bluuebunny/crossref_metadata_2025_split huggingface dataset:
Die Progression der Nierenerkrankung – wie ist sie zu verhindern?
Authors: Schneider Markus , Hilgers Karl 
Published: August 2017

AbstractEnd stage chronic kidney disease (CKD) requiring renal replacement therapy is related to poor quality of life and high mortality. Thus, slowing the progression of CKD is an important purpose of therapy. Some general therapeutic approaches aim to slow the decline of renal function and they can be applied in all patients with CKD – irrespective of the underlying cause of CKD. A key intervention is lowering blood pressure (target: ≤ 140/90 mmHg, and in patients with albuminuria ≤ 130/80 mmHg). Inhibitors of the renin angiotensin system preferentially should be used in case of albuminuria, depending on the diabetic status and the level of albuminuria: in diabetics with albuminuria ≥ 30 mg/d, in non-diabetics with albuminuria > 300 mg/d. Mineralocorticoid receptor blockers and endothelin receptors blockers promise novel anti-proteinuric strategies – but still validation of their positive effects on retarding CKD progression is necessary. In patients with diabetic kidney disease, glycemic control aiming for an HbA1c of ≈ 7.0 % has been established to slow CKD progression. Furthermore, SGLT-2 inhibition with empagliflozin may be considered as a new therapeutic approach that provides additional cardiovascular and renal protection. Finally, recent studies suggest: correction of metabolic acidosis and avoidance of episodes of acute renal failure may provide protection against the progression of CKD.
Granuloma anulare als mögliche kutane Paraneoplasie
Authors: Troyanova-Slavkova S. , Seidl C. , Schaarschmidt E. , Werner W. , Kowalzick L. 
Published: August 2017

ZusammenfassungDie paraneoplastische Variante des Granuloma anulare (GA) ist eine seltene kutane Manifestation einer zugrunde liegenden Malignität, die am häufigsten ein systemisches Lymphom ist. Wir berichten über den Fall eines Patienten mit Urothelkarzinom des Ureters und ca. 2 Jahre später mit Rezidiv-Urothelkarzinom der Harnblase mit disseminiertem und therapierefraktärem GA. Das GA trat nahezu gleichzeitig mit dem Urothelkarzinom auf, nach der Tumorentfernung bildete es sich etwas zurück und verschlechterte sich erneut bei dem Rezidiv des Karzinoms. Die enge zeitliche Korrelation der klinischen Verläufe dieser beiden Krankheiten weist darauf hin, dass ihre Koexistenz mehr als ein zufälliger Befund ist. Dieser Fall hebt hervor, wie wichtig es ist, ein paraneoplastisches GA auszuschließen, besonders in Fällen, in denen die Hautmanifestationen umfangreich und resistent gegen die Behandlung sind.
Epileptic Seizures Under Antidepressive Drug Treatment: Systematic Review
Authors: Steinert Tilman , Fröscher Walter 
Published: August 2017

Abstract
Objective This paper is a systematic review on seizures under treatment with substances licensed for major depression.
Method Systematic review protocol is available in PROSPERO registration number CRD42016034010. Twenty-five substances were selected according to frequencies of prescriptions and publications. A PubMed search was conducted with “substance name” and “seizure.”
Results A total of 2291 articles were screened, out of which 164 fulfilled inclusion criteria. Data synthesis was possible only to a limited extent due to heterogeneity of included patients, observation periods, methods, and outcomes. Evidence for an at most moderate, but still low, risk (>0.1% under regular doses) was found highest for clomipramine, followed by quetiapine, amitriptyline, venlafaxine, citalopram, sertraline, trazodone, mirtazapine, paroxetine, bupropion, and escitalopram. For fluoxetine and duloxetine, the risk seems to be negligible. For the other, mostly newer, substances, sufficient evidence was not available. An increased risk for lithium, as reported in many reviews and textbooks, could not be confirmed.
Conclusions Antidepressive treatment is rather safe in terms of risk of seizures and also can be generally recommended in the treatment of patients with epilepsy.
The molecular dynamics of long noncoding RNA control of transcription in PTEN and its pseudogene
Authors: Lister Nicholas , Shevchenko Galina , Walshe James L. , Groen Jessica , Johnsson Per , Vidarsdóttir Linda , Grander Dan , Ataide Sandro F. , Morris Kevin V. 
Published: August 2017

