bluuebunny/crossref_metadata_2025_split huggingface dataset:
D‐dimer levels and risk of recurrence following provoked venous thromboembolism: findings from the RIETE registry
Authors: Avnery O. , Martin M. , Bura‐Riviere A. , Barillari G. , Mazzolai L. , Mahé I. , Marchena P.J. , Verhamme P. , Monreal M. , Ellis M.H. ,   the RIETE Investigators
Published: August 2019

AbstractBackgroundPatients with venous thromboembolism (VTE) secondary to transient risk factors may develop VTE recurrences after discontinuing anticoagulation. Identifying at‐risk patients could help to guide the duration of therapy.MethodsWe used the RIETE database to assess the prognostic value of d‐dimer testing after discontinuing anticoagulation to identify patients at increased risk for recurrences. Transient risk factors were classified as major (postoperative) or minor (pregnancy, oestrogen use, immobilization or recent travel).ResultsIn December 2018, 1655 VTE patients with transient risk factors (major 460, minor 1195) underwent d‐dimer measurements after discontinuing anticoagulation. Amongst patients with major risk factors, the recurrence rate was 5.74 (95% CI: 3.19–9.57) events per 100 patient‐years in those with raised d‐dimer levels and 2.68 (95% CI: 1.45–4.56) in those with normal levels. Amongst patients with minor risk factors, the rates were 7.79 (95% CI: 5.71–10.4) and 3.34 (95% CI: 2.39–4.53), respectively. Patients with major risk factors and raised d‐dimer levels (n = 171) had a nonsignificantly higher rate of recurrences (hazard ratio [HR]: 2.14; 95% CI: 0.96–4.79) than those with normal levels. Patients with minor risk factors and raised d‐dimer levels (n = 382) had a higher rate of recurrences (HR: 2.34; 95% CI: 1.51–3.63) than those with normal levels. On multivariate analysis, raised d‐dimers (HR: 1.74; 95% CI: 1.09–2.77) were associated with an increased risk for recurrences in patients with minor risk factors, not in those with major risk factors.ConclusionsPatients with raised d‐dimer levels after discontinuing anticoagulant therapy for VTE provoked by a minor transient risk factor were at an increased risk for recurrences.
Tactile trigeminal region acuity in temporomandibular disorders: A reliability and cross‐sectional study
Authors: La Touche Roy , Cuenca‐Martínez Ferran , Suso‐Martí Luis , García‐Vicente Ana , Navarro‐Morales Beatriz , Paris‐Alemany Alba 
Published: August 2019

AbstractBackgroundTwo‐point discrimination (2‐PD) is a valuable test for measuring tactile acuity that provides relevant information about cortical reorganisation and somatosensory function.ObjectivesThe main objectives of the present study were to assess intra‐ and interexaminer reliability of the 2‐PD test in the trigeminal region in asymptomatic individuals and only intra‐examiner reliability in patients with temporomandibular disorders (TMD). The secondary objective was to observe the correlations of the 2‐PD test with regard to pain intensity and psychological and disability variables.MethodsIntra‐ and interexaminer reliability of 2‐PD in the trigeminal region was assessed in 40 asymptomatic individuals and 54 patients with TMD. Each clinician received training in the assessment of 2‐PD using an esthesiometer and following a standardised protocol for the three branches of trigeminal nerve.ResultsIn the asymptomatic participants, interexaminer (intra‐class correlation coefficient (ICC .64‐.88) and test‐retest (ICC .70‐.87) values were obtained. Given similar test‐retest values were shown in the group of patients with TMD (ICC .72‐.86), the reliability were considered good‐moderate. Statistically significant differences (P < .001) were obtained between the asymptomatic participants and the patients with TMD regarding the mean values from trials of the three trigeminal branch measurements, with a large effect size.ConclusionReliability of the 2‐PD test was considered good‐moderate. Patients with TMD showed greater distances in the 2‐PD test, suggesting that tactile acuity in the trigeminal region is impaired in patients with TMD. Assessment of tactile acuity with 2‐PD test in patients with TMD should be considered clinically.
The proteasome regulator PTRE1 contributes to the turnover of SNC1 immune receptor
Authors: Thulasi Devendrakumar Karen , Copeland Charles , Li Xin 
Published: August 2019

