bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequences of Klebsiella pneumoniae Clinical Type Strain ATCC 13883 and Three Multidrug-Resistant Clinical Isolates
Authors: Arivett Brock A. , Ream David C. , Fiester Steven E. , Mende Katrin , Murray Clinton K. , Thompson Mitchell G. , Kanduru Shrinidhi , Summers Amy M. , Roth Amanda L. , Zurawski Daniel V. , Actis Luis A. 
Published: January 2015

ABSTRACT

Klebsiella pneumoniae
is a Gram-negative human pathogen capable of causing hospital-acquired infections with an increasing risk to human health. The total DNA from four clinically relevant strains was sequenced to >100× coverage, providing high-quality genome assemblies for
K. pneumoniae
strains ATCC 13883, KP4640, 101488, and 101712.
Draft Genome Sequence of the Cyanobacterium Aphanizomenon flos-aquae Strain 2012/KM1/D3, Isolated from the Curonian Lagoon (Baltic Sea)
Authors: Šulčius Sigitas , Alzbutas Gediminas , Kvederavičiūtė Kotryna , Koreivienė Judita , Zakrys Linas , Lubys Arvydas , Paškauskas Ričardas 
Published: January 2015

ABSTRACT

We report here the
de novo
genome assembly of a cyanobacterium, Aphanizomenon flos-aquae strain 2012/KM1/D3, a harmful bloom-forming species in temperate aquatic ecosystems. The genome is 5.7 Mb with a G+C content of 38.2%, and it is enriched mostly with genes involved in amino acid and carbohydrate metabolism.
Complete Genome Sequence of Listeria monocytogenes NTSN, a Serovar 4b and Animal Source Strain
Authors: Tan Weijun , Wang Guoliang , Pan Zhiming , Yin Yuelan , Jiao Xin’an 
Published: January 2015

ABSTRACT

Listeria monocytogenes
is an important foodborne pathogen that causes infections in humans and animals and has a high mortality rate. The complete genome sequence of
L. monocytogenes
strain NTSN, a highly virulent and serovar 4b strain isolated from the brains of sheep in Jiangsu Province, China, is presented here.
Complete Genome Sequence of a Newcastle Disease Virus Isolate from an Outbreak in Central India
Authors: Gogoi Polakshee , Morla Sudhir , Kaore Megha , Kurkure Nitin Vasantrao , Kumar Sachin 
Published: January 2015

ABSTRACT
The complete genome sequence of a Newcastle disease virus (NDV) strain NDV/Chicken/Nagpur/01/12 was isolated from vaccinated chicken farms in India during outbreaks in 2012. The genome is 15,192 nucleotides in length and is classified as genotype VII in class II.
Draft Genome Sequence of Robinsoniella peoriensis Strain WTD, Isolated from the Fecal Material of a Wood Turtle
Authors: Braasch Jeanna L. , Lapin Carly N. , Dowd Scot E. , McLaughlin Richard W. 
Published: January 2015

ABSTRACT

Here, we report the draft genome of
Robinsoniella peoriensis
strain WTD, which was isolated from the fecal material of a wood turtle. The genome size was 7,391,415 bp with 41.1 mol% G+C.
Average Case and Distributional Analysis of Dual-Pivot Quicksort
Authors: Wild Sebastian , Nebel Markus E. , Neininger Ralph 
Published: January 2015

