bluuebunny/crossref_metadata_2025 huggingface dataset:
Transverse single spin asymmetry for very forward π0 production in polarized proton-proton collisions at √s = 510 GeV
Authors: Kim M. H. , Hong B. , Goto Y. , Nakagawa I. , Seidl R. , Park J. S. , Tanida K. , Itow Y. , Menjo H. , Sato K. , Ueno M. , Zhou Q. D. , Sako T. , Kasahara K. , Suzuki T. , Torii S. , Sakurai N. , Adriani O. , Bonechi L. , Berti E. , D'Alessandro R. , Tricomi A.
Published: May 2019

Transverse single spin asymmetry, AN, of very forward π0 production from polarized p + p collisions provides new information toward an understanding of its production mechanism. AN of forward π0 in the pseudorapidity region of 3 < η < 4 has been described by the partonic structure of the proton in the perturbative QCD framework. However, recent data indicates a potential contribution from not only partonic but also diffractive interactions. In order to provide a new insight on the origin of the AN, we measured the very forward π0 production in the pseudorapidity region of 6 < η from √s = 510 GeV polarized p + p collisions at RHIC in 2017. We report our measurement of the very forward π0 over the transverse momentum range of 0 < pT < 1 GeV/c and the preliminary result.
Atmospheric Muons Measured with IceCube
Authors: Soldin Dennis
Published: May 2019

IceCube is a cubic-kilometer Cherenkov detector in the deep ice at the geographic South Pole. The dominant event yield is produced by penetrating atmospheric muons with energies above several 100 GeV. Due to its large detector volume, IceCube provides unique opportunities to study atmospheric muons with large statistics in detail. Measurements of the energy spectrum and the lateral separation distribution of muons offer insights into hadronic interactions during the air shower development and can be used to test hadronic models. We will present an overview of various measurements of atmospheric muons in IceCube, including the energy spectrum of muons between 10 TeV and 1 PeV. This is used to derive an estimate of the prompt contribution of muons, originating from the decay of heavy (mainly charmed) hadrons and unflavored mesons. We will also present measurements of the lateral separation distributions of TeV muons between 150m and 450m for several initial cosmic ray energies between 1 PeV and 16 PeV. Finally, the angular distribution of atmospheric muons in IceCube will be discussed.
QGSJET-III model: physics and preliminary results
Authors: Ostapchenko Sergey
Published: May 2019

We discuss in some detail the physics content of the new model, QGSJET-III-01, focusing on major problems related to the treatment of semihard processes in the very high energy limit. A special attention has been payed to the main improvement, compared to the QGSJET-II model, which is related to a phenomenological treatment of leading power corrections corresponding to final parton rescattering off soft gluons. In particular, this allowed us to use a twice smaller separation scale between the soft and hard parton physics, compared to the previous model version, QGSJET-II-04. Preliminary results obtained with the new model are also presented.
Digital Archives for Nuclear Emulsion Data
Authors: Kodama Koichi , Kamiya Takehiro , Ichimura Masakatsu , Nakamura Mitsuhiro
Published: May 2019

Digital archives for nuclear emulsion data of past experiments, such as in cosmic-ray and accelerator physics, is being studied and prepared. Significant progress of HTS, which is an automatic read-out system for tracks recorded in emulsion, is achieving a read-out speed of about 1m2/hour and opens a possibility to read all tracks recorded in emulsion of past experiments. Current status of our first trial with RUNJOB emulsion plates is reported. Till now, the top-most 10 plates had been scanned by HTS and preliminary data is presented.
GRAINE project: precise gamma-ray observations with balloon-borne emulsion telescope
Authors: Rokujo Hiroki
Published: May 2019

Observation of cosmic gamma rays is important in the understanding of high-energy objects or phenomena in the universe. Since 2008, the Large Area Telescope onboard the Fermi Gamma-ray Space Telescope (Fermi-LAT) has surveyed the sub-GeV/GeV gamma-ray sky and achieved high statistics measurements. However, observation at low galactic latitudes remains difficult owing to the lack of angular resolution, and new issues following the operation of Fermi-LAT have arisen. We devised a precise gamma-ray observation project, Gamma-Ray Astro-Imager with Nuclear Emulsion (GRAINE), using balloon-borne emulsion gammaray telescopes to realize high angular resolution, polarization-sensitive, and large-aperture observations in the 10 MeV–100 GeV energy region. Following basic developments on the ground, we performed three balloon-borne experiments with upgraded instruments. In this paper, we present results from the second balloon experiment in 2015, a report on the latest balloon experiment conducted on April 26, 2018, and a recent study on hadronic interactions using proton beams.
Baksan Air Shower Array: new prospects for old facility
Authors: Lidvansky Alexander S.
Published: May 2019

