gebhart/patrepeval huggingface dataset:
Network Properties Revealed through Matrix Functions (2010)

The emerging field of network science deals with the tasks of modeling, comparing, and summarizing large data sets that describe complex interactions. Because pairwise affinity data can be stored in a two-dimensional array, graph theory and applied linear algebra provide extremely useful tools. Here, we focus on the general concepts of centrality, communicability, and betweenness, each of which quantifies important features in a network. Some recent work in the mathematical physics literature has shown that the exponential of a network's adjacency matrix can be used as the basis for defining and computing specific versions of these measures. We introduce here a general class of measures based on matrix functions, and show that a particular case involving a matrix resolvent arises naturally from graph-theoretic arguments. We also point out connections between these measures and the quantities typically computed when spectral methods are used for data mining tasks such as clustering and ordering. We finish with computational examples showing the new matrix resolvent version applied to real networks.
Large-Scale Modelling of the Divergent Spectrin Repeats in Nesprins: Giant Modular Proteins (2013)

Nesprin-1 and nesprin-2 are nuclear envelope (NE) proteins characterized by a common structure of an SR (spectrin repeat) rod domain and a C-terminal transmembrane KASH [Klarsicht-ANC-Syne-homology] domain and display N-terminal actin-binding CH (calponin homology) domains. Mutations in these proteins have been described in Emery-Dreifuss muscular dystrophy and attributed to disruptions of interactions at the NE with nesprins binding partners, lamin A/C and emerin. Evolutionary analysis of the rod domains of the nesprins has shown that they are almost entirely composed of unbroken SR-like structures. We present a bioinformatical approach to accurate definition of the boundaries of each SR by comparison with canonical SR structures, allowing for a large-scale homology modelling of the 74 nesprin-1 and 56 nesprin-2 SRs. The exposed and evolutionary conserved residues identify important pbs for protein-protein interactions that can guide tailored binding experiments. Most importantly, the bioinformatics analyses and the 3D models have been central to the design of selected constructs for protein expression. 1D NMR and CD spectra have been performed of the expressed SRs, showing a folded, stable, high content α-helical structure, typical of SRs. Molecular Dynamics simulations have been performed to study the structural and elastic properties of consecutive SRs, revealing insights in the mechanical properties adopted by these modules in the cell.
Poor Long-Term Blood Pressure Control After Intracerebral Hemorrhage (2012)

Long-term BP control is inadequate in patients after intracerebral hemorrhage, particularly in blacks. Further studies are needed to understand the role of social support and barriers to control to identify optimal approaches to improve BP in this high-risk population.
Nano-reinforcement of Epoxy Adhesives with POSS (2005)

The reinforcement of epoxy adhesives with polyhedral-Oligomeric-SilSesquioxane (POSS) was studied. Shear performance of the nano-filled adhesive was evaluated as a function of filler content using the single-strap bonded joint configuration. It is found that maximal stress and maximum shear strain both increase with the POSS loading. X-ray diffraction (XRD) analyses indicated that aggregation and crystallization of POSS occurred over the curing cycle. Dynamic mechanical analyses (DMA) showed an increased storage modulus with the addition of POSS and decreased loss modulus, hence enhanced network elasticity. The increased chain relaxation enhanced the polymer/aluminum interaction at the interface, resulting in increased interfacial strength and toughness, which was evident from the observed shift in failure mode from adhesive to cohesive for the bonded joints with increased POSS content.
TETRASOMIC SEGREGATION FOR MULTIPLE ALLELES IN ALFALFA (1982)

Evidence of tetrasomic inheritance in alfalfa, Medicago sativa L. and M. falcata L., for multiple codominant alleles at three isozymic loci is reported in this study. The locus Prx-1 governing anodal peroxidase and the loci Lap-1 and Lap-2 governing anodal leucine-aminopeptidase were studied by starch gel electrophoresis in seedling root tissue or seeds. The progenies from several di-, tri- or tetra-allelic plants belong to the species M. sativa and M. falcata and their hybrids were studied for the segregation of the three genes. In all cases, tetrasomic inheritance of chromosomal-type segregation was observed. In another progeny resulting from the crossing of two plants involving four different alleles at locus Lap-2, tetrasomic segregation with the possible occurrence of double reduction was observed. This study presents direct evidence of autotetraploidy and the existence of tetra-allelic loci in alfalfa. It also supports the concept that the species M. sativa and M. falcata are genetically close enough to be considered biotypes of a common species.
Software-only system-level record and replay in wireless sensor networks (2015)

