bluuebunny/crossref_metadata_2025_split huggingface dataset:
On enhancing variation detection through pan-genome indexing
Authors: Valenzuela Daniel , Välimäki Niko , Pitkänen Esa , Mäkinen Veli 
Published: June 2015

ABSTRACTDetection of genomic variants is commonly conducted by aligning a set of reads sequenced from an individual to the reference genome of the species and analyzing the resultingread pileup. Typically, this process finds a subset of variants already reported in databases and additional novel variants characteristic to the sequenced individual. Most of the effort in the literature has been put to the alignment problem on a single reference sequence, although our gathered knowledge on species such as human ispan-genomic: We know most of the common variation in addition to the reference sequence. There have been some efforts to exploitpan-genome indexing, where the most widely adopted approach is to build an index structure on a set of reference sequences containing observed variation combinations.The enhancement in alignment accuracy when using pan-genome indexing has been demonstrated in experiments, but so far the abovemultiple referencespan-genome indexing approach has not that much been tested on its final goal, that is, in enhancing variation detection. This is the focus of this article: We study a generic approach to add variation detection support on top of the multiple references pan-genomic indexing approach. Namely, we study the read pileup on a multiple alignment of reference genomes, and propose a heaviest path algorithm to extract a new recombined reference sequence. This recombined reference sequence can then be utilized in any standard read alignment and variation detection workflow. We demonstrate that the approach enhances variation detection on realistic data sets.
Expression, purification, crystallization and crystallographic study of theAspergillus terreusaromatic prenyltransferase AtaPT
Authors: Gao Bingquan , Chen Ridao , Liu Xiao , Dai Jungui , Sun Fei 
Published: June 2015

Prenylated aromatics are produced by aromatic prenyltransferases during the secondary metabolism of bacteria, fungi and plants. The prenylation of nonprenylated precursors can lead to great chemical diversity and extensive biological properties.Aspergillus terreusaromatic prenyltransferase (AtaPT), which has recently been discovered and characterized, is such an enzyme and is responsible for the prenylation of various aromatic compounds. Here, recombinant AtaPT was overexpressed inEscherichia coli, purified and crystallized. Diffraction data were collected to a resolution of 1.71 Å and the crystal belonged to space groupP21212, with unit-cell parametersa= 96.2,b = 135.8,c= 69.5 Å, α = β = γ = 90°. Analysis of the calculated Matthews coefficient and the self-rotation function suggested that there are two AtaPT molecules in the asymmetric unit.
Service experiences and dyadic value co-creation in healthcare service delivery: a CIT approach
Authors: Osei-Frimpong Kofi , Wilson Alan , Owusu-Frimpong Nana 
Published: June 2015

Purpose
– The purpose of this paper is to investigate value co-creation processes from the focal dyad of the patient and the physician and how their experiences in the consulting room affect the value that is created.

Design/methodology/approach
– Semi-structured interviews incorporating the critical incident technique (CIT) were conducted with 8 doctors and 24 outpatients in selected hospitals in Ghana, exploring their experiences during their encounter in the service delivery impacting on the value creating healthcare opportunities. An abductive and thematic analytical approach was used to identify 76 useable critical incidents that had clear consequences on both the outcome of the service and the service experiences of the patient.

Findings
– The study reveals three critical areas needed to support the value co-creation process and respective elements or activities to be considered during the service encounter. The critical areas comprise of the social context, beliefs and perceptions, and partnership between the focal dyad. The findings also suggests that patients do not consider “getting well” as the only value that they seek, but also the total experiences they go through in the consulting room. Also some physicians find it difficult to accept the recent changes in the patients’ behaviour and attitudes, resulting in knowledge conflict that adversely affects actors’ experiences in the consulting room.

Research limitations/implications
– The study considered only one of the many professionals in the healthcare delivery, which may affect the true value perceptions of the patient.

Practical implications
– The study provides service providers understanding of the processes that influence the patients’ experiences and value creation and the changing trends in the patient’s attitudes. The findings suggest a need for providers to take a holistic view of the service delivery and consider the critical areas, which could impact on the overall service outcomes.