SummaryPlants have evolved a sophisticated immune system in order to recognize and respond to microbes in their environments. Nucleotide‐binding leucine‐rich repeat (NLR) proteins detect the presence of specific effector molecules delivered into host cells by pathogens and activate strong defence responses. However, as excessive accumulation of NLRs can result in inappropriate immune responses, their abundance must be tightly regulated. Targeted degradation of NLRs through the ubiquitin proteasome pathway is an important mechanism to limit NLR accumulation. Mutations that perturb NLR degradation can cause autoimmune phenotypes. In this study, we show that the proteasome regulator PTRE1 also contributes to NLR degradation. ptre1 mutant plants exhibit increased defence marker gene expression and enhanced disease resistance against virulent pathogens. The stability of the NLR, SUPPRESSOR OF npr1‐1 CONSTITUTIVE 1 (SNC1) is also increased in the ptre1 mutant. Although the mouse homologue of PTRE1 was reported to interact with a Cell Division Control protein 48 (CDC48) homologue in vitro (Clemen et al., 2015), we only observed interaction between PTRE1 and AtCDC48A in a split luciferase assay, but not in co‐immunoprecipitation. In addition, a related Arabidopsis protein PTRE1h shares partial redundancy with PTRE1. Together, PTRE1 acts as a negative regulator of plant immunity partly by facilitating the degradation of immune receptors such as SNC1.
Comparative sensitivity of 1,3 beta‐D‐glucan for common causes of candidaemia in South Africa
Authors: Chibabhai Vindana , Fadana Vuyolwethu , Bosman Norma , Nana Trusha 
Published: August 2019

SummaryCulture‐based diagnosis of candidaemia suffers poor sensitivity and prolonged turnaround time. The 1,3‐beta‐D‐glucan (BDG) assay is a non‐culture‐based broad fungal antigen with rapid turnaround time. To assess overall, species‐specific and population‐specific sensitivity of the BDG assay for candidaemia, to determine if the BDG assay is able to detect candidaemia prior to blood culture collection, and to evaluate the performance of the assay for the detection of Candida auris candidaemia. A retrospective review of all blood cultures (BC) with C albicans, C parapsilosis, C glabrata, C krusei and C auris was performed. A corresponding BDG result (Fungitell®) within 10 days of the BC was sought on the laboratory information system. Overall sensitivity of the assay was 79% (95% CI 73‐85; 173/218). Per species sensitivity was 81% (95% CI 72‐90; 66/81) for C albicans, 72% (61‐83; 60/83) for C parapsilosis, 90% (95% CI 79‐100; 27/30) for C glabrata, 71% (95% CI 43‐99; 10/14) C auris and 100% (10/10) for C krusei. No statistically significant difference in sensitivity between species was noted (P = .093). The assay demonstrated 92% (59/64) sensitivity in neonatal ICU (P = .047) compared to 94% (15/16) in surgery, 81% (59/73) in adult ICUs and 71% (15/21) in Oncology. BDG results were positive up to 10 days prior to blood culture collection with no significant difference in detection rate (P = .563). BDG results were positive up to 10 days prior to blood culture collection. BDG when collected a mean of 2.5 days (range 1‐10 days) prior to blood culture collection were positive.
A Japanese patient with a VCP mutation c.290G > A (p.G97E) presenting a rapid progressive respiratory failure
Authors: Nomura Emi , Ohta Yasuyuki , Sato Kota , Kawahara Yuko , Takemoto Mami , Takahashi Yoshiaki , Matsumoto Namiko , Yunoki Taijun , Yamashita Toru , Hishikawa Nozomi , Nishino Ichizo , Abe Koji 
Published: August 2019

