bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genome sequence of acute viral necrosis virus associated with massive mortality outbreaks in the Chinese scallop, Chlamys farreri
Authors: Ren Weicheng , Chen Haixia , Renault Tristan , Cai Yuyong , Bai Changming , Wang Chongming , Huang Jie 
Published: April 2013

Abstract

Background
Acute viral necrosis virus (AVNV) is the causative agent of a serious disease resulting in high mortality in cultured Chinese scallops, Chlamys farreri. We have sequenced and analyzed the complete genome of AVNV.

Results
The AVNV genome is a linear, double-stranded DNA molecule of 210,993 bp with a nucleotide composition of 38.5% G + C. A total of 123 open reading frames were predicted to encode functional proteins, ranging from 41 to 1,878 amino acid residues. The DNA sequence of AVNV is 97% identical to that of ostreid herpesvirus 1 (OsHV-1), and the amino acid sequences of the encoded proteins of these two viruses are 94-100% identical. The genomic organization of AVNV is similar to that of OsHV-1, and consists of two unique regions (170.4 kb and 3.4 kb, respectively), each flanked by two inverted repeats (7.6 kb and 10.2 kb, respectively), with a third unique region (1.5 kb) situated between the two internal repeats.

Conclusions
Our results indicate that AVNV is a variant of OsHV-1. The AVNV genome sequence provides information useful for understanding the evolution and divergence of OsHV-1 in marine molluscs.
Oncological outcomes in patients with stage I testicular seminoma and nonseminoma: pathological risk factors for relapse and feasibility of surveillance after orchiectomy
Authors: Kobayashi Kazuhiro , Saito Toshihiro , Kitamura Yasuo , Nobushita Tomohiro , Kawasaki Takashi , Hara Noboru , Takahashi Kota 
Published: April 2013

Abstract

Background
Surveillance after orchiectomy has recently been a management option in patients with stage I seminoma, while it remains controversial in those with stage I nonseminoma, and the risk factor associated with relapse is still a matter of concern in both entities. This study was performed to explore pathological risk factors for post-orchiectomy relapse in patients with stage I seminoma and nonseminoma, and to assess oncological outcomes in those managed with surveillance.

Methods
In this single institution study, 118 and 40 consecutive patients with stage I seminoma and nonseminoma were reviewed, respectively. Of the 118 patients with stage I seminoma, 56 and one received adjuvant radiotherapy and chemotherapy, respectively, and 61 were managed with surveillance. Of the 40 men with stage I nonseminoma, 4 underwent adjuvant chemotherapy and 36 were managed with surveillance.

Results
No patient had cause-specific death during the mean observation period of 104 and 99 months in men with seminoma and nonseminoma, respectively. In men with stage I seminoma, 1 (1.7%) receiving radiotherapy and 4 (6.6%) men managed with surveillance had disease relapse; the 10-year relapse-free survival (RFS) rate was 93.4% in men managed with surveillance, and their RFS was not different from that in patients receiving adjuvant radiotherapy (logrank P=0.15). Patients with tunica albuginea involvement showed a poorer RFS than those without (10-year RFS rate 80.0% vs. 94.1%), although the difference was of borderline significance (P=0.09). In men with stage I nonseminoma, 9 (22.5%) patients experienced relapse. Patients with lymphovascular invasion seemingly had a poorer RFS than those without; 40.0% and 18.7% of the patients with and without lymphovascular invasion had disease relapse, respectively, although the difference was not significant (logrank P=0.17).

Conclusion
In both men with stage I seminoma and nonseminoma, surveillance after orchiectomy is a feasible option. However, disease extension through tunica albuginea might be a factor associated with disease relapse in patients with organ-confined seminoma, and those with stage I nonseminoma showing lymphovascular invasion may possibly be at high risk for disease relapse.
Reconciliation and local gene tree rearrangement can be of mutual profit
Authors: Nguyen Thi Hau , Ranwez Vincent , Pointet Stéphanie , Chifolleau Anne-Muriel Arigon , Doyon Jean-Philippe , Berry Vincent 
Published: April 2013

Abstract

Background
Reconciliation methods compare gene trees and species trees to recover evolutionary events such as duplications, transfers and losses explaining the history and composition of genomes. It is well-known that gene trees inferred from molecular sequences can be partly erroneous due to incorrect sequence alignments as well as phylogenetic reconstruction artifacts such as long branch attraction. In practice, this leads reconciliation methods to overestimate the number of evolutionary events. Several methods have been proposed to circumvent this problem, by collapsing the unsupported edges and then resolving the obtained multifurcating nodes, or by directly rearranging the binary gene trees. Yet these methods have been defined for models of evolution accounting only for duplications and losses, i.e. can not be applied to handle prokaryotic gene families.

