bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequences of Propionibacterium acnes Type Strain ATCC6919 and Antibiotic-Resistant Strain HL411PA1
Authors: Liu Jared , Cheng Alison , Bangayan Nathanael Joshua , Barnard Emma , Curd Emily , Craft Noah , Li Huiying 
Published: August 2014

ABSTRACT

Propionibacterium acnes
is a major skin commensal and is associated with acne vulgaris, the most common skin disease. Here we report the draft genome sequences of two
P. acnes
strains, the type strain ATCC6919 and an antibiotic-resistant strain, HL411PA1.
Whole-Genome Sequence of Streptococcus suis Serotype 4 Reference Strain 6407
Authors: Wang Kaicheng , Chen Jiming , Yao Huochun , Lu Chengping 
Published: August 2014

ABSTRACT

We report here the second complete genome sequence of
Streptococcus suis
serotype 4 (strain 6407). The genome is 2,292,360 bp in length, covering 2,239 coding sequences, 58 tRNAs, and 4 rRNA loci.
Whole-Genome Sequences of Three Symbiotic
Endozoicomonas
Strains
Authors: Neave Matthew J. , Michell Craig T. , Apprill Amy , Voolstra Christian R. 
Published: August 2014

ABSTRACT

Members of the genus
Endozoicomonas
associate with a wide range of marine organisms. Here, we report on the whole-genome sequencing, assembly, and annotation of three
Endozoicomonas
type strains. These data will assist in exploring interactions between
Endozoicomonas
organisms and their hosts, and it will aid in the assembly of genomes from uncultivated
Endozoicomonas
spp.
Draft Genome Sequence of Staphylococcus chromogenes Strain MU 970, Isolated from a Case of Chronic Bovine Mastitis
Authors: Fry Pamela R. , Calcutt Michael J. , Foecking Mark F. , Hsieh Hsin-Yeh , Suntrup Douglas G. , Perry Jeanette , Stewart George C. , Middleton John R. 
Published: August 2014

ABSTRACT

Coagulase-negative staphylococcal species are a common cause of subclinical bovine mastitis, with
Staphylococcus chromogenes
being one of the most frequently identified species in these cases. The draft genome sequence of an
S. chromogenes
isolate (MU 970) recovered from the milk of a cow with a chronic intramammary infection is reported here.
Draft Genome Sequence of Rifamycin Derivatives Producing Amycolatopsis mediterranei Strain DSM 46096/S955
Authors: Singh Priya , Kumari Rashmi , Mukherjee Udita , Saxena Anjali , Sood Utkarsh , Lal Rup 
Published: August 2014

ABSTRACT

Amycolatopsis mediterranei
DSM 46096 produces antibiotics of the rifamycin family, 27-demethoxy-27-hydroxyrifamycin B, 25-desacetyl-27-demethoxy-27-hydroxyrifamycin, and 27-demethoxy-27-hydroxyrifamycin SV, which are effective against Gram-negative bacteria. Here, we present the draft genome of
A. mediterranei
46096 (approx. 10.2 Mbp) having 104 contigs with a GC content of 71.3% and 9,382 coding sequences.
Reducing caregiver stress with internet-based interventions: a systematic review of open-label and randomized controlled trials
Authors: Hu Chunling , Kung Simon , Rummans Teresa A , Clark Matthew M , Lapid Maria I 
Published: August 2014

AbstractObjective The high level of stress associated with caring for others with medical conditions has been recognized for some time. Reducing caregiver stress can improve caregiver quality of life as well as improve the care they provide to loved ones. This systematic review assesses the effectiveness of internet-based interventions to decrease caregiver stress.Materials and methods A comprehensive literature search of Ovid MEDLINE (1946–2013), Embase (1988–2013), PsycINFO (1987–2013), and CINAHL was conducted using terms related to caregiver and internet-based interventions. Internet-based interventions involving informal caregivers in an open-label or randomized controlled trial setting were included. A pair of raters independently reviewed all published abstracts. Data regarding participants, interventions, and outcomes were extracted and, for randomized trials, methodology quality was also reviewed.Results Eight open-label trials met the review criteria: three showed positive benefit in reducing caregiver stress, four were partially positive (some outcomes positive, others negative), and one was a negative study. Sixteen randomized trials met the review criteria: six showed positive benefit, five were partially positive, and five were negative. There were no clear patterns as to the variables (such as study duration and complexity of intervention) associated with better outcomes, although earlier studies typically had more negative outcomes.Discussion Internet-based interventions were mostly effective in reducing aspects of caregiver stress and improving their well-being. Further studies to assess outcomes for caregivers and their recipients’ health, different technology delivery methods, and the cost of such interventions are needed.
Potential risk of TNF inhibitors on the progression of interstitial lung disease in patients with rheumatoid arthritis
Authors: Nakashita Tamao , Ando Katsutoshi , Kaneko Norihiro , Takahashi Kazuhisa , Motojima Shinji 
Published: August 2014

