bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐performance SIMD implementation of the lattice‐Boltzmann method on the Xeon Phi processor
Authors: Robertsén Fredrik , Mattila Keijo , Westerholm Jan 
Published: November 2018

SummaryWe present a high‐performance implementation of the lattice‐Boltzmann method (LBM) on the Knights Landing generation of Xeon Phi. The Knights Landing architecture includes 16GB of high‐speed memory (MCDRAM) with a reported bandwidth of over 400 GB/s, and a subset of the AVX‐512 single instruction multiple data (SIMD) instruction set. We explain five critical implementation aspects for high performance on this architecture: (1) the choice of appropriate LBM algorithm, (2) suitable data layout, (3) vectorization of the computation, (4) data prefetching, and (5) running our LBM simulations exclusively from the MCDRAM. The effects of these implementation aspects on the computational performance are demonstrated with the lattice‐Boltzmann scheme involving the D3Q19 discrete velocity set and the TRT collision operator. In our benchmark simulations of fluid flow through porous media, using double‐precision floating‐point arithmetic, the observed performance exceeds 960 million fluid lattice site updates per second.
Computational Prediction of 1H and 13C NMR Chemical Shifts for Protonated Alkylpyrroles: Electron Correlation and Not Solvation is the Salvation
Authors: Lacerda Evanildo G. , Kamounah Fadhil S. , Coutinho Kaline , Sauer Stephan P. A. , Hansen Poul Erik , Hammerich Ole 
Published: November 2018

AbstractPrediction of chemical shifts in organic cations is known to be a challenge. In this article we meet this challenge for α‐protonated alkylpyrroles, a class of compounds not yet studied in this context, and present a combined experimental and theoretical study of the 13C and 1H chemical shifts in three selected pyrroles. We have investigated the importance of the solvation model, basis set, and quantum chemical method with the goal of developing a simple computational protocol, which allows prediction of 13C and 1H chemical shifts with sufficient accuracy for identifying such compounds in mixtures. We find that density functional theory with the B3LYP functional is not sufficient for reproducing all 13C chemical shifts, whereas already the simplest correlated wave function model, Møller–Plesset perturbation theory (MP2), leads to almost perfect agreement with the experimental data. Treatment of solvent effects generally improves the agreement with experiment to some extent and can in most cases be accomplished by a simple polarizable continuum model. The only exception is the NH proton, which requires inclusion of explicit solvent molecules in the calculation.
Secure and efficient protection for HTTP cookies with self‐verification
Authors: Lee Wei‐Bin , Chen Hsing‐Bai , Chang Shun‐Shyan , Chen Tzung‐Her 
Published: November 2018

SummaryHypertext transfer protocol (HTTP) cookies are used to store user‐related information sent by a website, and they can be read again later to maintain a link between a user's computer and the website and to remember the user's previous state on the website. In cloud services, cookies are used by service providers to maintain smooth operation for users. As cookies are sent in a public networking environment and saved on users' browsers, two problems are encountered when using cookies: (a) how to protect sensitive information on a cookie from disclosure and (b) how to determine whether cookies have been modified maliciously. Several studies have been conducted on web security to assess problems that occur when cookies are injected and hijacked. In the present study, a secure and efficient cookie protection scheme is proposed. The scheme is designed with the following principles: (a) a key is hidden within a cookie, (b) the integrity of the cookie is verified by both the web server and the web browser, and (c) the key and sensitive information in the cookie can only be read by the website. The proposed method was analyzed for its security and efficiency. Moreover, the methods from related studies and the proposed method were compared. The results revealed that the proposed cookie scheme is effective at improving cookie security.
Range‐wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod
Authors: Fairweather Robert , Bradbury Ian R. , Helyar Sarah J. , de Bruyn Mark , Therkildsen Nina O. , Bentzen Paul , Hemmer‐Hansen Jakob , Carvalho Gary R. 
Published: November 2018

