bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization and review of MTHFD1 deficiency: four new patients, cellular delineation and response to folic and folinic acid treatment
Authors: Burda P. , Kuster A. , Hjalmarson O. , Suormala T. , Bürer C. , Lutz S. , Roussey G. , Christa L. , Asin‐Cayuela J. , Kollberg G. , Andersson B. A. , Watkins D. , Rosenblatt D. S. , Fowler B. , Holme E. , Froese D. S. , Baumgartner M. R. 
Published: January 2015

AbstractIn the folate cycle MTHFD1, encoded by MTHFD1, is a trifunctional enzyme containing 5,10‐methylenetetrahydrofolate dehydrogenase, 5,10‐methenyltetrahydrofolate cyclohydrolase and 10‐formyltetrahydrofolate synthetase activity. To date, only one patient with MTHFD1 deficiency, presenting with hyperhomocysteinemia, megaloblastic anaemia, hemolytic uremic syndrome (HUS) and severe combined immunodeficiency, has been identified (Watkins et al J Med Genet 48:590–2, 2011). We now describe four additional patients from two different families. The second patient presented with hyperhomocysteinemia, megaloblastic anaemia, HUS, microangiopathy and retinopathy; all except the retinopathy resolved after treatment with hydroxocobalamin, betaine and folinic acid. The third patient developed megaloblastic anaemia, infection, autoimmune disease and moderate liver fibrosis but not hyperhomocysteinemia, and was successfully treated with a regime that included and was eventually reduced to folic acid. The other two, elder siblings of the third patient, died at 9 weeks of age with megaloblastic anaemia, infection and severe acidosis and had MTFHD1 deficiency diagnosed retrospectively. We identified a missense mutation (c.806C > T, p.Thr296Ile) and a splice site mutation (c.1674G > A) leading to exon skipping in the second patient, while the other three harboured a missense mutation (c.146C > T, p.Ser49Phe) and a premature stop mutation (c.673G > T, p.Glu225*), all of which were novel. Patient fibroblast studies revealed severely reduced methionine formation from [14C]‐formate, which did not increase in cobalamin supplemented culture medium but was responsive to folic and folinic acid. These additional cases increase the clinical spectrum of this intriguing defect, provide in vitro evidence of disturbed methionine synthesis and substantiate the effectiveness of folic or folinic acid treatment.
Evaluation of Some Nonionic Surfactants Derived From Vanillin as Corrosion Inhibitors for Carbon Steel During Drilling Processes
Authors: Negm Nabel A. , Tawfik Salah M. , Badr Emad A. , Abdou Mahmoud I. , Ghuiba Ferial M. 
Published: January 2015

AbstractFour eco‐friendly nonionic surfactants based on vanillin were investigated as corrosion inhibitors against carbon steel dissolution during the drilling process in the oil field. The corrosion inhibition efficiencies of the tested compounds were determined using weight loss, electrochemical polarization, and electrochemical impedance techniques. The data obtained show that the nonionic surfactants prevent the corrosion of drilling tools and their inhibition efficiency increased with an increase in their concentration. Tafel curves revealed that the surfactants under study act as mixed inhibitors. The adsorption of the inhibitors on carbon steel surface decreases the double‐layer capacitance. The inhibition efficiencies of the surfactants were influenced by their chemical structure and surface activity.
Prediction of AD dementia by biomarkers following the NIA‐AA and IWG diagnostic criteria in MCI patients from three European memory clinics
Authors: Prestia Annapaola , Caroli Anna , Wade Sara K. , van der Flier Wiesjie M. , Ossenkoppele Rik , Van Berckel Bart , Barkhof Frederik , Teunissen Charlotte E. , Wall Anders , Carter Stephen F. , Schöll Michael , Choo Il Han , Nordberg Agneta , Scheltens Philip , Frisoni Giovanni B. 
Published: January 2015

