bluuebunny/crossref_metadata_2025_split huggingface dataset:
VikNGS: a C++ variant integration kit for next generation sequencing association analysis
Authors: Baskurt Zeynep , Mastromatteo Scott , Gong Jiafen , Wintle Richard F , Scherer Stephen W , Strug Lisa J 
Published: September 2019

Abstract

Summary
Integration of next generation sequencing data (NGS) across different research studies can improve the power of genetic association testing by increasing sample size and can obviate the need for sequencing controls. If differential genotype uncertainty across studies is not accounted for, combining datasets can produce spurious association results. We developed the Variant Integration Kit for NGS (VikNGS), a fast cross-platform software package, to enable aggregation of several datasets for rare and common variant genetic association analysis of quantitative and binary traits with covariate adjustment. VikNGS also includes a graphical user interface, power simulation functionality and data visualization tools.

Availability and implementation
The VikNGS package can be downloaded at http://www.tcag.ca/tools/index.html.

Supplementary information
Supplementary data are available at Bioinformatics online.
MitoTrack, a user-friendly semi-automatic software for lineage tracking in living embryos
Authors: Trullo A , Dufourt J , Lagha M 
Published: September 2019

Abstract

Motivation
During development, progenitor cells undergo multiple rounds of cellular divisions during which transcriptional programs must be faithfully propagated. Investigating the timing of transcriptional activation, which is a highly stochastic phenomenon, requires the analysis of large amounts of data. In order to perform automatic image analysis of transcriptional activation, we developed a software that segments and tracks both small and large objects, leading the user from raw data up to the results in their final form.

Results
MitoTrack is a user-friendly open-access integrated software that performs the specific dual task of reporting the precise timing of transcriptional activation while keeping lineage tree history for each nucleus of a living developing embryo. The software works automatically but provides the possibility to easily supervise, correct and validate each step.

Availability and implementation
MitoTrack is an open source Python software, embedded within a graphical user interface (download here).

Supplementary information
Supplementary data are available at Bioinformatics online.
Deep-learning with synthetic data enables automated picking of cryo-EM particle images of biological macromolecules
Authors: Yao Ruijie , Qian Jiaqiang , Huang Qiang 
Published: September 2019

Abstract

Motivation
Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique for determining 3D structures of biological macromolecules at near-atomic resolution. However, this approach requires picking huge numbers of macromolecular particle images from thousands of low-contrast, high-noisy electron micrographs. Although machine-learning methods were developed to get rid of this bottleneck, it still lacks universal methods that could automatically picking the noisy cryo-EM particles of various macromolecules.

Results
Here, we present a deep-learning segmentation model that employs fully convolutional networks trained with synthetic data of known 3D structures, called PARSED (PARticle SEgmentation Detector). Without using any experimental information, PARSED could automatically segment the cryo-EM particles in a whole micrograph at a time, enabling faster particle picking than previous template/feature-matching and particle-classification methods. Applications to six large public cryo-EM datasets clearly validated its universal ability to pick macromolecular particles of various sizes. Thus, our deep-learning method could break the particle-picking bottleneck in the single-particle analysis, and thereby accelerates the high-resolution structure determination by cryo-EM.

Availability and implementation
The PARSED package and user manual for noncommercial use are available as Supplementary Material (in the compressed file: parsed_v1.zip).

Supplementary information
Supplementary data are available at Bioinformatics online.
Topology-based classification of tetrads and quadruplex structures
Authors: Popenda Mariusz , Miskiewicz Joanna , Sarzynska Joanna , Zok Tomasz , Szachniuk Marta 
Published: September 2019

Abstract

Motivation
Quadruplexes attract the attention of researchers from many fields of bio-science. Due to a specific structure, these tertiary motifs are involved in various biological processes. They are also promising therapeutic targets in many strategies of drug development, including anticancer and neurological disease treatment. The uniqueness and diversity of their forms cause that quadruplexes show great potential in novel biological applications. The existing approaches for quadruplex analysis are based on sequence or 3D structure features and address canonical motifs only.