ObjectivesBiological therapy represents important advances in alleviating rheumatoid arthritis (RA), but the effect on interstitial lung disease (ILD) has been controversial. The objective of this study was to assess the risk of such treatment for patients with ILD.DesignCase–control cohorts.SettingSingle centre in Japan.ParticipantsThis study included 163 patients with RA who underwent biological therapy.Outcome measuredWe assessed chest CT before initiation of biological therapy and grouped 163 patients according to the presence of ILD (with (n=58) and without pre-existing ILD (n=105)). Next, we evaluated serial changes of chest CT after treatment and visually assessed the emergence of ILD or its progression, which was referred to as an ‘ILD event’. Then, we also classified the patients according to the presence of ILD events and analysed their characteristics.ResultsTumour necrosis factor (TNF) inhibitors were administered to more patients with ILD events than those without ILD events (88% vs 60%, p<0.05), but recipients of tocilizumab or abatacept did not differ in this respect. Of 58 patients with pre-existing ILD, 14 had ILD events, and that proportion was greater than for those without pre-existing ILD (24% vs 3%, p<0.001). Of these 14 patients, all were treated with TNF inhibitors. Four patients developed generalised lung disease and two died from ILD progression. Baseline levels of KL-6 were similar in both groups, but increased in patients with ILD events.ConclusionsTNF inhibitors have the potential risk of ILD events, particularly for patients with pre-existing ILD, and KL-6 is a valuable surrogate marker for detecting ILD events. Our data suggest that non-TNF inhibitors are a better treatment option for these patients.
Shear-wave velocity structure of the Chilean subduction zone (39–40°S) based on Rayleigh wave dispersion: evidence of fluid release and melts in the mantle beneath the Villarrica volcano
Authors: Thorwart Martin , Dzierma Yvonne , Lieser Kathrin , Buhs Heiko , Rabbel Wolfgang 
Published: August 2014

Abstract

A seismic network operated from December 2008 to November 2009 in south-central Chile covering the Chile subduction zone from
c.
39°S to 40°S. This segment of the subduction zone includes the highly active Villarrica volcano and the maximum slip area of the 1960
M
w
9.5 earthquake. We applied surface wave dispersion analysis to data from a linear array of broadband stations and to records of four areal sub-arrays. Fifty regional and teleseismic events were used to produce dispersion curves of Rayleigh waves. From the dispersion curves, we determined depth functions of the shear-wave velocity for 4 subregions of the subduction zone: the Coastal Range, the Central Valley, the Volcanic Arc and the Back-arc Region in Argentina. The resulting models reveal the structure of the crust and the depth of the Moho discontinuity. Below the volcanic arc, the shear-wave velocities of the continental mantle are reduced by
c.
7% with respect to a background value of 4.3 km s
−1
. This low-velocity zone coincides with a zone of reduced electrical resistivity that was previously determined from magnetotelluric measurements. The combined occurrences of minima in the S-wave velocity and resistivity can be interpreted as an indicator of partial melts.
EGFR Blockade Enriches for Lung Cancer Stem–like Cells through Notch3-Dependent Signaling
Authors: Arasada Rajeswara Rao , Amann Joseph M. , Rahman Mohammad A. , Huppert Stacey S. , Carbone David P. 
Published: August 2014

Abstract
Mutations in the epidermal growth factor receptor (EGFR) are the most common actionable genetic abnormalities yet discovered in lung cancer. However, targeting these mutations with kinase inhibitors is not curative in advanced disease and has yet to demonstrate an impact on potentially curable, early-stage disease, with some data suggesting adverse outcomes. Here, we report that treatment of EGFR-mutated lung cancer cell lines with erlotinib, while showing robust cell death, enriches the ALDH+ stem-like cells through EGFR-dependent activation of Notch3. In addition, we demonstrate that erlotinib treatment increases the clonogenicity of lung cancer cells in a sphere-forming assay, suggesting increased stem-like cell potential. We demonstrate that inhibition of EGFR kinase activity leads to activation of Notch transcriptional targets in a γ secretase inhibitor-sensitive manner and causes Notch activation, leading to an increase in ALDH high+ cells. We also find a kinase-dependent physical association between the Notch3 and EGFR receptors and tyrosine phosphorylation of Notch3. This could explain the worsened survival observed in some studies of erlotinib treatment at early-stage disease, and suggests that specific dual targeting might overcome this adverse effect. Cancer Res; 74(19); 5572–84. ©2014 AACR.
PAK1 Tyrosine Phosphorylation Is Required to Induce Epithelial–Mesenchymal Transition and Radioresistance in Lung Cancer Cells
Authors: Kim EunGi , Youn HyeSook , Kwon TaeWoo , Son Beomseok , Kang JiHoon , Yang Hee Jung , Seong Ki Moon , Kim Wanyeon , Youn BuHyun 
Published: August 2014