Results
We propose a reconciliation method accounting for gene duplications, losses and horizontal transfers, that specifically takes into account the uncertainties in gene trees by rearranging their weakly supported edges. Rearrangements are performed on edges having a low confidence value, and are accepted whenever they improve the reconciliation cost. We prove useful properties on the dynamic programming matrix used to compute reconciliations, which allows to speed-up the tree space exploration when rearrangements are generated by Nearest Neighbor Interchanges (NNI) edit operations. Experiments on synthetic data show that gene trees modified by such NNI rearrangements are closer to the correct simulated trees and lead to better event predictions on average. Experiments on real data demonstrate that the proposed method leads to a decrease in the reconciliation cost and the number of inferred events. Finally on a dataset of 30 k gene families, this reconciliation method shows a ranking of prokaryotic phyla by transfer rates identical to that proposed by a different approach dedicated to transfer detection [BMCBIOINF 11:324, 2010, PNAS 109(13):4962–4967, 2012].

Conclusions
Prokaryotic gene trees can now be reconciled with their species phylogeny while accounting for the uncertainty of the gene tree. More accurate and more precise reconciliations are obtained with respect to previous parsimony algorithms not accounting for such uncertainties [LNCS 6398:93–108, 2010, BIOINF 28(12): i283–i291, 2012].
A software implementing the method is freely available at http://www.atgc-montpellier.fr/Mowgli/.
Hydroxyethyl starch 6%, 130/0.4 vs. a balanced crystalloid solution in cardiopulmonary bypass priming: a randomized, prospective study
Authors: Gurbuz Hasan Alper , Durukan Ahmet Baris , Salman Nevriye , Tavlasoglu Murat , Durukan Elif , Ucar Halil İbrahim , Yorgancioglu Cem 
Published: April 2013

Abstract

Background
Since the advent of cardiopulmonary bypass, many efforts have been made to avoid the complications related with it. Any component of the pump participates in occurrence of these adverse events, one of which is the type of prime solution. In this study, we aimed to compare the effects of 6% hydroxyethyl starch 130/0.4 with a commonly used balanced electrolyte solution on postoperative outcomes following coronary bypass surgery.

Methods
Two hundred patients undergoing elective coronary bypass surgery were prospectively studied. The patients were randomized in to two groups. First group received a balanced electrolyte solution and the second group received 6% hydoxyethyl starch 130/0.4 as prime solution. The postoperative outcomes of the patients were studied.

Results
The mean age of the patients was 61.81 ± 10.12 in the crystalloid group whereas 61.52 ± 9.29 in the HES group. There were 77 male patients in crystalloid group and 74 in HES group. 6% hydroxyethyl starch 130/0.4 did not have any detrimental effects on renal and pulmonary functions. The intensive care unit stay and postoperative hospital length of stay were shorter in hydroxyethyl starch group (p < 0.05 for each). Hydroxyethyl starch did not increase postoperative blood loss, amount of blood and fresh frozen plasma used, but it decreased platelet concentrate requirement. It did not have any effect on occurrence of post-coronary bypass atrial fibrillation (p > 0.05).

Conclusions
6% hydroxyethyl starch 130/0.4 when used as a prime solution did not adversely affect postoperative outcomes including renal functions and postoperative blood transfusion following coronary bypass surgery.
CoreGenes3.5: a webserver for the determination of core genes from sets of viral and small bacterial genomes
Authors: Turner Dann , Reynolds Darren , Seto Donald , Mahadevan Padmanabhan 
Published: April 2013

Abstract

Background
CoreGenes3.5 is a webserver that determines sets of core genes from viral and small bacterial genomes as an automated batch process. Previous versions of CoreGenes have been used to classify bacteriophage genomes and mine data from pathogen genomes.

Findings
CoreGenes3.5 accepts as input GenBank accession numbers of genomes and performs iterative BLASTP analyses to output a set of core genes. After completion of the program run, the results can be either displayed in a new window for one pair of reference and query genomes or emailed to the user for multiple pairs of small genomes in tabular format.