Results
In our study, we analyzed tetrads and quadruplexes contained in nucleic acid molecules deposited in Protein Data Bank. Focusing on their secondary structure topology, we adjusted its graphical diagram and proposed new dot-bracket and arc representations. We defined the novel classification of these motifs. It can handle both canonical and non-canonical cases. Based on this new taxonomy, we implemented a method that automatically recognizes the types of tetrads and quadruplexes occurring as unimolecular structures. Finally, we conducted a statistical analysis of these motifs found in experimentally determined nucleic acid structures in relation to the new classification.

Availability and implementation
https://github.com/tzok/eltetrado/

Supplementary information
Supplementary data are available at Bioinformatics online.
EvoEF2: accurate and fast energy function for computational protein design
Authors: Huang Xiaoqiang , Pearce Robin , Zhang Yang 
Published: September 2019

Abstract

Motivation
The accuracy and success rate of de novo protein design remain limited, mainly due to the parameter over-fitting of current energy functions and their inability to discriminate incorrect designs from correct designs.

Results
We developed an extended energy function, EvoEF2, for efficient de novo protein sequence design, based on a previously proposed physical energy function, EvoEF. Remarkably, EvoEF2 recovered 32.5%, 47.9% and 22.3% of all, core and surface residues for 148 test monomers, and was generally applicable to protein–protein interaction design, as it recapitulated 30.9%, 42.4%, 31.3% and 21.4% of all, core, interface and surface residues for 88 test dimers, significantly outperforming EvoEF on the native sequence recapitulation. We further used I-TASSER to evaluate the foldability of the 148 designed monomer sequences, where all of them were predicted to fold into structures with high fold- and atomic-level similarity to their corresponding native structures, as demonstrated by the fact that 87.8% of the predicted structures shared a root-mean-square-deviation less than 2 Å to their native counterparts. The study also demonstrated that the usefulness of physical energy functions is highly correlated with the parameter optimization processes, and EvoEF2, with parameters optimized using sequence recapitulation, is more suitable for computational protein sequence design than EvoEF, which was optimized on thermodynamic mutation data.

Availability and implementation
The source code of EvoEF2 and the benchmark datasets are freely available at https://zhanglab.ccmb.med.umich.edu/EvoEF.

Supplementary information
Supplementary data are available at Bioinformatics online.
Is Pteropyrum a pathway to C4 evolution in Polygonaceae? An integrative approach to the taxonomy and anatomy of Pteropyrum (C3), an immediate relative of Calligonum (C4)
Authors: Doostmohammadi Moslem , Malekmohammadi Maryam , Djamali Morteza , Akhani Hossein 
Published: September 2019

AbstractPteropyrum is a small genus of Polygonaceae with four species from the arid regions of Iran and adjacent countries. Pteropyrum spp. are not precisely delimitated and are difficult to identify because of their high plasticity in morphological characters. Pteropyrum (C3) has a close affinity to Calligonum (C4) and is therefore a suitable case for C4 evolutionary studies. We investigated the morphology and micromorphology (including pollen morphology) of Pteropyrum and elucidated the phylogenetic relationships with Atraphaxis and Calligonum using nuclear ITS sequences. Characteristics of the photosynthetic tissues such as volume and number of layers of primary carbon assimilation tissues (PCA) and photosynthetic carbon reduction tissue (PCR) were studied. In addition, the leaf and cotyledon anatomical characters of Pteropyrum (C3), Atraphaxis (C3) and Calligonum (C4), and their δ 13C values were compared to look for evolutionary changes in assimilating organs. The molecular phylogenetic tree identifies two strongly supported clades in Pteropyrum and its close relationship with Calligonum, confirming previous studies. Some morphologically similar species belong to different clades, which is probably due to convergent evolution and homoplasy. Leaf anatomical studies show that Atraphaxis has a multilayered mesophyll tissue, whereas Calligonum has one-layered mesophyll cells. The volume and layer number of mesophyll tissue cells decreases, whereas water storage tissue area significantly increases from Atraphaxis to Pteropyrum and Calligonum. This phenomenon confirms previous studies in other lineages with C4 salsoloid anatomy that have evolved through increasing of water storage tissue and succulence of assimilating organs. In the taxonomic part of the paper, a key to identification of accepted taxa of Pteropyrum, description of species and distribution maps are presented based on numerous herbarium specimens and our own rich collections from the field. Four new species are described based on a combination of morphology of seedlings and mature plants, pollen morphology and molecular data. A subspecific classification is suggested to show morpho-geographical variation of Pteropyrum aucheri s.l.
Official Acts and Beyond: Towards an Accurate Interpretation of Diplomatic Immunity Ratione Materiae under the Vienna Convention on Diplomatic Relations
Authors: Shi Xinxiang 
Published: September 2019

