bluuebunny/crossref_metadata_2025_split huggingface dataset:
On an Irrelevant Regress
Authors: Avnur Yuval 
Published: April 2015

AbstractIn a recent article, Wilson argues that Cartesian Scepticism leads to a vicious regress that can only be stopped by rejecting Cartesian Scepticism. If she is right, Wilson has solved one of philosophy's enduring problems. However, her regress is irrelevant to Cartesian Scepticism. This is evident once the proposition that we should have doubts, the person who has doubts, and the person who thinks that we should have doubts are carefully distinguished.
Karyotype evolution in apomictic Boechera and the origin of the aberrant chromosomes
Authors: Mandáková Terezie , Schranz M. Eric , Sharbel Timothy F. , de Jong Hans , Lysak Martin A. 
Published: April 2015

SummaryChromosome rearrangements may result in both decrease and increase of chromosome numbers. Here we have used comparative chromosome painting (CCP) to reconstruct the pathways of descending and ascending dysploidy in the genus Boechera (tribe Boechereae, Brassicaceae). We describe the origin and structure of three Boechera genomes and establish the origin of the previously described aberrant Het and Del chromosomes found in Boechera apomicts with euploid (2n = 14) and aneuploid (2n = 15) chromosome number. CCP analysis allowed us to reconstruct the origin of seven chromosomes in sexual B. stricta and apomictic B. divaricarpa from the ancestral karyotype (n = 8) of Brassicaceae lineage I. Whereas three chromosomes (BS4, BS6, and BS7) retained their ancestral structure, five chromosomes were reshuffled by reciprocal translocations to form chromosomes BS1‐BS3 and BS5. The reduction of the chromosome number (from x = 8 to x = 7) was accomplished through the inactivation of a paleocentromere on chromosome BS5. In apomictic 2n = 14 plants, CCP identifies the largely heterochromatic chromosome (Het) being one of the BS1 homologues with the expansion of pericentromeric heterochromatin. In apomictic B. polyantha (2n = 15), the Het has undergone a centric fission resulting in two smaller chromosomes – the submetacentric Het′ and telocentric Del. Here we show that new chromosomes can be formed by a centric fission and can be fixed in populations due to the apomictic mode of reproduction.
Hedgehog signaling is activated in canine transitional cell carcinoma and contributes to cell proliferation and survival
Authors: Gustafson T. L. , Kitchell B. E. , Biller B. 
Published: April 2015

AbstractTransitional cell carcinoma (TCC) is the most commonly diagnosed tumor of the canine urinary system. Hedgehog (HH) signaling represents one possible novel therapeutic target, based on its recently identified central role in human urothelial carcinoma. The purpose of this study was to determine if HH mediators are expressed in canine TCC and the effect of inhibition of this pathway on cell growth and survival. HH pathway mediators were found to be expressed in five canine TCC cell lines. Indian HH was expressed in tumor cells in five canine bladder tumor tissues, but not in normal canine bladder tissue. Inhibition of HH signaling with cyclopamine and GANT61 led to significantly decreased cell proliferation but had a smaller effect on apoptosis. These results support future investigation of inhibitors of HH signaling in the treatment of canine TCC.
Oxygen demand of perfused heart preparations: how electromechanical function and inadequate oxygenation affect physiology and optical measurements
Authors: Kuzmiak‐Glancy Sarah , Jaimes Rafael , Wengrowski Anastasia M. , Kay Matthew W. 
Published: April 2015

New Findings

What is the topic of this review?
This review discusses how the function and electrophysiology of isolated perfused hearts are affected by oxygenation and energy utilization. The impact of oxygenation on fluorescence measurements in perfused hearts is also discussed.

What advances does it highlight?
Recent studies have illuminated the inherent differences in electromechanical function, energy utilization rate and oxygen requirements between the primary types of excised heart preparations. A summary and analysis of how these variables affect experimental results are necessary to elevate the physiological relevance of these approaches in order to advance the field of whole‐heart research.

