bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of risk assessment strategies for not-high-risk pulmonary embolism
Authors: Hobohm Lukas , Hellenkamp Kristian , Hasenfuß Gerd , Münzel Thomas , Konstantinides Stavros , Lankeit Mareike 
Published: January 2016

We compared the prognostic performance of the 2014 European Society of Cardiology (ESC) risk stratification algorithm with the previous 2008 ESC algorithm, the Bova score and the modified FAST score (based on a positive heart-type fatty acid-binding protein (H-FABP) test, syncope and tachycardia, modified using high-sensitivity troponin T instead of H-FABP) in 388 normotensive pulmonary embolism patients included in a single-centre cohort study.Overall, 25 patients (6.4%) had an adverse 30-day outcome. Regardless of the score or algorithm used, the rate of an adverse outcome was highest in the intermediate-high-risk classes, while all patients classified as low-risk had a favourable outcome (no pulmonary embolism-related deaths, 0–1.4% adverse outcome). The area under the curve for predicting an adverse outcome was higher for the 2014 ESC algorithm (0.76, 95% CI 0.68–0.84) compared with the 2008 ESC algorithm (0.65, 95% CI 0.56–0.73) and highest for the modified FAST score (0.82, 95% CI 0.75–0.89). Patients classified as intermediate-high-risk by the 2014 ESC algorithm had a 8.9-fold increased risk for an adverse outcome (3.2–24.2, p<0.001 compared with intermediate-low- and low-risk patients), while the highest OR was observed for a modified FAST score ≥3 points (OR 15.9, 95% CI 5.3–47.6, p<0.001).The 2014 ESC algorithm improves risk stratification of not-high-risk pulmonary embolism compared with the 2008 ESC algorithm. All scores and algorithms accurately identified low-risk patients, while the modified FAST score appears more suitable to identify intermediate-high-risk patients.
Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts
Authors: Hakenberg Jörg , Cheng Wei-Yi , Thomas Philippe , Wang Ying-Chih , Uzilov Andrew V. , Chen Rong 
Published: January 2016

Abstract
Background
Data from a plethora of high-throughput sequencing studies is readily available to researchers, providing genetic variants detected in a variety of healthy and disease populations. While each individual cohort helps gain insights into polymorphic and disease-associated variants, a joint perspective can be more powerful in identifying polymorphisms, rare variants, disease-associations, genetic burden, somatic variants, and disease mechanisms.

Description
We have set up a Reference Variant Store (RVS) containing variants observed in a number of large-scale sequencing efforts, such as 1000 Genomes, ExAC, Scripps Wellderly, UK10K; various genotyping studies; and disease association databases. RVS holds extensive annotations pertaining to affected genes, functional impacts, disease associations, and population frequencies. RVS currently stores 400 million distinct variants observed in more than 80,000 human samples.

Conclusions
RVS facilitates cross-study analysis to discover novel genetic risk factors, gene–disease associations, potential disease mechanisms, and actionable variants. Due to its large reference populations, RVS can also be employed for variant filtration and gene prioritization.

Availability
A web interface to public datasets and annotations in RVS is available at https://rvs.u.hpc.mssm.edu/.
Infancy-Onset T1DM, Short Stature, and Severe Immunodysregulation in Two Siblings With a Homozygous LRBA Mutation
Authors: Schreiner Felix , Plamper Michaela , Dueker Gesche , Schoenberger Stefan , Gámez-Díaz Laura , Grimbacher Bodo , Hilger Alina C. , Gohlke Bettina , Reutter Heiko , Woelfle Joachim 
Published: January 2016

Abstract

Context:
Type 1 diabetes mellitus (T1DM) is caused by autoimmunity against pancreatic β-cells. Although a significant number of T1DM patients have or will develop further autoimmune disorders during their lifetime, coexisting severe immunodysregulation is rare.

Objective:
Presuming autosomal-recessive inheritance in a complex immunodysregulation disorder including T1DM and short stature in two siblings, we performed whole-exome sequencing.

Case Presentation:
Two Libyan siblings born to consanguineous parents were presented to our diabetology department at ages 12 and 5 years, respectively. Apart from T1DM diagnosed at age 2 years, patient 1 suffered from chronic restrictive lung disease, mild enteropathy, hypogammaglobulinemia, and GH deficiency. Fluorescence-activated cell sorting analysis revealed B-cell deficiency. In addition, CD4+/CD25+ and CD25high/FoxP3+ cells were diminished, whereas an unusual CD25−/FoxP3+ population was detectable. The younger brother, patient 2, also developed T1DM during infancy. Although his enteropathy was more severe and electrolyte derangements repeatedly led to hospitalization, he did not have significant pulmonary problems. IgG levels and B-lymphocytes were within normal ranges.