The Carpet air shower array of the Baksan Neutrino Observatory is in operation for a long time, and it was modernized more than once. A short review of important results obtained with this array is given, as well as future prospects, since at the moment the new project called Carpet-3 is in progress, using the old array as its basis. The purpose of the new project is to substantially increase the muon detector area (quite soon up to 400 m2 and later up to 600 m2). This improvement will allow one to reach a very good sensitivity to diffuse cosmic photons by selecting muon-poor showers. The energy range where the new experiment will be competitive with other experiments of gamma-ray astronomy is near and below 100 TeV.
Impact of Initialization on Gradient Descent Method in Localization Using Received Signal Strength
Authors: Hijazi Hussein , Kandil Nahi , Zaarour Nour , Hakem Nadir
Published: May 2019

In this article we present a localization technique based on received signal strength (RSS) combined with the gradient descent optimization method. The goal of this article is to show the importance of gradient descent in localization domain over the trilateration technique, and that by reducing the number of needed anchor nodes. Furthermore, we demonstrate the effect of the initialization technique on the localization accuracy. Results have shown that the selection of the initialization type (4 types of initialization were tested) has an efficient impact on the accuracy of the target sensors location estimation.
Blind Channel Equalization of Star QAM using Dual Dispersion MCMA Algorithm
Authors: Zaheer Faizan , Amin Sheikh Shahzad
Published: May 2019

An algorithm for blind channel equalization is presented for 16 and 32 Star QAM, namely, Dual Dispersion MCMA algorithm. The algorithm taking the concept from MCMA, uses the Dual Dispersion minimization approach for blind channel equalization. As Star QAM constellation contains two rings, so instead of one, dual dispersion minimization approach is used for its both rings. With modification in MCMA cost function, the new algorithm results improved performance in convergence rate of Residual ISI and MSE against MCMA algorithm. By incorporating decision directed approach, the performance increases drastically. Simulation results show effectiveness of proposed algorithm in removing the ISI and correcting the errors in symbols of received signal.
Using Deep Learning Detection Of Arrhythmia
Authors: Yue Zhang , Feng Li
Published: May 2019

The field of deep learning applications is becoming more widespread. The use of traditional algorithms for arrhythmia detection is cumbersome and the algorithm complexity is relatively high. Using the deep learning model to directly input data into the model will make it difficult to effectively segment the data, which will have a large error in the recognition accuracy. We collected data from six commonly used ECG databases and then used the label shuffling method to amplify the samples, effectively overcoming the effects of sample imbalance. The LSTM model is used for feature point detection to effectively locate the key feature points of the ECG signal, thereby completing the segmentation and processing of the data. Finally, the use of a multiple input model single output for arrhythmia detection has achieved significant results. The average accuracy of the final arrhythmia classification of the model reached 0.711. The accuracy of detecting the fusion of ventricular and normal beat and the aberrated atrial premature beat exceeds 0.9.
An optimistic-pessimistic DEA model based on game cross efficiency approach
Authors: Örkcü Mediha , Özsoy Volkan Soner , Örkcü H. Hasan
Published: May 2019

The ranking of the decision making units (DMUs) is an essential problem in data envelopment analysis (DEA). Numerous approaches have been proposed for fully ranking of units. Majority of these methods consider DMUs with optimistic approach, whereas their weaknesses are ignored. In this study, for fully ranking of the units, a modified optimistic–pessimistic approach, which is based on game cross efficiency idea is proposed. The proposed game like iterative optimistic-pessimistic DEA procedure calculates the efficiency scores according to weaknesses and strengths of units and is based on non-cooperative game. This study extends the optimistic-pessimistic DEA approach to obtain robust rank values for DMUs. The proposed approach yields Nash equilibrium solution, thus overcomes the problem of non-uniqueness of the DEA optimal weights that can possibly reduce the usefulness of cross efficiency. Finally, in order to verify the validity of the proposed model and to show the practicability of algorithm, we apply a real-world example for selection of industrial R&D projects. The proposed model can increase the discriminating power of DMUs and can fully rank the DMUs.
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