Abstract
This article explores the scope of diplomatic immunity ratione materiae under the Vienna Convention on Diplomatic Relations. The difficulty regarding the topic lies in the interpretation of what constitutes an act performed “in the exercise of” diplomatic functions. Based on a critique of differing views, it is argued that diplomatic immunity ratione materiae covers not only official acts stricto sensu, but also certain private acts ancillary or incidental to the performance of diplomatic functions. In practice, the availability of the immunity is heavily dependent on the factual end of a case. Therefore, instead of using general exceptions or standards to denote the scope of the immunity, it is better to determine the immunity on a case-by-case basis in light of the seriousness of an act and the connection between the act and the functions performed.
Severe Human Metapneumovirus and Group A Streptococcus Pneumonia in an Immunocompetent Adult
Authors: Biggs Holly M , Van Beneden Chris A , Kurkjian Katie , Kobayashi Miwako , Peret Teresa C T , Watson John T , Schneider Eileen , Gerber Susan I , Ravishankar Jayashree 
Published: September 2019

Abstract
An immunocompetent adult with asthma developed severe human metapneumovirus (HMPV) illness complicated by group A Streptococcus coinfection, progressing to acute respiratory distress syndrome and shock. Several coworkers had less severe HMPV infection. HMPV can cause severe respiratory illness in healthy adults and should be considered as a potential cause of community respiratory outbreaks.
A case report: ‘happy heart’ syndrome in a patient treated with atomoxetine for attention deficit hyperactivity disorder
Authors: Athanassopoulos Petros , Y-Hassan Shams 
Published: September 2019

Abstract

Background
Takotsubo syndrome (TS) is an acute cardiac disease entity with a clinical presentation resembling that of an acute coronary syndrome. Numerous physical stress factors including pheochromocytoma, epinephrine, and norepinephrine administration, and even physiological exercise have been reported to induce TS. Takotsubo syndrome induced by medications causing elevation of plasma norepinephrine as serotonin-norepinephrine reuptake inhibitor or selective norepinephrine reuptake inhibitor (atomoxetine) has been reported.

Case summary
We report on the case of a 49-year-old woman who was on atomoxetine treatment for attention deficit hyperactivity disorder, developed TS in association with sexual intercourse.

Discussion
The TS pattern in this patient was the type of mid-apical ballooning with apical tip-sparing at presentation. Two days later, TS evolved to mid-ventricular pattern. Takotsubo syndrome resolved completely 1 month after the index presentation.
Jones & Sufrin's EU Competition Law
Authors: Jones Alison , Sufrin Brenda , Dunne Niamh 
Published: September 2019