Results:
By whole-exome sequencing we identified a homozygous truncating mutation (c.2445_2447del(C)3ins(C)2, p.P816Lfs*4) in the lipopolysaccharide-responsive beige-like anchor (LRBA) gene in both siblings. The diagnosis of LRBA deficiency was confirmed by a fluorescence-activated cell sorting-based immunoassay showing the absence of LRBA protein in phytohemagglutinin-stimulated peripheral blood mononuclear cells.

Conclusion:
We identified a novel truncating LRBA mutation in two siblings with T1DM, short stature, and severe immunodysregulation. LRBA mutations have previously been reported to cause multiorgan autoimmunity and immunodysfunction. In light of the variable phenotypes reported so far in LRBA-mutant individuals, LRBA deficiency should be considered in all patients presenting with T1DM and signs of severe immunodysregulation.
Fascial Manipulation® for chronic aspecific low back pain: a single blinded randomized controlled trial
Authors: Branchini Mirco , Lopopolo Francesca , Andreoli Ernesto , Loreti Ivano , Marchand Aurélie M , Stecco Antonio 
Published: January 2016

Background: The therapeutic approach to chronic aspecific low back pain (CALBP) has to consider the multifactorial aetiology of the disorder. International guidelines do not agree on unequivocal treatment indications. Recommendations for fascial therapy are few and of low level evidence but several studies indicate strong correlations between fascial thickness and low back pain. This study aims at comparing the effectiveness of Fascial Manipulation® associated with a physiotherapy program following guidelines for CALBP compared to a physiotherapy program alone.Methods: 24 subjects were randomized into two groups, both received eight treatments over 4 weeks. Outcomes were measured at baseline, at the end of therapy and at a 1 month and a 3 months follow-up. Pain was measured with the visual analogue scale (VAS) and the brief pain inventory (BPI), function with the Rolland-Morris disability questionnaire (RMDQ), state of well-being with the short-form 36 health-survey (SF-36). The mean clinical important difference (MCID) was also measured.Results: Patients receiving Fascial Manipulation® showed statistically and clinically significant improvements at the end of care for all outcomes, in the short (RMDQ, VAS, BPI) and medium term for VAS and BPI compared to manual therapy. The MCID show significant improvements in the means and percentage of subjects in groups in all outcomes post-treatment, in the short and medium term.Conclusion: Fascial tissues were implicated in the aetiology of CALBP and treatment led to decreased symptomatic, improved functional and perceived well-being outcomes that were of greater amplitude compared to manual therapy alone.
How to put plant root uptake into a soil water flow model
Authors: Dong Xuejun 
Published: January 2016

The need for improved crop water use efficiency calls for flexible modeling platforms to implement new ideas in plant root uptake and its regulation mechanisms. This paper documents the details of modifying a soil infiltration and redistribution model to include (a) dynamic root growth, (b) non-uniform root distribution and water uptake, (c) the effect of water stress on plant water uptake, and (d) soil evaporation. The paper also demonstrates strategies of using the modified model to simulate soil water dynamics and plant transpiration considering different sensitivity of plants to soil dryness and different mechanisms of root water uptake. In particular, the flexibility of simulating various degrees of compensated uptake (whereby plants tend to maintain potential transpiration under mild water stress) is emphasized. The paper also describes how to estimate unknown root distribution and rooting depth parameters by the use of a simulation-based searching method. The full documentation of the computer code will allow further applications and new development.
Paper-Based Quantification of Male Fertility Potential
Authors: Nosrati Reza , Gong Max M , San Gabriel Maria C , Pedraza Claudio E , Zini Armand , Sinton David 
Published: January 2016

Abstract

BACKGROUND
More than 70 million couples worldwide are affected by infertility, with male-factor infertility accounting for about half of the cases. Semen analysis is critical for determining male fertility potential, but conventional testing is costly and complex. Here, we demonstrate a paper-based microfluidic approach to quantify male fertility potential, simultaneously measuring 3 critical semen parameters in 10 min: live and motile sperm concentrations and sperm motility.

METHODS
The device measures the colorimetric change of yellow tetrazolium dye to purple formazan by the diaphorase flavoprotein enzyme present in metabolically active human sperm to quantify live and motile sperm concentration. Sperm motility was determined as the ratio of motile to live sperm. We assessed the performance of the device by use of clinical semen samples, in parallel with standard clinical approaches.