Conclusions
With the number of genomes sequenced increasing daily and interest in determining phylogenetic relationships, CoreGenes3.5 provides a user-friendly web interface for wet-bench biologists to process multiple small genomes for core gene determinations. CoreGenes3.5 is available at http://binf.gmu.edu:8080/CoreGenes3.5.
Natural infection of synathropic rodent species Mus musculus and Rattus norvegicus by Leishmania infantum in Sesimbra and Sintra – Portugal
Authors: Helhazar Marcos , Leitão José , Duarte Ana , Tavares Luís , da Fonseca Isabel Pereira 
Published: April 2013

AbstractBackgroundCanine leishmaniosis caused byLeishmania infantumis a parasitic zoonotic disease transmitted by phlebotomine sandflies (Diptera: Psychodidae). GenusPhlebotomusis the biological vector in the Old World andLutzomyiain the New World. The dog is the domestic reservoir host but other animals like the fox (Vulpes vulpes) and rodents are known to maintain the infection in both sylvatic and domestic cycles.MethodsTo identify the role of synanthropic rodentsMus musculusandRattus norvegicusas reservoir hosts forLeishmania infantumnatural infection, 30 rodents were captured under a trap rodent control program in two private dog shelters from Sintra and Sesimbra, located in the Lisbon Metropolitan Area, known to be endemic for canine leishmaniosis in Portugal. Tissue samples were screened for the presence ofLeishmaniaamastigotes by qPCR and parasitological analysis.ResultsA total of 33.3% (9/27) ofMus musculusrodents revealed the presence ofLeishmaniaspp. DNA while 29.6% (8/27) were positive in the parasitological analysis. ConcerningRattus norvegicus(n=3), one animal revealed infection only by parasitological analysis.ConclusionsOur results identified for the first time in Portugal the presence ofLeishmaniainfection in both rodent species. As susceptible hosts, infectedMus musculusandRattus norvegicusmay increase the risk for dog and human infection in households and surrounding areas, enhancing the need for efficient rodent control measures in shelters and risk zones to prevent transmission of the infection.
Fragile X mental retardation protein and synaptic plasticity
Authors: Sidorov Michael S , Auerbach Benjamin D , Bear Mark F 
Published: April 2013

Abstract
Loss of the translational repressor FMRP causes Fragile X syndrome. In healthy neurons, FMRP modulates the local translation of numerous synaptic proteins. Synthesis of these proteins is required for the maintenance and regulation of long-lasting changes in synaptic strength. In this role as a translational inhibitor, FMRP exerts profound effects on synaptic plasticity.
Antimicrobial susceptibility profiles of human and piglet Clostridium difficile PCR-ribotype 078
Authors: Keessen Elisabeth C , Hensgens Marjolein PM , Spigaglia Patrizia , Barbanti Fabrizio , Sanders Ingrid MJG , Kuijper Ed J , Lipman Len JA 
Published: April 2013

Abstract
In the last decade, outbreaks of nosocomial Clostridium difficile infections (CDI) occurred worldwide. A new emerging type, PCR-ribotype 027, was the associated pathogen. Antimicrobial susceptibility profiles of this type were extensively investigated and used to partly explain its spread. In Europe, the incidence of C. difficile PCR-ribotype 078 recently increased in humans and piglets. Using recommendations of the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and the Clinical and Laboratory Standards Institute (CLSI) we studied the antimicrobial susceptibility to eight antimicrobials, mechanisms of resistance and the relation with previously prescribed antimicrobials in human (n=49) and porcine (n=50) type 078 isolates. Human and porcine type 078 isolates showed similar antimicrobial susceptibility patterns for the antimicrobials tested. In total, 37% of the isolates were resistant to four or more antimicrobial agents. The majority of the human and porcine isolates were susceptible to amoxicillin (100%), tetracycline (100%) and clindamycin (96%) and resistant to ciprofloxacin (96%). More variation was found for resistance patterns to erythromycin (76% in human and 59% in porcine isolates), imipenem (29% in human and 50% in porcine isolates) and moxifloxacin (16% for both human and porcine isolates). MIC values of cefuroxim were high (MICs >256 mg/L) in 96% of the isolates. Resistance to moxifloxacin and clindamycin was associated with a gyr(A) mutation and the presence of the erm(B) gene, respectively. A large proportion (96%) of the erythromycin resistant isolates did not carry the erm(B) gene. The use of ciprofloxacin (humans) and enrofloxacin (pigs) was significantly associated with isolation of moxifloxacin resistant isolates. Increased fluoroquinolone use could have contributed to the spread of C. difficile type 078.
Resumption of menses in anorexia nervosa during a course of family-based treatment
Authors: Faust Julianne P , Goldschmidt Andrea B , Anderson Kristen E , Glunz Catherine , Brown Melanie , Loeb Katharine L , Katzman Debra K , Le Grange Daniel 
Published: April 2013

