gebhart/patrepeval huggingface dataset:
From gigabyte to kilobyte (2015)

RNA-Seq techniques generate hundreds of millions of short RNA reads using next-generation sequencing (NGS). These RNA reads can be mapped to reference genomes to investigate changes of gene expression but improved procedures for mining large RNA-Seq datasets to extract valuable biological knowledge are needed. RNAMiner -- a multi-level bioinformatics protocol and pipeline -- has been developed for such datasets. It includes five steps: mapping RNA-Seq reads to a reference genome, calculating gene expression values, identifying differentially expressed genes, predicting gene functions, and constructing gene regulatory networks. To demonstrate its utility, we applied RNAMiner to datasets generated from Human, Mouse, Arabidopsis thaliana, and Drosophila melanogaster cells, and successfully identified differentially expressed genes, clustered them into cohesive functional groups, and constructed novel gene regulatory networks. The RNAMiner web service is available at http://calla.rnet.missouri.edu/rnaminer/index.html.
Antibacterial agents from the cashew Anacardium occidentale (Anacardiaceae) nut shell oil (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAntibacterial agents from the cashew Anacardium occidentale (Anacardiaceae) nut shell oilMasaki Himejima and Isao KuboCite this: J. Agric. Food Chem. 1991, 39, 2, 418–421Publication Date (Print):February 1, 1991Publication History Published online1 May 2002Published inissue 1 February 1991https://doi.org/10.1021/jf00002a039RIGHTS & PERMISSIONSArticle Views1172Altmetric-Citations157LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (437 KB) Get e-Alertsclose Get e-Alerts
Modeling a Million-Node Slim Fly Network Using Parallel Discrete-Event Simulation (2016)

As supercomputers close in on exascale performance, the increased number of processors and processing power translates to an increased demand on the underlying network interconnect. The Slim Fly network topology, a new lowdiameter and low-latency interconnection network, is gaining interest as one possible solution for next-generation supercomputing interconnect systems. In this paper, we present a high-fidelity Slim Fly it-level model leveraging the Rensselaer Optimistic Simulation System (ROSS) and Co-Design of Exascale Storage (CODES) frameworks. We validate our Slim Fly model with the Kathareios et al. Slim Fly model results provided at moderately sized network scales. We further scale the model size up to n unprecedented 1 million compute nodes; and through visualization of network simulation metrics such as link bandwidth, packet latency, and port occupancy, we get an insight into the network behavior at the million-node scale. We also show linear strong scaling of the Slim Fly model on an Intel cluster achieving a peak event rate of 36 million events per second using 128 MPI tasks to process 7 billion events. Detailed analysis of the underlying discrete-event simulation performance shows how the million-node Slim Fly model simulation executes in 198 seconds on the Intel cluster.
H/D exchange at sp3 carbons in the coordination sphere of platinum(ii) (2013)

The [PtCl(η(1)-CH2CH2OR)(Me2phen)], Me2phen = 2,9-dimethyl-1,10-phenanthroline, complex is indefinitely stable in the solid state; however, when dissolved in protic deuterated solvents at basic pH, it undergoes H-D exchange at the Me2phen Me's. An analogous H-D exchange process takes place in the related [PtCl2(Me2phen)] complex which is sterically strained and very easily can detach one nitrogen of Me2phen yielding a T-shaped species. In contrast, the H-D exchange is considerably slower in the [Pt(OR)2(Me2phen)] complex characterized by smaller size and lower trans-labilizing effect of the oxygen donor ligands. It is suggested that the formation of a T-shaped intermediate could foster the C-H activation via oxidative addition to the metal centre. In accord with this hypothesis, the H/D exchange was found to be considerably slower in analogous complexes with 6,6'-dimethyl-2,2'-bipyridyl (Me2bpy), where the greater flexibility of Me2bpy, as compared to Me2phen, reduces the strain in the four coordinate substrate and hence the propensity to dissociate one end of the bidentate ligand.
Lipophilic Guanylhydrazone Analogues as Promising Trypanocidal Agents: An Extended SAR Study (2020)

In this report, we extend the SAR analysis of a number of lipophilic guanylhydrazone analogues with respect to in vitro growth inhibition of Trypanosoma brucei and Trypanosoma cruzi. Sleeping sickness and Chagas disease, caused by the tropical parasites T. brucei and T. cruzi, constitute a significant socioeconomic burden in low-income countries of sub-Saharan Africa and Latin America, respectively. Drug development is underfunded. Moreover, current treatments are outdated and difficult to administer, while drug resistance is an emerging concern. The synthesis of adamantane-based compounds that have potential as antitrypanosomal agents is extensively reviewed. The critical role of the adamantane ring was further investigated by synthesizing and testing a number of novel lipophilic guanylhydrazones. The introduction of hydrophobic bulky substituents onto the adamantane ring generated the most active analogues, illustrating the synergistic effect of the lipophilic character of the C1 side chain and guanylhydrazone moiety on trypanocidal activity. The n-decyl C1-substituted compound G8 proved to be the most potent adamantane derivative against T. brucei with activity in the nanomolar range (EC50=90 nM). Molecular simulations were also performed to better understand the structure-activity relationships between the studied guanylhydrazone analogues and their potential enzyme target.
Table S4 from SHP2 Inhibition Sensitizes Diverse Oncogene-Addicted Solid Tumors to Re-treatment with Targeted Therapy (2023)