Abstract
EU Competition Law: Text, Cases, and Materials provides a complete guide to European competition law in a single authoritative volume. Carefully selected extracts from key cases, academic articles, and statutory materials are accompanied by in-depth author commentary from three experienced academics in the field. Thorough footnoting and referencing give a tour of the available literature, making this an ideal text and stand-alone resource for undergraduate and postgraduate students, as well as for competition law scholars engaged in specialized study. This seventh edition has been fully updated with detailed coverage and commentary on recent developments. These include the EU Courts’ judgments on Articles 101, 102 and 106 including Intel; cases on the Commission’s enforcement powers and judicial review; new legislation and guidelines on technology transfer; the revised de minimis notice; Commission actions in the digital economy, including the Google case; the directive on damages; and thorough discussion of ongoing developments in competition law such as the Commission's enforcement policy against cartels, the appraisal of mergers, the use of commitments decisions and the compatibility of EU competition procedures with human rights provisions.
Horizontal Cooperation Agreements
Authors: Jones Alison , Sufrin Brenda , Dunne Niamh 
Published: September 2019

Abstract
This chapter discusses EU competition policy towards horizontal cooperation agreements. It covers joint ventures; the contents of the 2010 Guidelines; the general approach to horizontal cooperation agreements in the Guidelines; information agreements; research and development agreements, including the block emption, Regulation 1217/2010; production agreements, including the block exemption on specialisation agreements, Regulation 1218/2010 ; purchasing agreements; commercialisation agreements; standardisation agreements; and agreements in particular sectors, such as the joint buying or selling of media rights to sports events.
Licensing Agreements and Other Agreements Involving Intellectual Property Rights
Authors: Jones Alison , Sufrin Brenda , Dunne Niamh 
Published: September 2019

Abstract
This chapter examines some of the different types of intellectual property rights (IPRs) before outlining the relationship between intellectual property and both EU competition law and the EU free movement rules. It focuses, however, on IP licensing agreements and their treatment under Article 101. The chapter traces the development of EU competition policy to IP licensing agreements and examine the current Technology Transfer Block Exemption and the Guidelines in detail. It also examines patent settlement agreements (including pay for delay agreements), patnet pools, trade mark licences, trade mark delimitation agreements, and copyright (other than software) licences not covered by the TTBER and Guidelines.
Large deletions and untargeted substitutions induced by abasic site analog on leading versus lagging strand templates in human cells
Authors: Suzuki Tetsuya , Katayama Yuri , Komatsu Yasuo , Kamiya Hiroyuki 
Published: September 2019

Abstract
The tetrahydrofuran-type abasic site analog (THF) induces large deletion mutations in human cells. To compare the large deletions induced by THF on leading and lagging strand templates, plasmid DNAs bearing the analog at a specific position outside the supF gene were introduced into human U2OS cells. The replicated DNAs recovered from the transfected cells were electroporated into an Escherichia coli indicator strain. THF on the lagging strand template produced more supF mutants than THF on the leading strand template. This unequal mutagenicity was due to the higher frequencies of not only large deletions but also untargeted base substitutions induced in the gene. These results suggested that both types of mutations occur more frequently when abasic sites are formed on the lagging strand template.
Multimodal Magnetic Resonance Imaging reveals alterations of sensorimotor circuits in restless legs syndrome
Authors: Stefani Ambra , Mitterling Thomas , Heidbreder Anna , Steiger Ruth , Kremser Christian , Frauscher Birgit , Gizewski Elke R , Poewe Werner , Högl Birgit , Scherfler Christoph 
Published: September 2019

