gebhart/patrepeval huggingface dataset:
The impact of blood on liver metabolite profiling – a combined metabolomic and proteomic approach (2013)

Metabolomics has entered the well-established omic sciences as it is an indispensable information resource to achieve a global picture of biological systems. The aim of the present study was to estimate the influence of blood removal from mice liver as part of sample preparation for metabolomic and proteomic studies. For this purpose, perfused mice liver tissue (i.e. with blood removed) and unperfused mice liver tissue (i.e. containing blood) were compared by two-dimensional gas chromatography time of flight mass spectrometry (GC × GC-TOFMS) for the metabolomic part, and by liquid chromatography tandem mass spectrometry (LC-MS/MS) for the proteomic part. Our data showed significant differences between the unperfused and perfused liver tissue samples. Furthermore, we also observed an overlap of blood and tissue metabolite profiles in our data, suggesting that the perfusion of liver tissue prior to analysis is beneficial for an accurate metabolic profile of this organ.
A statistical approach to texture description of medical images: a preliminary study (2003)

The article deals with the problem of texture description. It presents a statistical approach. Specifically, it introduces the use of first- and second-order statistics on texture color spaces. At the end of the article, we also give estimations of the computational time complexities of the parameter calculations presented in this article and describe our experience on one application domain. This study is a preliminary preparation for the application of these methods to medical images.
A105 Study on pressure serge prevention in aqua drive system (2011)

This study focuses on how to prevent a pressure surge form happening in a water hydraulic system. In the water hydraulic system, pressure surge emerging after cavitation invokes a serious damage on water hydraulic devices, and also has undesired influence which might make the system unstable. Both controlling a water hydraulic actuator's motion and suppressing a rapid pressure decrease must be archived simultaneously. However this is not possible to achieve with a conventional water hydraulic system, which has only one degree of freedom in its control. Thus, a new control method using two servo valves is proposed. In this paper, the problem of the conventional water hydraulic system is described and a control method to control two servo valves for the purpose of preventing the pressure surge is discussed. As result, validity of the proposed new control method is proved experimentally.
Efficient Utilization of a CPU-GPU Cluster (2012)

This paper will investigate the performance of a mixture of central processing unit (CPU) and graphical processing unit (GPU) codes on a multi-CPU, multi-GPU cluster. This cluster attempts to balance IO, GPU, and CPU performance to accommodate a wide variety of codes. When designing this cluster, the design goal of a balanced system was one of many options that could have been taken. The GPU, is essentially a video graphics card, found in every desktop or laptop computer. High-end graphics cards such as those used by a computer gamer are capable of extremely high floating point performance. The GPU utilizes the CPU to initialize the GPU, to transfer data from memory/storage to and from the GPU, and to launch the computation kernels that run on the GPU. The Jet Engine Noise Reduction (JENRE) code implements a compressible flow solver which is under development for the simulation of supersonic jet flow and its acoustic properties. A major emphasis of this code's development is on ensuring that the code is capable of fully exploiting emerging massively parallel, high-performance computing architectures for either GPUs or multi-core CPUs. The JENRE code's performance using GPUs is currently 2.1 times that with CPUs, and thus is run typically on the GPUs in the cluster. The cluster is also used for a variety of MPI-based jobs as well as single node OpenMP shared-memory jobs. These jobs utilize the CPU only, and the GPUs are left idle. Typically, a user requests that an entire node (or set of nodes) is allocated to a single job (CPU or GPU) so that there is no contention for resources with other jobs. Since jobs are either CPU or GPU-based, this leads to significant under-utilization of the computational resources. This paper will examine the overall utilization of the cluster and performance of a mix of CPU codes with the GPU-based JENRE code running simultaneously on the same nodes of the cluster. Results indicate that careful and cooperative scheduling of jobs can result in a tripling of the computational capability of the cluster.
CRESCIMENTO VEGETATIVO DO CAFEEIRO ARÁBICA EM FUNÇÃO DO NÚMERO DE RAMOS ORTOTRÓPICOS ORIUNDOS DO ARQUEAMENTO DA MUDA APÓS O PLANTIO (2019)

