bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective Particle Filtering in a Large Acoustophoretic Serpentine Channel
Authors: Kandemir M. H. , Wagterveld R. M. , Yntema D. R. , Keesman K. J. 
Published: May 2019

AbstractThe objective of this study is to investigate the performance of a serpentine channel for acoustically driven selective particle filtering. The channel consists of sharp corners and straight sections, and the acoustic field is affecting the particles throughout the channel. A prototype of the separator channel is manufactured using 3D printing. Acoustic waves are generated by a piezoelectric transducer operating near 2 MHz. Computer simulations are carried out to explore and visualize the flow field and acoustic field in the separator. Selective particle trapping is aimed to be achieved in the hairpin sections, which is confirmed by experiments. Spherical polyethylene particles of 34 µm, 70 µm and 100 µm diameter are used to demonstrate selective trapping by adjusting the flow rate in the channel or voltage input to the transducer. In addition, wheat beer containing yeast up to 20 µm size is selectively filtered by adjusting the flow rate to the channel. Experiments demonstrate that selective particle filtering is possible in the serpentine channel as both methods yield clear separation thresholds.
Direct-acting oral anticoagulants (DOACs) in pregnancy: new insight from VigiBase®
Authors: Sessa Maurizio , Mascolo Annamaria , Callréus Torbjörn , Capuano Annalisa , Rossi Francesco , Andersen Morten 
Published: May 2019

AbstractWe aimed to perform an analysis of individual case safety reports retrieved after the Standardized MedDRA Query “Pregnancy and neonatal topics” for which Direct-Acting Oral Anticoagulants (DOACs) were claimed as suspected/interacting drugs. Additionally, to investigate if exists a disproportion of cases reporting “Pregnancy and neonatal topics” adverse events rather than other adverse events for DOACs in comparison with all other drugs registered in VigiBase or warfarin. VigiBase, the World Health Organization (WHO)’s global database of individual case safety reports was used as data source. Forty-two cases of abortion were detected of which 18 (42.8%) had alternative causes for its occurrence. Fourteen cases reported congenital anomaly (8 cases) or low birth weight baby/fetal growth restriction (6 cases) of which 62.5% and 33.3% had at least one confounder, respectively. In the disproportionality analyses, a potential safety signal for spontaneous abortion emerged for rivaroxaban (Reporting Odds Ratio, ROR 2.70; 95% CI 1.79–4.07) and apixaban (ROR 6.76; 95% CI 2.99–15.25). However, when the same analyses were performed using only cases without alternative causes, no statistically significant associations for rivaroxaban when compared to all other drugs (ROR 1.05; 95% CI 0.54–2.02) or warfarin (ROR 0.79; 95% CI 0.47–1.32) were found. For apixaban, we found a statistically significant ROR for induced abortion when compared to all other drugs or warfarin. For the majority of cases claiming DOACs-induced teratogenic effects, spontaneous or induced abortion there was at least one alternative cause explaining the occurrence of the adverse events. For rivaroxaban, when cases without confounders were considered, no safety signals emerged. However, for apixaban, we found a potential safety signal suggesting an increased probability of reporting spontaneous/induced abortion rather than other events when compared to all other drugs or warfarin.
Qualitätssicherung mit Routinedaten bei Cholelithiasis – Veränderungen und aktueller Stand
Authors: Jeschke Elke , Günster Christian , Fahlenbrach Claus , Heller Günther , Maneck Matthias , Meyer Hans-Joachim , Rolle Udo , Schuler Ekkehard , Waibel Beate , Heidecke Claus-Dieter 
Published: May 2019