Originality/value
– This study extends the research on CIT to exploring the value co-creating processes in the healthcare setting. This also provides clarity in understanding the interdependence of the two actors and how this is managed as a resource in the value co-creation process at the micro level.
Physical and functional interaction between hepatitis C virus NS5A protein and ovarian tumor protein deubiquitinase 7B
Authors: Sianipar Imelda Rosalyn , Matsui Chieko , Minami Nanae , Gan Xiang , Deng Lin , Hotta Hak , Shoji Ikuo 
Published: June 2015

ABSTRACTHepatitis C virus (HCV) NS5A protein plays crucial roles in viral RNA replication, virus assembly, and viral pathogenesis. Although NS5A has no known enzymatic activity, it modulates various cellular pathways through interaction with cellular proteins. HCV NS5A (and other HCV proteins) are reportedly degraded through the ubiquitin–proteasome pathway; however, the physiological roles of ubiquitylation and deubiquitylation in HCV infection are largely unknown. To elucidate the role of deubiquitylation in HCV infection, an attempt was made to identify a deubiquitinase (DUB) that can interact with NS5A protein. An ovarian tumor protein (OTU), deubiquitinase 7B (OTUD7B), was identified as a novel NS5A‐binding protein. Co‐immunoprecipitation analyses showed that NS5A interacts with OTUD7B in both Huh‐7 and HCV RNA replicon cells. Immunofluorescence staining revealed that HCV NS5A protein colocalizes with OTUD7B in the cytoplasm. Moreover, HCV infection was found to enhance the nuclear localization of OTUD7B. The OTUD7B‐binding domain on NS5A was mapped using a series of NS5A deletion mutants. The present findings suggest that the domain I of NS5A is important and the region from amino acid 121 to 126 of NS5A essential for the interaction. Either V121A or V124A mutation in NS5A disrupts the NS5A‐OTUD7B interaction. The results of this in vivo ubiquitylation assay suggest that HCV NS5A enhances OTUD7B DUB activity. Taken together, these results suggest that HCV NS5A protein interacts with OTUD7B, thereby modulating its DUB activity.
Persistent natural infection of a Culex tritaeniorhynchus cell line with a novel Culex tritaeniorhynchus rhabdovirus strain
Authors: Gillich Nadine , Kuwata Ryusei , Isawa Haruhiko , Horie Masayuki 
Published: June 2015

ABSTRACTCulex tritaeniorhynchus rhabdovirus (CTRV) is a mosquito virus that establishes persistent infection without any obvious cell death. Therefore, occult infection by CTRV can be present in mosquito cell lines. In this study, it is shown that NIID‐CTR cells, which were derived from Cx. tritaeniorhynchus, are persistently infected with a novel strain of CTRV. Complete genome sequencing of the infecting strain revealed that it is genetically similar but distinct from the previously isolated CTRV strain, excluding the possibility of contamination. These findings raise the importance of further CTRV studies, such as screening of CTRV in other mosquito cell lines.
Circulating irisin levels are associated with lipid and uric acid metabolism in a Chinese population
Authors: Tang Shanshan , Zhang Rong , Jiang Feng , Wang Jie , Chen Miao , Peng Danfeng , Yan Jing , Wang Shiyun , Bao Yuqian , Hu Cheng , Jia Weiping 
Published: June 2015

SummaryIrisin is a novel hormone secreted by skeletal muscle after exercise, which may ameliorate insulin resistance. In this study, we aimed to explore the relationship between circulating irisin levels and type 2 diabetes mellitus (T2DM) as well as related metabolic traits in a Chinese population. A total of 203 subjects were recruited. Of these, 68 subjects with normal glucose tolerance (NGT), 63 subjects with impaired glucose regulation (IGR) and 72 subjects with new‐onset T2DM. Circulating irisin levels were measured by enzyme‐linked immunosorbent assay (ELISA). Detailed clinical investigations and biochemistry measurements were carried out in all of the subjects. Multivariate linear regression analysis was performed to assess the association between irisin levels and related metabolic characteristics. All subjects were classified into normal weight and overweight/obese subgroups according to body mass index (BMI). No significant differences in circulating irisin levels were identified among the three groups (P = 0.9741). After adjusting for covariates, multiple linear regression analysis revealed that serum irisin level was independently and significantly associated with total cholesterol (P = 0.0005), low‐density lipoprotein cholesterol (P = 0.0014), fasting fatty acids (P = 0.0402) and uric acid (P = 0.0062). By dividing the serum irisin levels into three tertile groups, the values of total cholesterol, low‐density lipoprotein cholesterol, fasting fatty acids and uric acid were all increased significantly with the increase of irisin (P < 0.05). Moreover, serum irisin levels remain closely related to total cholesterol in both normal weight and overweight/obese subgroups. Our study suggests that circulating irisin concentrations are significantly associated with lipid and uric acid metabolism in a Chinese population.
Hyperbaric oxygen pre‐treatment impairs anoxic tolerance but improves hyperglycemic tolerance in peripheral nerve
Authors: Stecker Mark M , Stevenson Matthew 
Published: June 2015

