here the draft genome sequence of a multidrug-resistant
Escherichia coli
strain (NIVEDI-P44) isolated from a chicken fecal sample. The estimated genome size is 4.76 Mb, with a G+C content of 50.65%. The genome harbors multiple antibiotic resistance genes,
bla
DHA-1
,
mph
(A),
strA
,
strB
,
dfrA14
,
sul-2
,
tet
(A), and
qnrS1
.
Draft Genome Sequence of the Putative Marine Pathogen Aquimarina sp. Strain I32.4
Authors: Ranson Hilary J. , LaPorte Jason , Spinard Edward , Chistoserdov Andrei Y. , Gomez-Chiarri Marta , Nelson David R. , Rowley David C. 
Published: April 2018

ABSTRACT

Aquimarina
sp. strain I32.4 (formerly
Aquimarina
sp. ‘
homaria
’) is a putative pathogen involved in epizootic shell disease in the American lobster (
Homarus americanus
). We report here the draft genome sequence for
Aquimarina
sp. strain I32.4 and describe virulence factors that may provide insight into its mechanism of pathogenicity.
Draft Genome Sequence of Bacillus sp. Strain M21, Isolated from the Arid Area of Matmata, Tunisia
Authors: Nasfi Zina , Poehlein Anja , Harms Henrik , Goralski Emilie , Fisch Katja M. , Daniel Rolf , König Gabriele M. , Schäberle Till F. , Bachoual Rafik 
Published: April 2018

ABSTRACT

Bacillus
sp. strain M21 was isolated from an environmental sample. In antibacterial screenings, the strain inhibited growth of Gram-positive and Gram-negative test strains. The genome was assembled into 69 contigs with a total size of 5.178 Mb. The strain contains at least nine biosynthetic gene clusters for the production of specialized metabolites.
Draft Genome Sequence of Burkholderia cepacia ATCC 17759, a Polyhydroxybutyrate-Co-Valerate Copolymer-Producing Bacterium
Authors: Crooks Casey , Palmer Jonathan M. , Lindner Daniel L. 
Published: April 2018

ABSTRACT

Burkholderia cepacia
ATCC 17759, isolated from forest soils in Trinidad, accumulates large amounts of polyhydroxyalkanoate copolymers when grown on xylose, mannose, arabinose, other carbohydrates, and organic acid cosubstrates. This 8.72-Mb draft genome sequence of
B. cepacia
ATCC 17759 will provide better insight into this organism's utility in lignocellulose bioconversion.
Draft Genome Sequence of the Thermophilic Acetogen
Moorella humiferrea
DSM 23265
Authors: Poehlein Anja , Keyl Alisa , Milsch Jan C. , Daniel Rolf 
Published: April 2018

ABSTRACT

Moorella humiferrea
is an endospore-forming, anaerobic, and thermophilic bacterium which was isolated from a terrestrial hydrothermal spring.
M. humiferrea
is able to use humic acid or 10-anthraquinone-2,6-disulfonate as an electron-shuttling compound for growth and Fe(III) reduction. The genome has a size of 2.629 Mb and contains 2,668 predicted protein-coding genes.
Complete Genome Sequences of Two Bacillus pumilus Strains from Cuatrociénegas, Coahuila, Mexico
Authors: Zarza Eugenia , Alcaraz Luis D. , Aguilar-Salinas Bernardo , Islas Africa , Olmedo-Álvarez Gabriela 
Published: April 2018

ABSTRACT

We assembled the complete genome sequences of
Bacillus pumilus
strains 145 and 150a from Cuatrociénegas, Mexico. We detected genes codifying for proteins potentially involved in antagonism (bacteriocins) and defense mechanisms (abortive infection bacteriophage proteins and 4-azaleucine resistance). Both strains harbored prophage sequences. Our results provide insights into understanding the establishment of microbial interactions.
Systematic development of a tennis injury prevention programme
Authors: Pas Haiko I M F L , Bodde Stefan , Kerkhoffs Gino M M J , Pluim Babette , Tiemessen Ivo J H , Tol Johannes L , Verhagen Evert , Gouttebarge Vincent 
Published: April 2018