ZusammenfassungQualitätssicherung mit Routinedaten (QSR) ist ein relativ neues Verfahren zur Bewertung der Ergebnisqualität, das sich von der externen Qualitätssicherung und der Qualitätssicherung über Registerdaten im methodischen Ansatz unterscheidet. Seitens des Wissenschaftlichen Instituts der AOK (WIdO) wird QSR seit 2011 für den Bereich Cholelithiasis bei AOK-Patienten vorgehalten. Nach Einführung eines Expertenpanels im Jahr 2013 wurden zahlreiche Veränderungen vorgenommen, die die Indikatorraten für „Transfusion/Blutung“, „Sonstige Komplikationen“ sowie den Gesamtindikator verringert, aber die risikoadjustierten Qualitätsunterschiede zwischen Kliniken keineswegs aufgehoben haben.
Normal Pressure Hydrocephalus with Primary Presentation of Psychiatric Disturbance: Case Report
Authors: Kogan Michael , Agyei Justice , Cuddahee Kevin J. , Gibbons Kevin J. 
Published: May 2019

Background and Objective Progressive impairment of cognitive function is a common feature seen in patients with normal pressure hydrocephalus (NPH). Along with cognitive decline, many of the other classic symptoms of NPH are chronic and rarely present with overwhelming anxiety. We report the case of a 63-year-old man who presented with recent primary psychiatric manifestation of severe disabling anxiety and otherwise a minimal change in gait and no urinary disturbance.
Clinical Presentation The patient's work-up consisted of magnetic resonance imaging that showed moderate ventriculomegaly but no findings concerning for acute obstructive hydrocephalus. A single-photon emission computed tomography scan was markedly abnormal with severe hypoperfusion consistent with hydrocephalus. Initially shunting was not advised but was eventually performed after a dramatic response to a large-volume lumbar puncture. After considerable discussion, he underwent elective ventriculoperitoneal shunt placement and had dramatic and sustained improvement in his anxiety.
Conclusion We believe this case report is a unique description of NPH symptomology and might guide future research or clinical decision making.
Radiofrequency Ablation of Pancreatic Cancer
Authors: Sarno Alessandro , Beleù Alessandro , De Robertis Riccardo , Giannotti Gabriele , Tedesco Giorgia , Paiella Salvatore , D'Onofrio Mirko 
Published: May 2019

AbstractRadiofrequency ablation (RFA) is emerging as a safe and feasible technique to treat various pancreatic lesions. In particular, pancreatic ductal adenocarcinoma (PDAC) is the most frequent treated lesion. Nowadays, PDAC treatment by means of RFA is limited to locally advanced, non-resectable, but non-metastatic lesions. The aim of this article is to describe the RFA technique, its results and possible complications.
Change of Element Settlement in Musi Riverside Palembang
Authors: Wicaksono Bambang , Siswanto Ari , Kusdiwanggo Susilo , Anwar Widya Fransiska Febriati 
Published: May 2019

Abstract
The development of the city in the modern era has had an impact on the culture of people living in the riverside. The river-oriented settlement culture is transformed into a land-based settlement culture. In this development, changes in the form of a settlement environment depend on the position of environmental elements in cultural systems such as nature, man, society, shells, and network. Changes in the form of environment affect the elements of the settlement. Some of them are repaired in building structures but material changes and others change following the development of the settlement orientation process. These changes undermine the identity, character, and potential of river architecture and settled cultures that were originally in harmony with river life. The purpose of this study was to explore the incidence and explanation of changes in the settlement elements in the Musi River and the architectural aspects of the house and residential type through a qualitative approach. Data collection is done qualitatively by using data collecting technique that is field observation, depth interview, and literature study. The analytical technique used is through qualitative approach of case study with a combination of strategies that identify elements of rural community settlements with triangulation. This study found the change of the settlement elements of the Musi River Palembang River from the river-oriented to the land-oriented. This study concludes that changes in the architecture and building system of river settlements that include changes in the orientation of buildings to rivers, the addition of space under the stilts, material changes, changes in the function of house space, and changes in river environmental infrastructure caused by the influence and development of land-oriented culture settlements, based on the elements of settlement on the banks of the River Musi Palembang.
Marine mammal ecology and health: finding common ground between conventional science and indigenous knowledge to track arctic ecosystem variability
Authors: Moore Sue E , Hauser Donna D W 
Published: May 2019