AbstractInclusion body myopathy with Paget's disease of bone and frontotemporal dementia (IBMPFD) is an autosomal dominant disorder caused by mutations in the valosin‐containing protein (VCP) gene. IBMPFD usually presents progressive limb muscle weakness resulting in wheelchaired after mean course of 9 years with myopathy, and Paget's osteolytic lesions and frontotemporal dementia (FTD) rarely present respiratory failure. Different from previous reports, we reported a Japanese IBMPFD patient with a VCP mutation c.290G > A (p.G97E), presenting a progressive respiratory failure accompanied by wheelchaired in only 6 years after myopathy onset, suggesting unique relationship between clinical severity and c.290G > A (p.G97E) mutation of VCP gene in Japanese.
Adaptive introgression as a driver of local adaptation to climate in European white oaks
Authors: Leroy Thibault , Louvet Jean‐Marc , Lalanne Céline , Le Provost Grégoire , Labadie Karine , Aury Jean‐Marc , Delzon Sylvain , Plomion Christophe , Kremer Antoine 
Published: August 2019

Summary

Latitudinal and elevational gradients provide valuable experimental settings for studies of the potential impact of global warming on forest tree species. The availability of long‐term phenological surveys in common garden experiments for traits associated with climate, such as bud flushing for sessile oaks (Quercus petraea), provide an ideal opportunity to investigate this impact.

We sequenced 18 sessile oak populations and used available sequencing data for three other closely related European white oak species (Quercus pyrenaica, Quercus pubescens, and Quercus robur) to explore the evolutionary processes responsible for shaping the genetic variation across latitudinal and elevational gradients in extant sessile oaks. We used phenotypic surveys in common garden experiments and climatic data for the population of origin to perform genome‐wide scans for population differentiation and genotype–environment and genotype–phenotype associations.

The inferred historical relationships between Q. petraea populations suggest that interspecific gene flow occurred between Q. robur and Q. petraea populations from cooler or wetter areas. A genome‐wide scan of differentiation between Q. petraea populations identified single nucleotide polymorphisms (SNPs) displaying strong interspecific relative divergence between these two species. These SNPs followed genetic clines along climatic or phenotypic gradients, providing further support for the likely contribution of introgression to the adaptive divergence of Q. petraea populations.

Overall, the results indicate that outliers and associated SNPs are Q. robur ancestry‐informative. We discuss the results of this study in the framework of the postglacial colonization scenario, in which introgression and diversifying selection have been proposed as essential drivers of Q. petraea microevolution.
Comprehensive construction strategy of bidirectional green tissue‐specific synthetic promoters
Authors: Bai Jiuyuan , Wang Xin , Wu Hao , Ling Fei , Zhao Yun , Lin Yongjun , Wang Rui 
Published: August 2019

SummaryBidirectional green tissue‐specific promoters have important application prospects in genetic engineering and crop genetic improvement. However, there is no report on the application of them, mainly due to undiscovered natural bidirectional green tissue‐specific promoters and the lack of a comprehensive approach for the synthesis of these promoters. In order to compensate for this vacancy, the present study reports a novel strategy for the expression regulatory sequence selection and the bidirectional green tissue‐specific synthetic promoter construction. Based on this strategy, seven promoters were synthesized and introduced into rice by agrobacterium‐mediated transformation. The functional identification of these synthetic promoters was performed by the expression pattern of GFP and GUS reporter genes in two reverse directions in transgenic rice. The results indicated that all the synthetic promoters possessed bidirectional expression activities in transgenic rice, and four synthetic promoters (BiGSSP2, BiGSSP3, BiGSSP6, BiGSSP7) showed highly bidirectional expression efficiencies specifically in green tissues (leaf, sheath, panicle, stem), which could be widely applied to agricultural biotechnology. Our study provided a feasible strategy for the construction of synthetic promoters, and we successfully created four bidirectional green tissue‐specific synthetic promoters. It is the first report on bidirectional green tissue‐specific promoters that could be efficiently applied in genetic engineering.
Combination therapy with traditional medicines for perianal abscess in children
Authors: Sueyoshi Ryo , Lane Geoffrey J. , Kusafuka Junichi , Yamataka Atsuyuki , Doi Takashi 
Published: August 2019