AbstractIntroductionProposed diagnostic criteria (international working group and National Institute on Aging and Alzheimer's Association) for Alzheimer's disease (AD) include markers of amyloidosis (abnormal cerebrospinal fluid [CSF] amyloid beta [Aβ]42) and neurodegeneration (hippocampal atrophy, temporo‐parietal hypometabolism on [18F]‐fluorodeoxyglucose‐positron emission tomography (FDG‐PET), and abnormal CSF tau). We aim to compare the accuracy of these biomarkers, individually and in combination, in predicting AD among mild cognitive impairment (MCI) patients.MethodsIn 73 MCI patients, followed to ascertain AD progression, markers were measured. Sensitivity and specificity, positive (LR+) and negative (LR−) likelihood ratios, and crude and adjusted hazard ratios were computed.ResultsTwenty‐nine MCI patients progressed and 44 remained stable. Positivity to any marker achieved the lowest LR− (0.0), whereas the combination Aβ42 plus FDG‐PET achieved the highest LR+ (6.45). In a survival analysis, positivity to any marker was associated with 100% conversion rate, whereas negativity to all markers was associated with 100% stability.DiscussionThe best criteria combined amyloidosis and neurodegeneration biomarkers, whereas the individual biomarker with the best performance was FDG‐PET.
The psychosocial indicators related to neuroticism in both sexes: A study of incoming university students
Authors: Chang Wei‐Hung , Cheng Shu‐Hui , Sun Zih‐Jie , Lee I‐Hui , Lee Chih‐Ting , Chen Kao‐Chin , Tsai Chung‐Hung , Yang Yen‐Kuang , Yang Yi‐Ching 
Published: January 2015

AbstractNeuroticism may have great impact on mental and physical health in both sexes. The aims of this study were to explore whether relationships between neuroticism scores and psychosocial indicators as well as metabolic syndrome in a population of incoming university students existed in the different sexes. In total, 4266 incoming students were included in this study. The test battery comprised a self‐administered structured questionnaire, including the neuroticism subscale of the Maudsley Personality Inventory, the 12‐item Chinese Health Questionnaire, the Chinese Internet Addiction Scale‐Revision, the measurement of support functions, and the Pittsburgh Sleep Quality Index. Multivariate logistic regression showed that higher Pittsburgh Sleep Quality Index scores, higher Chinese Internet Addiction Scale‐Revision scores, and higher 12‐item Chinese Health Questionnaire scores were significantly correlated with neuroticism in both sexes, but lower perceived routine support: measurement of support functions scores were associated only with the male participants. No significant differences were found in terms of body mass index or other metabolic profiles. Individuals with poorer mental health and a poorer personal lifestyle had higher neuroticism scores, and sex effects may influence the scale of perceived social support in the neuroticism group. However, the lack of an association between neuroticism score and metabolic syndrome may be due to the recruitment of younger participants in this study.
RESTORING CROPLAND PRODUCTIVITY AND PROFITABILITY IN NORTHERN ETHIOPIAN DRYLANDS AFTER NINE YEARS OF RESOURCE-CONSERVING AGRICULTURE
Authors: ARAYA TESFAY , NYSSEN JAN , GOVAERTS BRAM , BAUDRON FRÉDÉRIC , CARPENTIER LOUISE , BAUER HANS , LANCKRIET SIL , DECKERS JOZEF , CORNELIS WIM M. 
Published: January 2015

SUMMARYLong-termin situsoil and water conservation experiments are rare in sub-Saharan Africa, particularly in Eastern Africa. A long-term experiment was conducted (2005–2013) on a Vertisol to quantify the impacts of resource-conserving agriculture (RCA) on runoff, soil loss, soil fertility and crop productivity and economic profitability in northern Ethiopia. Two RCA practices were developed from traditional furrow tillage practices: (i)derdero+(DER+) andterwah+ (TER+). DER+ is a furrow and permanent raised bed planting system, tilled once at planting time by refreshing the furrow and 30% of crop residue is retained. TER+ is ploughed once at planting, furrows are made at 1.5 m intervals and 30% crop residue is retained. The third treatment was a conventional tillage (CT) with a minimum of three tillage operations and complete removal of crop residues. Wheat, teff, barley and grass pea crops were grown in rotation. Runoff, and soil and nutrient loss were measured in plastic sheet-lined collector trenches. Significantly different (P< 0.05) runoff coefficients (%) and soil losses (t ha−1) averaged over 9 yrs were 14 and 3, 22 and 11 and 30 and 17 for DER+, TER+ and CT, respectively. Significant improvements in crop yield and gross margin were observed after a period of three years of cropping This study demonstrated that RCA systems in semi-arid agro-ecosystems constitute a field rainwater conservation and soil fertility improvement strategy that enhances crop productivity and economic profitability. Adoption of RCA systems (DER+ and TER+) in the study area requires further work to improve smallholder farmers’ awareness on benefits, to guarantee high standards during implementation and to design appropriate weed management strategies.
The lichen genusKroswiais a synonym ofFuscopannaria(Pannariaceae)
Authors: MAGAIN Nicolas , SÉRUSIAUX Emmanuël 
Published: January 2015