&lt;p&gt;Supplementary Table 4: Pharmacokinetics of PF-07284892 in preclinical species&lt;/p&gt;
Chipless RFID tag using high‐impedance surfaces with resistor loading (2017)

ABSTRACT This study presents a novel chipless radio frequency identification tag based on HIS structure with loaded resistors. The scatters are designed to be period nesting loops. The power of the back scatted signal is controlled by varying the resistance of loaded resistors. Its operation principle is described through an equivalent transmission line model. By applying the ASK coding technology, a coding density of 11.1 bits is obtained. Polarization independence is validated by measuring the tag in different polarization directions. The cases excited with an oblique incidence wave are also discussed. Experimental validations of the proposed tag have been presented together with considerations about practical implementation. © 2017 Wiley Periodicals, Inc. Microwave Opt Technol Lett 59:1136–1140, 2017
Bioceramic Hydroxyapatite Granules for Purification of Biotechnological Products (2011)

Sorption experiments of bovine serum albumin (BSA) on hydroxyapatite (HAp) ceramic granules, prepared at three temperatures 900°C, 1000°C and 1150°C were performed at room temperature 18,6 °C and phosphate buffer, pH 5,83; 6.38 and 7,39. Thermal treatment contributed to the decrease of bovine serum albumin immobilization indicating that sorption process depended on HAp ceramics specific surface area and pH values of phosphate buffer solution. However, it was confirmed that granule size was also an important parameter for bovine serum albumin adsorption. As a result of these experiments, the most appropriate adsorption conditions and phosphate buffer pH values influence on to BSA sorption were analyzed.
Healthy Lifestyle Behaviors Are Major Predictors of Mental Wellbeing During COVID-19 Pandemic Confinement: A Study on Adult Arabs in Higher Educational Institutions (2020)

Abstract Background: In previous times, infectious diseases affected the quality of human life during home confinement. This study investigated the influence of home confinement during the COVID-19 pandemic outbreak on lifestyle, mental wellbeing, nutritional status, and sleeping pattern. Method: An online multicategory questionnaire was distributed to collect Demographical information and combined the following tools: Food Frequency Questionnaire (FFQ), International Physical Activity Questionnaire (IPAQ), WHO-5 wellbeing score, and Pittsburgh Sleep Quality Index (PSQI). A snowball none-discriminate sampling procedure was followed to collect data from people attending or working at higher institution had covering the period between Mar/00/2020 and Apr/24/2020. A total of 1723 completed responses (917 Males 37.4 ±13.4 yrs. old and (806 Females 32.2 ± 11.5 yrs. old) were collected. Results: Female participants had significantly lower mental health scores as compared to males (53.9% vs 46.1%). on Mental wellbeing score was better among participants with medium and high Physical Activity Levels (p &lt; 0.00). Additionally, mental wellbeing score was significantly improved by dietary quality and sleeping score (p &lt; 0.001). However, physical activity was by far the major determinants of mental health score. Conclusion: Factors such as PA, Diet, sleeping patterns were associated with mental wellbeing during COVID-19 confinement among Arab participants.
The Effect of High Power Laser on Organic-Rich Shales (2021)

Abstract The objective of this work is to characterize the effect of a high power laser (HPL) on organic-rich shales. The analysis combines machine learning with advanced characterizations to reveal the geochemical and mechanical transformations induced by high power laser in source rocks. Lab results showed that HPL improves permeability, increases porosity, modifies the mechanical structure of the rock, and may positively affect the maturity of source rocks. A high power laser was used in the lab to perforate and heat different types of source rocks with varying organic content. The process was characterized in real time using near-infrared spectroscopy and mid-IR thermography. The pre- and post-characterization process draws on different tools to evaluate the chemical and structural transformations induced by the HPL processes. This step included several spectroscopy techniques (e.g., FTIR, UV/VIS/NIR), Rock-Eval, and differential thermal analysis (DTA). The analysis leverages on clustering techniques to reveal the distinct effects of HPL on source rocks. The spectroscopy and geochemical analyses revealed that that HPL modifies the molecular structure of the rock. Yet, the fundamental structure of the rock remains intact. The changes are revealed by clustering analysis of the FTIR data before and after laser heating. The analysis show the formation of clusters after the process, which correspond to the maturation of the organic content. The success of the lab work proved that high power laser could enhance the properties of source rocks. The effects include permeability improvement, enhanced porosity, and changes in the molecular distribution of the organic content. The results of the analyses suggest that the laser can drive forward the maturity of the source rock. This work also illustrates how machine learning and multiphysics characterization can reveal the dynamics of the HPL processes and their effects. Ultimately, the outcome of this study will contribute to the development of novel HPL applications.
SAFT imaging using immersed capacitive micromachined ultrasonic transducers (2003)

