bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endoscopic ultrasonography in pancreatic diseases: advances in tissue acquisition
Authors: Mitselos Ioannis V. , Karoumpalis Ioannis , Theopistos Vasileios I. , Tzilves Dimitrios , Christodoulou Dimitrios K. 
Published: July 2019

Abstract
Background and study aims Endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) improved the diagnostic performance and upgraded the role of endoscopic ultrasonography (EUS) into an interventional modality, able to guide patient management and treatment.This review aimed to highlight the advances, emerging practices, procedural techniques and technological innovations in EUS tissue acquisition in pancreatic diseases.
Methods A thorough review of the literature was performed using PubMed to identify articles that describe techniques, advances, and practices in EUS tissue acquisition in gastrointestinal diseases.
Conclusion Since the first EUS-FNA procedure, EUS guided-tissue acquisition has been evolving continuously. Development of needles with innovative tip design enabled procurement of larger samples with preserved histological architecture. Moreover, sampling techniques and complementary methods, such as contrast harmonic imaging and EUS-elastography, have been introduced in an effort to improve diagnostic performance and sample adequacy.
Effect and Complications of Everolimus Use for Giant Cardiac Rhabdomyomas with Neonatal Tuberous Sclerosis
Authors: Shibata Yuka , Maruyama Hidehiko , Hayashi Taiyu , Ono Hiroshi , Wada Yuka , Fujinaga Hideshi , Fujino Shuhei , Nagasawa Junko , Amari Shoichiro , Tsukamoto Keiko , Ito Yushi 
Published: July 2019

AbstractMost cardiac rhabdomyomas with tuberous sclerosis (TS) are asymptomatic and spontaneously regress. However, some cases require surgical intervention due to arrhythmia and severe obstruction of cardiac inflow or outflow. We report herein a neonatal case of giant cardiac rhabdomyomas with TS and insufficient pulmonary blood flow from the right ventricle. Lipoprostaglandin E1 was necessary to maintain patency of the ductus arteriosus. We used everolimus, a mammalian target of rapamycin inhibitor, to diminish the cardiac rhabdomyomas. After treatment, the rhabdomyomas shrank rapidly, but the serum concentration of everolimus increased sharply (maximum serum trough level: 76.1 ng/mL) and induced complications including pulmonary hemorrhage, liver dysfunction, and acne. After the everolimus level decreased, the complications resolved. Everolimus may be a viable treatment option for rhabdomyomas, but its concentration requires close monitoring to circumvent complications associated with its use.
Metaphyseal Core Decompression and Anterograde Fixation for Scaphoid Proximal Pole Fracture Nonunion without Avascular Necrosis
Authors: Rellan Ignacio , Gallucci Gerardo Luis , Boretto Jorge Guillermo , Donndorff Agustin Guillermo , Zaidenberg Ezequiel Ernesto , De Carli Pablo 
Published: July 2019

Objective To report the consolidation rate and the results of a series of 22 patients with metaphyseal core decompression of the distal radius and an antegrade compression screw.
Methods We present a prospective series of patients with scaphoid proximal pole nonunion in whom the presence of intraoperative bleeding was confirmed in both fragments. Patients with displacement, degenerative changes, fragmentation of the proximal pole, cavitation of the focus, loss of height, and necrosis, as well as those with carpal instability, were excluded. The patients were evaluated with X-rays and computed tomography to evaluate their consolidation; their mobility and fist strength were recorded and an analog visual scale (VAS) of pain at rest, pain in activity, subjective functional status, and DASH questionnaire were completed.
Results Of the 23 patients, 21 accomplished union. The average follow-up was 19 months and the average final range of motion was flexion 86%, extension 85%, radial deviation 79%, ulnar deviation 84%, and grip strength 84%. The average VAS for pain at rest was 1 point, the average VAS for activity pain was 2 points, the average VAS for function was 9 points, and the average DASH score was 8.
Conclusions Using this simple and reliable technique, we obtained 91% union and very good functional results. Metaphyseal core decompression of the distal radius associated with an antegrade scaphoid screw is a reasonable and effective option for the treatment of proximal pole scaphoid nonunions without avascular necrosis in carefully selected patients.
Level of Evidence This is Level IV study.
Towards a framework for collective behavior in growth-driven systems, based on plant-inspired allotropic pairwise interactions
Authors: Bastien Renaud , Porat Amir , Meroz Yasmine 
Published: July 2019