Qualitätssicherung 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

Radiofrequency 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.
Magnetization switching in nanoelements induced by the spin-transfer torque: Study by massively parallel micromagnetic simulations
Authors: Semenova Elena K. , Berkov Dmitry V.
Published: May 2019

In this paper we present a detailed numerical study of magnetization switching in shape-anisotropic thin-film nanoelements. These elements are at present of the major interest for the applied solid state magnetism as main components of a new generation of conventional and spin-transfer-torque (STT) magnetic random access memory (MRAM) cells. To conduct this study, we have developed a highly efficient method for massively parallel micromagnetic simulations of the magnetization reversal in small-size nanoelements, which allows to fully exploit the large performance gain available on the GPU architecture (usually achievable only for large systems). We apply our method to the spin-torque-induced magnetization switching in elliptical nanoelements in presence of thermal fluctuations. Being able to compute simultaneously the reversal of up to 1000 such elements, we obtain the dependence of (i) the average switching time and (ii) the distribution density of switching times for individual elements on the element size with a high statistical accuracy. Analysis of these dependencies provides important insights into the physics of magnetization reversal in such systems. Comparison with analogous simulations in the macrospin approximation allows to determine the validity limits of the macrospin model. Our methodology can be applied for the optimization of the MRAM design regarding the information life time and significantly improve the prediction accuracy of write and read error rates of conventional and STT-based MRAM cells.
Aluminum acceptor activation and charge compensation in implanted p-type 4H-SiC
Authors: Weiße J. , Hauck M. , Krieger M. , Bauer A. J. , Erlbacher T.
Published: May 2019

In 4H silicon carbide, aluminum implantation causes unusual high compensation ratios as obtained from Hall effect investigations by fitting the neutrality equation with a single acceptor. We show that this approach cannot fully describe the experimental data, in particular in case of moderate doping and at high measurement temperatures above 450 K. We develop two extended models by adding an additional acceptor- or donor-like defect to the equation. Both approaches describe the data well. However, it turns out that an additional aluminum-correlated acceptor is the more reasonable choice. In this case, the compensation ratio stays almost independent of the implantation dose between 30 % and 40 %. The deep acceptor is located at EV + (280–400) meV.
Unraveling the mystery of histone tail function in nucleosome unwinding
Authors: Frank Jodi Ackerman
Published: May 2019

Study reveals source of layer separation to provide a fuller picture of how histone tails influence the free-energy landscape of nucleosome unwinding.
Influence of thermal radiation on hot cluster decay rates and abundances
Authors: Hansen Klavs , Ferrari P.
Published: May 2019

The influence of radiative cooling on the unimolecular decay rates of free, hot clusters and molecules with unspecified excitation energies is quantified. Two different regimes, defined by the magnitude of the energy of the photons emitted, are identified and the boundary between them is given. The boundary is determined in terms of the photon emission rate constants and thermal properties of the particles. Also the abundance spectra are calculated for the continuous cooling case, corresponding to small photon energies. The two regimes correspond to continuous cooling and single photon quenching of the unimolecular decay. The radiative effect can be parametrized by a redefinition of the time each individual cluster has available to undergo evaporation, expressed by an effective radiative time constant.
Composition dependent magnetic coupling in Fe-Cr alloy cluster arrays
Authors: Xu Zhong-qi , Liu Chang , Luo Wei-feng , Liu Fei , Han Min
Published: May 2019

Dense arrays of Fe-Cr alloy clusters with different Cr ratios were fabricated by gas-phase cluster beam deposition. The complex multiphase structure and various coupling effects in the cluster arrays were studied. A lattice mismatched tetragonal-like morphology of the Fe-Cr alloy cluster was observed at large Cr ratio. An exchange bias effect was observed and was shown to be dependent on the proportion of the Cr components in the alloy. With the increase of the Cr composition, the exchange bias field became smaller and stronger dipolar interactions between the clusters developed. Residual coercivity and magnetization, which were more remarkable in the tetragonal-like clusters, were observed above the ferromagnetic-superparamagnetic transition temperature. The experimental results of the coercive field and the bias field at different temperatures demonstrated that the tetragonal-like clusters had better thermal stability and greater anisotropy.
Well dispersed SnO2 nanoclusters preparation and modulation of metal-insulator transition induced by ionic liquid
Authors: Liu Zhong-hu , Chen Xing , Zhu Yi-yu , Zhao Si-han , Wang Zhi-qiang , Wang Feng , Meng Qiang-qiang , Zhu Lei , Zhang Qin-fang , Wang Bao-lin , Fan Le-le
Published: May 2019