AbstractMolecular inferences of three loci within a phylogenetic framework of a subset of thePannariaceaeconfirm that the genusKroswiais nested within the genusFuscopannaria. The formal combination of the type species ofKroswiaintoFuscopannariais therefore made here, andKroswiais reduced into synonymy with the latter genus.
From Beginning to End: Perspectives of the Dementia Journey in Northern Ontario
Authors: Gregorio Deanna Di , Ferguson Shannon , Wiersma Elaine 
Published: January 2015

RÉSUMÉLa recherche sur les soins de la démence continue à se développer, mais peu d'attention est accordée à l'expérience de la démence dans les lieux ruraux et nordiques. Cette étude explore la démence à travers les points de vue des services de santé, les soignants, les membres de la communauté, et les personnes atteintes de démence. Les résultats mettent en évidence la complexité de la prise de conscience et la compréhension de ce phénomène dans des lieux ruraux. La perspective des gens vivants avec une démence, la compréhension des services disponibles et une prise de conscience communautaire, sont essentiels à la prise en charge rural. La nécessité d'accroître les connaissances et l’emphase sur le développement des services de santé et bien-être en milieux ruraux sont discutée.
Triple splitting and z-rays in polar ionograms
Authors: Scotto Carlo 
Published: January 2015

AbstractThe theory of propagation in a direction almost parallel to the Earth’s magnetic field is reviewed, calculating the group refractive index of the ordinary ray in the presence of electron-neutral collisions. An electron density profile is estimated from the ordinary trace and is used to compute the z-ray trace. It is shown that this reconstruction can help to identify the rare cases of z-rays from among the numerous cases of duplicate ordinary traces, due to reflection from two different directions.
Inhibition of immunoproteasome reduces infarction volume and attenuates inflammatory reaction in a rat model of ischemic stroke
Authors: Chen X , Zhang X , Wang Y , Lei H , Su H , Zeng J , Pei Z , Huang R 
Published: January 2015

AbstractThe detailed knowledge about the contribution of immunoproteasome to the neuroinflammation in ischemic stroke is still not available. The immunoreactivity of low molecular mass peptide 2 (LMP2) and low molecular mass peptide 7 (LMP7) was evident in the ipsilateral ischemic cerebral cortex and striatum following transient middle cerebral artery occlusion (MCAO). Both LMP2 and LMP7 increased as early as 4 h after the MCAO, further increased at 24 h, peaked at 72 h and decreased 7 days later. LMP2 and LMP7 were mainly present in astrocytes and microglia/macrophage cells, respectively. LMP2 knockdown by shRNA (short hairpin RNA) markedly reduced the levels of LMP2 and LMP7 protein and caused 75.5 and 78.6% decrease in the caspase-like (C-L) and chymotrypsin-like (CT-L) activities, respectively. Compared with cont-shRNA group (39.7%, infarction volumes/total ipsilateral hemisphere), the infarction volumes were reduced to 22.5% in LMP2-shRNA group. Additionally, LMP2 knockdown significantly reduced activated astrocytes and microglia, the expression nuclear factor kappa B (NF-κB) p65, tumor necrosis factor-α(TNF-α) and interleukin-1β(IL-1β) and caused less accumulation of ischemia-induced protein ubiquitination compared with MG132. These findings demonstrate that inhibition of LMP2 significantly attenuates inflammatory reaction and offers neuroprotection against focal cerebral ischemia in rats, suggesting that selective immunoproteasome inhibitors may be a promising strategy for stroke treatment.
Base-CP proteasome can serve as a platform for stepwise lid formation
Authors: Yu Zanlin , Livnat-Levanon Nurit , Kleifeld Oded , Mansour Wissam , Nakasone Mark A. , Castaneda Carlos A. , Dixon Emma K. , Fushman David , Reis Noa , Pick Elah , Glickman Michael H. 
Published: January 2015