Abstract
A variety of biological systems are not motile, but sessile in nature, relying on growth as the main driver of their movement. Groups of such growing organisms can form complex structures, such as the functional architecture of growing axons, or the adaptive structure of plant root systems. These processes are not yet understood, however the decentralized growth dynamics bear similarities to the collective behavior observed in groups of motile organisms, such as flocks of birds or schools of fish. Equivalent growth mechanisms make these systems amenable to a theoretical framework inspired by tropic responses of plants, where growth is considered implicitly as the driver of the observed bending towards a stimulus. We introduce two new concepts related to plant tropisms: point tropism, the response of a plant to a nearby point signal source, and allotropism, the growth-driven response of plant organs to neighboring plants. We first analytically and numerically investigate the 2D dynamics of single organs responding to point signals fixed in space. Building on this we study pairs of organs interacting via allotropism, i.e. each organ senses signals emitted at the tip of their neighbor and responds accordingly. In the case of local sensing we find a rich state-space. We describe the different states, as well as the sharp transitions between them. We also find that the form of the state-space depends on initial conditions. This work sets the stage towards a theoretical framework for the investigation and understanding of systems of interacting growth-driven individuals.
Sediment accumulation expectations for growing desert cities: a realistic desired outcome to be used in constructing appropriately sized sediment storage of flood control structures
Authors: Jeong Ara 
Published: July 2019

Abstract
Many rapidly urbanizing desert cities (RUDC) around the globe experience an acute risk of flooding. To reduce this risk, properly engineered flood control structures (FCS) must account for sediment accumulation as well as flood waters. While the Phoenix area, USA, uses regional data from non-urban, non-desert watersheds to generate sediment yield rates, the proposed desired outcome for RUDCs is to base FCS on data related to urbanization. Wolman (1967 Geogr. Ann. A 49 385–95) recognized that sediment yields spike during a relatively short period of bare-ground exposure associated with urban growth, followed by surface sealing resulting in a great reduction in sediment yield. This research presents a new analysis of empirical data where two regression models provide estimates of a more realistic sediment accumulation for arid regions and also urbanization of a desert cities: (i) linear regression between drainage area and sediment yield based on a compilation of more than 150 global sediment yield data for warm desert (BWh Köppen‐Geiger) climate; and (ii) linear regression relating percent urban growth with sediment yield using available data on urbanization-generated sediment associated with growth of a desert city. The new model can be used to predict the realistic sediment accumulation for helping provide data where few data exists in urbanizing parts of arid Africa, southwest Asia, and India.
Riverine plastic emission from Jakarta into the ocean
Authors: van Emmerik Tim , Loozen Michelle , van Oeveren Kees , Buschman Frans , Prinsen Geert 
Published: July 2019

Abstract
Plastic pollution in aquatic environments is an increasing global risk. In recent years, marine plastic pollution has been studied to a great extent, and it has been hypothesized that land-based plastics are its main source. Global modeling efforts have suggested that rivers in South East Asia are in fact the main contributors to plastic transport from land to the oceans. However, due to a lack of plastic transport observations, the origin and fate of riverine plastic waste is yet unclear. Here, we present results from a first assessment of riverine macroplastic emission from rivers and canals that run through a densely populated coastal urban city. Using a combination of field measurements, empirical relations and hydraulic modeling, we provide an estimate of total riverine plastic export originating from Jakarta, Indonesia, into the ocean. Furthermore, we provide insights in its composition, and variation in time and space. We found that most macroplastics in Jakarta consists of films and foils. We estimate that 2.1 × 103 tonnes of plastic waste, is transported from land to sea annually, equaling 3% of the total annual unsoundly disposed plastic waste in the Jakarta area.
Molecular signal communication during arbuscular mycorrhizal formation induces significant transcriptional reprogramming of wheat (Triticum aestivum) roots
Authors: Tian Hui , Wang Runze , Li Mengjiao , Dang Haiyan , Solaiman Zakaria M 
Published: July 2019