AbstractThe p21-activated Ser/Thr kinase 1 (PAK1) kinase has an essential role in tumorigenesis and cell survival in many cancers, but its regulation is not fully understood. In this study, we showed that in response to irradiation of lung cancer cells, PAK1 was upregulated, tyrosine phosphorylated, and translocated to the nucleus. Tyrosine phosphorylation relied upon JAK2 kinase activity and was essential for PAK1 protein stability and binding to Snail. This radiation-induced JAK2–PAK1–Snail signaling pathway increased epithelial–mesenchymal transition (EMT) by regulating epithelial and mesenchymal cell markers. Notably, JAK2 inhibitors mediated radiosensitization and EMT blockade in a mouse xenograft model of lung cancer. Taken together, our findings offered evidence that JAK2 phosphorylates and stabilizes functions of PAK1 that promote EMT and radioresistance in lung cancer cells, with additional implications for the use of JAK2 inhibitors as radiosensitizers in lung cancer treatment. Cancer Res; 74(19); 5520–31. ©2014 AACR.
Transcriptional Dynamics in Colorectal Carcinogenesis: New Insights into the Role of c-Myc and miR17 in Benign to Cancer Transformation
Authors: Ben-David Eyal , Bester Assaf C. , Shifman Sagiv , Kerem Batsheva 
Published: August 2014

AbstractColorectal cancer develops in a sequential, evolutionary process, leading to a heterogenic tumor. Comprehensive molecular studies of colorectal cancer have been previously performed; still, the process of carcinogenesis is not fully understood. We utilized gene expression patterns from 94 samples including normal, adenoma, and adenocarcinoma colon biopsies and performed a coexpression network analysis to determine gene expression trajectories of 8,000 genes across carcinogenesis. We found that the majority of gene expression changes occur in the transition from normal tissue to adenoma. The upregulated genes, known to be involved in cellular proliferation, included c-Myc along with its targets. In a cellular model system, we show that physiologic upregulation of c-Myc can lead to cellular proliferation without DNA replication stress. Our analysis also found that carcinogenesis involves a progressive downregulation of genes that are markers of colonic tissue and propose that this reflects a perturbed differentiation of colon cells during carcinogenesis. The analysis of miRNAs targets pointed toward the involvement of miR17 in the regulation of colon cell differentiation. Finally, we found that copy-number variations (CNV) enriched in colon adenocarcinoma tend to occur in genes whose expression changes already in adenoma, with deletions occurring in genes downregulated and duplications in genes upregulated in adenomas. We suggest that the CNVs are selected to reinforce changes in gene expression, rather than initiate them. Together, these findings shed new light into the molecular processes that underlie the transformation of colon tissue from normal to cancer and add a temporal context that has been hitherto lacking. Cancer Res; 74(19); 5532–40. ©2014 AACR.
Clinical Implications of Phosphorylated STAT3 Expression in De Novo Diffuse Large B-cell Lymphoma
Authors: Ok Chi Young , Chen Jiayu , Xu-Monette Zijun Y. , Tzankov Alexandar , Manyam Ganiraju C. , Li Ling , Visco Carlo , Montes-Moreno Santiago , Dybkær Karen , Chiu April , Orazi Attilio , Zu Youli , Bhagat Govind , Richards Kristy L. , Hsi Eric D. , Choi William W.L. , van Krieken J. Han , Huh Jooryung , Zhao Xiaoying , Ponzoni Maurilio , Ferreri Andrés J.M. , Bertoni Francesco , Farnen John P. , Møller Michael B. , Piris Miguel A. , Winter Jane N. , Medeiros L. Jeffrey , Young Ken H. 
Published: August 2014