Wireless sensor networks (WSNs) are plagued by the possibility of bugs manifesting only at deployment. However, debugging deployed WSNs is challenging for several reasons---the remote location of deployed sensor nodes, the non- determinism of execution that can make it difficult to replicate a buggy run, and the limited hardware resources available on a node. In particular, existing solutions to record and replay debugging in WSNs fail to capture the complete code execution, thus negating the possibility of a faithful replay and causing a large class of bugs to go unnoticed. In short, record and replay logs a trace of predefined events while a deployed application is executing, enabling replaying of events later using debugging tools. Existing recording methods fail due to the many sources of non-determinism and the scarcity of resources on nodes.
Cytotoxicity and Anti-inflammatory Activity of Flavonoid Derivatives Targeting NF-kappaB (2016)

compound (10b) was found to be the most potent as both anti-inflammatory and cytotoxic agents. In silico approach was in good tune with the wet lab experiments. The promising compounds have shown to induce cell cycle arrest at G2/M Phase.
Liquid–liquid distribution studies on moderately labile metal chelates. Kinetics of hydrolysis of tris(thenoyltrifluoroacetonate)thallium(III) (2005)

Summary Kinetics of hydrolysis of tris(thenoyltrifluoroacetonate)thallium(III) in water was studied by back extraction of this moderately labile metal chelate, labelled with 204 Tl, from a water-immiscible organic solvent to aqueous solutions. A function of the distribution ratio of the metal was derived, which linearly depended on time after reaching quasi-equilibrium of chelate partition. Its extrapolation to zero time made it possible to evaluate the partition constant of the chelate. The rate constant of its hydrolysis was determined from the slope. The dependence of the rate constant on pH and on the ligand concentration shows that both acid and base hydrolysis of the chelate studied took place. The approach used can be helpful for determining partition constants of moderately labile metal complexes and the lability of the complexes in aqueous solutions.
Amplifier linearization using a digital predistorter with fast adaptation and low memory requirements (1990)

A method is described for linearizing a power amplifier by predistorting its input. It is particularly well suited to baseband implementation with digital signal processor hardware. In comparison with the most powerful previously published predistorter, it requires four orders of magnitude less memory, reduces convergence time by over three orders of magnitude, eliminates reconvergence time following a channel switch, and eliminates the need for a phase shifter in the feedback path. The predistorter structure is described. Its ability to suppress intermodulation products using only a small table is demonstrated. The effect of predistorter nonidealities (especially limited table size) on the power amplifier's output are analyzed. A fast adaptation algorithm is introduced.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Optically Pumped Mid-Infrared Stimulated Emission of ZnSe:Cr Crystals (2004)

a W e dem onstr ate that Zn Se:C r is an ex cellent solid state laser material for mid -inf rared re gion w ith a broad am pli cation band from 2.2 m to 3 m , and with a high quantum ecienc y of a radiati ve recombination. 46% external total eciency and 56 mW threshold power w ere achieved, when pump ed w ith a C W YA l O:H o laser at resonant excitation conditions. Such laser system can ha ve w idespread applica tion s in medicine as laser scalp els w ith regulated cutting depth. W e further demonstrate a stimulated emission under C r 2+ to 1+ photo-ioni zati on pumping. T he latter op ens chances for laser emission under carrier in j ection conditions.
Vegetable processing wasteflows: liability or asset (1982)

