bluuebunny/crossref_metadata_2025_split huggingface dataset:
First Report of Rice stripe necrosis virus Infecting Rice in Burkina Faso
Authors: Sereme D. , Neya B. J. , Bangratz M. , Brugidou C. , Ouedraogo I. 
Published: August 2014

Rice stripe necrosis virus (RSNV) was first described in 1977 as a new virus infecting rice in Cote d'Ivoire (3) and was subsequently observed in Liberia, Nigeria, and Sierra Leone (2). RSNV is a soil-borne virus transmitted by the fungus Polymyxa graminis (1) and belongs to the genus Benyvirus (4). During a survey carried out in April of 2013, severe symptoms characterized by seedling death, severe plant malformation, and foliar striping were observed on rice plants in an experimental field of INERA at Banfora located in western Burkina Faso. Disease incidence in the field was estimated to be 80 ± 5%. The symptoms of disease were successfully transmitted to the susceptible rice (Oryza sativa) cultivar IR64 by soil transmission experiments (1). RSNV was detected by ELISA using a polyclonal antiserum (1), kindly provided by Dr. Denis Fargette, IRD, Montpellier, France. Total nucleic acid was extracted with TRIzol reagent (Invitrogen) from IR64 and field infected samples. The presence of the virus was confirmed by RT-PCR using primers 5′-CATCTTGTCGAGATGAG-3′ and 5′-GCGTTGTCTTTATCAGTG-3′ for specific sequences flanking the RNA2 CP gene. The RT-PCR product was directly sequenced and the sequence was deposited in GenBank (Accession No. LK023710). Sequence analysis showed that the CP gene of the RSNV isolate from Burkina Faso shared the highest nucleotide sequence identity (97.6%) with the known RSNV CP gene sequence from the Colombian isolate (EU099845) available in GenBank, confirming the presence of RSNV in the rice crops in Burkina Faso. To our knowledge, this is the first confirmed report of RSNV in Burkina Faso. Further studies are needed to determine its incidence and spread in the country. Detection of RSNV in Burkina Faso signals the urgent need for adoption of appropriate measures to restrict the spread and impact of this virus within Africa. References: (1) C. Fauquet and J. C. Thouvenel. Proc. Acad. Sci. Ser. D 296:575, 1983. (2) C. Fauquet et al. Develop. Appl. Biol. 2:71, 1988. (3) D. Louvel and J.-M. Bidaux. Agronomie Tropicale 32:257, 1977. (4) I. Lozano and F. Morales. Eur. J. Plant Pathol. 124:673, 2009.
Intraoperative Transitions of Anesthesia Care and Postoperative Adverse Outcomes
Authors: Saager Leif , Hesler Brian D. , You Jing , Turan Alparslan , Mascha Edward J. , Sessler Daniel I. , Kurz Andrea 
Published: August 2014

Abstract

Background:
Transfers of patient care and responsibility among caregivers, “handovers,” are common. Whether handovers worsen patient outcome remains unclear. The authors tested the hypothesis that intraoperative care transitions among anesthesia providers are associated with postoperative complications.

Methods:
From the records of 138,932 adult Cleveland Clinic (Cleveland, Ohio) surgical patients, the authors assessed the association between total number of anesthesia handovers during a case and an adjusted collapsed composite of in-hospital mortality and major morbidities using multivariable logistic regression.

Results:
Anesthesia care transitions were significantly associated with higher odds of experiencing any major in-hospital mortality/morbidity (incidence of 8.8, 11.6, 14.2, 17.0, and 21.2% for patients with 0, 1, 2, 3, and ≥4 transitions; odds ratio 1.08 [95% CI, 1.05 to 1.10] for an increase of 1 transition category, P < 0.001). Care transitions among attending anesthesiologists and residents or nurse anesthetists were similarly associated with harm (odds ratio 1.07 [98.3% CI, 1.03 to 1.12] for attending [incidence of 9.4, 13.9, 17.4, and 21.5% for patients with 0, 1, 2, and ≥3 transitions] and 1.07 [1.04 to 1.11] for residents or nurses [incidence of 9.4, 13.0, 15.4, and 21.2% for patients with 0, 1, 2, and ≥3 transitions], both P < 0.001). There was no difference between matched resident only (8.5%) and nurse anesthetist only (8.8%) cases on the collapsed composite outcome (odds ratio, 1.00 [98.3%, 0.93 to 1.07]; P = 0.92).

