bluuebunny/crossref_metadata_2025_split huggingface dataset:
Poverty hits children first?
Authors: Fegert J. M. , Harsch D. , Kölch M. 
Published: September 2018

SummaryPoverty is a risk factor for mental health problems during childhood and adolescence in general. The economic crisis (2007–2013) seemed to have intensified poverty in families within the most affected countries, esp. in the southern countries of Europe. Within a selective literature review, existing data on the risk of poverty, mental disorders in parents and further risk factors on mental health of children are analyzed. Direct effects like limited access to mental health care system may exist, but are not proved in general. From a developmental perspective, effects of the crisis seem more indirectly mediated by well-known risk factors for psychiatric disorders of children and adolescents: substance abuse in families, mental disorders of parents and loss of perspectives within families are risk factors both on mental health of a child but also for a low educational level which would be a resilience factor. There is evidence that an increase of child abuse and neglect (adverse childhood experiences, ACE) was linked to the economic crisis. Long-term effects e.g. due to ACE may be observed in later times, when children are grown-up.
Therapieresistente Depression - Perspektiven durch Hirnstimulationsverfahren
Authors: Plichta M. , Köstner N.-C. , Zwanzger P. , Fallgatter A. J. 
Published: September 2018

ZusammenfassungEine leitliniengerechte Therapie der Depression umfasst heute gleichermaßen pharmakologische sowie psychotherapeutische Ansätze. Allerdings sprechen nach wie vor ca. 20-25% der Patienten nicht ausreichend auf die Therapie an. Im Fall von Therapieresistenz ist nationalen wie internationalen Standards zufolge derzeit die Elektrokonvulsionstherapie (EKT) Mittel der Wahl. Demgegenüber ist der aktuelle Stellenwert moderner Hirnstimulationsverfahren unterschiedlich zu beurteilen. Während mittlerweile gute Daten zum Einsatz der repetitiven transkraniellen Magnetstimulation (rTMS) sowie begrenzt zum Einsatz der transkraniellen Gleichstromstimulation (tDCS) bei Depression vorliegen, erfordern die vielversprechenden Befunde zur Vagusnervstimulation (VNS) sowie zur tiefen Hirnstimulation (THS) weitere Forschungsaktivitäten.
The Influence of Implant Position on Final Clinical Outcome and Gait Analysis after Total Knee Arthroplasty
Authors: Jabłoński Jarosław , Sibiński Marcin , Polguj Michał , Kowalczewski Jacek , Marczak Dariusz , Faflik Łukasz , Jabłońska Dorota 
Published: September 2018

AbstractThe aim of the study was to evaluate the impact of implant component alignment on objective and subjective outcomes after total knee arthroplasty (TKA). The rotation of the femoral component and its influence on the final results were also examined. After exclusion, the study examined 102 patients (mean age, 66.28 years; range, 51–79 years) who had undergone unilateral TKA. All of the operative procedures were performed by one surgeon with one type of implant. One year after the operation, improvements in Knee Society's Knee Scoring System, functional score, Western Ontario and McMaster Universities Osteoarthritis Index, and Visual Analog Scale were observed; however, none showed a significant correlation with any of the parameters analyzed by X-ray or computed tomography (CT) (α, β, γ, δ angles and posterior condylar angle [PCA]). Significant improvements were found for the vast majority of the parameters used for gate analysis at the final follow-up. Significant correlations were found between PCA angle and differences in stance phase, swing phase of the operated limb, and step width (all p = 0.03). No other significant relationships were found between gait parameters and indicators measured by X-ray and CT. None of the analyzed radiographic parameters, including rotation of the femoral component, correlated with final clinical results. Neither femoral internal rotation of 3° to 6°, nor rotation of 0° ± 3° or 0° ± 6° influenced the outcome. One year after TKA, a significant improvement was observed in both functional and gait parameters.
Pure Endoscopic Lateral Orbitotomy Approach to the Cavernous Sinus, Posterior, and Infratemporal Fossae: Anatomic Study
Authors: Laleva Lili , Spiriev Toma , Dallan Iacopo , Prats-Galino Alberto , Catapano Giuseppe , Nakov Vladimir , de Notaris Matteo 
Published: September 2018