IntroductionDespite an injury incidence of up to 3.0/1000 hours of play, there are no published tennis injury prevention programmes. This article aims to describe the developmental process of TennisReady, an e-health tennis-specific injury programme for adult recreational tennis players.Five-step approachA bottom-up, five-step approach was used with the Knowledge Transfer Scheme as a guideline. During the first step, a problem statement among targeted users was carried out. 475 (partially) completed surveys and group interviews (n=8) revealed a preference for an app-based prevention intervention of 10–15 min. As a second step, a systematic review was performed to identify prevention strategies in tennis. None were found. In step 3, during two expert group meetings (n=18), the findings of the first two steps were discussed and goals were formulated. Relevant and potential exercises for the programme were discussed. A subgroup of a total of six physical therapists, physicians and trainers developed the content of the programme in step 4. Step 5 included an evaluation of the exercises in 33 recreational tennis players. Participants evaluated the exercises during training sessions with trainers involved in the programme’s development or their colleagues. Participants evaluated the programme through standardised surveys or group interviews. Based on this evaluation, the programme was adjusted by altering exercises and frequencies, and it was evaluated in a second target group (n=27). The second evaluation did not result in any major changes to the final prevention programme.ConclusionThrough a five-step approach guided by the Knowledge Transfer Scheme, we developed an e-health tennis-specific prevention programme for adult tennis players. This 10 min intervention will require testing in a randomised controlled setting.
KRASfluorescence in situ hybridisation testing for the detection and diagnosis of pancreatic adenocarcinoma
Authors: Shiroma Noriyuki , Arihiro Koji , Oda Miyo , Orita Makoto 
Published: April 2018

AimsThe aim of our study was to analyse correlations betweenKRASmutation status, chromosomal changes that affectKRASstatus in cells from pancreatic tumours.MethodsWe collected 69 cases of surgically resected pancreatic ductal adenocarcinoma (PDA) and seven cases of chronic pancreatitis (CP). Chromosomal abnormalities ofKRASand CEP12 were detected using fluorescence in situ hybridisation (FISH).ResultsThe number of CEP12 signals per cell ranged from 1.78 to 2.04 and 1.46 to 4.88 in CP and PDA samples, respectively, while the number ofKRASsignals per cell ranged from 1.94 to 2.06 and 1.88 to 8.18 in CP and PDA samples, respectively. The ‘chromosomal instability index’, which was defined as the percentage of cells with any chromosomal abnormality, was over 5.7 times greater in PDA than in CP. We performedKRASmutation analysis by direct sequencing and found that tumours withKRASmutations have a significantly higher meanKRASsignal per cell from PDA samples compared with tumours with wild-typeKRAS. KRASamplification was noted in 10% of cases. Although we found that lymph node metastasis and distal metastasis of PDA were more frequent in cases withKRASamplification, this was not correlated with overall survival. Using a threshold of 40%, we found that the chromosomal instability index robustly discriminated PDA cells from CP cells.ConclusionsBased on these findings, we concluded that FISH testing ofKRASusing cytology samples may represent an accurate approach for the diagnosis of PDA.
Intermediate catheter placement distal to the cerebral aneurysm during flow diversion embolization with the Surpass device
Authors: Topcuoglu Osman Melih , Arat Anil , Peker Ahmet , Sarikaya Basar 
Published: April 2018

PurposeWe present the preliminary angiographic and clinical results of the combined utilization of an AXS Catalyst 5 (Cat5) distal access catheter and a Surpass flow diverter (SFD) for the endovascular treatment of intracranial aneurysms.Materials and methodsInterventional neuroradiology case records were evaluated retrospectively to identify patients treated with an SFD in combination with Cat5. Demographic data, technical success, location of the catheter tip, aneurysm occlusion rate, and procedure-related morbidity and mortality were noted.ResultsThe analysis yielded 24 patients with 25 aneurysms with a mean age of 52.3±19.7 years. The mean aneurysm diameter was 15.7±8.8 mm. Twenty-one were anterior circulation (seven supraclinoid, one middle cerebral, one anterior choroidal and 12 petrocavernous) and four were posterior circulation (three basilar tip, one posterior inferior cerebellar) aneurysms. Only two of these aneurysms were re-treatments for recurrences. For SFD deployment, the distal tip of Cat5 was placed intradurally and at, or distal to, M1 segment in 88% and 48% of patients, respectively. Aneurysms were bypassed with Cat5 in 80% of the procedures. In one patient, flow diversion was abandoned totally due to arterial tortuosity. With the exclusion of this patient, the technical success rate was 91.7%. There was no permanent procedure-related morbidity or mortality. Of the 22 aneurysms treated successfully with the Surpass device, 20 had imaging follow-up at 6.3±3.8 months and 95% were totally occluded.ConclusionThe Cat5 catheter, which was manufactured for the navigation of large-bore stent-like devices, is a useful adjunct to the Surpass device and allowed us to deploy the device safely.
Does medical students’ gender affect their clinical learning of gynaecological examination? A retrospective cohort study
Authors: Wallbridge Thomas , Holden Angela , Picton Aled , Gupta Janesh 
Published: April 2018