Micromachined ultrasonic transducers (cMUTs) capable of operating in immersion mode have been designed and fabricated. As with previously reported airborne results, these immersable transducers possess extremely wide bandwidths, with operation typically ranging from low MHz extending beyond 10 MHz in water. Such wide bandwidths are of interest for many imaging applications. A range of transducer arrays have been fabricated with individual element sizes ranging from 200 /spl mu/m - 1 mm. The transducers are fabricated using an electronics-compatible micromachining process, which would allow analogue front-end electronics and transducers to be implemented on the same silicon substrate. Results will be presented from small aperture synthetic line arrays of cMUT receivers, which have been used in conjunction with a series of piezoelectric sources to allow images to be presented of reflective targets. The data is processed using a 2D Synthetic Aperture Focussing Technique (SAFT) algorithm.
A Survey of Big Data and Computational Intelligence in Networking (2017)

Networking has become an indispensable part of the modern world, providing convenient access to the Internet, remote communication, and information exchange. Big data also has a great influence on networking. Networked big data, in fact, is not simply another way of saying &quot;analytics&quot; or large amount of data. In addition to the common features of veracity and value, networked big data has higher volume, velocity, and variety compared with other forms of big data. A network application in the era of big data usually involves data sources from different geographically distributed data centers. Under the distributed and decentralized control of large volume, heterogeneous, autonomous sources, big data seeks to explore the complex and ever-changing relationship among data. Networked big data possesses unstructured, semistructured, and structured formats. Big data security issues are related to a set of risk areas, which includes information lifecycle, data creation, and collection processes.
Research of dynamic routing based on improved Dynamic Ant Colony algorithm (2010)

The reliability and distance of Power Line Communication (PLC) are the most important factors, which limit the application of PLC in practice seriously. This paper discusses the specialties and the methods of building up the PLC networks, uses an improved Dynamic Ant Colony System algorithm (DACS) in dynamic routing of PLC networks, and the multi-path storage technology is given. The improved DACS enhanced the accuracy and efficiency of dynamic routing in two aspects, that is the best tours and the worst tours. A dynamic penalty on worst tours will open up chances for ants to navigate, limit intentions and provide cautions in an ant's decision to move. And ants can get better search guidance by concentrating only the best tours from all groups. The simulation and experimentation indicate that the improved DACS provides an effective dynamic routing method for the expansion of PLC. It is an effective method of improving the reliability of PLC.
Transport architecture evolution in UMTS/IMT-2000 cellular networks (2000)

Mobile evolution from the second generation (2G) to the third generation (3G) raises several important questions for operators and manufacturers. How to ensure that the old and current investments can still be utilized in the future? What is the optimum architecture? ATM or IP? Voice or data? There is no single correct answer to these questions, as it all depends on individual cases. In this paper, we discuss the transport architecture evolution for the universal mobile telecommunications system (UMTS)/international mobile telecommunications—year 2000 (IMT-2000), or 3G cellular networks and interworking aspects between 2G and 3G cellular networks. The interfaces between access nodes in a cellular network and the changes incorporated to support packet data services are described. Emerging services such as mobile data, virtual private networks (VPN) and location aware networking are described. Role of ATM and IP in this new transport architecture is presented. Control and data plane interworking issues between different transport technologies are described. The new ATM standard, ATM adaptation layer type 2 (AAL2) and its applicability for transporting compressed speech in an ATM based cellular network is described. A similar approach in IP, multiplexing in real-time transport protocol (RTP) payload to transport compressed speech on selective interfaces of 3G network, is introduced. Transport network architecture evolution within four different scenarios is evaluated. Special interest is focused on the protocol stacks and flexible layered solutions that allow smooth migration from one transport technology to another. Copyright © 2000 John Wiley & Sons, Ltd.
Coupled mechanical-electrostatic FE-BE analysis with FMM acceleration (2004)

This paper deals with the coupled mechanical-electrostatic analysis of a shunt capacitive MEMS switch. The mechanical and electrostatic parts of the problem are modelled by the FE and BE methods, respectively. The fast multipole method is applied to reduce the storage requirements and the computational cost of the BE electrostatic model. An adaptive truncation expansion of the 3D Laplace Green function is employed. The strong interaction between the mechanical and electrostatic systems is considered iteratively.
Mucosal eosinophils, mast cells, and intraepithelial lymphocytes in youth with rumination syndrome (2021)