Tin dioxide (SnO2) has attracted broad interest due to its particular gas-sensor property. Nano- or atom-scale SnO2 material has always been the aim in order to ultimately improve the sensitivity. However, until now, it remains difficult to synthesize SnO2 nanoclusters by using traditional methods. In the present work, we have achieved the preparation of SnO2 nanoclusters by using the cluster beam deposition technique. The obtained nanoclusters were well characterized by high resolution transmission electron microscope HR-TEM. Results indicated the formation of the well-dispersed SnO2 nanoclusters with uniform size distribution (5–7 nm). Furthermore, an obvious metal insulator transition was observed by gating with ionic liquid. Combined with theory calculation, the corresponding mechanism was systematically analyzed from oxygen vacancy induced electron doping.
Defining the key attributes of resilience in mixed ration dairy systems
Authors: Barber D. G. , Auldist M. J. , Anstis A. R. , Ho C. K. M.
Published: May 2019

Dairy feeding systems in Australia and New Zealand have seen an increase in the use of mixed rations to manage variability in climate and market conditions and enable a certain degree of resilience in the operating environment. In this review, resilience was defined as the ability of the farm system to respond to challenges, optimise productivity and profitability for a given set of circumstances, and persist over time. Specific attributes of a dairy system that contribute to resilience were considered as flexibility, consistency, adaptation, sustainability and profitability. A flexible forage base that uses water efficient forage species provides a consistent supply of nutrients from home-grown forages across the year and is a key driver of resilience. Consistent milk production from purchased concentrates adds value to the forage base and will ensure that the system is profitable in the long term. Appropriate investment in infrastructure and careful management of debt has a positive impact on technical and financial efficiency and improves overall economic performance and resilience of the system. Nutrients, feed wastage, cow comfort and welfare were also identified as key areas to focus on for improved sustainability. Future research investigating the interaction between forages and concentrates, and the subsequent milk production response will be important for the future resilience of mixed ration systems. Adaptive management at a tactical and strategic level across several technical areas will further underpin the resilience of a mixed ration dairy system, and minimise the impact of climate and price variability. This will have flow on benefits to animal welfare and resource sustainability, which will have a positive impact of the public perception of these systems within the Australian and New Zealand dairy industries.
The labile zinc pool in plant cells
Authors: Zlobin Ilya E. , Kartashov Alexander V. , Nosov Alexander V. , Fomenkov Artem A. , Kuznetsov Vladimir V.
Published: May 2019

Zinc is the most abundant and important transition metal in plants; however, the dynamic aspects of zinc homeostasis in plant cells are poorly understood. In this study we explored the pool of labile exchangeable zinc complexes in plant cells, and the potential influence of changes in intracellular zinc availability on cellular physiology. Work was performed on cultivated cell extracts of Arabidopsis thaliana (L.) Heynh. and Thellungiella salsuginea (Pall.) O.E. Schulz grown under control (3.48 µM Zn2+), 10-fold Zn excess or Zn starvation conditions. The free and labile Zn contents in the extracts were then determined by fluorimetric titration. We observed for the first time that plant cells contain micromolar concentrations of labile zinc complexes that account for a low percentage of the total zinc content. Labile zinc is mainly protein bound. Zn starvation inhibits cell proliferation and leads to the disappearance of the labile zinc pool, whereas Zn excess drastically increases the labile zinc pool. Free Zn2+ is buffered at picomolar concentrations in the intracellular milieu, and the increase in free Zn2+ concentrations to low nanomolar values clearly modulates enzyme activity by direct reversible binding. Such increases in free Zn2+ can be achieved by the substantial influx of additional zinc or by the oxidation of zinc-binding thiols. The observed features of the labile zinc pool in plant cells suggest it has a role in intracellular zinc trafficking and zinc signalling.
Oleanolic acid causes reversible contraception in male mice by increasing the permeability of the germinal epithelium
Authors: Fisher David , Mosaval Faizel , Tharp Darla L. , Bowles Doug K. , Henkel Ralf
Published: May 2019