SummaryPrior research has suggested that treatment with hyperbaric oxygen (HBO) may change energy metabolism in the peripheral nerve, potentially resulting in improved tolerance to hyperglycemia and anoxia. In this paper, the in vitro rat sciatic nerve model was used to explore the effects of a single 90 min treatment with either 1 or 3 atmospheres of: oxygen, nitrogen or air on the ability of the peripheral nerve to tolerate intermittent anoxia or hyperglycemia. After this treatment, the nerve was placed in a perfusion system where the nerve action potential (NAP) was continuously recorded over the duration of a 16 h experiment. The amplitude, paired pulse response, velocity and duration of the NAP were used as markers of peripheral nerve function. The perfusate contained either 5 mmol/L or 55 mmol/L glucose and was either continuously oxygenated or intermittently replaced by an oxygen free solution of identical composition. HBO treatment primarily affected the amplitude and duration of the NAP. HBO improved the NAP in continuously oxygenated nerves exposed to the 55 mmol/L glucose perfusate but not the 5 mmol/L. However, it worsened the NAP in nerves exposed to intermittent anoxia and increased the rate at which the amplitude of the NAP declined during anoxia. Pressure had an effect on the NAP only for oxygen but not nitrogen or air. The effect of the HBO treatment persisted more than 1 h after the end of the treatment.
Reproductive biology of Pachira aquatica Aubl. (Malvaceae: Bombacoideae): a tropical tree pollinated by bats, sphingid moths and honey bees
Authors: Hernández‐Montero Jesús R. , Sosa Vinicio J. 
Published: June 2015

AbstractWe investigated the reproductive biology, including the floral biology, pollination biology, breeding system and reproductive success, of Pachira aquatica, a native and dominant tropical tree of fresh water wetlands, throughout the coastal plain of the Gulf of Mexico. The flowers present nocturnal anthesis, copious nectar production and sugar concentration (range 18–23%) suitable for nocturnal visitors such as bats and sphingid moths. The main nocturnal visitors were bats and sphingid moths while bees were the main diurnal visitors. There were no differences in legitimate visitation rates among bats, moths and honey bees. Bats and honey bees fed mainly on pollen while moths fed on nectar, suggesting resource partitioning. Eight species of bats carried pollen but Leptonycteris yerbabuenae is probably the most effective pollinator due to its higher pollen loads. The sphingid moths Manduca rustica, Cocytius duponchel and Eumorpha satellitia were recorded visiting flowers. Hand pollination experiments indicated a predominant outcrossing breeding system. Open pollination experiments resulted in a null fruit set, indicating pollen limitation; however, mean reproductive success, according to a seasonal census, was 17 ± 3%; these contrasting results could be explained by the seasonal availability of pollinators. We conclude that P. aquatica is an outcrossing species with a pollination system originally specialized for bats and sphingid moths, which could be driven to a multimodal pollination system due to the introduction of honey bees to tropical America.
Comparison of different methods of monitoring the secondary stage of oxidation of ghee
Authors: Mehta Bhavbhuti M , Aparnathi Kishorkumar D , Darji Vijaykumar B 
Published: June 2015