AbstractMarine mammals respond to, and thereby reflect, changes in Arctic ecosystems that are important both to practitioners of conventional science (CS) and to holders of indigenous knowledge (IK). Although often seen as contrasting approaches to tracking ecosystem variability, when CS and IK are combined they can provide complementary and synergistic information. Despite exceptions, ecosystem-focused CS is often spatially broad and time shallow (1000 s km, decades) while IK is comparatively narrow spatially and time deep (10 s km, centuries). In addition, differences in how information is gathered, stored, applied and communicated can confound information integration from these two knowledge systems. Over the past four decades, research partnerships between CS practitioners and IK holders have provided novel insights to an Alaskan Arctic marine ecosystem in rapid transition. We identify insights from some of those projects, as they relate to changes in sea ice, oceanography, and more broadly to marine mammal ecology and health. From those insights and the protocols of existing community-based programs, we suggest that the strong seasonal cycle of Arctic environmental events should be leveraged as a shared framework to provide common ground for communication when developing projects related to marine mammal health and ecology. Adopting a shared temporal framework would foster joint CS–IK thinking and support the development of novel and nonlinear approaches to shared questions and concerns regarding marine mammals. The overarching goal is to extend the range and depth of a common understanding of marine mammal health and ecology during a period of rapid ecosystem alteration. The current focus on CS–IK co-production of knowledge and recent inclusion of marine mammals as essential variables in global ocean observatories makes this an opportune time to find common ground for understanding and adapting to the rapid changes now underway in Arctic marine ecosystems.
Using the evaporative stress index to monitor flash drought in Australia
Authors: Nguyen Hanh , Wheeler Matthew C , Otkin Jason A , Cowan Tim , Frost Andrew , Stone Roger 
Published: May 2019

Abstract
Flash drought is a term and concept that has gained increasing attention in the research literature and media since it was first coined in the United States in the early 2000s to describe a drought that has undergone rapid intensification. In Australia the term has recently been used in reference to the 2017/18 drought in eastern Australia. Due to its rapid intensification, the impacts of flash droughts will likely occur too quickly for many of the usual drought-coping mechanisms to be deployed. This study proposes the use of the evaporative stress index (ESI), the standardized anomaly of the actual evapotranspiration to potential evapotranspiration ratio, to identify flash droughts in Australia computed using daily outputs from the Bureau of Meteorology’s land surface water balance model AWRA-L. The case study of the January 2018 flash drought in eastern Australia is used to assess and demonstrate the suitability of the ESI. Results show that the ESI accurately highlighted the event and offered potential for flash drought pre-warning by a few weeks. In addition, the availability of long term high-resolution outputs from AWRA-L offers the ability to investigate multiple flash drought events in detail for greater understanding and to inform stakeholders.
Multiscale hierarchical bioresorbable scaffolds for the regeneration of tendons and ligaments
Authors: Sensini Alberto , Gualandi Chiara , Focarete Maria Letizia , Belcari Juri , Zucchelli Andrea , Boyle Liam , Reilly Gwendolen C , Kao Alexander P , Tozzi Gianluca , Cristofolini Luca 
Published: May 2019

Abstract
Lesions of tendons and ligaments account for over 40% of the musculoskeletal lesions. Surgical techniques and materials for repair and regeneration are currently not satisfactory. The high rate of post-operative complications and failures mainly relates to the technical difficulties in replicating the complex multiscale hierarchical structure and the mechanical properties of the native tendons and ligaments. With the aim of overcoming the limitations of non-biomimetic devices, we developed a hierarchical structure replicating the organization of tendons and ligaments. The scaffold consists of multiple bundles made of resorbable electrospun nanofibers of Poly-L-Lactic acid (PLLA) having tailored dimensions, wrapped in a sheath of nanofibers able to compact the construct. The bundles in turn consist of electrospun nanofibers with a preferential direction. High-resolution x-ray tomographic investigation at nanometer resolution confirmed that the morphology of the single bundles and of the entire scaffold replicated the hierarchical arrangement in the natural tendons and ligaments. To confirm that these structures could adequately restore tendons and ligaments, we measured the tensile stiffness, strength and toughness. The mechanical properties were in the range required to replace and repair tendons and ligaments. Furthermore, human fibroblasts were able to attach to the scaffolds and showed an increase in cell number, indicated by an increase in metabolic activity over time. Fibroblasts were preferentially aligned along the electrospun nanofibers. These encouraging in vitro results open the way for the next steps towards in vivo regeneration of tendons and ligaments.
Comparison of Two Commercial Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Systems for Identification of Nontuberculous Mycobacteria
Authors: Brown-Elliott Barbara A , Fritsche Thomas R , Olson Brooke J , Vasireddy Sruthi , Vasireddy Ravikiran , Iakhiaeva Elena , Alame Diana , Wallace Richard J , Branda John A 
Published: May 2019

