bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of Bacillus cereus LA2007, a Human-Pathogenic Isolate Harboring Anthrax-Like Plasmids
Authors: Pena-Gonzalez Angela , Marston Chung K. , Rodriguez-R Luis M. , Kolton Cari B. , Garcia-Diaz Julia , Theppote Amanda , Frace Michael , Konstantinidis Konstantinos T. , Hoffmaster Alex R. 
Published: April 2017

ABSTRACT

We present the genome sequence of
Bacillus cereus
LA2007, a strain isolated in 2007 from a fatal pneumonia case in Louisiana. Sequence-based genome analysis revealed that LA2007 carries a plasmid highly similar to
Bacillus anthracis
pXO1, including the genes responsible for the production and regulation of anthrax toxin.
Multiple Genome Sequences of Heteropolysaccharide-Forming Acetic Acid Bacteria
Authors: Brandt Julia U. , Jakob Frank , Geissler Andreas J. , Behr Jürgen , Vogel Rudi F. 
Published: April 2017

ABSTRACT

We report here the complete genome sequences of the acetic acid bacteria (AAB)
Acetobacter aceti
TMW 2.1153,
A. persici
TMW 2.1084, and
Neoasaia chiangmaiensis
NBRC 101099, which secrete biotechnologically relevant heteropolysaccharides (HePSs) into their environments. Upon genome sequencing of these AAB strains, the corresponding HePS biosynthesis pathways were identified.
Complete Genome Sequences of Mycobacterium kansasii Strains Isolated from Rhesus Macaques
Authors: Panda Aruna , Nagaraj Sushma , Zhao Xuechu , Tettelin Hervé , DeTolla Louis J. 
Published: April 2017

ABSTRACT

Mycobacterium kansasii
is a nontuberculous mycobacterium. It causes opportunistic infections with pulmonary and extrapulmonary manifestations. We report here the complete genome sequences of two
M. kansasii
strains isolated from rhesus macaques. We performed genome comparisons with human and environmental isolates of
M. kansasii
to assess the genomic diversity of this species.
Complete Genome Sequence of Mycobacterium avium subsp.
hominissuis
Strain H87 Isolated from an Indoor Water Sample
Authors: Zhao Xueyan , Epperson L. Elaine , Hasan Nabeeh A. , Honda Jennifer R. , Chan Edward D. , Strong Michael , Walter Nicholas D. , Davidson Rebecca M. 
Published: April 2017

ABSTRACT

Mycobacterium avium
subsp.
hominissuis
is an environmentally acquired bacterium known to cause pulmonary and soft tissue infections, lymphadenitis, and disseminated disease in humans. We report here the complete genome sequence of strain H87, isolated from an indoor water sample, as a single circular chromosome of 5,626,623 bp with a G+C content of 68.8%.
Whole-Genome Sequence of Corynebacterium pseudotuberculosis PA04, Isolated from the Lymph Node of a Sheep in the Amazon, Brazil
Authors: Costa Wana L. O. , Alves Jorianne T. C. , Dias Larissa M. , Araújo Carlos Leonardo de Aragão , Morais Eziquiel , Silva André G. M. , Andrade Soraya S. , Ramos Rommel T. J. , Silva Artur , Folador Adriana R. C. 
Published: April 2017

ABSTRACT

This study reports the complete genome sequence of
Corynebacterium pseudotuberculosis
strain PA04, isolated from a sheep in the Amazon, Brazil. This bacterium is the etiological agent of caseous lymphadenitis. This genome contains 2,338,093 bp, 52.2% G+C content, and a total of 2,104 coding sequences (CDSs), 41 pseudogenes, 12 rRNAs, and 49 tRNAs.
Draft Genome Sequences of Three Listeria monocytogenes Isolates from Foods in China
Authors: Su Xudong , Cao Guojie , Kuang Dai , Zhang Jianmin , Chen Yi , Allard Marc , Brown Eric , Shi Xianming , Meng Jianghong , Xu Xuebin 
Published: April 2017