Significance
In recent years, noncoding RNA transcripts have been found to interact with genes and modulate their ability to be transcribed and made into protein. Here we uncover many of the mechanistic underpinnings involved in how noncoding RNAs control gene transcription. Notably, we find that noncoding RNA control of gene transcription is based on a combination of structural and sequence components of the noncoding RNA and targeted gene. Collectively, the observations presented here suggest that a much more complex and vibrant RNA regulatory world is operative in gene expression and evolution of the genome.
Role for the EWS domain of EWS/FLI in binding GGAA-microsatellites required for Ewing sarcoma anchorage independent growth
Authors: Johnson Kirsten M. , Mahler Nathan R. , Saund Ranajeet S. , Theisen Emily R. , Taslim Cenny , Callender Nathan W. , Crow Jesse C. , Miller Kyle R. , Lessnick Stephen L. 
Published: August 2017

Significance
Ewing sarcoma is a pediatric bone malignancy driven by the fusion protein EWS/FLI. EWS/FLI mediates oncogenesis through its role as an aberrant transcription factor, but little is known about molecular mechanisms underlying this function. We demonstrate in Ewing sarcoma cells that EWS/FLI activates gene targets through binding at associated GGAA-microsatellites, and these repetitive sequences are necessary for Ewing sarcoma cell proliferation and anchorage-independent growth. Furthermore, we show a previously unknown role for the EWS portion of the fusion protein as critical in binding at EWS/FLI targets. Understanding the mechanism of EWS/FLI transcriptional regulation is imperative to expose novel, targetable biology to inhibit its function. Additionally, these insights provide a useful model for understanding the molecular complexities of other pediatric cancers.
Affinity of IDPs to their targets is modulated by ion-specific changes in kinetics and residual structure
Authors: Wicky Basile I. M. , Shammas Sarah L. , Clarke Jane 
Published: August 2017

Significance
Intrinsically disordered proteins (IDPs) rapidly exchange between conformations of marginal stability. These transient structures are much more sensitive to solution conditions than ordered proteins. Here we reveal that coupled folding and binding of IDPs are affected by the presence of different common salts beyond simple electrostatic effects, such that their affinities are ion-specific, and occur at physiological concentrations. We demonstrate that the phenomenon is rooted in the structural sensitivity of IDPs to co-solutes, which in turn affects binding rates and affinities. We suggest that the sensitivity of coupled folding and binding reactions to the environment might be a functional consequence of protein disorder. Considering the role of ions in biology, it might be a regulatory mechanism of physiological significance.
Seed dispersal increases local species richness and reduces spatial turnover of tropical tree seedlings
Authors: Wandrag Elizabeth M. , Dunham Amy E. , Duncan Richard P. , Rogers Haldre S. 
Published: August 2017

SignificanceDispersal is considered a key process underlying the high spatial diversity of tropical forests, with the seeds of most tropical tree species dispersed by vertebrates, particularly birds. Although it has proven very difficult to quantify the contribution of dispersal to tree species diversity, it is increasingly important to do so in the face of global declines in vertebrate disperser populations. We show that the complete loss of native seed dispersers on the island of Guam is having a major impact on tree seedling regeneration in canopy gaps, leading to species-poor and spatially aggregated seedling communities. These pronounced changes in patterns of seedling regeneration highlight the importance of dispersal in maintaining patterns of diversity in tropical forests.
Feeding Ecology of Pacific Sand Lance in the San Juan Archipelago
Authors: Sisson Nicholas B. , Baker Matthew R. 
Published: August 2017

Abstract
Forage fishes such as Pacific Sand Lance Ammodytes personatus are a crucial link between lower and upper elements in marine food webs, as they transfer energy from plankton to higher trophic levels. Despite their importance to marine food webs, little is known about the population structure and feeding ecology of Pacific Sand Lance. In this study, we examined the population density and diet composition of Pacific Sand Lance as well as feeding patterns and movement in response to tidal, diel, and seasonal cycles in a prominent sand wave field in the San Juan Channel, Washington. A generalized linear model was applied to account for the corresponding effects of tidal, diel, and seasonal trends as well as habitat affinity related to substrate type. We showed that fish distributions were predominantly driven by sediment type and that time of day had a significant influence on foraging behavior with distinct crepuscular feeding patterns. Our results also provide evidence for the cessation of feeding over the fall transition and the onset of a winter dormant period, as observed by increased densities of fish within the sand wave field (177%), a marked increase in the number of empty stomachs (511%), and a significant decrease in condition factor. These trends correspond with the expectations that Pacific Sand Lances exhibit a winter dormant phase and burrow in sediments throughout the winter months to conserve energy and reduce predation risk during periods of low productivity. We anticipate our study to be a starting point for understanding the foraging ecology of the Pacific Sand Lance, particularly in the San Juan Archipelago and Salish Sea. The results of this study may improve the understanding of Pacific Sand Lance habitat and availability to pelagic predators, inform fisheries management, and increase the resolution of marine food web models.
RUCS: rapid identification of PCR primers for unique core sequences
Authors: Thomsen Martin Christen Frølund , Hasman Henrik , Westh Henrik , Kaya Hülya , Lund Ole 
Published: August 2017