Abstract

Background and Aims
Arbuscular mycorrhizal (AM) symbiosis begins with molecular signal communication (MSC) between AM fungi and the roots of the host plant. We aimed to test the hypothesis that the transcriptional profiles of wheat roots can be changed significantly by AM symbiotic signals, without direct contact.

Methods
Non-mycorrhizal (NM) and MSC treatments involved burying filter membrane bags containing sterilized and un-sterilized inoculum of the AM fungus Rhizophagus irregularis, respectively. The bags physically separated roots and AM structures but allowed molecular signals to pass through. Extracted RNA from wheat roots was sequenced by high-throughput sequencing.

Results
Shoot total nitrogen and phosphorus content of wheat plants was decreased by the MSC treatment. A total of 2360 differentially expressed genes (DEGs), including 1888 up-regulated DEGs and 472 down-regulated DEGs, were found dominantly distributed on chromosomes 2A, 2B, 2D, 3B, 5B and 5D. The expression of 59 and 121 genes was greatly up- and down-regulated, respectively. Only a portion of DEGs could be enriched into known terms during gene ontology analysis, and were mostly annotated to ‘catalytic activity’, ‘protein metabolic process’ and ‘membrane’ in the molecular function, biological process and cellular component ontology categories, respectively. More than 120 genes that may be involved in key processes during AM symbiosis development were regulated at the pre-physical contact stages.

Conclusions
The transcriptional profiles of wheat roots can be changed dramatically by MSC. Much of the information provided by our study is of great importance for understanding the mechanisms underlying the development of AM symbiosis.
A comprehensive review and evaluation of computational methods for identifying protein complexes from protein–protein interaction networks
Authors: Wu Zhourun , Liao Qing , Liu Bin 
Published: July 2019

AbstractProtein complexes are the fundamental units for many cellular processes. Identifying protein complexes accurately is critical for understanding the functions and organizations of cells. With the increment of genome-scale protein–protein interaction (PPI) data for different species, various computational methods focus on identifying protein complexes from PPI networks. In this article, we give a comprehensive and updated review on the state-of-the-art computational methods in the field of protein complex identification, especially focusing on the newly developed approaches. The computational methods are organized into three categories, including cluster-quality-based methods, node-affinity-based methods and ensemble clustering methods. Furthermore, the advantages and disadvantages of different methods are discussed, and then, the performance of 17 state-of-the-art methods is evaluated on two widely used benchmark data sets. Finally, the bottleneck problems and their potential solutions in this important field are discussed.
Computational approaches to therapeutic antibody design: established methods and emerging trends
Authors: Norman Richard A , Ambrosetti Francesco , Bonvin Alexandre M J J , Colwell Lucy J , Kelm Sebastian , Kumar Sandeep , Krawczyk Konrad 
Published: July 2019

AbstractAntibodies are proteins that recognize the molecular surfaces of potentially noxious molecules to mount an adaptive immune response or, in the case of autoimmune diseases, molecules that are part of healthy cells and tissues. Due to their binding versatility, antibodies are currently the largest class of biotherapeutics, with five monoclonal antibodies ranked in the top 10 blockbuster drugs. Computational advances in protein modelling and design can have a tangible impact on antibody-based therapeutic development. Antibody-specific computational protocols currently benefit from an increasing volume of data provided by next generation sequencing and application to related drug modalities based on traditional antibodies, such as nanobodies. Here we present a structured overview of available databases, methods and emerging trends in computational antibody analysis and contextualize them towards the engineering of candidate antibody therapeutics.
DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks
Authors: Bartoszewicz Jakub M , Seidel Anja , Rentzsch Robert , Renard Bernhard Y 
Published: July 2019