AbstractRecent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range‐wide examinations suggest significant transatlantic divergence, although the fine‐scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data‐synthesis approach, integrating multiple genome‐wide single‐nucleotide polymorphism (SNP) datasets representative of different regions to create a single range‐wide dataset containing 1,494 individuals from 54 locations and genotyped at 796 common loci. Our analysis highlights significant transatlantic divergence and supports the hypothesis of westward post‐glacial colonization of Greenland from the East Atlantic. Accordingly, our analysis suggests the presence of transatlantic secondary contact off eastern North America and supports existing perspectives on the phylogeographic history of Atlantic cod with an unprecedented combination of genetic and geographic resolution. Moreover, we demonstrate the utility of integrating distinct SNP databases of high comparability.
Seascape genetics of the spiny lobster Panulirus homarus in the Western Indian Ocean: Understanding how oceanographic features shape the genetic structure of species with high larval dispersal potential
Authors: Singh Sohana P. , Groeneveld Johan C. , Hart‐Davis Michael G. , Backeberg Björn C. , Willows‐Munro Sandi 
Published: November 2018

AbstractThis study examines the fine‐scale population genetic structure and phylogeography of the spiny lobster Panulirus homarus in the Western Indian Ocean. A seascape genetics approach was used to relate the observed genetic structure based on 21 microsatellite loci to ocean circulation patterns, and to determine the influence of latitude, sea surface temperature (SST), and ocean turbidity (KD490) on population‐level processes. At a geospatial level, the genetic clusters recovered corresponded to three putative subspecies, P. h. rubellus from the SW Indian Ocean, P. h. megasculptus from the NW Indian Ocean, and P. h. homarus from the tropical region in‐between. Virtual passive Lagrangian particles advected using satellite‐derived ocean surface currents were used to simulate larval dispersal. In the SW Indian Ocean, the dispersion of particles tracked over a 4‐month period provided insight into a steep genetic gradient observed at the Delagoa Bight, which separates P. h. rubellus and P. h. homarus. South of the contact zone, particles were advected southwestwards by prevailing boundary currents or were retained in nearshore eddies close to release locations. Some particles released in southeast Madagascar dispersed across the Mozambique Channel and reached the African shelf. Dispersal was characterized by high seasonal and inter‐annual variability, and a large proportion of particles were dispersed far offshore and presumably lost. In the NW Indian Ocean, particles were retained within the Arabian Sea. Larval retention and self‐recruitment in the Arabian Sea could explain the recent genetic divergence between P. h. megasculptus and P. h. homarus. Geographic distance and minimum SST were significantly associated with genetic differentiation in multivariate analysis, suggesting that larval tolerance to SST plays a role in shaping the population structure of P. homarus.
The sensitivity of snow ephemerality to warming climate across an arid to montane vegetation gradient
Authors: Petersky Rose S. , Shoemaker Kevin T. , Weisberg Peter J. , Harpold Adrian A. 
Published: November 2018

AbstractShifts from longer seasonal snowpacks to shorter, ephemeral snowpacks (snowpacks that persist for <60 days) due to climate change will alter the timing and rates of water availability. Ephemeral snowmelt has less predictable timing and lowers soil water availability during the growing season. The Great Basin, United States is an ideal system to study snow ephemerality across a broad climate gradient. To identify the climatic controls on snow ephemerality, we analysed moderate resolution imaging spectroradiometer (MODIS) snow‐covered products from water years 2001–2015 using an object‐based mapping approach and a random forest model. Winter temperature and precipitation were the most influential variables on the maximum snow duration. We predict that warming the average winter air temperature by 2 and 4°C would reduce the areal extent of seasonal snow by 14.7 and 47.8%, respectively (8.8% of the Great Basin's areal extent is seasonal in the historical record), with shifts to ephemeral snowpack concentrated in lower elevations and warmer regions. The combination of warming and interannual precipitation variability (i.e., reductions of 25%) had different effects on vegetation types. Vegetation types that have had consistent seasonal snow cover in their historical record are likely to have lower resilience to a new hydrologic regime, with earlier and more intermittent snowmelt causing a longer but drier growing season. Implications of increased snow ephemerality on vegetation productivity and susceptibility to disturbance will depend on local topography, subsurface water storage, and physiological adaptations. Nevertheless, patterns found in this study can help target management intervention to species that are most at risk.
Seismic responses of bridges with rocking column‐foundation: A dimensionless regression analysis
Authors: Zhang Jian , Xie Yazhou , Wu Gang 
Published: November 2018