RESUMO: Objetivou-se com o presente estudo avaliar o crescimento vegetativo do cafeeiro arabica em funcao do numero de ramos ortotropicos oriundos do arqueamento da muda apos o plantio. O experimento foi desenvolvido na Fazenda Experimental de Venda Nova (INCAPER), em altitude de 740 m. A lavoura onde se conduziu o experimento foi implantada em marco de 2016, utilizando mudas de Coffea arabica L. da cultivar Catuai IAC 81 e no espacamento de 2,5 x 1,0 m. Apos 270 dias do plantio, as mudas foram arqueadas para estimular as brotacoes e permitir o estabelecimento dos numeros de ramos ortotropicos. O experimento foi conduzido com quatro tratamentos, sendo estes: um, dois, tres e quatro ramos ortotropicos por planta, em delineamento de blocos casualizados, com seis repeticoes. Aos 17 meses apos o arqueamento das mudas, avaliou-se a altura das plantas, a area da copa das plantas, o diâmetro do caule, o numero de ramos plagiotropicos das plantas, o comprimento do ramo plagiotropico e o numero de nos no ramo plagiotropico. Percebeu-se que o emprego da tecnica do arqueamento da muda apos o plantio se mostrou eficiente para o estabelecimento do numero de ramos ortotropicos no cafeeiro arabica. De modo geral, o crescimento vegetativo inicial do cafeeiro arabica foi influenciado pelo manejo do numero de ramos ortotropicos, sendo observados incrementos consideraveis na area da copa e na quantidade de ramos plagiotropicos das plantas com o aumento do numero de ramos ortotropicos, o que certamente refletira nas primeiras safras produtivas.
The Compression of Bonded Rubber Blocks (1959)

Experimental measurements are described of the load-deflection relations for rubber blocks having a wide range of thicknesses and varied shapes of cross-section. An approximate theoretical treatment is presented for classically small compressions of circular discs and infinitely long rectangular bars. The measured stiffnesses for small compressions are shown to be in good agreement with the theoretical predictions for a vulcanízate containing no carbon black, and, when an empirically obtained modification is made for thixotropic effects, for vulcanizates containing various quantities of carbon black. The behaviour under moderately large compressions is also examined.
Permanent Pacing in Nonagenarians Over 20‐Year Period (2014)

Introduction Life expectancy increases progressively and nonagenarians are a growing population. We report trends in pacing and long‐term outcome in nonagenarians over a 20‐year period in a single center compared with those of younger patients. Methods We retrospectively reviewed all the patients who underwent their first pacemaker implantation from January 1, 1991 to December 31, 2010 and were followed through December 31, 2013. Results During the study period, 1,009 patients underwent first pacemaker implantation: 45 patients were older than 90 years (mean age 92.5 ± 2.6) (4.5%); 21 were men. Battery replacement was performed in four patients in whom first implant was made at age ≥90 years (8.9%) and in 231 patients aged &lt;90 (24%; P &lt; 0.01). Syncope was the most common symptom leading to pacing, followed by dizziness and fatigue in all age groups; no significant difference of symptoms was found between patient age groups. In patients aged ≥90 atrioventricular block and atrial fibrillation with slow ventricular response were more frequent, while sick sinus syndrome and carotid sinus hypersensitivity were less frequent than in younger patients. Ventricular chamber pacemakers were implanted with significant growing frequency, according to the older patients' age. Neither the indication for pacemaker implantation nor pacing mode influenced survival. Conclusions Nonagenarians are a growing population. Symptoms leading to pacing in patients aged ≥90 were similar to those of younger patients, but different frequency was found in the electrocardiographic indications. Ventricular chamber pacemakers were significantly more implanted than dual‐chamber pacemakers but without negative survival influence.
Adrenergic agents. 3. Synthesis and adrenergic activity of some catecholamine analogs bearing a substituted sulfonyl or sulfonylalkyl group in the meta position (1975)