AbstractMotivationWe expect novel pathogens to arise due to their fast-paced evolution, and new species to be discovered thanks to advances in DNA sequencing and metagenomics. Moreover, recent developments in synthetic biology raise concerns that some strains of bacteria could be modified for malicious purposes. Traditional approaches to open-view pathogen detection depend on databases of known organisms, which limits their performance on unknown, unrecognized and unmapped sequences. In contrast, machine learning methods can infer pathogenic phenotypes from single NGS reads, even though the biological context is unavailable.ResultsWe present DeePaC, a Deep Learning Approach to Pathogenicity Classification. It includes a flexible framework allowing easy evaluation of neural architectures with reverse-complement parameter sharing. We show that convolutional neural networks and LSTMs outperform the state-of-the-art based on both sequence homology and machine learning. Combining a deep learning approach with integrating the predictions for both mates in a read pair results in cutting the error rate almost in half in comparison to the previous state-of-the-art.Availability and implementationThe code and the models are available at: https://gitlab.com/rki_bioinformatics/DeePaC.Supplementary informationSupplementary data are available at Bioinformatics online.
In vitro reconstitution of germ cell development†
Authors: Hayashi Katsuhiko 
Published: July 2019

AbstractGerm cell development is a series of highly specialized processes through which diploid pluripotent cells differentiate into haploid gametes. The processes include biologically important events such as epigenetic reprogramming, sex determination, and meiosis. The mechanisms underlying these events are key issues in reproductive and developmental biology, yet they still remain elusive. As a tool to elucidate these mechanisms, in vitro gametogenesis, which reproduces germ cell development in culture, has long been sought for decades. Recently, methods of in vitro gametogenesis have undergone rapid development in association with stem cell biology, opening many possibilities in this field. This new technology is considered an alternative source of gametes for the reproduction of animals and perhaps humans. This review summarizes current advances and problems in in vitro gametogenesis.
Aminophylline and progesterone prevent inflammation-induced preterm parturition in the mouse†
Authors: Herbert Bronwen R , Markovic Danijela , Georgiou Ektoras , Lai Pei F , Singh Natasha , Yulia Angela , Johnson Mark R 
Published: July 2019

Abstract
Although progesterone (P4) supplementation is the most widely used therapy for the prevention of preterm labor (PTL), reports of its clinical efficacy have been conflicting. We have previously shown that the anti-inflammatory effects of P4 can be enhanced by increasing intracellular cyclic adenosine monophosphate (cAMP) levels in primary human myometrial cells. Here, we have examined whether adding aminophylline (Am), a non-specific phosphodiesterase inhibitor that increases intracellular cAMP levels, to P4 might improve its efficacy using in vivo and in vitro models of PTL. In a mouse model of lipopolysaccharide (LPS)-induced PTL, we found that the combination of P4 and Am delayed the onset of LPS-induced PTL, while the same dose of P4 and Am alone had no effect. Pup survival was not improved by either agent alone or in combination. Myometrial prolabor and inflammatory cytokine gene expression was reduced, but the reduction was similar in P4 and P4/Am treated mice. There was no effect of the combination of P4 and Am on an ex vivo assessment of myometrial contractility. In human myometrial cells and myometrial tissue explants, we found that the combination had marked anti-inflammatory effects, reducing cytokine and COX-2 mRNA and protein levels to a greater extent than either agent alone. These data suggest that the combination of P4 and Am has a more potent anti-inflammatory effect than either agent alone and may be an effective combination in women at high-risk of PTL.
Oxidative stress-induced downregulation of glycogen synthase kinase 3 beta in fetal membranes promotes cellular senescence†
Authors: Lavu Narmada , Richardson Lauren , Radnaa Enkhtuya , Kechichian Talar , Urrabaz-Garza Rheanna , Sheller-Miller Samantha , Bonney Elizabeth , Menon Ramkumar 
Published: July 2019