AbstractBackgroundCombination therapy with two different traditional medicine formulations called hainosankyuto and juzentaihoto (TJ‐122 and TJ‐48; Tsumura & Co, Tokyo, Japan) may be effective for perianal abscess (PA), but their effectiveness has not been established. The present study investigated the effectiveness of combination therapy with TJ‐122 and TJ‐48 as the most effective conservative treatment for PA.MethodsWe identified 69 patients with PA under 2 years of age and divided them into four groups according to the formulations used: group 1, TJ‐122 (n = 17); group 2, TJ‐48 (n = 14); group 3, TJ‐122 and TJ‐48 (n = 19); and group 4, no traditional medicines (n = 19). Treatment was continued for 3–6 months after resolution of the PA in groups 1 and 2, and for 1 year in group 3. Age at presentation, duration of purulent discharge (PD), frequency of surgical intervention (incision and drainage [ID]; fistulotomy/fistulectomy), and recurrence rates were statistically analyzed.ResultsMean age (months) was 8.6 ± 9.2, 6.9 ± 7.3, 5.2 ± 4.7, and 3.8 ± 3.1 in groups 1, 2, 3, and 4, respectively (P = n.s.). Mean PD (weeks) was 2.5 ± 2.2, 7.1 ± 10.8, 2.0 ± 0.0, and 2.7 ± 1.0, respectively. Duration of PD was significantly longer in group 2 than in groups 1 and 3 (P < 0.05). Mean number of ID procedures was 1.0 ± 0.2, 2.3 ± 0.5, 0, and 1.6 ± 0.2, respectively. Group 1 had significantly less ID than group 2 (P < 0.01). Recurrence rates were 6%, 36%, 0%, and 32%, respectively. Groups 1 and 3 had significantly less recurrence than group 2 (P < 0.05), and group 3 had significantly less recurrence than group 4 (P < 0.01).ConclusionsCombination therapy with TJ‐122 and TJ‐48 decreased recurrence and surgical intervention to zero in this study, demonstrating high effectiveness for treating PA in children.
The microbial diversity and structure in peatland forest in Indonesia
Authors: Liu Bing , Talukder Muhamed Jamal Hosen , Terhonen Eeva , Lampela Maija , Vasander Harry , Sun Hui , Asiegbu Fred 
Published: August 2019

AbstractThe microbial community structure and function under forest in tropical peatlands are poorly understood. In this study, we investigated the microbial community structure and diversity in natural peat swamp forest soil, disturbed peat soil and mineral soil in Central Kalimantan, Indonesia, using 454 pyrosequencing. The results showed that the natural peat soil had the greatest fungal species richness (Chao1), which was significantly (p < .05) larger than that in the other two soils. Community structure of both fungi and bacteria in natural peat soil differed significantly from that in the disturbed peat soil (p = .039 and p = .045, respectively). Ascomycota (40.5%) was the most abundant phylum across the three soils followed by Basidiomycota (18.8%), Zygomycota (<0.1%) and Glomeromycota (<0.1%). The linear discriminant analysis with effect size (LEfSe) showed that Ascomycota (p < .05) and genus Gliocephalotrichum (p < .05) dominated in natural peat soil. Functionally, pathotrophs were more abundant in disturbed peat soil (p < .05). Proteobacteria (43.8%) were the most abundant phylum followed by Acidobacteria (32.6%), Actinobacteria (9.8%), Planctomycetes (1.7%). Methylocystis, Telmatospirillum, Syntrophobacter, Sorangium and Opitutus were the more abundant genera in disturbed peat soil, whereas Nevskia and Schlesneria were more abundant in mineral soil and natural peat soil, respectively. The natural peat forest soil supported a more diverse microbiology; however, the land use of such a soil can change its microbial community structure. The results provide evidence that the disturbance of tropical peat land could lead to the introduction and spread of a large number of fungal diseases
U‐Pb zircon dating of metaigneous rocks from the Nordbreen Nappe of Svalbard’s Ny‐Friesland suggests their affinity to Northeast Greenland
Authors: Bazarnik Jakub , Majka Jarosław , McClelland William C. , Strauss Justin V. , Kośmińska Karolina , Piepjohn Karsten , Elvevold Synnøve , Czupyt Zbigniew , Mikuš Tomáš 
Published: August 2019