In conclusion, we found an increase in eosinophil and mast cell densities in the gastric antrum and an increase in intraepithelial lymphocytes in the duodenum in youth with rumination syndrome which was independent of the presence of abdominal pain or early satiety. These findings suggest a potential role for inflammation in the pathophysiology of rumination syndrome. Future studies should address whether treatment directed at these cells are beneficial in treating rumination syndrome.
Review of transplantation in HIV patients during the HAART era. (2004)

Human immunodeficiency virus (HIV) infection was once thought to be a relative or even absolute contraindication to transplantation. With the recent advent of highly active antiretroviral therapy (HAART), those infected with HIV are now living longer and dying from illnesses other than acquired immunodeficiency syndrome (AIDS). Although studies prior to the HAART era suggested poor outcomes might occur with transplantation in those infected with HIV, more recent studies have demonstrated results comparable to those of recipients without HIV infection. A number of issues persist regarding ethics, patient selection, post-operative management, and drug interactions between antiretroviral and immunosuppression agents. In this review, kidney, liver, and heart transplantation in the HIV-positive population were analyzed using data from the Organ Procurement and Transplantation Network/ Scientific Registry of Transplant Recipients.
A Risk Score for Predicting Near-Term Incidence of Hypertension: The Framingham Heart Study (2008)

The hypertension risk prediction score can be used to estimate an individual's absolute risk for hypertension on short-term follow-up, and it represents a simple, office-based tool that may facilitate management of high-risk individuals with prehypertension.
Targeted genomic landscape of metastases compared to primary tumours in clear cell metastatic renal cell carcinoma (2018)

These data support the theory that ccRCC primary tumours and metastases encompass a uniform distribution of common genomic alterations tested by next-generation sequencing targeted panels. This study does not address variability between matched primary tumours and metastases or the change in genomic alterations over time and after sequential systemic therapies.
Optimal variable selection in multi-group sparse discriminant analysis (2015)

This article considers the problem of multi-group classification in the setting where the number of variables $p$ is larger than the number of observations $n$. Several methods have been proposed in the literature that address this problem, however their variable selection performance is either unknown or suboptimal to the results known in the two-group case. In this work we provide sharp conditions for the consistent recovery of relevant variables in the multi-group case using the discriminant analysis proposal of Gaynanova et al. [7]. We achieve the rates of convergence that attain the optimal scaling of the sample size $n$, number of variables $p$ and the sparsity level $s$. These rates are significantly faster than the best known results in the multi-group case. Moreover, they coincide with the minimax optimal rates for the two-group case. We validate our theoretical results with numerical analysis.
Benchmarking nanotechnology for high-performance and low power logic transistor applications (2005)

Recently there has been tremendous progress made in the research of novel nanotechnology for future nanoelectronics applications. In particular, several novel nanoelectronic devices such as carbon-nanotube field effect transistor (FET), Si nanowire FET, and planar III-V compound semiconductor FET, all hold promise as device candidates to be integrated onto the silicon platform for enhancing circuit functionality and also for extending Moore's law. For high-performance and low-power logic transistor applications, it is important that these research devices are frequently benchmarked against the existing Si logic transistor data in order to gauge the progress of research. In this work, we compare these novel nanoelectronic devices to the state-of-the-art planar and nonplanar Si logic transistors in terms of intrinsic speed, energy-delay product, and electrostatics. The results of this benchmarking exercise indicate that while these novel nanoelectronic devices show promise and opportunities for future logic applications, their device characteristics and electrostatics still need to be improved. We believe that BENCHMARKING is a key element in accelerating the progress of nanotechnology research for logic transistor applications.
Anisotropy and Temperature Dependence of the Zero Field Uniform Mode Relaxation Rate in (1974)

Using derivative detection we have measured dχ″ (ω,H)/dH for a RF field applied along either the c (antiferromagnetic) axis or the a axis, in the presence of a static field H applied perpendicular to the RF field. Measurements were made with ω/2π ≃ 14 MHzand 58 MHz, and with H between O and 15KOe. These data were put on an approximate absolute scale by calibrating the spectrometer against the F19 NMR line. By numerical integration we then obtained the zero‐field absorption χ″ (ω,0). The results were then analyzed by assuming a single relaxation rate, i.e. χ″ (ω,0)/ω = χΓ/(ω2plus;Γ2), where χ is the known static susceptibility. For the case HRF∥ a. Γ aPPeared to diverge as TN was approached from above, with no detectable absorption observed below TN. However, for HRF∥ c, absorption was observed below, at and above TN. Thus there is no critical anomaly in the longitudinal uniform relaxation rate. This rate remained almost constant from room temperature down to TN, and increased with decreasing T below TN.