Abstract

Motivation
Designing PCR primers to target a specific selection of whole genome sequenced strains can be a long, arduous and sometimes impractical task. Such tasks would benefit greatly from an automated tool to both identify unique targets, and to validate the vast number of potential primer pairs for the targets in silico.

Results
Here we present RUCS, a program that will find PCR primer pairs and probes for the unique core sequences of a positive genome dataset complement to a negative genome dataset. The resulting primer pairs and probes are in addition to simple selection also validated through a complex in silico PCR simulation. We compared our method, which identifies the unique core sequences, against an existing tool called ssGeneFinder, and found that our method was 6.5–20 times more sensitive. We used RUCS to design primer pairs that would target a set of genomes known to contain the mcr-1 colistin resistance gene. Three of the predicted pairs were chosen for experimental validation using PCR and gel electrophoresis. All three pairs successfully produced an amplicon with the target length for the samples containing mcr-1 and no amplification products were produced for the negative samples. The novel methods presented in this manuscript can reduce the time needed to identify target sequences, and provide a quick virtual PCR validation to eliminate time wasted on ambiguously binding primers.

Availability and implementation
Source code is freely available on https://bitbucket.org/genomicepidemiology/rucs. Web service is freely available on https://cge.cbs.dtu.dk/services/RUCS.

Supplementary information
Supplementary data are available at Bioinformatics online.
NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis
Authors: Singer Jochen , Ruscheweyh Hans-Joachim , Hofmann Ariane L , Thurnherr Thomas , Singer Franziska , Toussaint Nora C , Ng Charlotte K Y , Piscuoglio Salvatore , Beisel Christian , Christofori Gerhard , Dummer Reinhard , Hall Michael N , Krek Wilhelm , Levesque Mitchell P , Manz Markus G , Moch Holger , Papassotiropoulos Andreas , Stekhoven Daniel J , Wild Peter , Wüst Thomas , Rinn Bernd , Beerenwinkel Niko 
Published: August 2017

Abstract

Motivation
Next-generation sequencing is now an established method in genomics, and massive amounts of sequencing data are being generated on a regular basis. Analysis of the sequencing data is typically performed by lab-specific in-house solutions, but the agreement of results from different facilities is often small. General standards for quality control, reproducibility and documentation are missing.

Results
We developed NGS-pipe, a flexible, transparent and easy-to-use framework for the design of pipelines to analyze whole-exome, whole-genome and transcriptome sequencing data. NGS-pipe facilitates the harmonization of genomic data analysis by supporting quality control, documentation, reproducibility, parallelization and easy adaptation to other NGS experiments.

Availability and implementation
https://github.com/cbg-ethz/NGS-pipe
A hybrid clustering and ranking method for best positioned logistics distribution centre in Balkan Peninsula
Authors: Simić Dragan , Ilin Vladimir , Svirčević Vasa , Simić Svetlana 
Published: August 2017

AbstractFacility location decisions are critical in strategic planning for a wide range of operational and logistical decisions. Facility location problem with focus on logistics distribution centre (LDC) in Balkan Peninsula (BP) is discussed in this article. Methodological hybrid genetic algorithm, Analytical Hierarchy Process, and fuzzy c-means method is proposed here and it is shown how such a model can be of assistance in analysing a multi criteria decision-making problem. This research represents continuation of three existing studies. The experimental results in our research could be well compared with other official results of the feasibility study of the LDC located in BP.
Cervical Alignment Changes in Patients Developing Proximal Junctional Kyphosis Following Surgical Correction of Adult Spinal Deformity
Authors: Passias Peter G , Horn Samantha R , Jalai Cyrus M , Ramchandran Subaraman , Poorman Gregory W , Kim Han Jo , Smith Justin S , Sciubba Daniel , Soroceanu Alexandra , Ames Christopher P , Hamilton D Kojo , Eastlack Robert , Burton Douglas , Gupta Munish , Bess Shay , Lafage Virginie , Schwab Frank 
Published: August 2017

Abstract

BACKGROUND
Proximal junctional kyphosis (PJK) following adult spinal deformity (ASD) surgery is a well-documented complication, but associations between radiographic PJK and cervical malalignment onset remain unexplored.