The m-phenolic group of catecholamine beta-adrenergic agonists may be replaced by various functionalities capable of undergoing H bonding. Considerable latitude in the nature of the OH simulating group is permissible with retention of activity; however, the most extensively studied analogs are ones in which a mobile proton is attached to an O or N atom. In a search for new selective bronchodilators a series of catecholamine analogs bearing a substituted sulfonyl or sulfonylalkyl group in the meta position (i.e., groups in which the mobile H is attached to a C atom) was examined. These compounds were studied for beta-adrenergic agonist activity in vitro by measuring their ability to relax tracheal smooth muscle and to increase the rate of spontaneously beating right atria of guinea pigs. Adrenergic activity was influenced by the nature of the alkylene bridge between the sulfonyl and aromatic groups, branching of the ethanolamine side chain, stereochemistry, and substitution of the sulfonyl and amino groups. Beta-adrenergic blockage was noted for some compounds having the sulfonyl attached directly to the ring. Greatest beta-adrenergic agonist potency and tissue selectivity was observed with a m-MeSO2CH2 substituent. One of these compounds, alpha-[[(1,1-dimethylethyl)amino]methyl]-4-hydroxy-3-[(methylsulfonyl)methyl]benzenemethanol hydrochloride (sulfonterol hydrochloride, USAN), was studied more extensively in animals and is presently being examined for bronchodilator activity in man.
634. Transcriptional Stimulation of Antiviral Response Components by the Structural and Accessory Human coronavirus OC43 Proteins (2018)

In Kuwait, human coronavirus OC43 (HCoV-OC43) causes 25–30% of common cold, and 8.8% of respiratory infections in hospitalised patients. It is also associated with severe respiratory symptoms in infants, elderly, and immunocompromised patients. Our previous results showed that the expression of antiviral genes in human embryonic kidney (HEK) 293 cells is downregulated in the presence of HCoV-OC43 proteins. To understand the role of HCoV-OC43 proteins in antagonizing antiviral responses of the host, we investigated the effect of HCoV-OC43 structural and accessory proteins on the transcriptional activation of interferon-stimulated response element (ISRE), interferon-β (IFN-β) promoter, and nuclear factor kappa B response element (NF-kappaB-RE). HCoV-OC43 ns2a, ns5a, membrane (M), and nucleocapsid (N) mRNA were amplified and cloned into the pAcGFP1-N expression vector, followed by transfection in HEK-293 cells. Two days post-transfection, the cells were co-transfected with a reporter vector containing firefly luciferase under the control of ISRE, IFN-β promoter, or NF-kappaB-RE. Renilla luciferase vector was used as an internal control for transfection efficiency. Following 24 hours of incubation, the cells were treated with either IFN or tumour necrosis factor (TNF) for 6 hours. Thereafter, promoter activity was assayed using the dual-luciferase reporter assay system. Influenza NS1 protein was used as positive control for antagonism. The transcriptional activity of ISRE, IFN-β promoter, and NF-kappaB-RE was downregulated in the presence of ns2a, ns5a, M, or N protein as there was a sharp fall in firefly luciferase levels. Overall, HCoV-OC43 proteins reduced firefly luciferase levels for ISRE and IFN-β promoter by at least ten fold, whereas for NF-kappaB-RE the firefly luciferase levels were reduced by at least fivefold. HCoV-OC43 has the ability to block the activation of different antiviral signaling pathways. All authors: No reported disclosures.
Graph Matching with Anchor Nodes: A Learning Approach (2013)

In this paper, we consider the weighted graph matching problem with partially disclosed correspondences between a number of anchor nodes. Our construction exploits recently introduced node signatures based on graph Laplacians, namely the Laplacian family signature (LFS) on the nodes, and the pair wise heat kernel map on the edges. In this paper, without assuming an explicit form of parametric dependence nor a distance metric between node signatures, we formulate an optimization problem which incorporates the knowledge of anchor nodes. Solving this problem gives us an optimized proximity measure specific to the graphs under consideration. Using this as a first order compatibility term, we then set up an integer quadratic program (IQP) to solve for a near optimal graph matching. Our experiments demonstrate the superior performance of our approach on randomly generated graphs and on two widely-used image sequences, when compared with other existing signature and adjacency matrix based graph matching methods.
Advanced Medical Displays: A Literature Review of Augmented Reality (2008)