The ex vivo perfused heart recreates important aspects of in vivo conditions to provide insight into whole‐organ function. In this review we discuss multiple types of ex vivo heart preparations, explain how closely each mimic in vivo function, and discuss how changes in electromechanical function and inadequate oxygenation of ex vivo perfused hearts may affect measurements of physiology. Hearts that perform physiological work have high oxygen demand and are likely to experience hypoxia when perfused with a crystalloid perfusate. Adequate myocardial oxygenation is critically important for obtaining physiologically relevant measurements, so when designing experiments the type of ex vivo preparation and the capacity of perfusate to deliver oxygen must be carefully considered. When workload is low, such as during interventions that inhibit contraction, oxygen demand is also low, which could dramatically alter a physiological response to experimental variables. Changes in oxygenation also alter the optical properties of cardiac tissue, an effect that may influence optical signals measured from both endogenous and exogenous fluorophores. Careful consideration of oxygen supply, working condition, and wavelengths used to acquire optical signals is critical for obtaining physiologically relevant measurements during ex vivo perfused heart studies.
Rethinking the Niche of Upper-Atmosphere Bacteria: Draft Genome Sequences of Bacillus aryabhattai C765 and Bacillus aerophilus C772, Isolated from Rice Fields
Authors: Ramos-Silva Paula , Brito Patrícia H. , Serrano Mónica , Henriques Adriano O. , Pereira-Leal José B. 
Published: April 2015

ABSTRACT

Here, we report two genome sequences of endospore-forming bacteria isolated from the rice fields of Comporta, Portugal, identified as
Bacillus aryabhattai
C765 and
Bacillus aerophilus
C772. Both species were previously identified in air samples from the upper atmosphere, but our findings suggest their presence in a wider range of environmental niches.
Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Myophage Mushroom
Authors: Tolen Tamra N. , Xie Yicheng , Hernandez Adriana C. , Kuty Everett Gabriel F. 
Published: April 2015

ABSTRACT

Salmonella enterica
serovar Typhimurium (
S
. Typhimurium) is a leading cause of foodborne illness worldwide. Over the past two decades, strains resistant to antibiotics have begun to emerge, highlighting the need for alternative treatment strategies such as bacteriophage therapy. Here, we present the complete genome of Mushroom, an
S
. Typhimurium myophage.
Genome Sequence of a Pseudomonas syringae pv. tabaci Strain, yuexi-1, Causing Wildfire Disease in Tobacco
Authors: Wang Tielin , Yang Yuwen , Zhao Tingchang 
Published: April 2015

ABSTRACT

We determined the draft genome sequence of the
Pseudomonas syringae
pv. tabaci strain yuexi-1. It was isolated from tobacco sample of yuexi-1, Sichuan province, China, by our laboratory. The genome contains 6,232,497 bp and has a G+C content of 58.2 mol%.
Genome Sequence of EU-Unauthorized Genetically Modified Bacillus subtilis Strain 2014-3557 Overproducing Riboflavin, Isolated from a Vitamin B2 80% Feed Additive
Authors: Barbau-Piednoir Elodie , De Keersmaecker Sigrid C. J. , Wuyts Véronique , Gau Céline , Pirovano Walter , Costessi Adalberto , Philipp Patrick , Roosens Nancy H. 
Published: April 2015

ABSTRACT

This paper announces the genome sequence and annotation of the genetically modified (GM)
Bacillus subtilis
strain 2014-3557 overproducing riboflavin (vitamin B2). This GM-strain is unauthorized in the European Union. Nevertheless, it has been isolated from a lot of vitamin B2 (riboflavin) 80% feed grade imported to Europe from China.
Complete Genome Sequence of a Novel Bacterium within the Family
Rhodocyclaceae
That Degrades Polycyclic Aromatic Hydrocarbons
Authors: Singleton David R. , Dickey Allison N. , Scholl Elizabeth H. , Wright Fred A. , Aitken Michael D. 
Published: April 2015

ABSTRACT

A polycyclic aromatic hydrocarbon-degrading bacterium designated strain Ca6, a member of the family
Rhodocyclaceae
and a representative of the uncharacterized pyrene group 1 (PG1), was isolated and its genome sequenced. The presence of several genes suspected to be associated with PG1 was confirmed, and additional genes for aromatic compound metabolism were detected.
Draft Genome Sequence of Shewanella sp. Strain CP20
Authors: Lutz Carla , Martin Tay Qi Xiang , Sun Shuyang , McDougald Diane 
Published: April 2015

ABSTRACT

Shewanella sp. CP20 is a marine bacterium that survives ingestion by
Tetrahymena pyriformis
and is expelled from the protozoan within membrane-bound vacuoles, where the bacterial cells show long-term survival. Here, we report the draft genome sequence of Shewanella sp. CP20 and discuss the potential mechanisms facilitating intraprotozoan survival.
Complete Genome Sequence of Methylobacterium aquaticum Strain 22A, Isolated from
Racomitrium japonicum
Moss
Authors: Tani Akio , Ogura Yoshitoshi , Hayashi Tetsuya , Kimbara Kazuhide 
Published: April 2015