26S proteasome, a major regulatory protease in eukaryotes, consists of a 20S proteolytic core particle (CP) capped by a 19S regulatory particle (RP). The 19S RP is divisible into base and lid sub-complexes. Even within the lid, subunits have been demarcated into two modules: module 1 (Rpn5, Rpn6, Rpn8, Rpn9 and Rpn11), which interacts with both CP and base sub-complexes and module 2 (Rpn3, Rpn7, Rpn12 and Rpn15) that is attached mainly to module 1. We now show that suppression of RPN11 expression halted lid assembly yet enabled the base and 20S CP to pre-assemble and form a base-CP. A key role for Regulatory particle non-ATPase 11 (Rpn11) in bridging lid module 1 and module 2 subunits together is inferred from observing defective proteasomes in rpn11–m1, a mutant expressing a truncated form of Rpn11 and displaying mitochondrial phenotypes. An incomplete lid made up of five module 1 subunits attached to base-CP was identified in proteasomes isolated from this mutant. Re-introducing the C-terminal portion of Rpn11 enabled recruitment of missing module 2 subunits. In vitro, module 1 was reconstituted stepwise, initiated by Rpn11–Rpn8 heterodimerization. Upon recruitment of Rpn6, the module 1 intermediate was competent to lock into base-CP and reconstitute an incomplete 26S proteasome. Thus, base-CP can serve as a platform for gradual incorporation of lid, along a proteasome assembly pathway. Identification of proteasome intermediates and reconstitution of minimal functional units should clarify aspects of the inner workings of this machine and how multiple catalytic processes are synchronized within the 26S proteasome holoenzymes.
Derivation of a Screening Tool to Identify Patients with Right Ventricular Dysfunction or Tricuspid Regurgitation after Negative Computerized Tomographic Pulmonary Angiography of the Chest
Authors: Kline Jeffrey A. , Russell Frances M. , Lahm Tim , Mastouri Ronald A. 
Published: January 2015

Many dyspneic patients who undergo computerized tomographic pulmonary angiography (CTPA) for presumed acute pulmonary embolism (PE) have no identified cause for their dyspnea yet have persistent symptoms, leading to more CTPA scanning. Right ventricular (RV) dysfunction or overload can signal treatable causes of dyspnea. We report the rate of isolated RV dysfunction or overload after negative CTPA and derive a clinical decision rule (CDR). We performed secondary analysis of a multicenter study of diagnostic accuracy for PE. Inclusion required persistent dyspnea and no PE. Echocardiography was ordered at clinician discretion. A characterization of isolated RV dysfunction or overload required normal left ventricular function and RV hypokinesis, or estimated RV systolic pressure of at least 40 mmHg. The CDR was derived from bivariate analysis of 97 candidate variables, followed by multivariate logistic regression. Of 647 patients, 431 had no PE and persistent dyspnea, and 184 (43%) of these 431 had echocardiography ordered. Of these, 64 patients (35% [95% confidence interval (CI): 28%–42%]) had isolated RV dysfunction or overload, and these patients were significantly more likely to have a repeat CTPA within 90 days (P =. 02, χ2 test). From univariate analysis, 4 variables predicted isolated RV dysfunction: complete right bundle branch block, normal CTPA scan, active malignancy, and CTPA with infiltrate, the last negatively. Logistic regression found only normal CTPA scanning significant. The final rule (persistent dyspnea + normal CTPA scan) had a positive predictive value of 53% (95% CI: 37%–69%). We conclude that a simple CDR consisting of persistent dyspnea plus a normal CTPA scan predicts a high probability of isolated RV dysfunction or overload on echocardiography.
SFA-SPA: a suffix array based short peptide assembler for metagenomic data
Authors: Yang Youngik , Zhong Cuncong , Yooseph Shibu 
Published: January 2015

Abstract
Summary: The determination of protein sequences from a metagenomic dataset enables the study of metabolism and functional roles of the organisms that are present in the sampled microbial community. We had previously introduced algorithm and software for the accurate reconstruction of protein sequences from short peptides identified on nucleotide reads in a metagenomic dataset. Here, we present significant computational improvements to the short peptide assembly algorithm that make it practical to reconstruct proteins from large metagenomic datasets containing several hundred million reads, while maintaining accuracy. The improved computational efficiency is achieved using a suffix array data structure that allows for fast querying during the assembly process, and a significant redesign of assembly steps that enables multi-threaded execution.
Availability and implementation: The program is available under the GPLv3 license from sourceforge.net/projects/spa-assembler.
Contact: syooseph@jcvi.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Computational identification of MoRFs in protein sequences
Authors: Malhis Nawar , Gsponer Jörg 
Published: January 2015