AbstractBackgroundThe resumption of menses (ROM) is considered an important clinical marker in weight restoration for patients with anorexia nervosa (AN). The purpose of this study was to examine ROM in relation to expected body weight (EBW) and psychosocial markers in adolescents with AN.MethodsWe conducted a retrospective chart review at The University of Chicago Eating Disorders Program from September 2001 to September 2011 (N = 225 females with AN). Eighty-four adolescents (Mean age = 15.1,SD = 2.2) with aDSM-IVdiagnosis of AN, presenting with secondary amenorrhea were identified. All participants had received a course of outpatient family-based treatment (FBT), i.e., ~20 sessions over 12 months. Weight and menstrual status were tracked at each therapy session throughout treatment. The primary outcome measures were weight (percent of expected for sex, age and height), and ROM.ResultsMean percent EBW at baseline was 82.0 (SD = 6.5). ROM was reported by 67.9% of participants (57/84), on average at 94.9 (SD = 9.3) percent EBW, and after having completed an average of 13.5 (SD = 10.7) FBT sessions (~70% of standard FBT). Compared to participants without ROM by treatment completion, those with ROM had significantly higher baseline Eating Disorder Examination Global scores (p = .004) as well as Shape Concern (p < .008) and Restraint (p < .002) subscale scores. No other differences were found.ConclusionsResults suggest that ROM occur at weights close to the reference norms for percent EBW, and that high pre-treatment eating disorder psychopathology is associated with ROM. Future research will be important to better understand these differences and their implications for the treatment of adolescents with AN.
A randomised controlled phase II trial of pre-operative celecoxib treatment reveals anti-tumour transcriptional response in primary breast cancer
Authors: Brandão Rita D , Veeck Jürgen , Van de Vijver Koen K , Lindsey Patrick , de Vries Bart , van Elssen Catharina HMJ , Blok Marinus J , Keymeulen Kristien , Ayoubi Torik , Smeets Hubert JM , Tjan-Heijnen Vivianne C , Hupperets Pierre S 
Published: April 2013

Abstract
Introduction
Cyclooxygenase-2 (COX-2) is frequently over-expressed in primary breast cancer. In transgenic breast cancer models, over-expression of COX-2 leads to tumour formation while COX-2 inhibition exerts anti-tumour effects in breast cancer cell lines. To further determine the effect of COX-2 inhibition in primary breast cancer, we aimed to identify transcriptional changes in breast cancer tissues of patients treated with the selective COX-2 inhibitor celecoxib.

Methods
In a single-centre double-blind phase II study, thirty-seven breast cancer patients were randomised to receive either pre-operative celecoxib (400 mg) twice daily for two to three weeks (n = 22) or a placebo according to the same schedule (n = 15). Gene expression in fresh-frozen pre-surgical biopsies (before treatment) and surgical excision specimens (after treatment) was profiled by using Affymetrix arrays. Differentially expressed genes and altered pathways were bioinformatically identified. Expression of selected genes was validated by quantitative PCR (qPCR). Immunohistochemical protein expression analyses of the proliferation marker Ki-67, the apoptosis marker cleaved caspase-3 and the neo-angiogenesis marker CD34 served to evaluate biological response.

Results
We identified 972 and 586 significantly up- and down-regulated genes, respectively, in celecoxib-treated specimens. Significant expression changes in six out of eight genes could be validated by qPCR. Pathway analyses revealed over-representation of deregulated genes in the networks of proliferation, cell cycle, extracellular matrix biology, and inflammatory immune response. The Ki-67 mean change relative to baseline was -29.1% (P = 0.019) and -8.2% (P = 0.384) in the treatment and control arm, respectively. Between treatment groups, the change in Ki-67 was statistically significant (P = 0.029). Cleaved caspase-3 and CD34 expression were not significantly different between the celecoxib-treated and placebo-treated groups.