The U.S. fruit and vegetable processing industry annually discards about 114 billion gallons of by-product liqud wasteflow. Because of high BOD levels, these wastestreams cannot be released to surface waters but must be processed at high expense to the generating industries. By selectively processing a portion of these wasteflows through ultrafiltration/reverse osmosis facilities, most of the fermentable sugars in fruit and vegetable processing wastes could be recovered as a 20% sugar concentrate suitable for bioconversion to liquid fuel. The value as feedstock of approximately 1.6 million tons of fermentable sugar, the major reduction in wasteflow BOD and disposal costs, and the reuse value of reverse osmosis permeate water would exceed process costs by a wide margin. Industrial participation in sugar concentrate production by membrane processes would turn a liability into an asset and provide sufficient feedstock to produce approximately 217 million gallons of alcohol annually. The net energy yield of the alcohol is about one-half of the total energy used by the fruit and vegetable processing industry.
Modelling heat and moisture transport in porous materials with CFD for building applications (2011)

Paper presented at the 8th International Conference on Heat Transfer, Fluid Mechanics and Thermodynamics, Mauritius, 11-13 July, 2011.
Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations (2019)

The proliferation, differentiation and survival of mononuclear phagocytes depend on signals from the receptor for macrophage colony-stimulating factor, CSF1R. The mammalian Csf1r locus contains a highly conserved super-enhancer, the fms-intronic regulatory element (FIRE). Here we show that genomic deletion of FIRE in mice selectively impacts CSF1R expression and tissue macrophage development in specific tissues. Deletion of FIRE ablates macrophage development from murine embryonic stem cells. Csf1r<sup>ΔFIRE/ΔFIRE</sup> mice lack macrophages in the embryo, brain microglia and resident macrophages in the skin, kidney, heart and peritoneum. The homeostasis of other macrophage populations and monocytes is unaffected, but monocytes and their progenitors in bone marrow lack surface CSF1R. Finally, Csf1r<sup>ΔFIRE/ΔFIRE</sup> mice are healthy and fertile without the growth, neurological or developmental abnormalities reported in Csf1r<sup>-/-</sup> rodents. Csf1r<sup>ΔFIRE/ΔFIRE</sup> mice thus provide a model to explore the homeostatic, physiological and immunological functions of tissue-specific macrophage populations in adult animals.
Association of ulcerative colitis symptom severity and proctocolectomy with multidimensional patient-reported outcomes: a cross-sectional study (2023)

Ulcerative colitis was associated with reduced mood, quality of life, fatigue, and work productivity even in patients with mild symptoms, suggesting that management of active ulcerative colitis may improve patient-reported outcomes irrespective of disease severity. (UMIN Clinical Trials Registry: UMIN000031995, https://www.umin.ac.jp/ctr/index-j.htm ).
Selective activity of butyrylcholinesterase in serum by a chemiluminescent assay (2001)

In a previous study, we showed that purified commercial esterase activity can be detected in a chemiluminescent assay based on the hydrolysis of 2-methyl-1-propenylbenzoate (MPB) to 2-methyl-1-propenol, which is subsequently oxidized by the horseradish peroxidase (HRP)-H(2)O(2) system. The purpose of this study was to verify the applicability of this assay to human serum. The existence of an esterase activity capable of hydrolysing MPB is indicated by the fact that the MPB-serum-HRP-H(2)O(2) system consumes oxygen and emits light. Both signals were abolished by prior serum heat inactivation and were preserved when serum was stored at < or =4 degrees C. Addition of aliesterase inhibitors, such as fluoride ion and trichlorfon or the cholinesterase inhibitor eserine, totally prevents light emission. The butyrylcholinesterase-specific substrate benzoylcholine causes a delay in both O(2) uptake and light emission, while the specific acetylcholinesterase substrate, acetyl-beta-methylcholine, had practically no effect. Purified butyrylcholinesterase, but not acetylcholinesterase, triggered light emission. The finding that butyrylcholinesterase is responsible for the hydrolysis of MPB in serum should serve as the basis for the development of a specific chemiluminescent assay for this enzyme.
Development of a shortwave infrared sinuscope for the detection of cerebrospinal fluid leaks (2023)

An endoscopic system based on SWIR narrowband imaging can provide an alternative in the future to invasive methods of CSF leak detection.
Report on ACM SIGIR 2006 workshop on evaluating exploratory search systems (2006)