AbstractIntroductionMedical graduates should be competent in gynaecological examination as well as associated skills including speculum use and swabbing. Male and female medical students may have different opportunities to practise these skills in clinical environments, potentially impacting on confidence and competence. This study explores this further via reviewing students’ learning experience in genitourinary medicine (GUM) and obstetrics and gynaecology (O&G) clinics.MethodsCross-sectional study of 759 year 4 and year 5 University of Birmingham medical students via an online questionnaire. This explored degree of participation, impact of gender and self-reported confidence.ResultsOverall response rate was 31% (233/759). Students of either gender who observed an examination being performed by a clinician were more likely to perform the same examination. Female students reported more opportunities to practise gynaecological examination and associated skills. Female students were more likely to be granted consent to perform speculum examinations, vaginal swabbing and vaginal bimanual examinations. Sixty-five per cent of male students felt that their gender affected their learning experience with female patients. Despite this, there was no significant difference in self-reported confidence level in performing gynaecological examinations between genders at the end of placement.ConclusionThe majority of male students perceived that their gender impacted their clinical experience in O&G and GUM. Self-reported confidence levels were unaffected, which could reflect varying approaches to competence between genders. The link between observing examinations and subsequent opportunities to practise is key. This could demonstrate students developing rapport and trust with patients, and clinicians’ roles as gatekeepers.
SABR
Authors: Bhat Divyashri , Rizk Amr , Zink Michael , Steinmetz Ralf 
Published: April 2018

State-of-the-art software-defined wide area networks (SD-WANs) provide the foundation for flexible and highly resilient networking. In this work, we design, implement, and evaluate a novel architecture (denoted as SABR) that leverages the benefits of software-defined networking (SDN) to provide network-assisted adaptive bitrate streaming. With clients retaining full control of their streaming algorithms, we clearly show that by this network assistance, both the clients and the content providers benefit significantly in terms of quality of experience (QoE) and content origin offloading. SABR utilizes information on available bandwidths per link and network cache contents to guide video streaming clients with the goal of improving the viewer’s QoE. In addition, SABR uses SDN capabilities to dynamically program flows to optimize the utilization of content delivery network caches.
Backed by our study of SDN-assisted streaming, we discuss the change in the requirements for network-to-player APIs that enables flexible video streaming. We illustrate the difficulty of the problem and the impact of SDN-assisted streaming on QoE metrics using various well-established player algorithms. We evaluate SABR together with state-of-the-art dynamic adaptive streaming over HTTP (DASH) quality adaptation algorithms through a series of experiments performed on a real-world, SDN-enabled testbed network with minimal modifications to an existing DASH client. In addition, we compare the performance of different caching strategies in combination with SABR. Our trace-based measurements show the substantial improvement in cache hit rates and QoE metrics in conjunction with SABR indicating a rich design space for jointly optimized SDN-assisted caching architectures for adaptive bitrate video streaming applications.
Invariant and heritable local cortical organization as revealed by fMRI
Authors: Christova Peka , Georgopoulos Apostolos P. 
Published: April 2018

Neural interactions in local cortical networks critically depend on the distance between interacting elements: the shorter the distance, the stronger the interactions. Here we quantified these interactions in six cortical areas of 854 individuals, including monozygotic and dizygotic twins, nontwin siblings, and nonrelated individuals. We found that the strength of zero-lag correlation between prewhitened, resting-state, blood level oxygenation-dependent functional magnetic resonance imaging time series decreased with distance as a power law. The rate of decrease, b, varied among individuals by ~1.9×, was highly correlated between hemispheres, but differed among areas (by ~1.2×) in a systematic fashion, becoming progressively less steep from frontal to occipital areas. With respect to twin status, b was significantly correlated between monozygotic twins, less so between dizygotic twins or nontwin siblings, and not at all in nonrelated individuals. These results quantify the lawful, distance-related cortical interactions and demonstrate, for the first time, the heritability of their power law. NEW & NOTEWORTHY Local cortical circuitry involves orderly neuronal interactions. A key feature of these interactions is that they are stronger the closer the interacting neurons. Here we quantified this crucial dependence of neural interactions on distance with functional magnetic resonance imaging and found that the strength of interactions decreases with distance as a power law that is very similar in all cortical lobes and heritable. These findings identify an invariant and heritable property of local cortical organization.
Inhibition of BDNF signaling in the paraventricular nucleus of the hypothalamus lowers acute stress-induced pressor responses
Authors: Schaich Chris L. , Wellman Theresa L. , Einwag Zachary , Dutko Richard A. , Erdos Benedek 
Published: April 2018