Abstract

Objectives
This multicenter study’s aim was to assess the performance of two commercially available matrix-assisted laser desorption/ionization time of flight mass spectrometry systems in identifying a challenge collection of clinically relevant nontuberculous mycobacteria (NTM).

Methods
NTM clinical isolates (n = 244) belonging to 23 species/subspecies were identified by gene sequencing and analyzed using Bruker Biotyper with Mycobacterial Library v5.0.0 and bioMérieux VITEK MS with v3.0 database.

Results
Using the Bruker or bioMérieux systems, 92% and 95% of NTM strains, respectively, were identified at least to the complex/group level; 62% and 57%, respectively, were identified to the highest taxonomic level. Differentiation between members of Mycobacterium abscessus, M fortuitum, M mucogenicum, M avium, and M terrae complexes/groups was problematic for both systems, as was identification of M chelonae for the Bruker system.

Conclusions
Both systems identified most NTM isolates to the group/complex level, and many to the highest taxonomic level. Performance was comparable.
hicGAN infers super resolution Hi-C data with generative adversarial networks
Authors: Liu Qiao , Lv Hairong , Jiang Rui 
Published: May 2019

Abstract

Motivation
Hi-C is a genome-wide technology for investigating 3D chromatin conformation by measuring physical contacts between pairs of genomic regions. The resolution of Hi-C data directly impacts the effectiveness and accuracy of downstream analysis such as identifying topologically associating domains (TADs) and meaningful chromatin loops. High resolution Hi-C data are valuable resources which implicate the relationship between 3D genome conformation and function, especially linking distal regulatory elements to their target genes. However, high resolution Hi-C data across various tissues and cell types are not always available due to the high sequencing cost. It is therefore indispensable to develop computational approaches for enhancing the resolution of Hi-C data.

Results
We proposed hicGAN, an open-sourced framework, for inferring high resolution Hi-C data from low resolution Hi-C data with generative adversarial networks (GANs). To the best of our knowledge, this is the first study to apply GANs to 3D genome analysis. We demonstrate that hicGAN effectively enhances the resolution of low resolution Hi-C data by generating matrices that are highly consistent with the original high resolution Hi-C matrices. A typical scenario of usage for our approach is to enhance low resolution Hi-C data in new cell types, especially where the high resolution Hi-C data are not available. Our study not only presents a novel approach for enhancing Hi-C data resolution, but also provides fascinating insights into disclosing complex mechanism underlying the formation of chromatin contacts.

Availability and implementation
We release hicGAN as an open-sourced software at https://github.com/kimmo1019/hicGAN.

Supplementary information
Supplementary data are available at Bioinformatics online.
Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype
Authors: Yin Bojian , Balvert Marleen , van der Spek Rick A A , Dutilh Bas E , Bohté Sander , Veldink Jan , Schönhuth Alexander 
Published: May 2019

Abstract

Motivation
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease caused by aberrations in the genome. While several disease-causing variants have been identified, a major part of heritability remains unexplained. ALS is believed to have a complex genetic basis where non-additive combinations of variants constitute disease, which cannot be picked up using the linear models employed in classical genotype–phenotype association studies. Deep learning on the other hand is highly promising for identifying such complex relations. We therefore developed a deep-learning based approach for the classification of ALS patients versus healthy individuals from the Dutch cohort of the Project MinE dataset. Based on recent insight that regulatory regions harbor the majority of disease-associated variants, we employ a two-step approach: first promoter regions that are likely associated to ALS are identified, and second individuals are classified based on their genotype in the selected genomic regions. Both steps employ a deep convolutional neural network. The network architecture accounts for the structure of genome data by applying convolution only to parts of the data where this makes sense from a genomics perspective.