The effects of oleanolic acid (OA) on the fertility of male mice were investigated using both invivo and invitro experimental models. The experimental group (n=12) was treated with a daily dose of 30mgOAkg−1 bodyweight (i.p.), while the control group (n=6) received a daily dose of 10% ethanol solution (1mLkg−1 bodyweight). The effect of OA on the permeability status of TM4 Sertoli monolayers was investigated by measuring the transepithelial electrical resistance (TER), intracellular electrical resistance and semiquantitative RT–PCR. After 45 days, OA-treated males produced no pregnancies but in the control group, all 12 females were impregnated (69 offspring). Male mice, which demonstrated sterility when exposed to OA, recovered their fertility after 30 days (78 offspring). Testicular histological observations of OA-treated mice showed detachment of adjacent Sertoli–Sertoli cells. A control monolayer developed TER of 300–400 Ω.cm2, but OA (50, 100, 200µgL−1) treated monolayers developed TER of approximately 100Ω.cm2. Intracellular electrophysiological and RT–PCR data supported the premise that OA compromised tight junctional permeability. The study demonstrated reversible contraception in male mice by increasing the permeability of the germinal epithelium and further postulates that contraceptive reversibility is brought about by the reconstitution of the paracellular junctions between adjacent Sertoli cells.
Change of Element Settlement in Musi Riverside Palembang
Authors: Wicaksono Bambang , Siswanto Ari , Kusdiwanggo Susilo , Anwar Widya Fransiska Febriati
Published: May 2019

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

Marine 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

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

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

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

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

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

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

A 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.
Keepingcrisprin check: diverse mechanisms of phage-encoded anti-crisprs
Authors: Trasanidou Despoina , Gerós Ana Sousa , Mohanraju Prarthana , Nieuwenweg Anna Cornelia , Nobrega Franklin L , Staals Raymond H J
Published: May 2019

CRISPR-Cas represents the only adaptive immune system of prokaryotes known to date. These immune systems are widespread among bacteria and archaea, and provide protection against invasion of mobile genetic elements, such as bacteriophages and plasmids. As a result of the arms-race between phages and their prokaryotic hosts, phages have evolved inhibitors known as anti-CRISPR (Acr) proteins to evade CRISPR immunity. In the recent years, several Acr proteins have been described in both temperate and virulent phages targeting diverse CRISPR-Cas systems. Here, we describe the strategies of Acr discovery and the multiple molecular mechanisms by which these proteins operate to inhibit CRISPR immunity. We discuss the biological relevance of Acr proteins and speculate on the implications of their activity for the development of improved CRISPR-based research and biotechnological tools.
Hepatitis D infection: from initial discovery to current investigational therapies
Authors: Da Ben L , Heller Theo , Koh Christopher
Published: May 2019

Hepatitis D is the most severe form of viral hepatitis associated with a more rapid progression to cirrhosis and an increased risk of hepatocellular carcinoma and mortality compared with hepatitis B mono-infection. Although once thought of as a disappearing disease, hepatitis D is now becoming recognized as a serious worldwide issue due to improvement in diagnostic testing and immigration from endemic countries. Despite these concerns, there is currently only one accepted medical therapy (pegylated-interferon-α) for the treatment of hepatitis D with less than desirable efficacy and significant side effects. Due to these reasons, many patients never undergo treatment. However, increasing knowledge about the virus and its life cycle has led to the clinical development of multiple promising new therapies that hope to alter the natural history of this disease and improve patient outcome. In this article, we will review the literature from discovery to the current investigational therapies.
Integral Hasse Principle and Strong Approximation for Markoff Surfaces
Authors: Loughran Daniel , Mitankin Vladimir
Published: May 2019

We study the failure of the integral Hasse principle and strong approximation for Markoff surfaces, as studied by Ghosh and Sarnak, using the Brauer–Manin obstruction.
A comparison of text versus audio for information comprehension with future uses for smart speakers
Authors: Leroy Gondy , Kauchak David
Published: May 2019

Objective

Audio is increasingly used to access information on the Internet through virtual assistants and smart speakers. Our objective is to evaluate the distribution of health information through audio.