In 2009, Oracle replaced the long-serving sorting algorithm in its Java 7 runtime library by a new dual-pivot Quicksort variant due to Vladimir Yaroslavskiy. The decision was based on the strikingly good performance of Yaroslavskiy's implementation in running time experiments. At that time, no precise investigations of the algorithm were available to explain its superior performance—on the contrary: previous theoretical studies of other dual-pivot Quicksort variants even discouraged the use of two pivots. In 2012, two of the authors gave an average case analysis of a simplified version of Yaroslavskiy's algorithm, proving that savings in the number of comparisons are possible. However, Yaroslavskiy's algorithm needs more swaps, which renders the analysis inconclusive.
To force the issue, we herein extend our analysis to the fully detailed style of Knuth: we determine the exact number of executed Java Bytecode instructions. Surprisingly, Yaroslavskiy's algorithm needs sightly more Bytecode instructions than a simple implementation of classic Quicksort—contradicting observed running times. As in Oracle's library implementation, we incorporate the use of Insertionsort on small subproblems and show that it indeed speeds up Yaroslavskiy's Quicksort in terms of Bytecodes; but even with optimal Insertionsort thresholds, the new Quicksort variant needs slightly more Bytecode instructions on average.

Finally, we show that the (suitably normalized) costs of Yaroslavskiy's algorithm converge to a random variable whose distribution is characterized by a fixed-point equation. From that, we compute variances of costs and show that for large
n
, costs are concentrated around their mean.
The Complexity of the Nucleolus in Compact Games
Authors: Greco Gianluigi , Malizia Enrico , Palopoli Luigi , Scarcello Francesco 
Published: January 2015

The nucleolus is a well-known solution concept for coalitional games to fairly distribute the total available worth among the players. The nucleolus is known to be
NP
-hard to compute over compact coalitional games, that is, over games whose functions specifying the worth associated with each coalition are encoded in terms of polynomially computable functions over combinatorial structures. In particular, hardness results have been exhibited over minimum spanning tree games, threshold games, and flow games. However, due to its intricate definition involving reasoning over exponentially many coalitions, a nontrivial upper bound on its complexity was missing in the literature and looked for.

This article faces this question and precisely characterizes the complexity of the nucleolus, by exhibiting an upper bound that holds on any class of compact games, and by showing that this bound is tight even on the (structurally simple) class of graph games. The upper bound is established by proposing a variant of the standard linear-programming based algorithm for nucleolus computation and by studying a framework for reasoning about succinctly specified linear programs, which are contributions of interest in their own. The hardness result is based on an elaborate combinatorial reduction, which is conceptually relevant for it provides a “measure” of the computational cost to be paid for guaranteeing voluntary participation to the distribution process. In fact, the pre-nucleolus is known to be efficiently computable over graph games, with this solution concept being defined as the nucleolus but without guaranteeing that each player is granted with it at least the worth she can get alone, that is, without collaborating with the other players.
Finally, this article identifies relevant tractable classes of coalitional games, based on the notion of type of a player. Indeed, in most applications where many players are involved, it is often the case that such players do belong in fact to a limited number of classes, which is known in advance and may be exploited for computing the nucleolus in a fast way.
ViFi
Authors: Guo Katherine , Sanadhya Shruti , Woo Thomas 
Published: January 2015

We consider an architecture in which the same WiFi infrastructure can be dynamically shared among multiple operators. Our system, ViFi, virtualizes WLAN resources, allowing for controlled sharing of both the uplink and downlink bandwidth. ViFi operates with stock 802.11 clients, and can be implemented entirely as a software add-on for commodity 802.11 APs.
ViFi puts users (customers) of different operators in separate groups, each creating a virtual WLAN. ViFi guarantees proportional fair share of channel access time at group level, and isolates traffic between groups. The key technical contribution of ViFi is a useful form of virtualization without requiring changes to the underlying WiFi protocol.
Long Noncoding RNA HULC Modulates Abnormal Lipid Metabolism in Hepatoma Cells through an miR-9–Mediated RXRA Signaling Pathway
Authors: Cui Ming , Xiao Zelin , Wang Yue , Zheng Minying , Song Tianqiang , Cai Xiaoli , Sun Baodi , Ye Lihong , Zhang Xiaodong 
Published: January 2015