ABSTRACT

Listeria monocytogenes
is a foodborne pathogen of global concern because of the high mortality rate among patients. The draft genome sequences of three
L. monocytogenes
strains isolated from foods are reported here. The availability of these genomes should provide useful information on the genomic diversity of
L. monocytogenes
isolated from foods in China.
Draft Genome Sequences of Two Highly Erythromycin-Resistant Streptococcus gallolyticus subsp.
gallolyticus
Isolates Containing a Novel Tn
916
-Like Element, Tn
6331
Authors: Kambarev Stanimir , Pecorari Frédéric , Corvec Stéphane 
Published: April 2017

ABSTRACT

Recently, we reported the draft genome sequence of
Streptococcus gallolyticus
NTS31106099. It was found to contain a previously unknown putative Tn
916
-like conjugative transposon, Tn
6263
. Here, we report the draft genome sequences of two other clinical isolates, NTS31301958 and NTS31307655. Both of them contain another novel element, Tn
6331
, which is highly similar to Tn
6263
.
Improved High-Quality Draft Genome Sequence and Annotation of Burkholderia contaminans LMG 23361
T
Authors: Jung Ji Young , Ahn Youngbeom , Kweon Ohgew , LiPuma John J. , Hussong David , Marasa Bernard S. , Cerniglia Carl E. 
Published: April 2017

ABSTRACT

Burkholderia contaminans
LMG 23361 is the type strain of the species isolated from the milk of a dairy sheep with mastitis. Some pharmaceutical products contain disinfectants such as benzalkonium chloride (BZK) and previously we reported that
B. contaminans
LMG 23361
T
possesses the ability to inactivate BZK with high biodegradation rates. Here, we report an improved high-quality draft genome sequence of this strain.
HuR Small-Molecule Inhibitor Elicits Differential Effects in Adenomatosis Polyposis and Colorectal Carcinogenesis
Authors: Lang Michaela , Berry David , Passecker Katharina , Mesteri Ildiko , Bhuju Sabin , Ebner Florian , Sedlyarov Vitaly , Evstatiev Rayko , Dammann Kyle , Loy Alexander , Kuzyk Orest , Kovarik Pavel , Khare Vineeta , Beibel Martin , Roma Guglielmo , Meisner-Kober Nicole , Gasche Christoph 
Published: April 2017

AbstractHuR is an RNA-binding protein implicated in immune homeostasis and various cancers, including colorectal cancer. HuR binding to AU-rich elements within the 3′ untranslated region of mRNAs encoding oncogenes, growth factors, and various cytokines leads message stability and translation. In this study, we evaluated HuR as a small-molecule target for preventing colorectal cancer in high-risk groups such as those with familial adenomatosis polyposis (FAP) or inflammatory bowel disease (IBD). In human specimens, levels of cytoplasmic HuR were increased in colonic epithelial cells from patients with IBD, IBD-cancer, FAP-adenoma, and colorectal cancer, but not in patients with IBD-dysplasia. Intraperitoneal injection of the HuR small-molecule inhibitor MS-444 in AOM/DSS mice, a model of IBD and inflammatory colon cancer, augmented DSS-induced weight loss and increased tumor multiplicity, size, and invasiveness. MS-444 treatment also abrogated tumor cell apoptosis and depleted tumor-associated eosinophils, accompanied by a decrease in IL18 and eotaxin-1. In contrast, HuR inhibition in APCMin mice, a model of FAP and colon cancer, diminished the number of small intestinal tumors generated. In this setting, fecal microbiota, evaluated by 16S rRNA gene amplicon sequencing, shifted to a state of reduced bacterial diversity, with an increased representation of Prevotella, Akkermansia, and Lachnospiraceae. Taken together, our results indicate that HuR activation is an early event in FAP-adenoma but is not present in IBD-dysplasia. Furthermore, our results offer a preclinical proof of concept for HuR inhibition as an effective means of FAP chemoprevention, with caution advised in the setting of IBD. Cancer Res; 77(9); 2424–38. ©2017 AACR.
Regulatory Aspects of Optical Methods and Exogenous Targets for Cancer Detection
Authors: Tummers Willemieke S. , Warram Jason M. , Tipirneni Kiranya E. , Fengler John , Jacobs Paula , Shankar Lalitha , Henderson Lori , Ballard Betsy , Pfefer T. Joshua , Pogue Brian W. , Weichert Jamey P. , Bouvet Michael , Sorger Jonathan , Contag Christopher H. , Frangioni John V. , Tweedle Michael F. , Basilion James P. , Gambhir Sanjiv S. , Rosenthal Eben L. 
Published: April 2017