SummaryRocking column‐foundation system is a new design concept for bridges that can reduce overall seismic damage, minimize construction and repair time, and achieve lower cost in general. However, such system involves complex dynamic responses due to impacts and highly nonlinear rocking behavior. This study presents a dimensionless regression analysis to estimate the rocking and shaking responses of the flexible column‐foundation system under near‐fault ground motions. First, the transient drift and rocking responses of the system are solved numerically using previously established analytical models. Subsequently, the peak column drifts and uplift angles are derived as functions of ground motion characteristics and the geometric and dynamic parameters of column‐foundation system in regressed dimensionless forms. The proposed response models are further examined by validating against the numerical simulations for several as‐built bridge cases. It is shown that the proposed model not only physically quantifies the influences of prominent parameters, but also consistently reflects the complex dynamics of the system. The seismic demands of rocking column‐foundation system can be realistically predicted directly from structural and ground motion characteristics. This can significantly benefit the design of bridges incorporating this new design concept.
The effectiveness of PEPFAR's funding for women and children with HIV/AIDS
Authors: Kim Yiyeon 
Published: November 2018

SummaryHas President's Emergency Plan for AIDS Relief's (PEPFAR) funding been effective in reducing the rate of HIV new infections and AIDS‐related deaths among women and children? While previous studies have found HIV/AIDS aid to be ineffective and PEPFAR funding to produce negative externalities, there is lack of empirical examination of the impact of PEPFAR on women and children despite the emphasis on prevention of mother‐to‐child transmission of HIV during the Bush and Obama administrations. Using descriptive analysis and difference‐in‐differences (DID) regression, this study finds that PEPFAR's funding has reduced the HIV new infections and AIDS‐related death rates of women and children for both focus countries and recipient countries, which are those that were added in a second phase. These findings show that PEPFAR's strategy for women and children has been effective and that it should be continued. However, while PEPFAR has contributed to the fight against HIV/AIDS, the effects of its work have been underestimated.
Enhancement of thermal efficiency and cost effectiveness by development of melting furnace by revamping and troubleshooting fuel‐fired furnace
Authors: Kumbhar Siddharaj V. , Sonage B. K. 
Published: November 2018

AbstractTechnological development of furnaces over conventional melting methods of diesel or gas‐fired furnaces is necessary. These furnaces have large amount of heat losses and hence their thermal efficiency is very low. Moreover, these furnaces do not produce good quality melt because of the chances of embedment of impurities from after‐combustion gases and agitation. The time required for melting in such furnaces is more. Also, insulation is not provided and there are heat losses which increase the time of melting. An electric resistance heating furnace is developed which overcomes all the problems associated with the fuel‐fired conventional furnace. The thermal efficiency of this developed furnace is found to increase quite drastically up to 85%, which is by about 33% more than conventional furnace; while reducing the operating cost of furnace. This benefits industry overall by profit of 70% and certainly can replace the existing conventional fuel‐fired furnaces.
CDC25A pathway toward tumorigenesis: Molecular targets of CDC25A in cell‐cycle regulation
Authors: Sadeghi Hossein , Golalipour Masoud , Yamchi Ahad , Farazmandfar Touraj , Shahbazi Majid 
Published: November 2018

AbstractThe cell division cycle 25 (CDC25) phosphatases regulate key transitions between cell‐cycle phases during normal cell division, and in the case of DNA damage, they are key targets of the checkpoint machinery that ensure genetic stability. Little is known about the mechanisms underlying dysregulation and downstream targets of CDC25. To understand these mechanisms, we silenced the CDC25A gene in breast cancer cell line MDA‐MB‐231 and studied downstream targets of CDC25A gene. MDA‐MB‐231 breast cancer cells were transfected and silenced by CDC25A small interfering RNA. Total messenger RNA (mRNA) was extracted and analyzed by quantitative real‐time polymerase chain reaction. CDC25A phosphatase level was visualized by Western blot analysis and was analyzed by 2D electrophoresis and LC‐ESI‐MS/MS. After CDC25A silencing, cell proliferation reduced, and the expression of 12 proteins changed. These proteins are involved in cell‐cycle regulation, programmed cell death, cell differentiation, regulation of gene expression, mRNA editing, protein folding, and cell signaling pathways. Five of these proteins, including ribosomal protein lateral stalk subunit P0, growth factor receptor bound protein 2, pyruvate kinase muscle 2, eukaryotic translation elongation factor 2, and calpain small subunit 1 increase the activity of cyclin D1. Our results suggest that CDC25A controls the cell proliferation and tumorigenesis by a change in expression of proteins involved in cyclin D1 regulation and G1/S transition.
Putative tumor suppressor cytoglobin promotes aryl hydrocarbon receptor ligand–mediated triple negative breast cancer cell death
Authors: Rowland Leah K. , Campbell Petreena S. , Mavingire Nicole , Wooten Jonathan V. , McLean Lancelot , Zylstra Dain , Thorne Gabriell , Daly Devin , Boyle Kristopher , Whang Sonya , Unternaehrer Juli , Brantley Eileen J. 
Published: November 2018