Abstract
HULC is a long noncoding RNA overexpressed in hepatocellular carcinoma (HCC), but its functional contributions in this setting have not been determined. In this study, we explored the hypothesis that HULC contributes to malignant development by supporting abnormal lipid metabolism in hepatoma cells. HULC modulated the deregulation of lipid metabolism in HCC by activating the acyl-CoA synthetase subunit ACSL1. Immunohistochemical analysis of tissue microarrays revealed that approximately 77% (180/233) of HCC tissues were positive for ACSL1. Moreover, HULC mRNA levels correlated positively with ACSL1 levels in 60 HCC cases according to real-time PCR analysis. Mechanistic investigations showed that HULC upregulated the transcriptional factor PPARA, which activated the ACSL1 promoter in hepatoma cells. HULC also suppressed miR-9 targeting of PPARA mRNA by eliciting methylation of CpG islands in the miR-9 promoter. We documented the ability of HULC to promote lipogenesis, thereby stimulating accumulation of intracellular triglycerides and cholesterol in vitro and in vivo. Strikingly, ACSL1 overexpression that generates cholesterol was sufficient to enhance the proliferation of hepatoma cells. Further, cholesterol addition was sufficient to upregulate HULC expression through a positive feedback loop involving the retinoid receptor RXRA, which activated the HULC promoter. Overall, we concluded that HULC functions as an oncogene in hepatoma cells, acting mechanistically by deregulating lipid metabolism through a signaling pathway involving miR-9, PPARA, and ACSL1 that is reinforced by a feed-forward pathway involving cholesterol and RXRA to drive HULC signaling. Cancer Res; 75(5); 846–57. ©2015 AACR.
Improvements in Radiographic Progression-Free Survival Stratified by ERG Gene Status in Metastatic Castration-Resistant Prostate Cancer Patients Treated with Abiraterone Acetate
Authors: Attard Gerhardt , de Bono Johann S. , Logothetis Christopher J. , Fizazi Karim , Mukherjee Som D. , Joshua Anthony M. , Schrijvers Dirk , van den Eertwegh Alfons J.M. , Li Weimin , Molina Arturo , Griffin Thomas W. , Kheoh Thian , Ricci Deborah S. , Zelinsky Kathy , Rathkopf Dana E. , Scher Howard I. , Ryan Charles J. 
Published: January 2015

Abstract
Purpose: Gene fusions leading to androgen receptor–modulated ERG overexpression occur in up to 70% of metastatic castration-resistant prostate cancers (mCRPC). We assessed the association between ERG rearrangement status and clinical benefit from abiraterone acetate.
Experimental Design: COU-AA-302 is a phase III trial comparing abiraterone acetate and prednisone versus prednisone in chemotherapy-naïve mCRPC. ERG status was evaluated by FISH on archival tumors. End points included radiographic progression-free survival (rPFS), time to PSA progression (TTPP), rate of ≥50% PSA decline from baseline, and overall survival (OS). Cox regression was used to evaluate association with time-to-event measures and Cochran–Mantel–Haenszel for PSA response.
Results: ERG status was defined for 348 of 1,088 intention-to-treat patients. ERG was rearranged in 121 of 348 patients with confirmed ERG status (35%). Cancers with an ERG fusion secondary to deletion of 21q22 and increased copy number of fusion sequences (class 2+ Edel) had a greater improvement in rPFS after abiraterone acetate and prednisone [22 vs. 5.4 months; HR (95% confidence interval, CI), 0.31 (0.15–0.68); P = 0.0033] than cancers with no ERG fusion [16.7 vs. 8.3 months; 0.53 (0.38–0.74); P = 0.0002] or other classes of ERG rearrangement. There was also greater benefit in this subgroup for TTPP.
Conclusions: Both ERG-rearranged and wild-type cancers had a significant improvement in rPFS with abiraterone acetate and prednisone in the COU-AA-302 trial. However, our data suggest that 2+ Edel cancers, accounting for 15% of all mCRPC patients and previously associated with a worse outcome, derived the greatest benefit. Clin Cancer Res; 21(7); 1621–7. ©2015 AACR.
Hedgehog Pathway Inhibitors Promote Adaptive Immune Responses in Basal Cell Carcinoma
Authors: Otsuka Atsushi , Dreier Jil , Cheng Phil F. , Nägeli Mirjam , Lehmann Holger , Felderer Lea , Frew Ian J. , Matsushita Shigeto , Levesque Mitchell P. , Dummer Reinhard 
Published: January 2015