Objective The aim of this anatomic study is to describe a fully endoscopic lateral orbitotomy extradural approach to the cavernous sinus, posterior, and infratemporal fossae.
Material and Methods Three prefixed latex-injected head specimens (six orbital exposures) were used in the study. Before and after dissection, a computed tomography scan was performed on each cadaver head and a neuronavigation system was used to guide the approach. The extent of bone removal and the area of exposure of the targeted corridor were evaluated with the aid of OsiriX software (Pixmeo, Bernex, Switzerland).
Results The lateral orbital approach offers four main endoscopic extradural routes: the anteromedial, posteromedial, posterior, and inferior. The anteromedial route allows a direct route to the optic canal by removal of the anterior clinoid process, whereas the posteromedial route allows for exposure of the lateral wall of the cavernous sinus. The posterior route is targeted to Meckel's cave and provides access to the posterior cranial fossa by exposure and drilling of the petrous apex, whereas the inferior route gives access to the pterygopalatine and infratemporal fossae by drilling the floor of the middle cranial fossa and the bone between the second and third branches of the trigeminal nerve.
Conclusion The lateral orbitotomy endoscopic approach provides direct access to the cavernous sinus, posterior, and infratemporal fossae. Advantages of the approach include a favorable angle of attack, minimal brain retraction, and the possibility of dissection within the two dural layers of the cavernous sinus without entering its neurovascular compartment.
Delayed Facial Nerve Paralysis after Vestibular Schwannoma Resection
Authors: Yawn Robert J. , Dedmon Matthew M. , Xie Deborah , Thompson Reid C. , O'Malley Matthew R. , Bennett Marc L. , Rivas Alejandro , Haynes David S. 
Published: September 2018

Objective To describe the incidence and clinical course of patients who develop delayed facial nerve paralysis (DFNP) after surgical resection of vestibular schwannoma.
Setting Tertiary skull base center.
Methods Retrospective chart review.
Results Two hundred and forty six consecutive patients, who underwent surgical resection for vestibular schwannoma at a single center between 2010 and 2015, were analyzed. Of these patients, 22 (8.9%) developed DFNP, defined here as deterioration of function by at least 2 House–Brackmann (HB) grades within 30 days in patients with immediate postoperative HB ≤ 3. The mean age of DFNP patients was 47.2 years (range: 17–67) and 16 (73%) were female. The mean tumor size in greatest dimension was 2.1 cm (range: 0.7–3.5 cm). At the conclusion of each case, the facial nerve stimulated at the brainstem. Mean immediate postoperative facial nerve function was HB 1.8 (range: 1–3). Average facial nerve function at the 3-week-postoperative visit was 4.4 (range: 2–6). In 1-year, 8 patients (36%) recovered HB 1 function, 10 patients (46%) recovered to HB 2, and 2 patients (9%) were HB 3. The remaining 2 patients did not recover function and were HB 6 at last follow-up. Initial postoperative facial nerve function (HB 1 or HB 2) was associated with improved recovery to normal (HB 1) function (p = 0.018).
Conclusion A majority of patients that develop delayed paralysis will recover excellent facial nerve function. Patients should be counseled; however, a small percentage of patients will not recover function long-term, despite having a previously functioning and anatomically intact nerve.
What Is the Price and Claimed Efficacy of Platelet-Rich Plasma Injections for the Treatment of Knee Osteoarthritis in the United States?
Authors: Piuzzi Nicolas S. , Ng Mitchell , Kantor Ariel , Ng Kenneth , Kha Stephanie , Mont Michael A. , Muschler George F. 
Published: September 2018