ABSTRACT

Methylobacterium
species colonize plant surfaces and utilize methanol emitted from plants.
Methylobacterium aquaticum
strain 22A was isolated from a hydroponic culture of a moss,
Racomitrium japonicum
, and is a potent plant growth promoter. The complete genome sequencing of the strain confirmed the presence of genes related to plant growth promotion and methylotrophy.
Draft Genome Sequence of the Piezotolerant and Crude Oil-Degrading Bacterium Rhodococcus qingshengii Strain TUHH-12
Authors: Lincoln Sara A. , Hamilton Trinity L. , Valladares Juárez Ana Gabriela , Schedler Martina , Macalady Jennifer L. , Müller Rudolf , Freeman Katherine H. 
Published: April 2015

ABSTRACT

We report here the draft genome sequence of
Rhodococcus qingshengii
strain TUHH-12. The ability of this piezotolerant bacterium to grow on crude oil and tetracosane as sole carbon sources at 150 × 10
5
Pa makes it useful in studies of hydrocarbon degradation under simulated deep-sea conditions.
Complete Genome Sequence of a Carbapenem-Resistant Extraintestinal Pathogenic Escherichia coli Strain Belonging to the Sequence Type 131
H
30R Subclade
Authors: Johnson Timothy J. , Hargreaves Melissa , Shaw Kristin , Snippes Paula , Lynfield Ruth , Aziz Maliha , Price Lance B. 
Published: April 2015

ABSTRACT

Here, we report the completed genome sequence of a carbapenem-resistant extraintestinal pathogenic
Escherichia coli
sequence type 131 (ST131) isolate, MNCRE44. The isolate was obtained in 2012 in Minnesota, USA, from a sputum sample from a hospitalized patient with multiple comorbidities, and it belongs to the
H
30R sublineage.
Genome Resequencing of the Virulent and Multidrug-Resistant Reference Strain Clostridium difficile 630
Authors: Riedel Thomas , Bunk Boyke , Thürmer Andrea , Spröer Cathrin , Brzuszkiewicz Elzbieta , Abt Birte , Gronow Sabine , Liesegang Heiko , Daniel Rolf , Overmann Jörg 
Published: April 2015

ABSTRACT

We resequenced the complete genome of the virulent and multidrug-resistant pathogen
Clostridium difficile
strain 630. A combination of single-molecule real-time and Illumina sequencing technology revealed the presence of an additional rRNA gene cluster, additional tRNAs, and the absence of a transposon in comparison to the published and reannotated genome sequence.
Draft Genome Sequence of the First Hypermucoviscous Klebsiella variicola Clinical Isolate
Authors: Garza-Ramos Ulises , Silva-Sanchez Jesus , Barrios Humberto , Rodriguez-Medina Nadia , Martínez-Barnetche Jesus , Andrade Veronica 
Published: April 2015

ABSTRACT

An antibiotic-susceptible and hypermucoviscous clinical isolate of
Klebsiella variicola
(
K. variicola
8917) was obtained from the sputum of an adult patient. This work reports the complete draft genome sequence of
K. variicola
8917 with 103 contigs and an annotation that revealed a 5,686,491-bp circular chromosome containing a total of 5,621 coding DNA sequences, 65 tRNA genes, and an average G+C content of 56.98%.
Complete Genome Sequence of an American Avian Leukosis Virus Subgroup J Isolate That Causes Hemangiomas and Myeloid Leukosis
Authors: Malhotra Sanandan , Justice James , Lee Nathan , Li Yingying , Zavala Guillermo , Ruano Miguel , Morgan Robin , Beemon Karen 
Published: April 2015

ABSTRACT
We report the complete genome sequence of avian leukosis virus subgroup J (ALV-J) isolate PDRC-59831, which causes myeloid leukosis and hemangiomas in chickens. This is an American ALV-J isolate, which was found in a 38-week-old broiler breeder chicken on a farm in Georgia in 2007.
Monitoring for proteinuria in patients with type 2 diabetes mellitus
Authors: Liang Huifang , Kennedy Caroline , Manne Sudhakar , Lin Jennifer Hsiang-Ling , Dolin Paul 
Published: April 2015