Abstract
Considerable advances in cancer-specific optical imaging have improved the precision of tumor resection. In comparison to traditional imaging modalities, this technology is unique in its ability to provide real-time feedback to the operating surgeon. Given the significant clinical implications of optical imaging, there is an urgent need to standardize surgical navigation tools and contrast agents to facilitate swift regulatory approval. Because fluorescence-enhanced surgery requires a combination of both device and drug, each may be developed in conjunction, or separately, which are important considerations in the approval process. This report is the result of a one-day meeting held on May 4, 2016 with officials from the National Cancer Institute, the FDA, members of the American Society of Image-Guided Surgery, and members of the World Molecular Imaging Society, which discussed consensus methods for FDA-directed human testing and approval of investigational optical imaging devices as well as contrast agents for surgical applications. The goal of this workshop was to discuss FDA approval requirements and the expectations for approval of these novel drugs and devices, packaged separately or in combination, within the context of optical surgical navigation. In addition, the workshop acted to provide clarity to the research community on data collection and trial design. Reported here are the specific discussion items and recommendations from this critical and timely meeting. Cancer Res; 77(9); 2197–206. ©2017 AACR.
Oncogenic Role of SND1 in Development and Progression of Hepatocellular Carcinoma
Authors: Jariwala Nidhi , Rajasekaran Devaraja , Mendoza Rachel G. , Shen Xue-Ning , Siddiq Ayesha , Akiel Maaged A. , Robertson Chadia L. , Subler Mark A. , Windle Jolene J. , Fisher Paul B. , Sanyal Arun J. , Sarkar Devanand 
Published: April 2017

Abstract
SND1, a subunit of the miRNA regulatory complex RISC, has been implicated as an oncogene in hepatocellular carcinoma (HCC). In this study, we show that hepatocyte-specific SND1 transgenic mice (Alb/SND1 mice) develop spontaneous HCC with partial penetrance and exhibit more highly aggressive HCC induced by chemical carcinogenesis. Livers from Alb/SND1 mice exhibited a relative increase in inflammatory markers and spheroid-generating tumor-initiating cells (TIC). Mechanistic investigations defined roles for Akt and NF-κB signaling pathways in promoting TIC formation in Alb/SND1 mice. In human xenograft models of subcutaneous or orthotopic HCC, administration of the selective SND1 inhibitor 3′, 5′-deoxythymidine bisphosphate (pdTp), inhibited tumor formation without effects on body weight or liver function. Our work establishes an oncogenic role for SND1 in promoting TIC formation and highlights pdTp as a highly selective SND1 inhibitor as a candidate therapeutic lead to treat advanced HCC. Cancer Res; 77(12); 3306–16. ©2017 AACR.
CMTM3 (CKLF-Like Marvel Transmembrane Domain 3) Mediates Angiogenesis by Regulating Cell Surface Availability of VE-Cadherin in Endothelial Adherens Junctions
Authors: Chrifi Ihsan , Louzao-Martinez Laura , Brandt Maarten , van Dijk Christian G.M. , Burgisser Petra , Zhu Changbin , Kros Johan M. , Duncker Dirk J. , Cheng Caroline 
Published: April 2017

Objective—

Decrease in VE-cadherin adherens junctions reduces vascular stability, whereas disruption of adherens junctions is a requirement for neovessel sprouting during angiogenesis. Endocytosis plays a key role in regulating junctional strength by altering bioavailability of cell surface proteins, including VE-cadherin. Identification of new mediators of endothelial endocytosis could enhance our understanding of angiogenesis. Here, we assessed the function of CMTM3 (CKLF-like MARVEL transmembrane domain 3), which we have previously identified as highly expressed in Flk1
+
endothelial progenitor cells during embryonic development.