The impressive development of medical imaging technology during the last decades provided physicians with an increasing amount of patient specific anatomical and functional data. In addition, the increasing use of non-ionizing real-time imaging, in particular ultrasound and optical imaging, during surgical procedures created the need for design and development of new visualization and display technology allowing physicians to take full advantage of rich sources of heterogeneous preoperative and intraoperative data. During 90's, medical augmented reality was proposed as a paradigm bringing new visualization and interaction solutions into perspective. This paper not only reviews the related literature but also establishes the relationship between subsets of this body of work in medical augmented reality. It finally discusses the remaining challenges for this young and active multidisciplinary research community.
Highly Sensitive Molecularly Imprinted Electrochemical Sensor Based on the Double Amplification by an Inorganic Prussian Blue Catalytic Polymer and the Enzymatic Effect of Glucose Oxidase (2012)

A novel strategy to improve the sensitivity of molecularly imprinted polymer (MIP) sensors was proposed. An electrocatalytic Prussian blue (PB) film was electrochemically polymerized on an electrode surface to fabricate an MIP electrochemical sensor using oxytetracycline (OTC) as a template. The OTC determination relied on a competition reaction between OTC and glucose-oxidase-labeled OTC and the catalytic reduction of hydrogen peroxide by the modified PB film. Experimental results show that double amplification, which is based on the catalysis of inorganic PB films and the enzymatic effect of glucose oxidase, can remarkably increase the assay sensitivity. The main experimental conditions (including electrocatalysis of the PB film, pH effects, incubation and competition times, and anti-interference) were optimized. This novel MIP sensor can offer an femtomole detection limit for OTC. In addition, the feasibility of its practical applications has been demonstrated in the analysis of a series of real milk samples.
THE AMAZING PLACENTA: EVOLUTION AND LIFELINE TO HUMANNESS (2020)

The placenta arose during mammalian evolution, which is recent in evolutionary terms. Genetic changes underlying placental development remain identifiable by the new science of comparative genomics (approximately post‐2000). Randomly arising features of genomes including endogenous retroviruses and transposable elements have provided structural genes and gene‐regulatory motifs responsible for innovations in placental biology. Stochastic genetic events indeed contribute to new functionality. Theologically, random mutations are part of the strategy by which the divine purpose for humanity is attained. Placental function critically underlies human brain development, and suboptimal function, associated with environmental conditions and maternal distress, contributes to mental health deficits in the offspring. Many enter life with handicaps arising from contingent events in utero, mandating understanding, compassion, and socioemotional support, imperatives native to moral including biblical values. The extended period of development afforded by placentation enables prenatal parenting, with implications for sensitive and devoted parental commitment.
Machine learning can guide experimental approaches for protein digestibility estimations (2022)

Food protein digestibility and bioavailability are critical aspects in addressing human nutritional demands, particularly when seeking sustainable alternatives to animal-based proteins. In this study, we propose a machine learning approach to predict the true ileal digestibility coefficient of food items. The model makes use of a unique curated dataset that combines nutritional information from different foods with FASTA sequences of some of their protein families. We extracted the biochemical properties of the proteins and combined these properties with embeddings from a Transformer-based protein Language Model (pLM). In addition, we used SHAP to identify features that contribute most to the model prediction and provide interpretability. This first AI-based model for predicting food protein digestibility has an accuracy of 90% compared to existing experimental techniques. With this accuracy, our model can eliminate the need for lengthy in-vivo or in-vitro experiments, making the process of creating new foods faster, cheaper, and more ethical.
In Reply (2017)

Many thanks for this great review article (1). I am a general practitioner who runs a sarcoidosis clinic, and as such I missed the psychosomatic aspect. This is relevant because almost all of my sarcoidosis patients experience depression. Little of relevance is to be found in the literature. An older article (2) from Gttingen offers the conclusion that sarcoidosis patients are "mostly in a chronic situation of conflict or overload" and that they can be "described as workaholic in some cases." The study included very few patients, and participants had completed and returned an extremely comprehensive questionnaire. My conclusion is that it was particularly conscientious and helpful patients that were studied in this setting.
ABCD-BIDS pipeline (2020)