ObjectiveThe UK National Institute for Health and Care Excellence (NICE) guideline on diabetes recommends at least annual monitoring of patients with type 2 diabetes mellitus (T2DM) for proteinuria. To date, little has been published on the frequency of proteinuria monitoring in T2DM, and its association with risk factors for renal complications. We aimed to describe proteinuria monitoring in patients with T2DM.DesignThis study identified patients with T2DM aged 40 years or older with the first antidiabetic drug use in 2007–2012 (cohort entry) in the UK Clinical Practice Research Datalink. At least 1 year of registration before and after cohort entry was required. A test was considered undertaken if a medical or laboratory code indicated a urinary albumin or protein test. The percentage of patients with at least one test performed was obtained in 1 year after cohort entry and any time during follow-up. A Cox proportional hazards model was used to estimate the HRs of patients having the first screening test while adjusting for baseline covariates.Results65 790 patients (mean age 63.0 years, men 57.5%, mean follow-up 41.0 months) were included, of whom 49 707 (75.6%) patients had at least one test in 1 year after antidiabetic drug initiation and 59 400 (90.3%) had at least one test any time during follow-up. Proteinuria monitoring decreased with time since initiation of antidiabetic drug therapy and with number of treatment changes and was independently associated with age, sex, smoking status, and year of antidiabetic drug initiation. 12.3% of patients with T2DM tested had a positive proteinuria test for the first screening performed in 1 year after initiation of antidiabetic drug therapy.ConclusionsThe findings suggested suboptimal compliance with the NICE guideline on proteinuria monitoring in patients with T2DM and that level of monitoring appeared to depend on multiple clinical factors.
Republished: A straightforward guide to the basic science behind arrhythmogenesis
Authors: Dumotier Berengere M 
Published: April 2015

ABSTRACT
The underlying mechanisms behind cardiac arrhythmias are described in this manuscript. In clinical practice, significant arrhythmias are unpredictable, and under some conditions, potentially life-threatening. How can basic science help improve our understanding of molecular entities and factors behind the arrhythmia to advance, develop, adapt or deliver available medications? Structural heart disease and remodelling (eg, heart failure, cardiomyopathy), the presence of modulating factors (ie, diabetes mellitus, autonomic nervous system), genetic predispositions (ie, channelopathies) are considerable preconditions, and influence the development of an arrhythmia. Cardiac arrhythmias may indeed share common basic mechanisms, while elements and substrates perpetuating these may be different and ultimately manifest as various ECG abnormalities. This article lists cellular and subcellular iatrogenic disorders responsible for abnormal impulse generation, or conduction disturbances, including the latest development in theories and biological research, for a better understanding of cellular disorders behind arrhythmogenesis.
Enterectomy for treatment of small intestinal segmental volvulus secondary to dietary obstruction in a dog
Authors: Allan Ross M 
Published: April 2015

A four‐year‐old 32 kg neutered female golden retriever dog presented with a two‐day history of intermittent vomiting, inappetence and lethargy whilst fed an exclusively bones and raw food diet. Clinical examination and radiography was consistent with intestinal obstruction, while biochemical and haematological samples were unremarkable. The dog recovered well after exploratory coeliotomy at which segmental small intestinal volvulus involving the jejunum was diagnosed and successfully managed with enterectomy. The presentation of segmental volvulus was atypical in this case due to its insidious onset in contrast to the dramatic findings at coeliotomy. Whilst segmental volvulus in the dog is a rare occurrence, this case serves to increase the description of its clinical onset as well as suggesting a likely dietary contribution in its occurrence.
miR-25 Modulates Invasiveness and Dissemination of Human Prostate Cancer Cells via Regulation of αv- and α6-Integrin Expression
Authors: Zoni E. , van der Horst G. , van de Merbel A.F. , Chen L. , Rane J.K. , Pelger R.C.M. , Collins A.T. , Visakorpi T. , Snaar-Jagalska B.E. , Maitland N.J. , van der Pluijm G. 
Published: April 2015