AbstractPlatelet-rich plasma (PRP) injections are often used for the treatment of knee osteoarthritis (OA), despite clinical value and cost-effectiveness not being definitely established. PRP injections are considered as a potential means of reducing pain and improving function in patients with knee OA, in the hope of delaying or avoiding the need for surgical intervention. Centers that offer PRP injections usually charge patients out of pocket and directly market services. Therefore, the purpose of this study was to quantify the current (1) prices and (2) marketed clinical efficacy of autologous PRP injections for knee OA. A prospective cross-sectional study was performed based on 286 centers identified in the United States offering PRP injections for knee OA. A total of 179 (73.4%) centers were successfully contacted via e-mail or phone, using a simulated 52-year-old male patient with knee OA. Scripted questions were asked by the simulated patient to determine the current marketed prices and clinical efficacy, either reported as “good results” or “symptomatic improvement,” claimed by each treating center. The mean price for a single unilateral knee same-day PRP injection was $714 with a standard deviation of $144 (95% confidence interval [CI]: $691–737, n = 153). The mean claim of clinical efficacy was 76% with a standard deviation of 11% (95% CI: 73.5–78.3%, n = 84). Out of the 84 clinics, 10 claimed “90 to 100% efficacy,” 27 claimed “80 to 90%,” 29 claimed “70 to 80%,” 9 claimed “60 to 70%,” 8 claimed “50 to 60%,” and 1 claimed “40 to 60%.” These findings provide a unique perspective on the PRP market for the treatment of knee OA that is valuable to physicians and health care providers in providing better education to patients on the associated costs and purported clinical benefits of PRP injections.
Basics of Neurointervention
Authors: Matin Tariq , Deshmukh Aviraj , Al-Schameri A. 
Published: September 2018

AbstractNeurointervention is a subspecialty of neurosciences which offers a minimally invasive therapy for the vascular lesions of the central nervous system. The resources, techniques, and indications of neurointervention therapy are rapidly expanding and becoming diverse. With the support of robust scientific data, neurointervention has established itself as a first line therapy for many neurovascular diseases. This article provides an overview about the various material used in neurointervention, basic steps followed in some common neurointerventional procedures, and its related complications. In the era of 21st century, any young physician or surgeon as well as residents-in-training dealing with neurovascular cases should have some insight into these basic concepts so as to provide better care to their patients.
β-Ga2O3 for wide-bandgap electronics and optoelectronics
Authors: Galazka Zbigniew 
Published: September 2018

Abstract

β-Ga2O3 is an emerging, ultra-wide bandgap (energy gap of 4.85 eV) transparent semiconducting oxide, which attracted recently much scientific and technological attention. Unique properties of that compound combined with its advanced development in growth and characterization place β-Ga2O3 in the frontline of future applications in electronics (Schottky barrier diodes, field-effect transistors), optoelectronics (solar- and visible-blind photodetectors, flame detectors, light emitting diodes), and sensing systems (gas sensors, nuclear radiation detectors). A capability of growing large bulk single crystals directly from the melt and epi-layers by a diversity of epitaxial techniques, as well as explored material properties and underlying physics, define a solid background for a device fabrication, which, indeed, has been boosted in recent years. This required, however, enormous efforts in different areas of science and technology that constitutes a chain linking together engineering, metrology and theory. The present review includes material preparation (bulk crystals, epi-layers, surfaces), an exploration of optical, electrical, thermal and mechanical properties, as well as device design/fabrication with resulted functionality suitable for different fields of applications. The review summarizes all of these aspects of β-Ga2O3 at the research level that spans from the material preparation through characterization to final devices.
Automatic rough alignment for key components in laser driven experiments using fiducial markers
Authors: Popescu D C , Cernaianu M O , Dumitrache I 
Published: September 2018