Brain-derived neurotrophic factor (BDNF) expression increases in the paraventricular nucleus of the hypothalamus (PVN) during stress, and our recent studies indicate that BDNF induces sympathoexcitatory and hypertensive responses when injected acutely or overexpressed chronically in the PVN. However, it remained to be investigated whether BDNF is involved in the mediation of stress-induced cardiovascular responses. Here we tested the hypothesis that inhibition of the high-affinity BDNF receptor TrkB in the PVN diminishes acute stress-induced cardiovascular responses. Male Sprague-Dawley rats were equipped with radiotelemetric transmitters for blood pressure measurement. BDNF-TrkB signaling was selectively inhibited by viral vector-mediated bilateral PVN overexpression of a dominant-negative truncated TrkB receptor (TrkB.T1, n = 7), while control animals ( n = 7) received green fluorescent protein (GFP)-expressing vector injections. Rats were subjected to acute water and restraint stress 3–4 wk after vector injections. We found that body weight, food intake, baseline mean arterial pressure (MAP), and heart rate were unaffected by TrkB.T1 overexpression. However, peak MAP increases were significantly reduced in the TrkB.T1 group compared with GFP both during water stress (GFP: 39 ± 2 mmHg, TrkB.T1: 27 ± 4 mmHg; P < 0.05) and restraint stress (GFP: 41 ± 3 mmHg, TrkB.T1: 34 ± 2 mmHg; P < 0.05). Average MAP elevations during the poststress period were also significantly reduced after both water and restraint stress in the TrkB.T1 group compared with GFP. In contrast, heart rate elevations to both stressors remained unaffected by TrkB.T1 overexpression. Our results demonstrate that activation of BDNF high-affinity TrkB receptors within the PVN is a major contributor to acute stress-induced blood pressure elevations. NEW & NOTEWORTHY We have shown that inhibition of the high-affinity brain-derived neurotrophic factor receptor TrkB in the paraventricular nucleus of the hypothalamus significantly reduces blood pressure elevations to acute stress without having a significant impact on resting blood pressure, body weight, and food intake.
Common Mitochondrial Haplogroups and Cutaneous Squamous Cell Carcinoma Risk
Authors: Jorgenson Eric , Choquet Hélène , Yin Jie , Asgari Maryam M. 
Published: April 2018

Abstract
Background: Cutaneous squamous cell carcinoma (cSCC) is the second most common cancer in United States, and its incidence is substantially higher in men than women, but the reasons for the difference are unknown. We explored whether common mitochondrial DNA (mtDNA) haplogroups, which have been associated with cancer risk, and in particular squamous cell carcinoma risk arising in other organs, could explain this biological sex difference in cSCC susceptibility.
Methods: We performed a retrospective cohort study using data from the Genetic Epidemiology Research in Adult Health and Aging cohort composed of 67,868 non-Hispanic white subjects (7,701 cSCC cases and 60,167 controls). Genotype information on &gt;665,000 SNPs was generated using Affymetrix Axiom arrays designed to maximize genome-wide coverage, and 102 high-quality mtDNA SNPs were used to determine mtDNA haplogroups. Associations between each mtDNA haplogroup and cSCC risk were evaluated by logistic regression analysis adjusting for age, sex, and population stratification using ancestry principal components.
Results: cSCC was more common in men (15.4% vs. 8.4% for women). Nine common mtDNA haplogroups (frequency ≥1%) were identified in addition to the most common haplogroup, H, used as the reference group. No association with cSCC risk was detected for any of the mtDNA haplogroups or overall or sex-stratified analyses.
Conclusions: Common mitochondrial variation is not associated with cSCC risk.
Impact: This well-powered study refutes the hypothesis that common mitochondrial haplogroups play a role in the differential sex predilection of cSCCs. Cancer Epidemiol Biomarkers Prev; 27(7); 838–41. ©2018 AACR.
Targeting AKT with Oridonin Inhibits Growth of Esophageal Squamous Cell Carcinoma In Vitro and Patient-Derived Xenografts In Vivo
Authors: Song Mengqiu , Liu Xuejiao , Liu Kangdong , Zhao Ran , Huang Hai , Shi Yuanyuan , Zhang Man , Zhou Silei , Xie Hua , Chen Hanyong , Li Yin , Zheng Yan , Wu Qiong , Liu Fangfang , Li Enmin , Bode Ann M. , Dong Zigang , Lee Mee-Hyun 
Published: April 2018