Thiobarbituric acid value (TBA), ρ‐anisidine value (ρ‐AnV) and carbonyl value (CV) were compared with sensory scores in monitoring the oxidation of ghee. The latter used a 9‐point hedonic scale for flavour. Six samples of ghee were stored at 80 °C and samples were removed at 48‐h intervals. Correlation coefficients of the chemical values with flavour scores were CV −0.664, TBA −0.521 and p‐AnV −0.356, suggesting that the CV was the most suitable of the methods tested.
Systematic approach to study temperature and time effects on yield of pasta filata cheese
Authors: Bähler Balz , Ruf Thomas , Samudrala Ravi , Schenkel Philipp , Hinrichs Jörg 
Published: June 2015

A batch cooker‐stretcher for pasta filata cheese production was developed based on the kitchen machine ‘Thermomix’. With this batch model system, the effect of kneading time (180, 420 and 600 s) and temperature (55, 60 and 70 °C) on the chemical composition of the pasta filata cheese and the yield was investigated. An increase in temperature from 55 to 70 °C reduced the yield of the pasta filata cheese production from 0.88 to 0.59 g/g, compared to initial curd weight. A correlation between process temperature and the water‐holding properties of protein (casein micelles) is proposed.
Invasive therapies for primary postpartum haemorrhage: a population‐based study in France
Authors: Kayem G , Dupont C , Bouvier‐Colle MH , Rudigoz RC , Deneux‐Tharaux C 
Published: June 2015

ObjectiveTo describe the characteristics, management, and outcomes of women undergoing invasive therapies for primary postpartum haemorrhage (PPH).DesignA population‐based observational study.SettingAll 106 maternity units of six French regions.PopulationA total of 146 781 women delivering between 2004 and 2006.MethodsProspective identification of women with PPH managed with invasive therapies, including uterine suture, pelvic vessel ligation, arterial embolisation, and hysterectomy.Main outcome measuresRate of use and failure rate of invasive therapies, with 95% confidence intervals (95% CIs).ResultsAn invasive therapy was used in 296 of 6660 women with PPH (4.4%, 95% CI 4.0–5.0), and in 0.2% of deliveries (95% CI 0.18–0.23). A hysterectomy was performed in 72/6660 women with PPH (1.1%, 95% CI 0.8–1.4%), and in 0.05% of deliveries (95% CI 0.04–0.06). A conservative invasive therapy was used in 262 women, including 183 (70%) who underwent arterial embolisation and 79 (30%) who had conservative surgery as the first‐line therapy. Embolisation was more frequently used after vaginal than caesarean delivery, and when arterial embolisation was available on site. The failure rate of conservative invasive therapies was 41/262 (15.6%, 95% CI 11.5–20.6) overall, and was higher after surgical than after embolisation procedures, in particular for vaginal deliveries.ConclusionsBoth maternal mortality as a result of obstetric haemorrhage and the rate of invasive therapies used for PPH are high in France. These findings suggest flaws in the initial management of PPH and/or the inadequate use of invasive procedures.Tweetable abstractMaternal mortality as a result of haemorrhage and the rate of invasive therapies used for PPH are high in France.
Methods of classification for women undergoing induction of labour: a systematic review and novel classification system
Authors: Nippita TA , Khambalia AZ , Seeho SK , Trevena JA , Patterson JA , Ford JB , Morris JM , Roberts CL 
Published: June 2015

BackgroundA lack of reproducible methods for classifying women having an induction of labour (IOL) has led to controversies regarding IOL and related maternal and perinatal health outcomes.ObjectivesTo evaluate articles that classify IOL and to develop a novel IOL classification system.Search strategyElectronic searches using CINAHL, EMBASE, WEB of KNOWLEDGE, and reference lists.Selection criteriaTwo reviewers independently assessed studies that classified women having an IOL.Data collection and analysisFor the systematic review, data were extracted on study characteristics, quality, and results. Pre‐specified criteria were used for evaluation. A multidisciplinary collaboration developed a new classification system using a clinically logical model and stakeholder feedback, demonstrating applicability in a population cohort of 909 702 maternities in New South Wales, Australia, over the period 2002–2011.Main resultsAll seven studies included in the systematic review categorised women according to the presence or absence of varying medical indications for IOL. Evaluation identified uncertainties or deficiencies across all studies, related to the criteria of total inclusivity, reproducibility, clinical utility, implementability, and data availability. A classification system of ten groups was developed based on parity, previous caesarean, gestational age, number, and presentation of the fetus. Nulliparous and parous women at full term were the largest groups (21.2 and 24.5%, respectively), and accounted for the highest proportion of all IOL (20.7 and 21.5%, respectively).Author's conclusionsCurrent methods of classifying women undertaking IOL based on medical indications are inadequate. We propose a classification system that has the attributes of simplicity and clarity, uses information that is readily and reliably collected, and enables the standard characterisation of populations of women having an IOL across and within jurisdictions.Tweetable abstractMethods classifying pregnant women having IOL are inadequate; we suggest a new classification system
Use of a high‐sensitivity troponin T assay in the assessment and disposition of patients attending a tertiary Australian emergency department: A cross‐sectional pilot study
Authors: Saad Yousef ME , McEwan James , Shugman Ibrahim M , Mussap Christian , Juergens Craig P , Ferguson Ian , French John K 
Published: June 2015