Abstract
In the laser - solid target experiments at ELI-NP, maximizing the availability of the laser system and hence the number of shots during a campaign is envisaged. One of the factors that affects this is the time for preparing the experiment and the time for changing the targets between shots. In this paper we present a method for automatic rough alignment of various experimental setup instruments like the target frames, microscopes and diagnostics. Giving the impossibility to define a global reference system that captures precisely enough the relative position of all equipment in a continuously changing experimental setup, the method developed is using relative optical measurements using fiducial markers. The method is conceived to be used along with other micron-level alignment methods as a pre-alignment phase. Along this work, a setup and the algorithms were developed in order to test the accuracy of the method. First tests revealed a rough alignment accuracy between 100-200μm which was achieved using only a low resolution imaging camera. The accuracy can be further improved using higher resolution imaging systems or by developing new key points in the algorithm that are discussed at the end of the paper.
Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb
Authors: Cossard Guillaume G , Toups Melissa A , Pannell John R 
Published: September 2018

AbstractBackground and AimsSexual dimorphism in morphology, physiology or life history traits is common in dioecious plants at reproductive maturity, but it is typically inconspicuous or absent in juveniles. Although plants of different sexes probably begin to diverge in gene expression both before their reproduction commences and before dimorphism becomes readily apparent, to our knowledge transcriptome-wide differential gene expression has yet to be demonstrated for any angiosperm species.MethodsThe present study documents differences in gene expression in both above- and below-ground tissues of early pre-reproductive individuals of the wind-pollinated dioecious annual herb, Mercurialis annua, which otherwise shows clear sexual dimorphism only at the adult stage.Key ResultsWhereas males and females differed in their gene expression at the first leaf stage, sex-biased gene expression peaked just prior to, and after, flowering, as might be expected if sexual dimorphism is partly a response to differential costs of reproduction. Sex-biased genes were over-represented among putative sex-linked genes in M. annua but showed no evidence for more rapid evolution than unbiased genes.ConclusionsSex-biased gene expression in M. annua occurs as early as the first whorl of leaves is produced, is highly dynamic during plant development and varies substantially between vegetative tissues
Development of a protein–ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions
Authors: Wójcikowski Maciej , Kukiełka Michał , Stepniewska-Dziubinska Marta M , Siedlecki Pawel 
Published: September 2018

Abstract

Motivation
Fingerprints (FPs) are the most common small molecule representation in cheminformatics. There are a wide variety of FPs, and the Extended Connectivity Fingerprint (ECFP) is one of the best-suited for general applications. Despite the overall FP abundance, only a few FPs represent the 3D structure of the molecule, and hardly any encode protein–ligand interactions.

Results
Here, we present a Protein–Ligand Extended Connectivity (PLEC) FP that implicitly encodes protein–ligand interactions by pairing the ECFP environments from the ligand and the protein. PLEC FPs were used to construct different machine learning models tailored for predicting protein–ligand affinities (pKi∕d). Even the simplest linear model built on the PLEC FP achieved Rp = 0.817 on the Protein Databank (PDB) bind v2016 ‘core set’, demonstrating its descriptive power.

Availability and implementation
The PLEC FP has been implemented in the Open Drug Discovery Toolkit (https://github.com/oddt/oddt).

Supplementary information
Supplementary data are available at Bioinformatics online.
Phylolink: phylogenetically-based profiling, visualisations and metrics for biodiversity
Authors: Miller Joseph T , Pirzl Rebecca , Rosauer Dan , Jolley-Rogers Garry , Varghese Temi 
Published: September 2018

Abstract

Summary
Phylolink is a research collaboration toolkit through which biodiversity can be explored from a phylogenetic perspective. It is an update of PhyloJiVE that has been integrated into the framework of the Atlas of Living Australia, including its spatial portal. Phylolink connects phylogenetic tree nodes with species occurrence records, environmental data, and species trait information. Features new to Phylolink allow users to upload and download spatial datasets, store files and link to the ALA spatial portal, improve graphics and provide the novel ability to analyze environmental attributes of species and clades distributions. Species richness and phylogenetic diversity comparisons can be made among geographic areas. The result is a powerful way of combining data to generate flexible and customizable visualizations, profiles and metrics for biodiversity.