Materials and Methods

We conducted 2 studies to compare comprehension after reading or listening to information using a new corpus containing short text snippets from Cochrane (N = 50) and Wikipedia (N = 50). In study 1, the snippets were first presented as audio or text followed by a multiple-choice question. Then, the same information was presented as text and the question was repeated in addition to questions about perceived difficulty, severity and the likelihood of encountering the disease. In study 2, the first multiple-choice question was replaced with a free recall question.

Results

Study 1 showed that information comprehension is very similar in both presentation modes (53% accuracy for text and 55% for audio). Study 2 showed that information retention is higher with text, but similar comprehension. Both studies show improvement in performance with repeated information presentation.

Discussion

Audio presentation of information is effective and the format novel. Performance was slightly lower with audio when asked to repeat information, but comparable to text for answering questions. Additional studies are needed with different types of information and presentation combinations.

Conclusion

The use of audio to provide health information is a promising field and will become increasingly important with the popularity of smart speakers and virtual assistants, particularly for consumers who do not use computers, for example minority groups, or those with limited sight or motor control.
Available energy and amino acid digestibility of yellow dent corn fed to growing pigs1
Authors: Lyu Zhiqian , Li Quanfeng , Zhang Shuai , Lai Changhua , Huang Chengfei
Published: May 2019

Two experiments were conducted to determine the DE and ME as well as the apparent ileal digestibility (AID) and standardized ileal digestibility (SID) of CP and AA in corn fed to growing pigs. All corn was yellow dent corn collected from different areas in China. In Exp. 1, 60 crossbred barrows (Duroc × Landrace × Yorkshire; 40.7 ± 3.5 kg BW) were randomly allotted to 1 of 10 diets to determine the DE and ME of corns. Diets were formulated to contain 96.8% of 1 of the 10 corn samples and 3.2% of other microingredients. In Exp. 2, 11 crossbred barrows (Duroc × Landrace × Yorkshire; 30.5 ± 2.3 kg) fitted with a T-cannula at the distal ileum were assigned to a 6 × 11 Youden square design with 6 periods and 11 diets. Diets included a N-free diet based on cornstarch and sucrose and 10 test diets formulated with 96.6% 1 of the 10 corns as the sole source of AA. Chromic oxide (0.3%) was added to each diet as an indigestible marker for calculating the AA digestibility. On a DM basis, the starch, ether extract (EE), CP, NDF, and ADF contents of corns averaged 74.05% (69.98 to 78.59%), 3.83% (2.04 to 4.73%), 9.63% (7.74 to 10.43%), 10.80% (10.27 to 11.46%), and 2.27% (2.03 to 2.57%), respectively. The CV of EE, CP, and ADF was 22.59, 8.22, and 8.21%, respectively. The DE and ME of corns averaged 4,087 and 3,981 kcal/kg, respectively, and ranged from 3,999 to 4,161 kcal/kg and from 3,898 to 4,067 kcal/kg, respectively. The DE and ME values were positively correlated (P < 0.05) with the EE content. Optimal prediction equations of ME were ME = 940.35 + (0.72 × DE) + (21.88 × EE) (R2 = 0.94) or ME = 1,051.50 + (0.82 × DE) − (282.05 × ash) (R2 = 0.99). In Exp. 2, significant differences (P < 0.05) were observed in the SID of Arg, His, Phe, Ala, Pro, Cys, and Tyr. The SID of Lys (average 73.79%), Met (average 87.32%), and Thr (average 80.06%) ranged from 61.45 to 78.47%, from 74.09 to 90.91%, and from 79.19 to 85.79%, respectively. The standardized ileal digestible Met was positively correlated (P < 0.01) with the Met and CP contents. The obtained prediction equations were standardized ileal digestible Met = 31.34 + (3.43 × CP) + (116.04 × Met) and standardized ileal digestible Met = 104.92 + (294.71 × Met) − (7.03 × NDF). In conclusion, sources had an effect on the energy values and ileal digestibility of most AA in corn. The ME can be predicted by the DE combined with either the EE or ash content. The AA concentrations and SID of AA in corn varied largely.