Abstract
Motivation: Intrinsically disordered regions of proteins play an essential role in the regulation of various biological processes. Key to their regulatory function is the binding of molecular recognition features (MoRFs) to globular protein domains in a process known as a disorder-to-order transition. Predicting the location of MoRFs in protein sequences with high accuracy remains an important computational challenge.
Method: In this study, we introduce MoRF CHiBi , a new computational approach for fast and accurate prediction of MoRFs in protein sequences. MoRF CHiBi combines the outcomes of two support vector machine (SVM) models that take advantage of two different kernels with high noise tolerance. The first, SVM S , is designed to extract maximal information from the general contrast in amino acid compositions between MoRFs, their surrounding regions (Flanks), and the remainders of the sequences. The second, SVM T , is used to identify similarities between regions in a query sequence and MoRFs of the training set.
Results: We evaluated the performance of our predictor by comparing its results with those of two currently available MoRF predictors, MoRFpred and ANCHOR. Using three test sets that have previously been collected and used to evaluate MoRFpred and ANCHOR, we demonstrate that MoRF CHiBi outperforms the other predictors with respect to different evaluation metrics. In addition, MoRF CHiBi is downloadable and fast, which makes it useful as a component in other computational prediction tools.
Availability and implementation: http://www.chibi.ubc.ca/morf/ .
Contact: gsponer@chibi.ubc.ca .
Supplementary information: Supplementary data are available at Bioinformatics online.
Use of Clinical and Neuroimaging Characteristics to Distinguish Temporal Lobe Herpes Simplex Encephalitis From Its Mimics
Authors: Chow Felicia C. , Glaser Carol A. , Sheriff Heather , Xia Dongxiang , Messenger Sharon , Whitley Richard , Venkatesan Arun 
Published: January 2015

Abstract
Background.  We describe the spectrum of etiologies associated with temporal lobe (TL) encephalitis and identify clinical and radiologic features that distinguish herpes simplex encephalitis (HSE) from its mimics.
Methods.  We reviewed all adult cases of encephalitis with TL abnormalities on magnetic resonance imaging (MRI) from the California Encephalitis Project. We evaluated the association between specific clinical and MRI characteristics and HSE compared with other causes of TL encephalitis and used multivariate logistic modeling to identify radiologic predictors of HSE.
Results.  Of 251 cases of TL encephalitis, 43% had an infectious etiology compared with 16% with a noninfectious etiology. Of infectious etiologies, herpes simplex virus was the most commonly identified agent (n = 60), followed by tuberculosis (n = 8) and varicella zoster virus (n = 7). Of noninfectious etiologies, more than half (n = 21) were due to autoimmune disease. Patients with HSE were older (56.8 vs 50.2 years; P = .012), more likely to be white (53% vs 35%; P = .013), more likely to present acutely (88% vs 64%; P = .001) and with a fever (80% vs 49%; P &lt; .001), and less likely to present with a rash (2% vs 15%; P = .010). In a multivariate model, bilateral TL involvement (odds ratio [OR], 0.38; 95% confidence interval [CI], .18–.79; P = .010) and lesions outside the TL, insula, or cingulate (OR, 0.37; 95% CI, .18–.74; P = .005) were associated with lower odds of HSE.
Conclusions.  In addition to HSE, other infectious and noninfectious etiologies should be considered in the differential diagnosis for TL encephalitis, depending on the presentation. Specific clinical and imaging features may aid in distinguishing HSE from non-HSE causes of TL encephalitis.
A novel mutation, D404N, in the connection subdomain of reverse transcriptase of HIV-1 CRF08_BC subtype confers cross-resistance to NNRTIs
Authors: Zhang Xiao-Min , Wu Hao , Zhang Qiwei , Lau Terrence Chi-Kong , Chu Hin , Chen Zhi-Wei , Jin Dong-Yan , Zheng Bo-Jian 
Published: January 2015

Abstract

Objectives
Growing evidence suggests that mutations in the connection domain of the HIV-1 reverse transcriptase (RT) can contribute to viral resistance to RT inhibitors. This work was designed to determine the effects of a novel mutation, D404N, in the connection subdomain of RT of HIV-1 CRF08_BC subtype on drug resistance, viral replication capacity (RC) and RT activity.

Methods
Mutation D404N, alone or together with the other reported mutations, was introduced into an HIV-1 CRF08_BC subtype infectious clone by site-directed mutagenesis. Viral susceptibility to nine RT inhibitors, viral RC and the DNA polymerase activity of viral RT of the constructed virus mutants were investigated. A modelling study using the server SWISS-MODEL was conducted to explore the possible structure-related drug resistance mechanism of the mutation D404N.

Results
Single mutations D404N and H221Y conferred low-level resistance to nevirapine, efavirenz, rilpivirine and zidovudine. Double mutations Y181C/D404N and Y181C/H221Y significantly reduced susceptibility to NNRTIs. The most pronounced resistance to NNRTIs was observed with the triple mutation Y181C/D404N/H221Y. Virus containing D404N as the only mutation displayed ∼50% RC compared with the WT virus. The modelling study suggested that the D404N mutation might abolish the hydrogen bonds between residues 404 and K30 in p51 or K431 in p66, leading to impaired RT subunit structure and enhanced drug resistance.

Conclusions
These results indicate that D404N is a novel NNRTI-associated mutation in the HIV-1 subtype CRF08_BC and provides information valuable for the monitoring of clinical RTI resistance.