Conclusion:
Intraoperative anesthesia care transitions are strongly associated with worse outcomes, with a similar effect size for attendings, residents, and nurse anesthetists.
NxTrim: optimized trimming of Illumina mate pair reads
Authors: O’Connell Jared , Schulz-Trieglaff Ole , Carlson Emma , Hims Matthew M. , Gormley Niall A. , Cox Anthony J. 
Published: August 2014

ABSTRACTMotivationMate pair protocols add to the utility of paired-end sequencing by boosting the genomic distance spanned by each pair of reads, potentially allowing larger repeats to be bridged and resolved. The Illumina Nextera Mate Pair (NMP) protocol employs a circularisation-based strategy that leaves behind 38bp adapter sequences which must be computationally removed from the data. While “adapter trimming” is a well-studied area of bioinformatics, existing tools do not fully exploit the particular properties of NMP data and discard more data than is necessary.ResultsWe present NxTrim, a tool that strives to discard as little sequence as possible from NMP reads. The sequence either side of the adapter site is triaged into “virtual libraries” of mate pairs, paired-end reads and single-ended reads. When combined, these data boost coverage and can substantially improve the de novo assembly of bacterial genomes.AvailabilityThe source code is available athttps://github.com/sequencing/NxTrimContactacox@illumina.com
How to make a kin selection model when marginal fitness is non-linear?
Authors: Schonmann R.H. , Boyd R. , Vicente R. 
Published: August 2014

AbstractWe observe that the Taylor-Frank method for making kin selection models when fitnesswis a nonlinear function of a continuous actor’s phenotypeyand the average phenotypezin its social environment requiresw(y, z) to be differentiable (as a function of two variables, i.e., jointly inyandz). This means that even ifw(y, z) is non-linear globally, locally it must be close to linear, meaning that its graph must be well approximated by a plane. When more than two individuals interact, this assumption is only satisfied when the marginal fitness of the actor is a linear function of the fraction of individuals in its social environment that share its phenotype. This assumption sometimes fails for biologically important fitness functions, for instance in microbial data and the theory of repeated n-person games. In these cases, the Taylor-Frank methodology cannot be used, and a more general form of direct fitness must replace it, to decide when a social mutant allele can invade a monomorphic population.
Can the site-frequency spectrum distinguish exponential population growth from multiple-merger coalescents?
Authors: Eldon Bjarki , Birkner Matthias , Blath Jochen , Freund Fabian 
Published: August 2014

AbstractThe ability of the site-frequency spectrum (SFS) to reflect the particularities of gene genealogies exhibiting multiple mergers of ancestral lines as opposed to those obtained in the presence of population growth is our focus. An excess of singletons is a well-known characteristic of both population growth and multiple mergers. Other aspects of the SFS, in particular the weight of the right tail, are, however, affected in specific ways by the two model classes. Using an approximate likelihood method and minimum-distance statistics, our estimates of statistical power indicate that exponential and algebraic growth can indeed be distinguished from multiple merger coalescents, even for moderate sample size, if the number of segregating sites is high enough. A normalized version of the SFS is also used as a summary statistic in an approximate Bayesian computation (ABC) approach. The results give further positive evidence as to the general eligibility of the SFS to distinguish between the different histories.
Biologics are more potent than other treatment modalities for improvement of quality of life in psoriasis patients
Authors: Takahashi Hidetoshi , Iinuma Shin , Tsuji Hitomi , Honma Masaru , Iizuka Hajime 
Published: August 2014