Results
Our approach identifies potentially ALS-associated promoter regions, and generally outperforms other classification methods. Test results support the hypothesis that non-additive combinations of variants contribute to ALS. Architectures and protocols developed are tailored toward processing population-scale, whole-genome data. We consider this a relevant first step toward deep learning assisted genotype–phenotype association in whole genome-sized data.

Availability and implementation
Our code will be available on Github, together with a synthetic dataset (https://github.com/byin-cwi/ALS-Deeplearning). The data used in this study is available to bona-fide researchers upon request.

Supplementary information
Supplementary data are available at Bioinformatics online.
Controlling large Boolean networks with single-step perturbations
Authors: Baudin Alexis , Paul Soumya , Su Cui , Pang Jun 
Published: May 2019

Abstract

Motivation
The control of Boolean networks has traditionally focussed on strategies where the perturbations are applied to the nodes of the network for an extended period of time. In this work, we study if and how a Boolean network can be controlled by perturbing a minimal set of nodes for a single-step and letting the system evolve afterwards according to its original dynamics. More precisely, given a Boolean network (BN), we compute a minimal subset Cmin of the nodes such that BN can be driven from any initial state in an attractor to another ‘desired’ attractor by perturbing some or all of the nodes of Cmin for a single-step. Such kind of control is attractive for biological systems because they are less time consuming than the traditional strategies for control while also being financially more viable. However, due to the phenomenon of state-space explosion, computing such a minimal subset is computationally inefficient and an approach that deals with the entire network in one-go, does not scale well for large networks.

Results
We develop a ‘divide-and-conquer’ approach by decomposing the network into smaller partitions, computing the minimal control on the projection of the attractors to these partitions and then composing the results to obtain Cmin for the whole network. We implement our method and test it on various real-life biological networks to demonstrate its applicability and efficiency.

Supplementary information
Supplementary data are available at Bioinformatics online.
A segregating human allele ofSPO11modeled in mice disrupts timing and amounts of meiotic recombination, causing oligospermia and a decreased ovarian reserve†
Authors: Tran Tina N , Schimenti John C 
Published: May 2019

AbstractA major challenge in medical genetics is to characterize variants of unknown significance (VUS). Doing so would help delineate underlying causes of disease and the design of customized treatments. Infertility has presented an especially difficult challenge with respect to not only determining if a given patient has a genetic basis, but also to identify the causative genetic factor(s). Though genome sequencing can identify candidate variants, in silico predictions of causation are not always sufficiently reliable so as to be actionable. Thus, experimental validation is crucial. Here, we describe the phenotype of mice containing a non-synonymous (proline-to-threonine at position 306) change in Spo11, corresponding to human SNP rs185545661. SPO11 is a topoisomerase-like protein that is essential for meiosis because it induces DNA double stranded breaks (DSBs) that stimulate pairing and recombination of homologous chromosomes. Although both male and female Spo11P306T/P306T mice were fertile, they had reduced sperm and oocytes, respectively. Spermatocyte chromosomes exhibited synapsis defects (especially between the X and Y chromosomes), elevated apoptotic cells, persistent markers of DSBs, and most importantly, fewer Type 1 crossovers that causes some chromosomes to have none. Spo11P306T/− mice were sterile and made fewer meiotic DSBs than Spo11+/- animals, suggesting that the Spo11P306T allele is a hypomorph and likely is delayed in making sufficient DSBs in a timely fashion. If the consequences are recapitulated in humans, it would predict phenotypes of premature ovarian failure, reduced sperm counts, and possible increased number of aneuploid gametes. These results emphasize the importance of deep phenotyping in order to accurately assess the impact of VUSs in reproduction genes.