Availability and implementation
Phylolink is available at the Atlas of Living Australia, http://phylolink.ala.org.au/. It works on any browser and users can select from a range of stored phylogenetic trees and spatial datasets, or upload their own.
SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data
Authors: Yang Yuchen , Huh Ruth , Culpepper Houston W , Lin Yuan , Love Michael I , Li Yun 
Published: September 2018

Abstract

Motivation
Accurately clustering cell types from a mass of heterogeneous cells is a crucial first step for the analysis of single-cell RNA-seq (scRNA-Seq) data. Although several methods have been recently developed, they utilize different characteristics of data and yield varying results in terms of both the number of clusters and actual cluster assignments.

Results
Here, we present SAFE-clustering, single-cell aggregated (From Ensemble) clustering, a flexible, accurate and robust method for clustering scRNA-Seq data. SAFE-clustering takes as input, results from multiple clustering methods, to build one consensus solution. SAFE-clustering currently embeds four state-of-the-art methods, SC3, CIDR, Seurat and t-SNE + k-means; and ensembles solutions from these four methods using three hypergraph-based partitioning algorithms. Extensive assessment across 12 datasets with the number of clusters ranging from 3 to 14, and the number of single cells ranging from 49 to 32, 695 showcases the advantages of SAFE-clustering in terms of both cluster number (18.2–58.1% reduction in absolute deviation to the truth) and cluster assignment (on average 36.0% improvement, and up to 18.5% over the best of the four methods, measured by adjusted rand index). Moreover, SAFE-clustering is computationally efficient to accommodate large datasets, taking &lt;10 min to process 28 733 cells.

Availability and implementation
SAFEclustering, including source codes and tutorial, is freely available at https://github.com/yycunc/SAFEclustering.

Supplementary information
Supplementary data are available at Bioinformatics online.
SequencEnG: an interactive knowledge base of sequencing techniques
Authors: Zhang Yi , Manjunath Mohith , Kim Yeonsung , Heintz Joerg , Song Jun S 
Published: September 2018

Abstract

summary
Next-generation sequencing (NGS) techniques are revolutionizing biomedical research by providing powerful methods for generating genomic and epigenomic profiles. The rapid progress is posing an acute challenge to students and researchers to stay acquainted with the numerous available methods. We have developed an interactive online educational resource called Sequencing Techniques Engine for Genomics (SequencEnG) to provide a tree-structured knowledge base of 66 different sequencing techniques and step-by-step NGS data analysis pipelines comparing popular tools. SequencEnG is designed to facilitate barrier-free learning of current NGS techniques and provides a user-friendly interface for searching through experimental and analysis methods.

Availability and implementation
SequencEnG is part of the project Knowledge Engine for Genomics (KnowEnG) and is freely available at http://education.knoweng.org/sequenceng/.
Resting-State Activity in High-Order Visual Areas as a Window into Natural Human Brain Activations
Authors: Strappini Francesca , Wilf Meytal , Karp Ofer , Goldberg Hagar , Harel Michal , Furman-Haran Edna , Golan Tal , Malach Rafael 
Published: September 2018

Abstract
A major limitation of conventional human brain research has been its basis in highly artificial laboratory experiments. Due to technical constraints, little is known about the nature of cortical activations during ecological real life. We have previously proposed the “spontaneous trait reactivation (STR)” hypothesis arguing that resting-state patterns, which emerge spontaneously in the absence of external stimulus, reflect the statistics of habitual cortical activations during real life. Therefore, these patterns can serve as a window into daily life cortical activity. A straightforward prediction of this hypothesis is that spontaneous patterns should preferentially correlate to patterns generated by naturalistic stimuli compared with artificial ones. Here we targeted high-level category-selective visual areas and tested this prediction by comparing BOLD functional connectivity patterns formed during rest to patterns formed in response to naturalistic stimuli, as well as to more artificial category-selective, dynamic stimuli. Our results revealed a significant correlation between the resting-state patterns and functional connectivity patterns generated by naturalistic stimuli. Furthermore, the correlations to naturalistic stimuli were significantly higher than those found between resting-state patterns and those generated by artificial control stimuli. These findings provide evidence of a stringent link between spontaneous patterns and the activation patterns during natural vision.