AbstractPurpose: Basal cell carcinomas (BCCs) are tumors ignored by immune surveillance. Activated Hedgehog (Hh) signaling within primary cilia is a key driver in the pathogenesis of BCCs. We examined immune alterations during treatment with systemic Hh inhibitors.Experimental Design: We investigated biopsies from patients with BCC before (23 patients) and after 4 weeks of treatment (5 patients) with Hh signaling inhibitor. Ber-Ep4, BCL-2, Ki-67, CD4, CD8, MHC class I, HLA-DR-class II, and SOX9 were analyzed by immunohistochemistry. Primary cilia were analyzed by double immunofluorescence of acetylated tubulin and SOX9. Differential gene expression for 84 cytokines and chemokines was analyzed in 3 patients.Results: After 4 weeks of treatment, we found reduction of Ki-67, SOX9, Ber-EP4, and BCL-2 expression in tumors associated with morphologic signs of squamous differentiation. In addition, the number of cilia-positive BCC cells was significantly decreased. An upregulation of MHC I expression on the cell membranes of residual tumor cells and an influx of CD4+, HLA-DR-class II+, and CD8+ cells with invasion into the tumor cell nests were found. Finally, qPCR arrays showed the differential expression of genes involved in modulating immune responses.Conclusions: We show that Hh pathway inhibitor–induced tumor regression is accompanied by a dynamic change of the microenvironment with a disruption of immune privilege involving an influx of cytotoxic T cells, activation of the adaptive immune functions, and a profound alteration of the local chemokine/cytokine network. Clin Cancer Res; 21(6); 1289–97. ©2015 AACR.
Vascular Smooth Muscle Cell Phenotypic Changes in Patients With Marfan Syndrome
Authors: Crosas-Molist Eva , Meirelles Thayna , López-Luque Judit , Serra-Peinado Carla , Selva Javier , Caja Laia , Gorbenko del Blanco Darya , Uriarte Juan José , Bertran Esther , Mendizábal Yolanda , Hernández Vanessa , García-Calero Carolina , Busnadiego Oscar , Condom Enric , Toral David , Castellà Manel , Forteza Alberto , Navajas Daniel , Sarri Elisabet , Rodríguez-Pascual Fernando , Dietz Harry C. , Fabregat Isabel , Egea Gustavo 
Published: January 2015

Objective—
Marfan’s syndrome is characterized by the formation of ascending aortic aneurysms resulting from altered assembly of extracellular matrix microfibrils and chronic tissue growth factor (TGF)-β signaling. TGF-β is a potent regulator of the vascular smooth muscle cell (VSMC) phenotype. We hypothesized that as a result of the chronic TGF-β signaling, VSMC would alter their basal differentiation phenotype, which could facilitate the formation of aneurysms. This study explores whether Marfan’s syndrome entails phenotypic alterations of VSMC and possible mechanisms at the subcellular level.

Approach and Results—
Immunohistochemical and Western blotting analyses of dilated aortas from Marfan patients showed overexpression of contractile protein markers (α-smooth muscle actin, smoothelin, smooth muscle protein 22 alpha, and calponin-1) and collagen I in comparison with healthy aortas. VSMC explanted from Marfan aortic aneurysms showed increased in vitro expression of these phenotypic markers and also of myocardin, a transcription factor essential for VSMC-specific differentiation. These alterations were generally reduced after pharmacological inhibition of the TGF-β pathway. Marfan VSMC in culture showed more robust actin stress fibers and enhanced RhoA-GTP levels, which was accompanied by increased focal adhesion components and higher nuclear localization of myosin-related transcription factor A. Marfan VSMC and extracellular matrix measured by atomic force microscopy were both stiffer than their respective controls.