Abstract
Purpose: Activated signal transducer and activator of transcription 3 (STAT3) regulates tumor growth, invasion, cell proliferation, angiogenesis, immune response, and survival. Data regarding expression of phosphorylated (activated) STAT3 in diffuse large B-cell lymphoma (DLBCL) and the impact of phosphorylated STAT3 (pSTAT3) on prognosis are limited.
Experimental Design: We evaluated expression of pSTAT3 in de novo DLBCL using immunohistochemistry, gene expression profiling (GEP), and gene set enrichment analysis (GSEA). Results were analyzed in correlation with cell-of-origin (COO), critical lymphoma biomarkers, and genetic translocations.
Results: pSTAT3 expression was observed in 16% of DLBCL and was associated with advanced stage, multiple extranodal sites of involvement, activated B-cell–like (ABC) subtype, MYC expression, and MYC/BCL2 expression. Expression of pSTAT3 predicted inferior overall survival (OS) and progression-free survival (PFS) in patients with de novo DLBCL. When DLBCL cases were stratified according to COO or MYC expression, pSTAT3 expression did not predict inferior outcome, respectively. Multivariate analysis showed that the prognostic predictability of pSTAT3 expression was due to its association with the ABC subtype, MYC expression, and adverse clinical features. GEP demonstrated upregulation of genes, which can potentiate function of STAT3. GSEA showed the JAK–STAT pathway to be enriched in pSTAT3+ DLBCL.
Conclusions: The results of this study provide a rationale for the ongoing successful clinical trials targeting the JAK–STAT pathway in DLBCL. Clin Cancer Res; 20(19); 5113–23. ©2014 AACR.
Carotid Plaque, Intima-Media Thickness, and Incident Aortic Stenosis
Authors: Martinsson Andreas , Östling Gerd , Persson Margaretha , Sundquist Kristina , Andersson Charlotte , Melander Olle , Engström Gunnar , Hedblad Bo , Smith J. Gustav 
Published: August 2014

Objective—
Aortic stenosis (AS) shares risk factors with atherosclerotic vascular disease. Carotid intima-media thickness (IMT) and plaque may reflect the cumulative damage from exposure to different atherosclerotic risk factors. We examined the relationship of carotid IMT and plaque with incident AS in a prospective population-based study.

Approach and Results—

A random sample of participants (age, 45–68 years) in the population-based Malmö Diet and Cancer Study underwent B-mode ultrasound with measurements of IMT and the presence of plaque in the common carotid artery (n=5079). Potential risk factors for incident AS were studied in age- and sex-adjusted and expanded multivariable-adjusted Cox regression models. A total of 69 (1.4%) participants developed AS during up to 20 years of follow-up. Significant risk factors for AS in age- and sex-adjusted analyses were (
P
<0.05) body mass index, low-density lipoprotein cholesterol, hypertension, diabetes mellitus, smoking, C-reactive protein, plaque, and IMT. In contrast, high-density lipoprotein cholesterol, triglycerides, height, and leukocyte count were not significantly associated with AS (
P
>0.05). After adjustments, IMT, plaque, age, smoking, C-reactive protein, low-density lipoprotein cholesterol, and diabetes mellitus remained significantly associated with incident AS. IMT was no longer significantly associated with AS after adjustments for plaque and systolic blood pressure, but plaque remained significantly associated with incident AS.

Conclusions—
Traditional cardiovascular risk factors were individually associated with incident AS, and in multivariable models low-density lipoprotein cholesterol, smoking, age, presence of plaque, C-reactive protein, and diabetes mellitus remained significant predictors of incident AS. AS represents a vascular disorder related to carotid plaque, with potential implications for the pathophysiology and prevention of this disease.
Aberrant Hetero-Disulfide Bond Formation by the Hypertriglyceridemia-Associated p.Gly185Cys
APOA5
Variant (rs2075291)
Authors: Sharma Vineeta , Witkowski Andrzej , Witkowska H. Ewa , Dykstra Andrew , Simonsen Jens B. , Nelbach Lisa , Beckstead Jennifer A. , Pullinger Clive R. , Kane John P. , Malloy Mary J. , Watson Gordon , Forte Trudy M. , Ryan Robert O. 
Published: August 2014

Objective—

Apolipoprotein A-V (apoA-V) is a low-abundance plasma protein that modulates triacylglycerol homeostasis. Gene transfer studies were undertaken in
apoa5
(−/−) mice to define the mechanism underlying the correlation between the single-nucleotide polymorphism c.553G>T in
APOA5
and hypertriglyceridemia.