AbstractObjectiveWe examined the disposition and outcomes of patients presenting to the ED with symptoms suggestive of acute coronary syndrome undergoing measurement of troponin T using a highly sensitive assay.MethodsTroponin T (TnT) was measured in 204 consecutive patients (mean age = 65 [±18] years, 55% men) presenting to the ED with symptoms suggestive of acute coronary syndrome.ResultsNinety‐four patients predominantly had chest pain, 34 had dyspnoea and the remainder had various symptoms. Overall, 96 patients had TnT >14 ng/L (upper reference limit), of whom 31 were admitted to the cardiology service (26 had final cardiac diagnosis [five ST‐elevation MI, 10 non‐ST‐elevation MI, one unstable angina and 10 other cardiac]). Among these 96 patients, 41 had chronic kidney disease, 17 had heart failure and seven had sepsis. At 30 days, death rates among patients who had TnT >14 ng/L with non‐cardiac diagnoses and in patients who had TnT >14 ng/L with a cardiac diagnosis were 6.6% and 2.9% (P = 0.652); no death and/or MI occurred in patients with normal TnT levels. At late follow up (median 6.8 months) that was obtained in 189 (93% of 204) patients, four had MI and 14 died (three cardiac deaths).ConclusionsDespite high‐sensitivity TnT assay having a high sensitivity and specificity for myocardial necrosis, the majority of unselected consecutive patients attending ED in whom TnT levels were elevated did not have an acute coronary syndrome. Our pilot study suggests that a larger study is needed to provide evidence to modify management algorithms.
Coenzyme Q10 restores oocyte mitochondrial function and fertility during reproductive aging
Authors: Ben‐Meir Assaf , Burstein Eliezer , Borrego‐Alvarez Aluet , Chong Jasmine , Wong Ellen , Yavorska Tetyana , Naranian Taline , Chi Maggie , Wang Ying , Bentov Yaakov , Alexis Jennifer , Meriano James , Sung Hoon‐Ki , Gasser David L. , Moley Kelle H. , Hekimi Siegfried , Casper Robert F. , Jurisicova Andrea 
Published: June 2015

SummaryFemale reproductive capacity declines dramatically in the fourth decade of life as a result of an age‐related decrease in oocyte quality and quantity. The primary causes of reproductive aging and the molecular factors responsible for decreased oocyte quality remain elusive. Here, we show that aging of the female germ line is accompanied by mitochondrial dysfunction associated with decreased oxidative phosphorylation and reduced Adenosine tri‐phosphate (ATP) level. Diminished expression of the enzymes responsible for CoQ production, Pdss2 and Coq6, was observed in oocytes of older females in both mouse and human. The age‐related decline in oocyte quality and quantity could be reversed by the administration of CoQ10. Oocyte‐specific disruption of Pdss2 recapitulated many of the mitochondrial and reproductive phenotypes observed in the old females including reduced ATP production and increased meiotic spindle abnormalities, resulting in infertility. Ovarian reserve in the oocyte‐specific Pdss2‐deficient animals was diminished, leading to premature ovarian failure which could be prevented by maternal dietary administration of CoQ10. We conclude that impaired mitochondrial performance created by suboptimal CoQ10 availability can drive age‐associated oocyte deficits causing infertility.