AbstractObjectiveOxidative stress (OS)-induced stress signaler p38 mitogen-activated protein kinase (p38MAPK) activation and fetal membrane senescence are associated with parturition. This study determined changes in glycogen synthase kinase 3 beta (GSK3β) and its regulation by p38MAPK in effecting senescence to further delineate the molecular mechanism involved in senescence.MethodsPrimary human amnion epithelial cells and amnion mesenchymal cells were treated with cigarette smoke extract (CSE, OS inducer). Expression of total and phosphorylated GSK3β and p38MAPK, and that of GSK3β’s downstream targets: beta-catenin (β-Cat) and nuclear factor erythroid 2-related factor 2 (Nrf2) (western blot analysis), cell cycle regulation and senescence (flow cytometry) were determined. The specificity of GSK3β and p38MAPK’s mechanistic role was tested by co-treating cells with their respective inhibitors, CHIR99021 and SB203580. Exosomal secretion of β-Cat from OS-induced cells was confirmed by immunofluorescence confocal microscopy and western blot.ResultsOS induced by CSE resulted in phosphorylation of GSK3β (inactivation) and p38MAPK (activation) that was associated with cell cycle arrest and senescence. Inhibitors to GSK3β and p38MAPK verified their roles. Glycogen synthase kinase 3 beta inactivation was associated with nuclear translocation of antioxidant Nrf2 and exosomal secretion of β-Cat.ConclusionsOS-induced P-p38MAPK activation is associated with functional downregulation of GSK3β and arrest of cell cycle progression and senescence of amnion cells. Lack of nuclear translocation of β-Cat and its excretion via exosomes further supports the postulation that GSK3β down-regulation by p38MAPK may stop cell proliferation preceding cell senescence. A better understanding of molecular mechanisms of senescence will help develop therapeutic strategies to prevent preterm birth.
Sustainability of Handshake Stewardship: Extending a Hand Is Effective Years Later
Authors: MacBrayne Christine E , Williams Manon C , Levek Claire , Child Jason , Pearce Kelly , Birkholz Meghan , Todd James K , Hurst Amanda L , Parker Sarah K 
Published: July 2019

AbstractBackgroundChildren’s Hospital Colorado created a unique method of antimicrobial stewardship, called handshake stewardship, that effectively decreased hospital anti-infective use and costs in its pilot year (2013). Handshake stewardship is distinguished by: (1) the lack of prior authorization; (2) a review of all prescribed anti-infectives; (3) a shared review by the physician and the pharmacist; and (4) a daily, rounding-based, in-person approach to supporting providers. We sought to reevaluate the outcomes of the program after 5 years of experience, totaling 8 years of data.MethodsWe retrospectively measured anti-infective (antibiotic, antiviral, antifungal) use hospital-wide by unit and by drug for an 8-year period spanning October 2010 to October 2018. Aggregated monthly use was measured in days of therapy per thousand patient days (DOT/1000 PD). The percentage of children admitted ever receiving an anti-infective was also measured, as well as severity-adjusted mortality, readmissions, and lengths of stay.ResultsHospital-wide mean anti-infective use significantly decreased, from 891 (95% confidence interval [CI] 859–923) in the pre-implementation phase to 655 (95% CI 637–694) DOT/1000 PD in post-implementation Year 5; in a segmented regression time series analysis, this was a rate of -2.6 DOT/1000 PD (95% CI -4.8 to -0.4). This is largely attributable to decreased antibacterial use, from 704 (95% CI 686–722) to 544 (95% CI 525 –562) DOT/1000 PD. The percentage of children ever receiving an anti-infective during admission likewise declined, from 65% to 52% (95% CI 49–54). There were no detrimental effects on severity adjusted mortality, readmissions, or lengths of stay.ConclusionsThe handshake method is an effective and sustainable approach to stewardship.