AbstractNearly 40 000 women die annually from breast cancer in the United States. Clinically available targeted breast cancer therapy is largely ineffective in triple negative breast cancer (TNBC), characterized by tumors that lack expression of the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (Her2). TNBC is associated with a poor prognosis. Previous reports show that aryl hydrocarbon receptor (AhR) partial agonist 2‐(4‐amino‐3‐methylphenyl)‐5‐fluorobenzothiazole (5F 203) selectively inhibits the growth of breast cancer cells, including those of the TNBC subtype. We previously demonstrated that 5F 203 induced the expression of putative tumor suppressor gene cytoglobin (CYGB) in breast cancer cells. In the current study, we determined that 5F 203 induces apoptosis and caspase‐3 activation in MDA‐MB‐468 TNBC cells and in T47D ER+ PR
+ Her2
− breast cancer cells. We also show that caspases and CYGB promote 5F 203–mediated apoptosis in MDA‐MB‐468 cells. 5F 203 induced lysosomal membrane permeabilization (LMP) and cathepsin B release in MDA‐MB‐468 and T47D cells. In addition, silencing CYGB attenuated the ability of 5F 203 to induce caspase‐3/‐7 activation, proapoptotic gene expression, LMP, and cathepsin B release in MDA‐MB‐468 cells. Moreover, 5F 203 induced CYGB protein expression, proapoptotic protein expression, and caspase‐3 cleavage in MDA‐MB‐468 cells and in MDA‐MB‐468 xenograft tumors grown orthotopically in athymic mice. These data provide a basis for the development of AhR ligands with the potential to restore CYGB expression as a novel strategy to treat TNBC.
Sodium–glucose cotransporter inhibitors and oxidative stress: An update
Authors: Yaribeygi Habib , Atkin Stephen L. , Butler Alexandra E. , Sahebkar Amirhossein 
Published: November 2018

AbstractSodium–glucose cotransporter 2 (SGLT2) inhibitors are therapeutic agents that have been used recently to reduce tubular absorption of glucose, leading to enhanced glycosuria, resulting in the reduction of blood glucose and improved diabetes control. Recent data suggest that SGLT2 inhibitors have antioxidant properties that may be key to the reduction in cardiovascular death found in clinical trials. Oxidative stress is involved in the development and progression of atherosclerosis, as well as underlying diabetes complications, and may result from either increased free‐radical production, a reduction in antioxidative capacity, or a combination of both. In this report, we have reviewed the recent evidence of the impact that SGLT2 inhibition may have on improved oxidative stress by either amelioration of free‐radical generation or potentiation of cellular antioxidative capacity, and its importance in the prevention of cardiovascular and diabetes complications.
MicroRNA‐99a‐5p suppresses breast cancer progression and cell‐cycle pathway through downregulating CDC25A
Authors: Qin Hongzhen , Liu Wenfei 
Published: November 2018