AbstractStudy ObjectivesIntegrated information on brain microstructural integrity and iron storage and its impact on the morphometric profile is not available in restless legs syndrome (RLS). We applied multimodal magnetic resonance imaging (MRI) including diffusion tensor imaging, the transverse relaxation rate (R2*), a marker for iron storage, as well as gray and white matter volume measures to characterize RLS-related MRI signal distribution patterns and to analyze their associations with clinical parameters.MethodsEighty-seven patients with RLS (mean age 51, range 20–72 years; disease duration, mean 13 years, range 1–46 years, of those untreated n = 30) and 87 healthy control subjects, individually matched for age and gender, were investigated with multimodal 3T MRI.ResultsVolume of the white matter compartment adjacent to the post- and precentral cortex and fractional anisotropy (FA) of the frontopontine tract were both significantly reduced in RLS compared to healthy controls, and these alterations were associated with disease duration (r = 0.25, p = 0.025 and r = 0.23, p = 0.037, respectively). Corresponding gray matter volume increases of the right primary motor cortex in RLS (p &lt; 0.001) were negatively correlated with the right FA signal of the frontopontine tract (r = −0.22; p &lt; 0.05). Iron content evaluated with R2* was reduced in the putamen as well as in temporal and occipital compartments of the RLS cohort compared to the control group (p &lt; 0.01).ConclusionsMultimodal MRI identified progressing white matter decline of key somatosensory circuits that may underlie the perception of sensory leg discomfort. Increases of gray matter volume of the premotor cortex are likely to be a consequence of functional neuronal reorganization.
III–1 The Benefit of LIPUS After Tibial Condylar Valgus Osteotomy (TCVO)
Authors: Nishii Yukinobu , Kinugasa Kiyoto 
Published: September 2019

Objective:
The purpose of this study is to investigate the benefit of LIPUS after Tibial Condylar Valgus Osteotomy (TCVO) for the osteoarthritis of the knee joint.

Materials and Methods:
This is retrospective study and the population of the study is 12 cases after TCVO with same locking plate and same artificial bone graft. Seven cases were treated LIPUS after TCVO (L group), and five cases were no LIPUS (NL group). Comparison was made of the period until bone fusion in L group and the NL group. The judgement of bone fusion was that the gap of the most proximal part of the osteotomy is no longer visible in the simple X-ray image.

Results:
The average of age was 63 (58–69) year old in L group, and 67 (59–76) year old in NL group. There was no significant difference in age between L group and the NL group. The average of the time of bone fusion was 73.6 (62–85) days in L group, and 95.0 (84–114) days in NL group. There were significant differences in the time of bone fusion between L group and the NL group (P < 0.05: Mann Whitney U test).

Discussion:
Usefulness of LIPUS after TCVO has been suggested in this study, although there is a limit to having a small number of surveys. There is a variation in the gap of the osteotomy, the time of bone fusion may be different depending on the size of the gap. There is a need to investigate the difference due to the treatment site of LIPUS.
A Prospective Analysis of Motor and Cognitive Skill Retention in Novice Learners of Point of Care Ultrasound
Authors: Rappaport Charles A. , McConomy Bryan C. , Arnold Nicholas R. , Vose Aaron T. , Schmidt Gregory A. , Nassar Boulos 
Published: September 2019

Objectives:
To identify the time at which point of care ultrasound static image recognition and image acquisition skills decay in novice learners.

Setting:
The University of Iowa Hospitals and Clinics.

Subjects:
Twenty-four subjects (23 first-year medical students and one first-year physician assistant student).

Design:
The subjects completed an initial didactic and hands-on session with immediate testing of learned image acquisition and static image identification skills.

Interventions:
Retesting occurred at 1, 4, and 8 weeks after the initial training session with no retraining in between. Image acquisition skills were obtained on the same healthy male volunteers, and the students were given no immediate feedback on their performance. The image identification skills were assessed with a 10 question test at each follow-up session.

Measurements and Main Results:
For pleural ultrasound by 4 weeks, there was a significant decline of the ability to identify A-lines (p = 0.0065). For pleural image acquisition, there was no significant decline in the ability to demonstrate lung sliding. Conversely, cardiac image recognition did not significantly decline throughout the study, while the ability to demonstrate cardiac images at 4 weeks (parasternal short axis view) did (p = 0.0008).

Conclusions:
Motor and cognitive skills decay at different times for pleural and cardiac images. Future ultrasound curricula should retrain skills at a maximum of 8 weeks from initial training. They should focus more on didactic sessions related to image identification for pleural images, and more hands-on image acquisition training for cardiac images, which represents a novel finding.