Approach and Results—

Using a 3-dimensional coculture of human umbilical vein endothelial cells-GFP (green fluorescent protein) and pericytes-RFP (red fluorescent protein), we demonstrated that siRNA-mediated CMTM3 silencing in human umbilical vein endothelial cells impairs angiogenesis. In vivo CMTM3 inhibition by morpholino injection in developing zebrafish larvae confirmed that CMTM3 expression is required for vascular sprouting. CMTM3 knockdown in human umbilical vein endothelial cells does not affect proliferation or migration. Intracellular staining demonstrated that CMTM3 colocalizes with early endosome markers EEA1 (early endosome marker 1) and Clathrin
+
vesicles and with cytosolic VE-cadherin in human umbilical vein endothelial cells. Adenovirus-mediated CMTM3 overexpression enhances endothelial endocytosis, shown by an increase in Clathrin
+
, EEA1
+
, Rab11
+
, Rab5
+
, and Rab7
+
vesicles. CMTM3 overexpression enhances, whereas CMTM3 knockdown decreases internalization of cell surface VE-cadherin in vitro. CMTM3 promotes loss of endothelial barrier function in thrombin-induced responses, shown by transendothelial electric resistance measurements in vitro.

Conclusions—
In this study, we have identified a new regulatory function for CMTM3 in angiogenesis. CMTM3 is involved in VE-cadherin turnover and is a regulator of the cell surface pool of VE-cadherin. Therefore, CMTM3 mediates cell–cell adhesion at adherens junctions and contributes to the control of vascular sprouting.
Circulating Levels of Interleukin 1-Receptor Antagonist and Risk of Cardiovascular Disease
Authors: Herder Christian , de las Heras Gala Tonia , Carstensen-Kirberg Maren , Huth Cornelia , Zierer Astrid , Wahl Simone , Sudduth-Klinger Julie , Kuulasmaa Kari , Peretz David , Ligthart Symen , Bongaerts Brenda W.C. , Dehghan Abbas , Ikram M. Arfan , Jula Antti , Kee Frank , Pietilä Arto , Saarela Olli , Zeller Tanja , Blankenberg Stefan , Meisinger Christa , Peters Annette , Roden Michael , Salomaa Veikko , Koenig Wolfgang , Thorand Barbara 
Published: April 2017

Objective—
Interleukin (IL)-1β represents a key cytokine in the development of cardiovascular disease (CVD). IL-1β is counter-regulated by IL-1 receptor antagonist (IL-1RA), an endogenous inhibitor. This study aimed to identify population-based studies on circulating IL-1RA and incident CVD in a systematic review, estimate the association between IL-1RA and incident CVD in a meta-analysis, and to test whether the association between IL-1RA and incident CVD is explained by other inflammation-related biomarkers in the MONICA/KORA Augsburg case–cohort study (Multinational Monitoring of Trends and Determinants in Cardiovascular Disease/Cooperative Health Research in the Region of Augsburg).