OBJECTIVE
To study cervical malalignment in ASD surgical patients that develop PJK.

METHODS
Retrospective review of prospective multicenter database. Inclusion: primary ASD patients (≥5 levels fused, upper instrumented vertebra [UIV] at T2 or above, and 1-yr minimum follow-up) without baseline cervical deformity (CD), defined as ≥2 of the following criteria: T1 slope minus cervical lordosis < 20°, cervical sagittal vertical axis < 4 cm, C2-C7 cervical lordosis < 10°. PJK presence (<10° change in UIV and UIV + 2 kyphosis) and angle were identified 1 yr postoperative. Propensity score matching between PJK and nonPJK groups controlled for baseline alignment. Preoperative and 1-yr postoperative cervical alignment were compared between PJK and nonPJK patients.

RESULTS
One hundred sixty-three patients without baseline CD (54.9 yr, 83.9% female) were included. PJK developed in 60 (36.8%) patients, with 27 (45%) having UIV above T7. PJK patients had significantly greater baseline T1 slope in unmatched and propensity score matching comparisons (P < .05). At 1 yr postoperative, PJK patients had significantly higher T1 slope (P < .001), C2-T3 Cobb (P = .04), and C2-T3 sagittal vertical axis (P = .02). New-onset CD rate in PJK patients was 15%, and 16.5% in nonPJK patients (P > .05). Increased PJK magnitude was associated with increasing T1 slope and C2-T3 SVA (P < .05).

CONCLUSION
Patients who develop PJK following surgical correction of ASD have a 15% incidence of development of new-onset CD. Patients developing PJK following surgical correction of ASD tend to have an increased preoperative T1 slope. Increased progression of C2-T3 Cobb angle and C2-T3 SVA are associated with development of PJK following surgical correction of thoracolumbar deformity.
Sex-Related Differences in the Developmental Morphology of the Atlas
Authors: Asukai Mitsuru , Fujita Tomotada , Suzuki Daisuke , Nishida Tatsuya , Ohishi Tsuyoshi , Matsuyama Yukihiro 
Published: August 2017

Study Design.
A retrospective study.

Objective.
To elucidate sex-related differences in the age at synchondroses closure, the normative size of the atlas, and the ossification patterns of the atlas in Japanese children.

Summary of Background Data.
The atlas develops from three ossification centers during childhood. The anterior and posterior synchondroses, which are separate ossification centers, mimic fracture lines on computed tomography (CT). Sex-related differences of age dependent morphological changes of the atlas in a large sample size have not been reported.

Methods.
This study analyzed data of 688 subjects (449 boys) between 0 and 18 years old who underwent CT examination of the head and/or neck between January 2010 and July 2016. The age at synchondroses closure, anteroposterior outer, inner, and spinal canal widths of the atlas, and variations of the ossification centers were examined.

Results.
Anterior synchondroses closed by 10 years in boys and by 7 years in girls. Significant earlier closure of anterior synchondroses was observed in girls than in boys (P < 0.05 at 4 and 5 years old). Posterior synchondrosis closed by 6 years in boys and by 5 years in girls. The outer, inner, and spinal canal widths increased up to 10 to 15 years in both sexes, although all three parameters in girls peaked 3 years earlier than those in boys. All parameters in boys were significantly larger than those in girls, except in the 10- to 12-year-old age category. Two or more ossification centers in the anterior arch were observed in 18.3% subjects, and 6% had midline ossification centers in the posterior arch of the atlas.

Conclusion.
Distinct sex-related differences in the age at anterior synchondroses closure and the size of the atlas were observed in Japanese children. Knowledge of morphological features of the atlas could help distinguish fractures from synchondroses.