Approach and Results—

Adeno-associated virus (AAV) 2/8–mediated gene transfer of wild-type apoA-V induced a dramatic lowering of plasma triacylglycerol in
apoa5
(−/−) mice, whereas AAV2/8-Gly162Cys apoA-V (corresponding to the c.553G>T single-nucleotide polymorphism: rs2075291; p.Gly185Cys when numbering includes signal sequence) had a modest effect. Characterization studies revealed that plasma levels of wild-type and G162C apoA-V in transduced mice were similar and within the physiological range. Fractionation of plasma from mice transduced with AAV2/8-G162C apoA-V indicated that, unlike wild-type apoA-V, >50% of G162C apoA-V was recovered in the lipoprotein-free fraction. Nonreducing SDS-PAGE immunoblot analysis provided evidence that G162C apoA-V present in the lipoprotein-free fraction, but not that portion associated with lipoproteins, displayed altered electrophoretic mobility consistent with disulfide-linked heterodimer formation. Immunoprecipitation followed by liquid chromatography/mass spectrometry of human plasma from subjects homozygous for wild-type
APOA5
and c.553G>T
APOA5
revealed that G162C apoA-V forms adducts with extraneous plasma proteins including fibronectin, kininogen-1, and others.

Conclusions—
Substitution of Cys for Gly at position 162 of mature apoA-V introduces a free cysteine that forms disulfide bonds with plasma proteins such that its lipoprotein-binding and triacylglycerol-modulation functions are compromised.
Twelve–Single Nucleotide Polymorphism Genetic Risk Score Identifies Individuals at Increased Risk for Future Atrial Fibrillation and Stroke
Authors: Tada Hayato , Shiffman Dov , Smith J. Gustav , Sjögren Marketa , Lubitz Steven A. , Ellinor Patrick T. , Louie Judy Z. , Catanese Joseph J. , Engström Gunnar , Devlin James J. , Kathiresan Sekar , Melander Olle 
Published: August 2014

Background and Purpose—
Atrial fibrillation (AF) is prevalent and there is a clinical need for biomarkers to identify individuals at higher risk for AF. Fixed throughout a life course and assayable early in life, genetic biomarkers may meet this need. Here, we investigate whether multiple single nucleotide polymorphisms together as an AF genetic risk score (AF-GRS) can improve prediction of one’s risk for AF.

Methods—
In 27 471 participants of the Malmö Diet and Cancer Study, a prospective, community-based cohort, we used Cox models that adjusted for established AF risk factors to assess the association of AF-GRS with incident AF and ischemic stroke. Median follow-up was 14.4 years for incident AF and 14.5 years for ischemic stroke. The AF-GRS comprised 12 single nucleotide polymorphisms that had been previously shown to be associated with AF at genome-wide significance.

Results—

During follow-up, 2160 participants experienced a first AF event and 1495 had a first ischemic stroke event. Participants in the top AF-GRS quintile were at increased risk for incident AF (hazard ratio, 2.00; 95% confidence interval, 1.73–2.31;
P
=2.7×10
–21
) and ischemic stroke (hazard ratio, 1.23; 95% confidence interval, 1.04–1.46;
P
=0.02) when compared with the bottom quintile. Addition of the AF-GRS to established AF risk factors modestly improved both discrimination and reclassification (
P
<0.0001 for both).

Conclusions—
An AF-GRS can identify 20% of individuals who are at ≈2-fold increased risk for incident AF and at 23% increased risk for ischemic stroke. Targeting diagnostic or therapeutic interventions to this subset may prove clinically useful.
Estimation of Ground-Level Reflectivity Factor in Operational Weather Radar Networks Using VPR-Based Correction Ensembles
Authors: Koistinen Jarmo , Pohjola Heikki 
Published: August 2014

AbstractAn operational method is presented that corrects the bias of radar-based quantitative precipitation estimations (QPE) in radar networks that is due to the vertical profile of reflectivity (VPR) factor. It is used in both rain and snowfall. Measured average VPRs are obtained from the volume scans of each radar at ranges of 2–40 km. At each radar, two time ensembles of the bias estimates are made use of: the first ensemble contains 0–24 members at each range gate, calculated by beam convolution from the measured VPRs at 15-min intervals during the most recent 6 h. The second ensemble similarly contains 24 members calculated from parameterized climatological VPRs. In each scan the precipitation type classification and the climatological VPR are matched with the freezing level obtained from a numerical weather prediction model. The members of the two ensembles are weighted for both time lapse and quality and are then combined. At each composite grid point, the value of the networked VPR correction is then determined as a distance-weighted mean of the time ensembles of biases from all radars located closer than 300 km. In the absence of calibration errors, the resulting estimate of the reflectivity factor at ground level Ze is a seamless continuous field. As verified by radar–radar and radar–gauge comparisons in the Finnish network of eight C-band Doppler radars, the method efficiently reduces the range-dependent bias in QPE. For example, at radar ranges of 141–219 km, the average bias in the ground level Ze was −8.7 and 1.2 dB before and after the VPR correction, respectively.