AbstractAlthough mental health is hampered in various skin disorders, few studies regarding anxiety in psoriasis patients are available, and specifically, no evaluation exists between mental health and psoriasis severity or the patients' quality of life. To examine the relation between mental health, psoriasis severity and patient's quality of life, 119 psoriasis vulgaris patients were assessed for anxiety using the General Health Questionnaire (GHQ)‐30. Psoriasis area and severity index (PASI) and Dermatological Life Quality Index (DLQI) scores were also measured. The average total GHQ‐30 score was significantly decreased from 4.41 to 2.11 (52.2% decrease) in biologics‐treated patients. That of patients treated with other systemic agents decreased from 4.36 to 3.32 (23.9% decrease) and that of those treated with topical agents from 4.21 to 3.48 (17.3% decrease). In the biologics‐treated group five of the six categories of GHQ‐30, i.e. general illness, somatic symptoms, sleep disturbance, social dysfunction, and anxiety and dysphoria, were significantly decreased after the treatment. In contrast, in the other systemic treatment and topical treatment groups, three of the six categories, general illness, somatic symptoms, and sleep disturbance were significantly decreased. There was a significant correlation between GHQ‐30 and DLQI, but not with PASI. The psoriasis patients show impaired mental health and among various treatment modalities biologics are superior to other systemic or topical treatments for improving the defective mental state.
HLA‐C*12:02 is a susceptibility factor in late‐onset type of psoriasis in Japanese
Authors: Mabuchi Tomotaka , Ota Tami , Manabe Yasuaki , Ikoma Norihiro , Ozawa Akira , Terui Tadashi , Ikeda Shigaku , Inoko Hidetoshi , Oka Akira 
Published: August 2014

AbstractPsoriasis is thought to be a multifactorial disease triggered by both genetic and environmental factors. The HLA‐C locus on chromosome 6p21.33 remains the strongest susceptibility candidate locus in psoriasis. The strong association between psoriasis and the HLA‐Cw6 allele has been well documented in various races. It is known that psoriatic patients with early onset are more likely to be familial and associated with HLA‐Cw6. Familial occurrence of Japanese psoriasis is smaller than other populations. Furthermore, males are predominant over females in Japanese psoriasis. We investigated the relation between HLA‐C alleles and age of onset, and in each gender for Japanese psoriasis, and discuss male predominance in the incidence of psoriasis in Japan. Four hundred forty six unrelated Japanese patients with psoriasis vulgaris and 557 sex‐ and age‐matched unrelated Japanese healthy controls were investigated by genotyping. We confirmed the association between early‐onset type of psoriasis with HLA‐C*06:02 allele in Japanese. In addition, we detected the association between the late‐onset type of psoriasis and the HLA‐C*12:02 allele in Japanese. No significant differences in allele frequency were observed between females and males. Our results suggest that there is no genetic factor effect on male predominance in Japanese. In contract, the effect of environmental risk factors on the onset of Japanese psoriatic patients is stronger in males than in females. As a result, male predominant in psoriasis may occur in Japan.
Post‐transcriptional regulation of the virulence‐associated enzyme AlgC by the σ22‐dependent small RNA ErsA of Pseudomonas aeruginosa
Authors: Ferrara Silvia , Carloni Sara , Fulco Roberta , Falcone Marilena , Macchi Raffaella , Bertoni Giovanni 
Published: August 2014

SummaryThe small RNA ErsA of Pseudomonas aeruginosa, transcribed from the same genomic context of the well‐known Escherichia coli Spot 42, has been characterized. We show that, different from Spot 42, ErsA is under the transcriptional control of the envelope stress response, which is known to impact the pathogenesis of P. aeruginosa through the activity of the alternative sigma factor σ22. The transcriptional responsiveness of ErsA RNA also spans infection‐relevant cues that P. aeruginosa can experience in mammalian hosts, such as limited iron availability, temperature shifts from environmental to body temperature and reduced oxygen conditions. Another difference between Spot 42 and ErsA is that ErsA does not seem to be involved in the regulation of carbon source catabolism. Instead, our results suggest that ErsA is linked to anabolic functions for the synthesis of exoproducts from sugar precursors. We show that ErsA directly operates in the negative post‐transcriptional regulation of the algC gene that encodes the virulence‐associated enzyme AlgC, which provides sugar precursors for the synthesis of several P. aeruginosa polysaccharides. Like ErsA, the activation of algC expression is also dependent on σ22. Altogether, our results suggest that ErsA and σ22 combine in an incoherent feed‐forward loop to fine‐tune AlgC enzyme expression.
Establishment and characterization of a novel cell line derived from thymoma with myasthenia gravis patients
Authors: Wang Guojin , Wang Yuanguo , Zhang Peng , Chen Yuan , Liu Yimei , Guo Feng , Zhang Hui 
Published: August 2014