Exploratory search systems (ESS) are designed to help users move beyond simply finding information toward using that information to support learning, analysis, and decision-making. The evaluation of the interactive systems designed specifically to help exploratory searchers is a challenging area, worthy of further discussion in the research community. In this article we report on a workshop conducted in conjunction with the ACM SIGIR Conference in Seattle, USA, in August 2006. The workshop involved researchers, academics, and practitioners discussing the formative and summative evaluation of ESS.
A Malicious Advertising Detection Scheme Based on the Depth of URL Strategy (2013)

With the development of the Internet, Web advertisements are increasingly used for illegal purposes such as propagating malware, scamming, click frauds etc. To detect these attacks, according to the characteristics of the malicious advertising attacks, we propose a detection scheme based on the depth of the URL strategy. Our scheme builds on the basis of Nutch and Modsecurity, which they are the famous open source software. By improving the Nutch we can obtain all suspicious URL from the website, then improve the Modsecurity response filtering part and deploy in the client to filter the suspicious response. We put this scheme compared with 360 secured browser in detecting malicious advertising, which is an effective tool to detect malicious advertising attacks for the Chinese website. The results show that this scheme is more effective in detecting malvertising cases.
Structural and Dielectric Studies of LLDPE/O-MMT Nanocomposites (2014)

Nanocomposites made of linear low density polyethylene (LLDPE) and organo-modified montmorillonite (O-MMT) were processed by melt compounding from a commercially available premixed LLDPE/nanoclay masterbatch, at different nanoclay loadings, by co-rotating twin-screw extruder. The morphological and dielectric properties of LLDPE/O-MMT nanocomposites were investigated to understand the structure-dielectric properties relationship in the nanocomposites. The microstructures of the materials were characterized by wide angle X-ray diffraction (WAXD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and atomic force microscopy (AFM). Initial findings by FTIR spectroscopy characterization indicated the absence of any chemical interaction between LLDPE and nanoclay during the extrusion process, while DSC showed that a 1% wt loading of nanoclay particles increased the degree of crystallinity of the nanocomposites samples. On the other hand, XRD, SEM, TEM and AFM indicated that nanoclay layers were intercalated or exfoliated in the LLDPE matrix. A correlation between the structure and dielectric properties of LLDPE/O-MMT nanocomposites was found and discussed.
Paramagnetic Oligonucleotides:  Contrast Agents for Magnetic Resonance Imaging with Proton Relaxation Enhancement Effects (1999)

An antisense paramagnetic oligonucleotide analogue targeted to a model macromolecular receptor (5S rRNA) was prepared. The paramagnetic agent's relaxivity (dependence of the relaxation rate on paramagnetic agent concentration) in the presence and absence of the macromolecular receptor was measured at 1.5 and 6.3 T. The relaxivity of the targeted agent increased specifically in the presence of the macromolecular receptor (16% at 6.3 T and 15% at 1.5 T). This effect was specific for a paramagnetic oligonucleotide targeted to the receptor and was larger than the relaxivity enhancement due simply to receptor-induced viscosity differences. Maximizing this relaxivity enhancement of tumor targeted paramagnetic oligonucleotides will aid in contrast agent development for magnetic resonance imaging.
Input-parallel output-series connection of isolated quasi-Z-source DC-DC converters (2014)

This paper proposes an input-parallel-output-series (IPOS) power system based on the isolated qZS DC-DC converter. Reported as a solution for the integration of renewable energy sources into the medium voltage grid, such power systems can also be used to integrate low voltage energy sources into a 230V/400V grid. We examined the basic switching stage with three different rectifier topologies whereas the steady state analysis was made for each topology. Criteria for our comparison were implementation complexity and current and voltage stress of the components. An experimental prototype of the proposed IPOS power system composed of two converters was built at a rated output power of 400 W. DC gain characteristics and efficiency curves are presented. The experimental waveforms for the input voltage 80 V and the output voltage 400 V were measured.
Chromosome 19q13 disruption alters expressions of CYP2A7, MIA and MIA-RAB4B lncRNA and contributes to FAP-like phenotype in APC mutation-negative familial colorectal cancer patients (2017)