The ABCD-BIDS pipeline is an updated version of the HCP pipeline designed to process the ABCD data across all sites and scanners.
MagPIe (1999)

Writing parallel applications for computational grids is a challenging task. To achieve good performance, algorithms designed for local area networks must be adapted to the differences in link speeds. An important class of algorithms are collective operations, such as broadcast and reduce. We have developed M AG PI E , a library of collective communication operations optimized for wide area systems. M AG PI E 's algorithms send the minimal amount of data over the slow wide area links, and only incur a single wide area latency. Using our system, existing MPI applications can be run unmodified on geographically distributed systems. On moderate cluster sizes, using a wide area latency of 10 milliseconds and a bandwidth of 1 MByte/s, M AG PI E executes operations up to 10 times faster than MPICH, a widely used MPI implementation; application kernels improve by up to a factor of 4. Due to the structure of our algorithms, M AG PI E 's advantage increases for higher wide area latencies.
Electrode assemblies, plasma apparatuses and systems including electrode assemblies, and methods for generating plasma (2023)

Electrode assemblies for plasma reactors include a structure or device for constraining an arc endpoint to a selected area or region on an electrode. In some embodiments, the structure or device may comprise one or more insulating members covering a portion of an electrode. In additional embodiments, the structure or device may provide a magnetic field configured to control a location of an arc endpoint on the electrode. Plasma generating modules, apparatus, and systems include such electrode assemblies. Methods for generating a plasma include covering at least a portion of a surface of an electrode with an electrically insulating member to constrain a location of an arc endpoint on the electrode. Additional methods for generating a plasma include generating a magnetic field to constrain a location of an arc endpoint on an electrode.
Cloning, Nucleotide Sequence, and Expression of the DNA Ligase-encoding Gene from Thermus filiformis (1998)

The gene encoding Thermus filiformis (Tfi) DNA ligase was cloned and its nucleotide sequence was determined by the chain-termination method. The primary structure of Tfi DNA ligase was deduced from its nucleotide sequence. The Tfi DNA ligase comprises of 667 amino acid residues and its molecular mass was determined to be 75,936 Da. The deduced amino acid sequence of Tfi DNA ligase showed a 86.5% homology to Tth DNA ligase and 43.5% to E. coli DNA ligase. The Lys-116 of Lys-Val-Asp-Gly motif was proposed to be the active residue of Tfi DNA ligase. In comparison with the amino acid composition of DNA ligase, Tfi DNA ligase showed a significant increase in the proportion of charged residues, Arg and Glu, compared to E. coli DNA ligase. The G + C content in the first, second, and third positions of the codons used were 70.3%, 40.3%, and 90.3%, respectively. Codon usage in Tfi DNA ligase was heavily biased towards the use of G + C in the third position. Under tac promoter control, Tfi DNA ligase was overproduced to greater than 9% of E. coli BL26Blue cellular proteins.
Preparation of N-doped graphene by reduction of graphene oxide with mixed microbial system and its haemocompatibility (2014)

A steady, effective and environment friendly method of introducing nitrogen into graphene is by microbial reduction of graphene oxide with mixed microorganisms from the anode chamber of microbial fuel cells (MFC). Using this method, N-doped graphene is easily obtained under mild conditions and by simple treatment processes, with the N/C ratio reaching 8.14%. Various characterizations demonstrate that the as-prepared N-doped graphene has excellent properties and is comparable with, and in some aspects, even better than, pristine graphene (containing only elemental C) prepared by chemical methods. The N-doped graphene (mainly substitution of C in the plane of the graphene sheet) with uniform distribution of N was haemocompatible, nontoxic, and water-dispersible, all of which are desirable properties for biomaterials and attributable to a synergetic metabolic effect of mixed microorganisms.
Integrated Couplers for OAM Fiber Modes using Compact Antennas and Circular Grating (2020)

We present and compare two novel integrated devices in SOI platform for the coupling of OAM modes into multimode fibers. Simulation results show generated OAM beams and mode overlap with a photonic bandgap fiber.