AbstractSIMS U‐Pb zircon dating of metaigneous rocks of the Nordbreen Nappe from the West Ny‐Friesland terrane (Eastern Basement Province of Svalbard) yields crystallization ages of 1,761 ± 4 Ma for a felsic metatuff and 1,373 ± 4 Ma for a metagabbro dyke. The Palaeoproterozoic age of the metatuff is similar to previously obtained ages for various felsic rocks from the study area, whereas the Mesoproterozoic age of the metagabbro has not been thus far documented on Svalbard. However, a similar age pattern has been reported from Northeast Greenland. Therefore, we conclude that the West Ny‐Friesland terrane can be correlated with age equivalent units of Northeast Greenland. We also explore similarities and dissimilarities between the study area and other terranes of Svalbard and speculate on regional‐scale correlations. Together, the presented new ages provide critical piercing points in palaeogeographic reconstructions of the relatively poorly understood circum‐Arctic region.
Toxoplasma gondii–induced brachial plexus neuropathy after allogeneic hematopoietic stem cell transplantation
Authors: De Clercq Jozefien , Crevits Ilse , Reynders Marijke , Deeren Dries 
Published: August 2019

AbstractBrachial plexus neuropathy is a rare, but underdiagnosed condition, characterized by intense analgesic‐resistant shoulder pain, followed by brachial plexus paresis and sensory symptoms. We present a case of brachial plexus neuropathy, induced by Toxoplasma gondii (T. gondii) 17 days after allogeneic hematopoietic stem cell transplantation (alloHSCT) in a patient with acute myeloid leukemia. The diagnosis was made based on the clinical presentation, magnetic resonance imaging (MRI) of the brachial plexus, and positive T. gondii polymerase chain reaction (PCR) in cerebrospinal fluid. The patient was treated with pyrimethamine, sulfadiazine, and levofolinic acid during 6 weeks, with a positive outcome.
Automated typing of red blood cell and platelet antigens from whole exome sequences
Authors: Lane William J. , Vege Sunitha , Mah Helen H. , Lomas‐Francis Christine , Aguad Maria , Smeland‐Wagman Robin , Koch Christopher , Killian Jacqueline M. , Gardner Cubby L. , De Castro Mauricio , Lebo Matthew S. , Kaufman Richard M. , Green Robert C. , Westhoff Connie M. ,   for the MilSeq Project
Published: August 2019

BACKGROUNDGenotyping has expanded the number red blood cell (RBC) and platelet (PLT) antigens that can readily be typed, but often represents an additional testing cost. The analysis of existing genomic data offers a cost‐effective approach. We recently developed automated software (bloodTyper) for determination of RBC and PLT antigens from whole genome sequencing. Here we extend the algorithm to whole exome sequencing (WES).STUDY DESIGN AND METHODSWhole exome sequencing was performed on samples from 75 individuals. WES‐based bloodTyper RBC and PLT typing was compared to conventional polymerase chain reaction (PCR)RHDzygosity testing and serologic and single‐nucleotide polymorphism (SNP) typing for 38 RBC antigens in 12 systems (17 serologic and 35 SNPs) and 22 PLT antigens (22 SNPs). Samples from the first 20 individuals were used to modify bloodTyper to interpret WES followed by blinded typing of 55 samples.RESULTSOver the first 20 samples, discordances were noted for C, M, and N antigens, which were due to WES‐specific biases. After modification, bloodTyper was 100% accurate on blinded evaluation of the last 55 samples and outperformed both serologic (99.67% accurate) and SNP typing (99.97% accurate) reflected by two Fyband one N serologic typing errors and one undetected SNP encoding a Jknullphenotype.RHDzygosity testing by bloodTyper was 100% concordant with a combination of hybrid Rhesus box PCR and PCR–restriction fragment length polymorphism for all samples.CONCLUSIONThe automated bloodTyper software was modified for WES biases to allow for accurate RBC and PLT antigen typing. Such analysis could become a routing part of future WES efforts.
Full annotation of serum virome in Chinese blood donors with elevated alanine aminotransferase levels
Authors: Li Gang , Zhou Zhihua , Yao Li , Xu Yanjuan , Wang Lan , Fan Xiaofeng 
Published: August 2019