AbstractBackgroundThymoma is a cancer with rare incidence, but it is a major malignancy in adult anterior mediastinum, occurring in about 40% of patients with myasthenia gravis. Because of the lack of thymic epithelial tumor cell lines, thymoma has lagged far behind other tumors in cytological studies. It is, therefore, quite necessary to establish a new thymic epithelial tumor cell line from Chinese patients to study the pathogenic mechanism and therapeutic methods.MethodsTwenty‐three samples of tumor tissues were collected from thymoma and thymic carcinoma patients for primary culture by tissue explant, suspension cell culture method, and collagenase digestion. We detected the biological characteristics and origin of the cell line after the establishment of a novel thymoma cell line.ResultsA novel cell line, designed as Thy0517, was established from thymoma type AB with myasthenia gravis patients by tissue explant. As an immortalized cell line, it always has a stable growth cycle, and there is no change in characteristics and morphology after culturing for 18 months and passing 160 generations in vitro. The experimental data demonstrate that the cell line exhibits the growth characteristics of tumor cells, the doubling time of 37 hours, with tumorigenicity in vitro and chromosome abnormality. Immunocytochemistry indicated that the cell line positive expression of CK7, CK8/18, CK19, CK‐pan, CD24, BCL‐2, P63, Vimentin, epithelial membrane antigen and epidermal growth factor receptor, lymphocyte related antigen CD99, and TdT were negatively expressed.ConclusionsThe newly established thymic epithelial tumor cell line from Chinese patients provides a model in the study of thymoma and molecularly targeted therapies.
Roles of miR‐182 in sensory organ development and cancer
Authors: Wei Qing , Lei Rong , Hu Guohong 
Published: August 2014

AbstractMicro ribonucleic acids (miRNAs) are a cluster of small non‐coding RNA molecules predicted to regulate more than 30% of coding messenger (m)RNAs in the human genome and proven to be essential in developmental and pathological processes. The miR‐182 gene was first found to be abundantly expressed in sensory organs and regulates the development of the retina and inner ear. Further studies revealed its roles in osteogenesis and T cell differentiation. In addition, the involvement of miR‐182 in cancer initiation and progression has recently been uncovered by a growing body of evidence, the majority of which supports its promoting effects in cell proliferation, angiogenesis, and invasion, as well as distant metastasis of various cancer types. Clinical analyses demonstrated the link of miR‐182 expression to poor prognosis in cancer patients. Mechanistically, multiple downstream genes including missing‐in‐metastasis, microphthalm‐associated transcription factor, FoxO1, cylindromatiosis, and others, can be targeted by miR‐182 and mediate its roles in cancer. miR‐182 is also interconnected with prominent cancer‐related signaling pathways, such as transforming growth factor beta and nuclear factor kappa beta. Interestingly, it was shown that in vivo targeting of miR‐182 prevented liver metastasis of melanoma. miR‐182 is emerging as an important regulator of malignancies, which warrants further study to establish the application potential of miR‐182 in cancer diagnosis and treatment.
Evaluation of quantitative trait loci affecting intramuscular fat and reproductive traits in pigs using marker‐assisted introgression
Authors: Sato S. , Ohnishi C. , Kikuchi T. , Kohira K. , Egawa S. , Terai S. , Nakamura T. , Arata S. , Komatsuda A. , Uemoto Y. 
Published: August 2014

SummaryWe investigated the effects of previously identified quantitative trait loci (QTL) in an experimental backcross (BC) between Chinese Meishan pigs and commercial Duroc pigs. We performed marker‐assisted introgression of two QTL for intramuscular fat (IMF) content (IMF population) and three QTL for reproductive traits (reproduction population) from a donor Meishan pig into a recipient Duroc pig. At the fourth BC generation of the IMF population and third BC generation of the reproduction population, carrier animals were selected for the production of animals homozygous for the QTL. Our previous studies have shown that the presence of a Meishan allele on the IMF QTL is associated with low IMF values, and the Meishan allele on the reproductive QTL is associated with large litters. In this study, the presence of a Duroc allele at the IMF QTL on SSC9 resulted in a 0.27% increase in IMF (additive effect = 0.27 ± 0.08), whereas the presence of a Meishan allele at the IMF QTL on SSC7 resulted in a 0.34% increase in IMF (additive effect = −0.34 ± 0.09). The presence of the Meishan allele at the IMF QTL on SSC7 thus had the opposite effect to our previous studies, that is, increased IMF. In the reproduction population, we observed no differences between the genotypes of the three QTL in regard to number of corpora lutea or litter size. Marker‐assisted introgression at these QTL is thus unlikely to result in an associated increase in litter size. These results show that it is possible to introgress alleles from other breeds into a selection population using molecular markers; any unexpected results might be associated with the genetic background.
Effect of ursodeoxycholic acid treatment on the altered progesterone and bile acid homeostasis in the mother‐placenta‐foetus trio during cholestasis of pregnancy
Authors: Estiú Maria C. , Monte Maria J. , Rivas Laura , Moirón Maria , Gomez‐Rodriguez Laura , Rodriguez‐Bravo Tomas , Marin Jose J.G. , Macias Rocio I.R. 
Published: August 2014