RESULTS
Detection limits of 8.46 and 15.18 million/mL were achieved for live and motile sperm concentrations, respectively. The live and motile sperm concentrations and motility values from our device correlated with those of the standard clinical approaches (R2 ≥ 0.84). In all cases, our device provided 100% agreement in terms of clinical outcome. The device was also robust and could tolerate conditions of high absolute humidity (22.8 g/m3) up to 16 weeks when packaged with desiccant.

CONCLUSIONS
Our device outperforms existing commercial paper-based assays by quantitatively measuring live and motile sperm concentrations and motility, in only 10 min. This approach is applicable to current clinical practices as well as self-diagnostic applications.
Las obras pías del VI conde de Fernán Núñez: Un ejemplo de distinción social a través de la caritas ilustrada.
Authors: Vigara Zafra José Antonio 
Published: January 2016

<p>Este trabajo pretende un análisis de las prácticas piadosas desarrolladas por el VI conde de Fernán Núñez en su villa. Para ello se estudian las etapas constructivas y las funciones simbólicas originadas en torno a estas obras. Con ello se esperan extraer consecuencias relativas al análisis de las nuevas estrategias de distinción social generadas por las élites nobiliarias durante la Ilustración.</p><p> </p>
Sobre narrativa de colegios jesuitas en Pérez de Ayala y Miró
Authors: Ezpeleta Aguilar Fermín 
Published: January 2016

<p><strong>Resumen</strong></p><p>La novela lírica, que caracteriza la producción literaria de Ramón Pérez de Ayala y Gabriel Miró, sirve a estos autores como estructura que acoge sus iniciales novelas autobiográficas de colegios jesuitas, particularmente, <em>A.M.D.G. </em>y <em>Amores de Antón Hernando</em> (posteriormente, <em>Niño y grande</em>). Se trata en los dos casos de novelas de aprendizaje, que se acercan a la modalidad «de artista», en las que se impugna, mediante recursos como la parodia y la ironía, la pedagogía jesuita. Importa, más en Pérez de Ayala que en Miró, el hilvanado de cuadros estudiantiles con anécdotas académicas de tipos docentes y discentes, al modo de las novelas de costumbres universitarias del momento. Se evidencia en ambos autores cómo el nuevo modo de novelar sigue aprovechando elementos de la tradición realista y naturalista del siglo xix.</p><p>Palabras clave: Ramón Pérez de Ayala, Gabriel Miró, colegios jesuitas, novela lírica, novela de formación, novela de artista.</p><p> </p><p><strong>Abstract</strong></p><p>The lyrical novel, which characterizes the literary production of Ramón Pérez de Ayala and Gabriel Miró, these authors serves as a structure that welcomes their initial autobiographical novels of Jesuit schools, particularly <em>A.M.D.G. </em>and <em>Amores de Antón Hernando</em> (later <em>Niño y grande</em>). It is in both cases <em>Bildungsromane</em> that are close to the mode «artist», which is challenged by resources such as parody and irony Jesuit pedagogy. In these novels is important composition of student academic painting with stories as they appear in the novels of university customs of the moment. It is evident in how both authors romanticize the new mode continues to build elements of the realist tradition and naturalist of the nineteenth century.</p><p>Key words: Ramón Pérez de Ayala, Gabriel Miró, Jesuit schools, lyrical novel, <em>Bildungsroman</em>, <em>Künstlerroman</em>.</p>
Volume 5 Index
Authors: Index GJFLT 
Published: January 2016