AbstractBACKGROUNDA serum alanine aminotransferase (ALT) test is currently demanded for blood donation in China. One of the major reasons to include such a test is possible etiology of known or unknown hepatotropic viruses. However, this hypothesis has never been examined convincingly.STUDY DESIGN AND METHODSThe study recruited 90 Chinese blood donors that were divided into three groups based on their ALT values. Serum virome from these donors was explored using a metagenomics approach with enhanced sensitivity resolved at single sequencing reads.RESULTSAnellovirus and pegivirus C (GBV‐C) were detected among these donors. None of them were found solely in donors with abnormal liver enzyme. Anellovirus was highly prevalent (93.3%) and the co‐infection with multiple genera (alpha, beta, and gammatorquevirus) were more common in the donors with normal ALT values in comparison to those with elevated ALT (single/double/triple Anellovirus genera, 1/3/24 vs. 7/7/14 or 6/7/13, p = 0.009). For unmapped reads that accounted for 15 ± 14.9% of the data, similarity‐based (BLASTN, BLASTP, and HMMER3) and similarity‐independent (k‐mer frequency) analysis identified several circular rep encoding ssDNA (CRESS‐DNA) genomes. Direct PCR testing indicated these genomes were likely reagent contaminants.CONCLUSIONViral etiology is not responsible for elevated ALT levels in Chinese blood donors. The ALT test, if not abandoned, should be adjusted for its cutoff in response to donor shortage in China.
Hybridization between resistant and susceptible fenugreek accessions and evaluation of Cercospora leaf spot resistance in segregating generations
Authors: Subedi U. , Acharya S. , Chatterton S. , Thomas J. , Friebel D. 
Published: August 2019

Cercospora leaf spot (CLS), caused by Cercospora traversoana, is an important phyto-pathological problem of self-pollinated fenugreek (Trigonella-foenum graecum). Developing resistant genotypes in crop plants has been considered the best option to control diseases for economic, environmental, and social reasons. However, before this can be accomplished, knowledge about the inheritance of disease-resistant genes is necessary for creating high-yielding resistant genotypes. One susceptible fenugreek cultivar, Tristar, and two resistant accessions L3717 and PI138687 were used in two-way crosses using hand emasculation and pollination technique in a greenhouse. F1 plants were grown in a greenhouse and allowed to grow till maturity to produce F2 seeds. Some flowers from F1 plants were crossed back to both resistant and susceptible parents separately to generate backcross (BC1) seeds. Parents, F1, F2, and BC1 populations were grown in the greenhouse using a RCBD with four replications. Plants were inoculated 30 d after sowing with a suspension of C. traversoana at 2 × 105 conidia mL−1. Symptoms were observed and rated on individual plants 25 d after inoculation, and plants were categorized according to susceptible or resistant reactions based on rating scores. Mean disease score was significantly different (p < 0.0001) among generations. In both the cross combinations, results showed CLS resistance in fenugreek (from L3717 and PI138687) was governed by a single dominant gene which is moderately heritable (46% narrow sense heritability). This indicates a relatively simple pathway for transfer of genes to adapted fenugreek cultivars.