AimIntrahepatic cholestasis of pregnancy (ICP) is characterized by pruritus and elevated bile acid concentrations in maternal serum. This is accompanied by an enhanced risk of intra‐uterine and perinatal complications. High concentrations of sulphated progesterone metabolites (PMS) have been suggested to be involved in the multifactorial aetiopathogenesis of ICP. The aim of this study was to investigate further the mechanism accounting for the beneficial effect of oral administration of ursodeoxycholic acid (UDCA), which is the standard treatment, regarding bile acid and PMS homeostasis in the mother‐placenta‐foetus trio.MethodUsing HPLC‐MS/MS bile acids and PMS were determined in maternal and foetal serum and placenta. The expression of ABC proteins in placenta was determined by real time quantitative PCR (RT‐QPCR) and immunofluorescence.ResultsIn ICP, markedly increased concentrations of bile acids (tauroconjugates > glycoconjugates >> unconjugated), progesterone and PMS in placenta and maternal serum were accompanied by enhanced concentrations in foetal serum of bile acids, but not of PMS. UDCA treatment reduced bile acid accumulation in the mother‐placenta‐foetus trio, but had no significant effect on progesterone and PMS concentrations. ABCG2 mRNA abundance was increased in placentas from ICP patients vs. controls and remained stable following UDCA treatment, despite an apparent further increase in ABCG2.ConclusionUDCA administration partially reduces ICP‐induced bile acid accumulation in mothers and foetuses despite the lack of effect on concentrations of progesterone and PMS in maternal serum. Up‐regulation of placental ABCG2 may play an important role in protecting the foetus from high concentrations of bile acids and PMS during ICP.
Diagnosing and following adult patients with acute myeloid leukaemia in the genomic age
Authors: Roug Anne S. , Hansen Marcus C. , Nederby Line , Hokland Peter 
Published: August 2014

SummaryThe diagnosis and follow‐up process of adult patients with acute myeloid leukaemia (AML) is challenging to clinicians and laboratory staff alike. While several sets of recommendations have been published over the years, the development of high throughput screening and characterization for both genetic and epigenetic events have evolved with astonishing speed. Here we attempt to provide a practical guide to diagnose and follow adult AML patients with a focus on how to balance the wealth of information on the one hand, with the restriction put on these processes in terms of time, feasibility and economy when caring for these patients, on the other.
L‐Leucine improves the anaemia in models of Diamond Blackfan anaemia and the 5q‐ syndrome in a TP53‐independent way
Authors: Narla Anupama , Payne Elspeth M. , Abayasekara Nirmalee , Hurst Slater N. , Raiser David M. , Look A. Thomas , Berliner Nancy , Ebert Benjamin L. , Khanna‐Gupta Arati 
Published: August 2014

SummaryHaploinsufficiency of ribosomal proteins (RPs) and upregulation of the tumour suppressor TP53 have been shown to be the common basis for the anaemia observed in Diamond Blackfan anaemia and 5q‐ myelodysplastic syndrome. We previously demonstrated that treatment with L‐Leucine resulted in a marked improvement in anaemia in disease models. To determine if the L‐Leucine effect was Tp53‐dependent, we used antisense MOs to rps19 and rps14 in zebrafish; expression of tp53 and its downstream target cdkn1a remained elevated following L‐leucine treatment. We confirmed this observation in human CD34+ cells. L‐Leucine thus alleviates anaemia in RP‐deficient cells in a TP53‐independent manner.