Abstract
Altered microRNA (miRNA; miR) expression is associated with tumor formation and progression of various solid cancers. A major challenge in miRNA expression profiling of bulk tumors is represented by the heterogeneity of the subpopulations of cells that constitute the organ, as well as the tumor tissue. Here, we analyzed the expression of miRNAs in a subpopulation of epithelial stem/progenitor-like cells in human prostate cancer [prostate cancer stem cell (PCSC)] and compared their expression profile to more differentiated cancer cells. In both cell lines and clinical prostate cancer specimens, we identified that miR-25 expression in PCSCs was low/absent and steadily increased during their differentiation into cells with a luminal epithelial phenotype. Functional studies revealed that overexpression of miR-25 in prostate cancer cell lines and selected subpopulation of highly metastatic and tumorigenic cells (ALDHhigh) strongly affected the invasive cytoskeleton, causing reduced migration in vitro and metastasis via attenuation of extravasation in vivo. Here, we show, for the first time, that miR-25 can act as a tumor suppressor in highly metastatic PCSCs by direct functional interaction with the 3′-untranslated regions of proinvasive αv- and α6-integrins. Taken together, our observations suggest that miR-25 is a key regulator of invasiveness in human prostate cancer through its direct interactions with αv- and α6-integrin expression. Cancer Res; 75(11); 2326–36. ©2015 AACR.
Lin28B/Let-7 Regulates Expression of Oct4 and Sox2 and Reprograms Oral Squamous Cell Carcinoma Cells to a Stem-like State
Authors: Chien Chian-Shiu , Wang Mong-Lien , Chu Pen-Yuan , Chang Yuh-Lih , Liu Wei-Hsiu , Yu Cheng-Chia , Lan Yuan-Tzu , Huang Pin-I. , Lee Yi-Yen , Chen Yi-Wei , Lo Wen-Liang , Chiou Shih-Hwa 
Published: April 2015

Abstract
Lin28, a key factor for cellular reprogramming and generation of induced pluripotent stem cell (iPSC), makes a critical contribution to tumorigenicity by suppressing Let-7. However, it is unclear whether Lin28 is involved in regulating cancer stem–like cells (CSC), including in oral squamous carcinoma cells (OSCC). In this study, we demonstrate a correlation between high levels of Lin28B, Oct4, and Sox2, and a high percentage of CD44+ALDH1+ CSC in OSCC. Ectopic Lin28B expression in CD44−ALDH1−/OSCC cells was sufficient to enhance Oct4/Sox2 expression and CSC properties, whereas Let7 co-overexpression effectively reversed these phenomena. We identified ARID3B and HMGA2 as downstream effectors of Lin28B/Let7 signaling in regulating endogenous Oct4 and Sox2 expression. Let7 targeted the 3′ untranslated region of ARID3B and HMGA2 and suppressed their expression, whereas ARID3B and HMGA2 increased the transcription of Oct4 and Sox2, respectively, through promoter binding. Chromatin immunoprecipitation assays revealed a direct association between ARID3B and a specific ARID3B-binding sequence in the Oct4 promoter. Notably, by modulating Oct4/Sox2 expression, the Lin28B–Let7 pathway not only regulated stemness properties in OSCC but also determined the efficiency by which normal human oral keratinocytes could be reprogrammed to iPSC. Clinically, a Lin28Bhigh-Let7low expression pattern was highly correlated with high levels of ARID3B, HMGA2, OCT4, and SOX2 expression in OSCC specimens. Taken together, our results show how Lin28B/Let7 regulates key cancer stem–like properties in oral squamous cancers. Cancer Res; 75(12); 2553–65. ©2015 AACR.
Hepcidin Regulation in Prostate and Its Disruption in Prostate Cancer
Authors: Tesfay Lia , Clausen Kathryn A. , Kim Jin Woo , Hegde Poornima , Wang Xiaohong , Miller Lance D. , Deng Zhiyong , Blanchette Nicole , Arvedson Tara , Miranti Cindy K. , Babitt Jodie L. , Lin Herbert Y. , Peehl Donna M. , Torti Frank M. , Torti Suzy V. 
Published: April 2015

Abstract
Hepcidin is a circulating peptide hormone made by the liver that is a central regulator of systemic iron uptake and recycling. Here, we report that prostate epithelial cells also synthesize hepcidin, and that synthesis and secretion of hepcidin are markedly increased in prostate cancer cells and tissue. Prostatic hepcidin functions as an autocrine hormone, decreasing cell surface ferroportin, an iron exporter, increasing intracellular iron retention, and promoting prostate cancer cell survival. Synthesis of hepcidin in prostate cancer is controlled by a unique intersection of pathways that involves BMP4/7, IL6, Wnt, and the dual BMP and Wnt antagonist, SOSTDC1. Epigenetic silencing of SOSTDC1 through methylation is increased in prostate cancer and is associated with accelerated disease progression in patients with prostate cancer. These results establish a new connection between iron metabolism and prostate cancer, and suggest that prostatic dysregulation of hepcidin contributes to prostate cancer growth and progression. Cancer Res; 75(11); 2254–63. ©2015 AACR.