Conclusions
Short-term COX-2 inhibition by celecoxib induces transcriptional programs supporting anti-tumour activity in primary breast cancer tissue. The impact on proliferation-associated genes is reflected by a reduction of Ki-67 positive cells. Therefore, COX-2 inhibition should be considered as a treatment strategy for further clinical testing in primary breast cancer.

Trial registration
ClinicalTrials.gov NCT01695226.
Relationship between red cell storage duration and outcomes in adults receiving red cell transfusions: a systematic review
Authors: Lelubre Christophe , Vincent Jean-Louis 
Published: April 2013

Abstract
Introduction
The duration of red blood cell (RBC) storage before transfusion may alter RBC function and supernatant and, therefore, influence the incidence of complications or even mortality.

Methods
A MEDLINE search from 1983 to December 2012 was performed to identify studies reporting age of transfused RBCs and mortality or morbidity in adult patients.

Results
Fifty-five studies were identified; most were single-center (93%) and retrospective (64%), with only a few, small randomized studies (eight studies, 14.5%). The numbers of subjects included ranged from eight to 364,037. Morbidity outcomes included hospital and intensive care unit (ICU) length of stay (LOS), infections, multiple organ failure, microcirculatory alterations, cancer recurrence, thrombosis, bleeding, vasospasm after subarachnoid hemorrhage, and cognitive dysfunction. Overall, half of the studies showed no deleterious effects of aged compared to fresh blood on any endpoint. Eleven of twenty-two (50%) studies reported no increased mortality, three of nine (33%) showed no increased LOS with older RBCs and eight of twelve (66%) studies showed no increased risks of organ failure. Ten of eighteen (55%) studies showed increased infections with transfusion of older RBCs. The considerable heterogeneity among studies and numerous methodological flaws precluded a formal meta-analysis.

Conclusions
In this systematic review, we could find no definitive argument to support the superiority of fresh over older RBCs for transfusion.
Evaluation of known-boundary and resistivity constraints for improving cross-borehole DC electrical resistivity imaging of discrete fractures
Authors: Robinson Judith , Johnson Timothy , Slater Lee 
Published: April 2013

There is a need to better characterize discrete fractures in contaminated hard rock aquifers to determine the fate of remediation injections away from boreholes and also to evaluate hydraulic fracturing performance. A synthetic cross-borehole electrical resistivity study was conducted assuming a discrete fracture model of an existing contaminated site with known fracture locations. Four boreholes and two discrete fracture zones, assumed to be the dominant electrical and hydraulically conductive pathways, were explicitly modeled within an unstructured tetrahedral mesh. We first evaluated different regularization constraints starting with an uninformed smoothness-constrained inversion, to which a priori information was incrementally added. We found major improvements when (1) smoothness regularization constraints were relaxed (or disconnected) along boreholes and fractures, (2) a homogeneous conductivity was assumed along boreholes, and (3) borehole conductivity constraints that could be determined from a specific conductance log were applied. We also evaluated the effect of including borehole packers on fracture zone model recovery. We found that the fracture zone conductivities with the inclusion of packers were comparable to similar trials excluding the use of packers regardless of electrical potential changes. The misplacement of fracture regularization disconnects (FRDs) can easily be misinterpreted as actual fracture locations. Conductivities within these misplaced disconnects were near the starting model value, and removing smoothing between boreholes and assumed fracture locations helped in identifying incorrectly located FRDs. We found that structural constraints used after careful evaluation of a priori information are critical to improve imaging of fracture electrical conductivities, locations, and orientations.
Die Vollendung des Deutschen Idealismus in Friedrich Heinrich JacobisSendschreibenan Fichte?
Authors: Schick Stefan 
Published: April 2013

AbstractBy denying the idea of an unprejudiced and presuppositionless reason and his assertion of a fundamental belief that underlies every performance of reason, Jacobi provoked both the German Enlighteners and the representatives of German Idealism. The paper tries to demonstrate the systematic importance of this provocation. To this end, it emphasizes Jacobi’s anticipation of Fichte’s and Schelling’s distinction between a negative (purely rational) and a positive philosophy. In particular, this study focuses on the idea of the self-annihilation of pure reason in its consequent self-realization.