Conclusions—
In Marfan VSMC, both in tissue and in culture, there are variable TGF-β-dependent phenotypic changes affecting contractile proteins and collagen I, leading to greater cellular and extracellular matrix stiffness. Altogether, these alterations may contribute to the known aortic rigidity that precedes or accompanies Marfan’s syndrome aneurysm formation.
Maternal High-Fat Diet Exaggerates Atherosclerosis in Adult Offspring by Augmenting Periaortic Adipose Tissue-Specific Proinflammatory Response
Authors: Wakana Noriyuki , Irie Daisuke , Kikai Masakazu , Terada Kensuke , Yamamoto Keita , Kawahito Hiroyuki , Kato Taku , Ogata Takehiro , Ueyama Tomomi , Matoba Satoaki , Yamada Hiroyuki 
Published: January 2015

Objective—
Maternal obesity elicits offspring’s metabolic disorders via developmental modifications of visceral adipose tissue; however, its effect on atherogenesis remains undefined. Perivascular adipose tissue has recently been implicated in vascular remodeling and vasoreactivity. We hypothesize that developmental modifications of perivascular adipose tissue by maternal high-fat diet (HFD) exposure promotes atherosclerosis in adult offspring.

Approach and Results—

Eight-week-old female apolipoprotein E-deficient mice were fed an HFD or normal diet (ND) during gestation and lactation. Offspring were fed a high-cholesterol diet from 8 weeks of age. Twenty-week-old male offspring of HFD-fed dams (O-HFD) showed a 2.1-fold increase in atherosclerotic lesion of the entire aorta compared with those of ND-fed dams (O-ND). Although mRNA expressions of interleukin-6, tumor necrosis factor, and monocyte chemotactic protein-1 and accumulation of macrophages in epididymal white adipose tissue were less in O-HFD than in O-ND, thoracic periaortic adipose tissue (tPAT) showed an exaggerated inflammatory response in O-HFD. Intra-abdominal transplantation of tPAT from 8-week-old O-HFD alongside the distal abdominal aorta exaggerated atherosclerosis development of the infrarenal aorta in recipient apolipoprotein E-deficient mice compared with tPAT from O-ND (210%,
P
<0.01). Although macrophage accumulation was rarely detected in tPAT of 8-week-old offspring, mRNA expression and protein levels of macrophage colony–stimulating factor were markedly elevated in O-HFD (2.3-fold, 3.3-fold, respectively,
P
<0.05), suggesting that increased macrophage colony–stimulating factor expression contributes to the augmented accumulation of macrophages, followed by the enhanced proinflammatory response.

Conclusions—
Our findings demonstrate that maternal HFD exaggerates atherosclerosis development in offspring by augmenting tPAT-specific inflammatory response proceeded by an increased expression of macrophage colony–stimulating factor.
Left Atrial Remodeling and Function in Advanced Heart Failure With Preserved or Reduced Ejection Fraction
Authors: Melenovsky Vojtech , Hwang Seok-Jae , Redfield Margaret M. , Zakeri Rosita , Lin Grace , Borlaug Barry A. 
Published: January 2015

Background—
Left atrial (LA) structure and function are altered in most heart failure (HF) patients, but there may be fundamental differences in LA properties between HF with preserved (HFpEF) and reduced ejection fraction (HFrEF).