Level of Evidence: 3
Idiopathic Spinal Epidural Fat Accumulation Is Associated With Hyperlipidemia
Authors: Ishihara Shinichi , Fujita Nobuyuki , Yagi Mitsuru , Tsuji Takashi , Michikawa Takehiro , Nishiwaki Yuji , Fukui Yasuyuki , Horiuchi Keisuke , Ishii Ken , Nakamura Masaya , Matsumoto Morio , Watanabe Kota 
Published: August 2017

Study Design.
Single-center retrospective analysis of consecutively collected data.

Objective.
To determine the clinical characteristics of idiopathic spinal epidural lipomatosis (SEL).

Summary of Background Data.
SEL is associated with the overt accumulation of nonencapsulated adipose tissue in the epidural space, leading to spinal cord or nerve root compression. The etiology of this condition is currently not completely understood.

Methods.
Data of 166 male patients who underwent primary surgery for lumbar spinal canal stenosis (LSS) from May 2013 to February 2016 were retrospectively reviewed. Participants were divided into three groups based on the degree of epidural lipomatous lesion. Patient data of age at surgery, body mass index, prevalence of common noncommunicable diseases, blood tests, arteriosclerotic index, and preoperative clinical scores (assessed using the Japanese Orthopedic Association Back Pain Evaluation Questionnaire) were evaluated. Multivariate analysis was performed to assess the potential associated factors for idiopathic SEL.

Results.
Patients with LSS with severe SEL had a significantly higher body mass index and elevated serum levels of total cholesterol and triglyceride compared with those without SEL. Analysis of preoperative clinical scores revealed that patients with SEL experienced pain more frequently and showed less walking ability than did those without SEL. Multivariate analysis revealed that hyperlipidemia was significantly associated with idiopathic SEL (odds ratio = 3.74, 95% confidence interval = 1.31–10.64).

Conclusion.
Our data suggest that aberrant lipid metabolism is related to the pathogenesis of idiopathic SEL and that patients with LSS with idiopathic SEL have more severe pain than do those without SEL.

Level of Evidence: 3
Effects of High-Flow Nasal Cannula on the Work of Breathing in Patients Recovering From Acute Respiratory Failure*
Authors: Delorme Mathieu , Bouchard Pierre-Alexandre , Simon Mathieu , Simard Serge , Lellouche François 
Published: August 2017

Objectives:
High-flow nasal cannula is increasingly used in the management of respiratory failure. However, little is known about its impact on respiratory effort, which could explain part of the benefits in terms of comfort and efficiency. This study was designed to assess the effects of high-flow nasal cannula on indexes of respiratory effort (i.e., esophageal pressure variations, esophageal pressure-time product/min, and work of breathing/min) in adults.

Design:
A randomized controlled crossover study was conducted in 12 patients with moderate respiratory distress (i.e., after partial recovery from an acute episode, allowing physiologic measurements).

Setting:
Institut Universitaire de Cardiologie et de Pneumologie de Québec, QC, Canada.

Subjects:
Twelve adult patients with respiratory distress symptoms were enrolled in this study.

Interventions:
Four experimental conditions were evaluated: baseline with conventional oxygen therapy and high-flow nasal cannula at 20, 40, and 60 L/min. The primary outcomes were the indexes of respiratory effort (i.e., esophageal pressure variations, esophageal pressure-time product/min, and work of breathing/min). Secondary outcomes included tidal volume, respiratory rate, minute volume, dynamic lung compliance, inspiratory resistance, and blood gases.

Measurements and Main Results:
Esophageal pressure variations decreased from 9.8 (5.8–14.6) cm H2O at baseline to 4.9 (2.1–9.1) cm H2O at 60 L/min (p = 0.035). Esophageal pressure-time product/min decreased from 165 (126–179) to 72 (54–137) cm H2O • s/min, respectively (p = 0.033). Work of breathing/min decreased from 4.3 (3.5–6.3) to 2.1 (1.5–5.0) J/min, respectively (p = 0.031). Respiratory pattern variables and capillary blood gases were not significantly modified between experimental conditions. Dynamic lung compliance increased from 38 (24–64) mL/cm H2O at baseline to 59 (43–175) mL/cm H2O at 60 L/min (p = 0.007), and inspiratory resistance decreased from 9.6 (5.5–13.4) to 5.0 (1.0–9.1) cm H2O/L/s, respectively (p = 0.07).

Conclusions:
High-flow nasal cannula, when set at 60 L/min, significantly reduces the indexes of respiratory effort in adult patients recovering from acute respiratory failure. This effect is associated with an improvement in respiratory mechanics.