<p> </p><p><strong>Vol 5, No 1 May (2015) </strong></p><p>University English: Issues and directions for curriculum development</p><p>Richard Kiely</p><p>01-14</p><p> </p><p>Intercultural communicative competence: A vital skill in the context of ASEAN economic community<br /> Thao Quoc Tran, Tham My Duong<br /> 15-22</p><p> </p><p>Analysis of teachers’ and students’ attitudes toward Iranian senior high school textbook series<br /> Amin Alani, Ali Jahangard<br /> 23-43</p><p> </p><p>Building english vocabulary through roots, prefixes and suffixes</p><p>Metin Yurtbaşı</p><p>44-51</p><p> </p><p>The effect of language proficiency on the negotiation in peer review in EFL context</p><p>Bahram Mowlaie, Parviz Maftoon</p><p>52-64</p><p> </p><p>Teaching lexical chunks on retention and production of referential and collocational meaning of lexis among the Iranian EFL learners<br /> Manochehr Jaafarigohar, Mohsen Nazari<br /> 65-75</p><p> </p><p>Formative assessment in the EFL context of kermanshah high schools: Teachers' familiarity and application<br /> Ferdos Jamali, Nouzar Gheisari<br /> 76-84</p><p> </p><p>The rhetorical organization of research article discussion sections: An investigation into genre evolution in applied linguistics<br /> Alireza Jalilifar, Mitra Baninajar, Soheil Saeedian<br /> 85-100</p><p>The metacognitive awareness listening questionnaire as a metacognitive-raising tool: Does it work?<br /> Rahman Sahragrard, Ali Kushki, M. Miri, Farzad Mahmooudi<br /> 101-113</p><p> </p><p><strong>Vol 5, No 2 November (2015)</strong></p><p><strong> </strong></p><p>From the editors</p><p>Assoc. Prof Dr. Ali Rahimi</p><p><strong> </strong></p><p>EFL teachers’ and learners’ perspectives on “english file series”</p><p><em>Masoud Rahimi</em></p><p><em>115-128</em></p><p> </p><p>Test-Taking strategies and Iranian EFL Learners’ vocabulary and structure test performance</p><p><em>Nouroddin Yousofi, Farkhondeh Pursiah, </em><em>Mohammad Ahmadnejad</em></p><p><em>129-142</em></p><p><em> </em></p><p>Impact of scaffolding on complexity and accuracy of Iranian EFL learners' narrative writing</p><p><em>Rouholah Askari Bigdeli, Ali Rahimi</em></p><p><em>143-156</em></p><p><em> </em></p><p>The effect of social class on Persian EFL learners’ pragmatic performance of Speech act of compliment responses</p><p><em>Saman Ebadi, Farkhondeh Pursiah</em></p><p><em>157-170</em></p><p><em> </em></p><p><em>The impact of self-perception on Iranian EFL learners' oral communication</em></p><p><em>Ali Soltani, Mohsen Ghafari</em></p><p><em>171-176</em></p>
Frequency and long-term follow-up of trapped fourth ventricle following neonatal posthemorrhagic hydrocephalus
Authors: Pomeraniec I. Jonathan , Ksendzovsky Alexander , Ellis Scott , Roberts Sarah E. , Jane John A. 
Published: January 2016

OBJECTIVE
Intraventricular hemorrhage (IVH) is a common complication of premature neonates with small birth weight, which often leads to hydrocephalus and treatment with ventriculoperitoneal (VP) shunting procedures. Trapped fourth ventricle (TFV) can be a devastating consequence of the subsequent occlusion of the cerebral aqueduct and foramina of Luschka and Magendie.

METHODS
The authors retrospectively reviewed 8 consecutive cases involving pediatric patients with TFV following VP shunting for IVH due to prematurity between 2003 and 2012. The patients ranged in gestational age from 23.0 to 32.0 weeks, with an average age at first shunting procedure of 6.1 weeks (range 3.1–12.7 weeks). Three patients were managed with surgery. Patients received long-term radiographic (mean 7.1 years; range 3.4–12.2 years) and clinical (mean 7.8 years; range 4.6–12.2 years) follow-up.

RESULTS
The frequency of TFV following VP shunting for neonatal posthemorrhagic hydrocephalus was found to be 15.4%. Three (37.5%) patients presented with symptoms of posterior fossa compression and were treated surgically. All of these patients showed signs of radiographic improvement with stable or improved clinical examinations during postoperative follow-up. Of the 5 patients treated conservatively, 80% experienced stable ventricular size and 1 patient experienced a slight increase (3 mm) on imaging. All of the nonsurgical patients showed stable to improved clinical examinations over the follow-up period.

CONCLUSIONS
The frequency of TFV among premature IVH patients is relatively high. Most patients with TFV are asymptomatic at presentation and can be managed without surgery. Symptomatic patients may be treated surgically for decompression of the fourth ventricle.
Comparison of the effectiveness of using the optic strut and tuberculum sellae as radiological landmarks in diagnosing paraclinoid aneurysms with CT angiography
Authors: Liao Chih-Hsiang , Lin Chung-Jung , Lin Chun-Fu , Huang Hsin-Yi , Chen Min-Hsiung , Hsu Sanford P. C. , Shih Yang-Hsin 
Published: January 2016

OBJECTIVE
The treatment of paraclinoid aneurysms remains challenging. It is important to determine the exact location of the paraclinoid aneurysm when considering treatment options. The authors herein evaluated the effectiveness of using the optic strut (OS) and tuberculum sellae (TS) as radiographic landmarks for distinguishing between intradural and extradural paraclinoid aneurysms on source images from CT angiography (CTA).