Methods and Results—

One hundred ninety-eight HF patients (51% HFpEF, New York Heart Association 3.1±0.7) and 40 HF-free controls underwent catheterization, echocardiography, and follow-up. Compared with controls, HF patients had larger and more dysfunctional left atria. At identical mean LA pressure (20 versus 20 mm Hg;
P
=0.9), HFrEF patients had larger LA volumes (LA volume index 50 versus 41 mL/m
2
;
P
<0.001), whereas HFpEF patients had higher LA peak pressures, lower LA minimal pressures, higher LA stiffness (0.79 versus 0.48 mm Hg/mL;
P
<0.001), greater LA pulsatility (19 versus 13 mm Hg;
P
<0.001), and higher wall stress variations. Despite smaller LA volumes, better function, and less mitral regurgitation, HFpEF patients had more atrial fibrillation (42 versus 26%;
P
=0.02). LA dysfunction was associated with increased pulmonary vascular resistance and right ventricular dysfunction in both HF phenotypes. After a median follow-up of 350 days, 31 HFpEF and 28 HFrEF patients died. LA function (total LA EF) was associated with lower mortality in HFpEF (hazard ratio 0.43; 95% confidence interval, 0.2–0.9;
P
<0.05), but not in HFrEF.

Conclusions—
HFrEF is characterized by greater eccentric LA remodeling, whereas HFpEF by increased LA stiffness, which might contribute to greater atrial fibrillation burden. LA function is associated with pulmonary vascular disease and right HF in both HF phenotypes, but is associated with outcome more closely in HFpEF, supporting efforts to improve LA function in this cohort.
Evaluation of Renal Function Before and After Percutaneous Mitral Valve Repair
Authors: Wang Andrew , Sangli Chithra , Lim Scott , Ailawadi Gorav , Kar Saibal , Herrmann Howard C. , Grayburn Paul , Foster Elyse , Weissman Neil J. , Glower Donald , Feldman Ted 
Published: January 2015

Background—
Chronic kidney disease (CKD) is strongly related to outcome in cardiovascular diseases. The relationship between treatment of mitral regurgitation (MR) and renal function is not well described. We sought to evaluate renal function before and after mitral valve repair by the MitraClip device.

Methods and Results—

Patients with moderate-to-severe or severe (3+ or 4+, respectively) MR by core laboratory determination who underwent transcatheter mitral valve repair with the MitraClip device in multicenter, investigational trials were included in this study. Estimated glomerular filtration rate (eGFR) was evaluated before and at hospital discharge, 30 days, 6 months, and 1 year after mitral valve repair. Eight hundred fifty-four patients with baseline mean eGFR 61.5±23.1 mL/min/1.73 m
2
were studied, including 438 (51.3%) with eGFR ≥60 mL/min/1.73 m
2
(CKD stage 1 or 2), 371 (42.6%) with eGFR 30 to 59 mL/min/1.73 m
2
(CKD stage 3), and 52 (6.1%) with eGFR <30 mL/min/1.73 m
2
(CKD stage 4 or 5). Baseline renal dysfunction was more prevalent in older patients with a history of heart failure, coronary artery disease, cerebrovascular disease, diabetes mellitus, hypertension, and atrial fibrillation. Baseline eGFR was associated with 1-year survival (
P
<0.001) after MitraClip repair. At 1-year follow-up, the mean change in eGFR for the overall cohort was −1.0±15.1 mL/min/1.73 m
2
; for patients with CKD stage 1 or 2, stage 3, or stage 4 or 5, mean change was −4.1±16.6, +2.6±12.4, and +4.8±9.5 mL/min/1.73 m
2
, respectively. Linear mixed effect modeling demonstrated a strong association between MR and eGFR, and a statistically significant improvement in eGFR in patients with CKD stage 4 or 5 associated with MR reduction to ≤2+ (
P
=0.007).

Conclusions—
Renal dysfunction is associated with lower survival in patients with severe MR even after percutaneous mitral valve repair. Reduction in MR severity by the MitraClip device is associated with improvement in renal function at 1 year in patients with baseline renal dysfunction.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifiers: NCT00209274, NCT01931956, NCT01940120.