Approach and Results—

We performed a systematic literature search and identified 5 cohort studies on IL-1RA and incident CVD in addition to the MONICA/KORA Augsburg case–cohort study for a meta-analysis based on a total of 1855 CVD cases and 18 745 noncases with follow-up times between 5 and 16 years. The pooled standardized hazard ratio (95% confidence interval) for incident CVD was 1.11 (1.06–1.17) after adjustment for age, sex, anthropometric, metabolic, and lifestyle factors (
P
<0.0001). There was no heterogeneity in effect sizes (I
2
=0%;
P
=0.88). More detailed analyses in the MONICA/KORA study showed that the excess risk for CVD was attenuated by ≥10% after additional separate adjustment for serum levels of high-sensitivity C-reactive protein, IL-6, myeloperoxidase, soluble E-selectin, or soluble intercellular adhesion molecule-1.

Conclusions—
Serum IL-1RA levels were positively associated with risk of CVD after adjustment for multiple confounders in a meta-analysis of 6 population-based cohorts. This association may at least partially reflect a response to triggers inducing subclinical inflammation, oxidative stress, and endothelial activation.
Thresholds for Ambulatory Blood Pressure Among African Americans in the Jackson Heart Study
Authors: Ravenell Joseph , Shimbo Daichi , Booth John N. , Sarpong Daniel F. , Agyemang Charles , Beatty Moody Danielle L. , Abdalla Marwah , Spruill Tanya M. , Shallcross Amanda J. , Bress Adam P. , Muntner Paul , Ogedegbe Gbenga 
Published: April 2017

Background:
Ambulatory blood pressure (BP) monitoring is the reference standard for out-of-clinic BP measurement. Thresholds for identifying ambulatory hypertension (daytime systolic BP [SBP]/diastolic BP [DBP] ≥135/85 mm Hg, 24-hour SBP/DBP ≥130/80 mm Hg, and nighttime SBP/DBP ≥120/70 mm Hg) have been derived from European, Asian, and South American populations. We determined BP thresholds for ambulatory hypertension in a US population-based sample of African American adults.

Methods:
We analyzed data from the Jackson Heart Study, a population-based cohort study comprised exclusively of African American adults (n=5306). Analyses were restricted to 1016 participants who completed ambulatory BP monitoring at baseline in 2000 to 2004. Mean SBP and DBP levels were calculated for daytime (10:00 am–8:00 pm), 24-hour (all available readings), and nighttime (midnight–6:00 am) periods, separately. Daytime, 24-hour, and nighttime BP thresholds for ambulatory hypertension were identified using regression- and outcome-derived approaches. The composite of a cardiovascular disease or an all-cause mortality event was used in the outcome-derived approach. For this latter approach, BP thresholds were identified only for SBP because clinic DBP was not associated with the outcome. Analyses were stratified by antihypertensive medication use.

Results:
Among participants not taking antihypertensive medication, the regression-derived thresholds for daytime, 24-hour, and nighttime SBP/DBP corresponding to clinic SBP/DBP of 140/90 mm Hg were 134/85 mm Hg, 130/81 mm Hg, and 123/73 mm Hg, respectively. The outcome-derived thresholds for daytime, 24-hour, and nighttime SBP corresponding to a clinic SBP ≥140 mm Hg were 138 mm Hg, 134 mm Hg, and 129 mm Hg, respectively. Among participants taking antihypertensive medication, the regression-derived thresholds for daytime, 24-hour, and nighttime SBP/DBP corresponding to clinic SBP/DBP of 140/90 mm Hg were 135/85 mm Hg, 133/82 mm Hg, and 128/76 mm Hg, respectively. The corresponding outcome-derived thresholds for daytime, 24-hour, and nighttime SBP were 140 mm Hg, 137 mm Hg, and 133 mm Hg, respectively, among those taking antihypertensive medication.