Abstract
Overexpression or activation of AKT is very well known to control cell growth, survival, and gene expression in solid tumors. Oridonin, an inflammatory medical and diterpenoid compound isolated from Rabdosia rubescens, has exhibited various pharmacologic and physiologic properties, including antitumor, antibacterial, and anti-inflammatory effects. In this study, we demonstrated that oridonin is an inhibitor of AKT and suppresses proliferation of esophageal squamous cell carcinoma (ESCC) in vitro and in vivo. The role of AKT in ESCC was studied using immuno-histochemical analysis of a tumor microarray, the effect of AKT knockdown on cell growth, and treatment of cells with MK-2206, an AKT inhibitor. Oridonin blocked AKT kinase activity and interacted with the ATP-binding pocket of AKT. It inhibited growth of KYSE70, KYSE410, and KYSE450 esophageal cancer cells in a time- and concentration-dependent manner. Oridonin induced arrest of cells in the G2–M cell-cycle phase, stimulated apoptosis, and increased expression of apoptotic biomarkers, including cleaved PARP, caspase-3, caspase-7, and Bims in ESCC cell lines. Mechanistically, we found that oridonin diminished the phosphorylation and activation of AKT signaling. Furthermore, a combination of oridonin and 5-fluorouracil or cisplatin (clinical chemotherapeutic agents) enhanced the inhibition of ESCC cell growth. The effects of oridonin were verified in patient-derived xenograft tumors expressing high levels of AKT. In summary, our results indicate that oridonin acts as an AKT inhibitor to suppress the growth of ESCC by attenuating AKT signaling. Mol Cancer Ther; 17(7); 1540–53. ©2018 AACR.
Molecular Profile of Advanced Thyroid Carcinomas by Next-Generation Sequencing: Characterizing Tumors Beyond Diagnosis for Targeted Therapy
Authors: Chen Hui , Luthra Rajyalakshmi , Routbort Mark J. , Patel Keyur P. , Cabanillas Maria E. , Broaddus Russell R. , Williams Michelle D. 
Published: April 2018

Abstract
Next-generation sequencing (NGS) for molecular diagnostics allows simultaneous testing of activating oncogenes and tumor suppressor mutations in multiple signal pathways. Extended mutational profiling of advanced thyroid cancers may enhance considerations for targeted therapies. We analyzed clinically derived molecular profiling of 216 patients with advanced thyroid carcinoma using NGS (Ion Torrent Personal Genome Machine) from April 2012 to February 2014. We examined substitutions and small indels in 46 or 50 cancer-related genes using Ampliseq Cancer Hotspot panel in respect to tumor diagnosis and clinical correlations.
Mutations were common in advanced thyroid carcinomas 154 (71%) predominately in targetable MAPK pathway (146/216, 68%), and several PI3K/AKT pathway (8, 4%; six as comutations). BRAF V600E mutation associated with papillary (94/139, 68%), poorly differentiated (4/39, 10%), and anaplastic (3/12, 25%) carcinomas. NRAS mutations occurred in follicular (5/12, 42%) and poorly differentiated thyroid carcinoma (12/39, 31%). Tumor suppressor mutations (16, 7%) occurred predominantly in TP53 in Hurthle cell (2/5, 40%, the only mutation), in anaplastic (3/12, 25%) and poorly differentiated thyroid carcinoma (4/39, 10%) some as comutations and in papillary thyroid carcinoma (5/139, 4%) always a comutation. Kaplan–Meier analysis of patients with poorly differentiated thyroid carcinoma containing activating mutations who received targeted therapeutics showed improved survival compared to similarly treated patients without mutations in targetable pathways (P = 0.02). In conclusion, MAPK pathway is the predominant target for therapy in advance thyroid carcinomas; adding NGS enables the identification of comutations associated with resistance (PI3K/AKT). Within poorly differentiated thyroid carcinoma, the molecular profile may hold prognostic value in the era of targeted therapy. Mol Cancer Ther; 17(7); 1575–84. ©2018 AACR.