Familial adenomatous polyposis (FAP) is an autosomal-dominantly inherited form of colorectal cancer (CRC) caused by mutation in the adenomatous polyposis coli (APC) gene. Our ability to exhaustively screen for APC mutations identify microsatellite-stable and APC-mutation negative familial CRC patients, enabling us to search for novel genes. We performed genome-wide scan on two affected siblings of one family and 88 ethnicity- and gender-matched healthy controls to identify deletions shared by the siblings. Combined loss of heterozygosity, copy number and allelic-specific copy number analysis uncovered 5 shared deletions. Long-range polymerase chain reaction (PCR) confirmed chromosome 19q13 deletion, which was subsequently found in one other family. The 32 kb deleted region harbors the CYP2A7 gene and was enriched with enhancer, repressor and insulator sites. The wildtype allele was lost in the polyps of the proband. Further, real-time RT-PCR assays showed that expressions of MIA and MIA-RAB4B located 35 kb upstream of the deletion, were up-regulated in the polyps compared to the matched mucosa of the proband. MIA-RAB4B, the read-through long non-coding RNA (lncRNA), RAB4B, PIM2 and TAOK1 share common binding site of a microRNA, miR-24, in their 3'UTRs. PIM2 and TAOK1, two target oncogenes of miR-24, were co-ordinately up-regulated with MIA-RAB4B in the polyps, suggesting that MIA-RAB4B could function as competitive endogenous RNA to titrate miR-24 away from its other targets. The data suggest that the 19.13 deletion disrupted chromatin boundary, leading to altered expression of several genes and lncRNA, could contribute to colorectal cancer via novel genetic and epigenetic mechanisms.
Properties of amino acid transport systems in K562 cells sensitive and resistant to cis-diamminedichloroplatinum(II). (1986)

When K562 cells were made resistant to cisplatin their neutral amino acid transport systems changed. K562 cells cloned in cisplatin developed a 6.7-fold resistance to the drug. The generation times for K562 cells sensitive (S) and resistant (DDP) to cisplatin were similar. The initial uptake and rapid efflux of cisplatin were similar in both cell lines. However, they differed in their sodium dependent neutral amino acid transport properties. In K562S cells the sodium-dependent uptake for methylaminoisobutyric acid was significantly inhibited by threonine (Ki = 10.3 mM), but in K562DDP the uptake of neutral amino acids was significantly lower, and methylaminoisobutyric acid uptake was minimally inhibited by threonine. When K562DDP cells were grown in the absence of cisplatin for 8 weeks, their amino acid transport properties reverted to those of K562S cells. In K562 cells, changes in plasma membrane essential amino acid transport systems were concomitant to both the development of resistance and the redevelopment of sensitivity to cisplatin. Therefore, human malignant cell sensitivity and resistance to cisplatin may be related to membrane nutrient transport systems.
Cannabinoid receptors in acute and chronic complications of atherosclerosis (2007)

Atherosclerosis is a chronic inflammatory disease that is the primary cause of myocardial infarction and stroke, which occur after sudden thrombotic occlusion of an artery. A growing body of evidence suggests that cannabinoid signalling plays a fundamental role in atherosclerosis development and its clinical manifestations. Thus, CB2 receptors are protective in myocardial ischaemia/reperfusion and implicated in the modulation of chemotaxis, which is crucial for the recruitment of leukocytes during inflammation. Delta-9-Tetrahydrocannabinol (THC)-mediated activation has been shown to inhibit atherosclerotic plaque progression in a CB2 dependent manner. Although CB1 and CB2 expression has been reported on platelets, their involvement in thrombus formation is still controversial. While several reports suggest that CB1 receptors may have a relevant role in neuroprotection after ischaemic stroke, recent studies show the protective effects in various forms of neuroprotection are not related to CB1 stimulation, and a protective role of CB1 blockade has also been reported. In addition, vascular and myocardial CB1 receptors contribute to the modulation of blood pressure and heart rate. It is tempting to suggest that pharmacological modulation of the endocannabinoid system is a potential novel therapeutic strategy in the treatment of atherosclerosis. For these purposes, it is important to better understand the complex mechanisms of endocannabinoid signalling and potential consequences of its pharmacological modulation, as it may have both pro- and anti-atherosclerotic effects.