AbstractIn this study, we aimed to explore the association between miR‐99a‐5p and CDC25A in breast cancer and the regulatory mechanisms of miR‐99a‐5p on breast cancer. The expressions of messenger RNA and microRNAs in breast cancer tissues and adjacent tissues were analyzed by the Cancer Genome Atlas microarray analysis. Quantitative real‐time polymerase chain reaction was conducted to find out the expression levels of miR‐99a‐5p and
CDC25A. The expression levels of proteins (CDC25A, ki67, cyclin D1, p21, BAX, BCL‐2, BCL‐XL, MMP2, and MMP9) were determined by Western blot analysis. The relationship between miR‐99a‐5p and
CDC25A was predicted and verified by bioinformatics analysis and dual luciferase assay. After transfection, cell proliferation, invasion, and apoptosis of breast cancer tissues were, respectively, observed by cell counting kit‐8 assay, transwell assay, and flow cytometry (FCM). Furthermore, the relationship among miR‐99a‐5p,
CDC25A, and cell‐cycle progression was determined by FCM assay. The nude mouse transplantation tumor experiment was performed to verify the influence of miR‐99a‐5p on breast cancer cell in vivo. The expression of miR‐99a‐5p in breast cancer tissues and cells was significantly downregulated, whereas
CDC25A expression was upregulated. MiR‐99a‐5p targeted
CDC25A and suppressed its expression in breast cancer cells. Overexpression of miR‐99a‐5p and decreased expression of
CDC25A could suppress breast cancer cell proliferation and invasion and facilitate apoptosis. Cell‐cycle progression was significantly activated by downregulated miR‐99a‐5p and upregulated
CDC25A. Moreover, miR‐99a‐5p overexpression repressed the expressions of CDC25A, marker ki67, and Cyclin D1 proteins, whereas it upregulated the expression of p21 protein. MicroRNA‐99a‐5p suppresses breast cancer progression and cell‐cycle pathway through downregulating
CDC25A.
A study of quiet eye's phenomenon in the shooting section of “laser run” of modern pentathlon
Authors: Chirico Andrea , Fegatelli Dario , Galli Federica , Mallia Luca , Alivernini Fabio , Cordone Susanna , Giancamilli Francesco , Pecci Stefano , Tosi Gian Marco , Giordano Antonio , Lucidi Fabio , Massaro Mina 
Published: November 2018

AbstractThe aim of the study was to evaluate the effects of the Quiet eye (QE) phenomenon on performances during the shooting section of “Laser Run” of Modern Pentathlon, in two samples of athletes (novices and experts). The “Laser Run” consists of running and shooting activities. The study involved 18 experienced athletes of the Italian National Team of Modern Pentathlon (i.e., “elite” group) and 18 young and nonexpert athletes of a local Pentathlon club (i.e., “novice” group). Participants performed, in ecological conditions, five trials of four series of shootings (as it occurs in the real competitions), for a total of 20 series. During the shooting trials, athletes wore a mobile Eye Tracking System to record eye movements (saccades, blinks, and fixations). Key measures of the study were QE parameters (QE Duration [QED], Relative QED [RQED], and QE Onset), as well as the performance (accuracy and time to perform the event). The results revealed that both groups of athletes had a longer QED, RQED, and an earlier onset during their best shots than during the worse ones. Furthermore, differences between the groups showed that elite athletes had an earlier onset and a shorter QED than the novice group of athletes. These results provide insightful information about different cognitive and perceptual processes involved in Modern Pentathlon's athletes' performances at both the elite and non‐elite level.
Organ‐on‐chip models: Implications in drug discovery and clinical applications
Authors: Mittal Rahul , Woo Frank W. , Castro Carlo S. , Cohen Madeline A. , Karanxha Joana , Mittal Jeenu , Chhibber Tanya , Jhaveri Vasanti M. 
Published: November 2018

AbstractBefore a lead compound goes through a clinical trial, preclinical studies utilize two‐dimensional (2D) in vitro models and animal models to study the pharmacodynamics and pharmacokinetics of that lead compound. However, these current preclinical studies may not accurately represent the efficacy and safety of a lead compound in humans, as there has been a high failure rate of drugs that enter clinical trials. All of these failures and the associated costs demonstrate a need for more representative models of human organ systems for screening in the preclinical phase of drug development. In this study, we review the recent advances in in vitro modeling including three‐dimensional (3D) organoids, 3D microfabrication, and 3D bioprinting for various organs including the heart, kidney, lung, gastrointestinal tract (intestine–gut–stomach), liver, placenta, adipose, retina, bone, and brain as well as multiorgan models. The availability of organ‐on‐chip models provides a wealth of opportunities to understand the pathogenesis of human diseases and provide a potentially better model to screen a drug, as these models utilize a dynamic 3D environment similar to the human body. Although there are limitations of organ‐on‐chip models, the emergence of new technologies have refined their capability for translational research as well as precision medicine.