Conclusions:
On the basis of the outcome-derived approach for SBP and regression-derived approach for DBP, the following definitions for daytime, 24-hour, and nighttime hypertension corresponding to clinic SBP/DBP ≥140/90 mm Hg are proposed for African American adults: daytime SBP/DBP ≥140/85 mm Hg, 24-hour SBP/DBP ≥135/80 mm Hg, and nighttime SBP/DBP ≥130/75 mm Hg, respectively.
Toll-Like Receptor 4 Mediates Hemorrhagic Transformation After Delayed Tissue Plasminogen Activator Administration in In Situ Thromboembolic Stroke
Authors: García-Culebras Alicia , Palma-Tortosa Sara , Moraga Ana , García-Yébenes Isaac , Durán-Laforet Violeta , Cuartero Maria I. , de la Parra Juan , Barrios-Muñoz Ana L. , Díaz-Guzmán Jaime , Pradillo Jesús M. , Moro María A. , Lizasoain Ignacio 
Published: April 2017

Background and Purpose—
Hemorrhagic transformation is the main complication of revascularization therapies after stroke. Toll-like receptor 4 (TLR4) is implicated in cerebral damage and inflammation in stroke. This study was designed to determine the role of TLR4 in hemorrhagic transformation development after tissue plasminogen activator (tPA) administration.

Methods—

Mice expressing (TLR4
+/+
) or lacking functional TLR4 (TLR4
−
/−
) were subjected to middle cerebral artery occlusion using an in situ thromboembolic model by thrombin injection into the middle cerebral artery, and tPA (10 mg/kg) was administered 20 minutes or 3 hours after ischemia. Infarct size, hemorrhages, IgG extravasation, matrix metalloproteinase 9 expression, and neutrophil infiltration were assessed 24 hours after ischemia.

Results—

In TLR4
+/+
, early reperfusion (tPA at 20 minutes) resulted infarct volume, whereas late recanalization (tPA at 3 hours) did not modify lesion size and increased the rate of the most severe hemorrhages. In TLR4
−
/−
mice, both early and late reperfusion did not modify lesion size. Importantly, late tPA administration did not result in worse hemorrhages and in an increased bleeding area as occurred in TLR4
+/+
group. In TLR4
−
/−
animals, late reperfusion produced a lesser increase in matrix metalloproteinase 9 expression when compared with TLR4
+/+
animals.

Conclusions—
Our results demonstrate TLR4 involvement in hemorrhagic transformation induced by delayed tPA administration, very likely by increasing matrix metalloproteinase 9 expression.
Integrative Modeling of Prefrontal Cortex
Authors: Alexander William H. , Vassena Eliana , Deraeve James , Langford Zachary D. 
Published: April 2017

AbstractpFC is generally regarded as a region critical for abstract reasoning and high-level cognitive behaviors. As such, it has become the focus of intense research involving a wide variety of subdisciplines of neuroscience and employing a diverse range of methods. However, even as the amount of data on pFC has increased exponentially, it appears that progress toward understanding the general function of the region across a broad array of contexts has not kept pace. Effects observed in pFC are legion, and their interpretations are generally informed by a particular perspective or methodology with little regard with how those effects may apply more broadly. Consequently, the number of specific roles and functions that have been identified makes the region a very crowded place indeed and one that appears unlikely to be explained by a single general principle. In this theoretical article, we describe how the function of large portions of pFC can be accommodated by a single explanatory framework based on the computation and manipulation of error signals and how this framework may be extended to account for additional parts of pFC.
Foraging Value, Risk Avoidance, and Multiple Control Signals: How the Anterior Cingulate Cortex Controls Value-based Decision-making
Authors: Brown Joshua W. , Alexander William H. 
Published: April 2017

Abstract
Recent work on the role of the ACC in cognition has focused on choice difficulty, action value, risk avoidance, conflict resolution, and the value of exerting control among other factors. A main underlying question is what are the output signals of ACC, and relatedly, what is their effect on downstream cognitive processes? Here we propose a model of how ACC influences cognitive processing in other brain regions that choose actions. The model builds on the earlier Predicted Response Outcome model and suggests that ACC learns to represent specifically the states in which the potential costs or risks of an action are high, on both short and long timescales. It then uses those cost signals as a basis to bias decisions to minimize losses while maximizing gains. The model simulates both proactive and reactive control signals and accounts for a variety of empirical findings regarding value-based decision-making.