METHODS
Between January 2010 and September 2013, a total of 49 surgical patients with the preoperative diagnoses of paraclinoid aneurysm and 1 symptomatic cavernous-clinoid aneurysm were retrospectively identified. With the source images from CTA, the OS and the TS were used as landmarks to predict the location of the paraclinoid aneurysm and its relation to the distal dural ring (DDR). The operative findings were examined to confirm the definitive location of the paraclinoid aneurysm. Statistical analysis was performed to determine the diagnostic effectiveness of the landmarks.

RESULTS
Nineteen patients without preoperative CTA were excluded. The remaining 30 patients comprised the current study. The intraoperative findings confirmed 12 intradural, 12 transitional, and 6 extradural paraclinoid aneurysms, the diagnoses of which were significantly related to the type of aneurysm (p < 0.05) but not factors like sex, age, laterality of aneurysm, or relation of the aneurysm to the ophthalmic artery on digital subtraction angiography. To measure agreement with the correct diagnosis, the OS as a reference point was far superior to the TS (Cohen's kappa coefficients 0.462 and 0.138 for the OS and the TS, respectively). For paraclinoid aneurysms of the medial or posterior type, using the base of the OS as a reference point tended to overestimate intradural paraclinoid aneurysms. The receiver operating characteristic curve indicated that if the aneurysmal neck traverses the axial plane 2 mm above the base of the OS, the aneurysm is most likely to grow across the DDR and present as a transitional aneurysm (sensitivity 0.806; specificity 0.792).

CONCLUSIONS
High-resolution thin-cut CTA is a fast and crucial tool for diagnosing paraclinoid aneurysms. The OS serves as an effective landmark in CTA source images for distinguishing between intradural and extradural paraclinoid aneurysms. The DDR is supposed to be located 2 mm above the base of the OS in axial planes.
Surgical outcomes following encephaloduroarteriosynangiosis in adult moyamoya disease associated with Type 2 diabetes
Authors: Ren Bin , Zhang Zheng-Shan , Liu Wei-Wei , Bao Xiang-Yang , Li De-Sheng , Han Cong , Xian Peng , Zhao Feng , Wang Hui , Wang Hai , Duan Lian 
Published: January 2016

OBJECTIVE
Debate exists regarding the merits and shortcomings of an indirect bypass procedure for treating adult patients with moyamoya disease (MMD). Considerable variation in neovascularization occurs among different organs in patients with diabetes mellitus. Here, the effect of encephaloduroarteriosynangiosis on MMD associated with Type 2 diabetes mellitus (T2DM) is evaluated.

METHODS
A retrospective and 1:2 matched case-control study was conducted in moyamoya patients with or without T2DM (n = 180). Postoperative collateral formations were graded according to the Modified Collateral Grading System that originated from the Matsushima Angiographic Stage Classification. Neurological function outcomes before and after the operation were evaluated according to the modified Rankin Scale. Univariate and multivariate logistic regression analyses were performed to determine the risk factors for clinical outcome.

RESULTS
There was no statistically significant difference in the constituent ratios of initial symptom and preoperative Suzuki stage between patients with and without T2DM. Progression of angiopathy around the circle of Willis was postoperatively observed in bilateral internal carotid arteries in both groups. Patients with T2DM had a higher postoperative Suzuki stage (p < 0.01) and more frequent development of collateral angiogenesis germinating from the external carotid after indirect revascularization procedures in the surgical cerebral hemisphere (82.7% vs 72.2%; p < 0.05). The extent of postoperative collateral formation in patients with diabetes mellitus was significantly higher (p < 0.01). Postoperative clinical improvement in the diabetes group was more common after revascularization procedures (p < 0.05), and the diabetes group had lower modified Rankin Scale scores (p < 0.05) in comparison with the nondiabetes group. Late postoperative stroke and posterior cerebral artery involvement were identified as predictors of unfavorable clinical outcome in both groups, while T2DM was associated with a favorable clinical outcome.

CONCLUSIONS
Encephaloduroarteriosynangiosis is an efficacious treatment for adult patients with MMD. Patients with T2DM could achieve better collateral circulation and clinical improvement following surgery.