gebhart/patrepeval huggingface dataset:
A combined biomarker and clinical panel for chronic graft versus host disease diagnosis (2016)

Whilst many chronic graft versus host disease (cGVHD) biomarkers have been previously reported, few have been verified in an independent cGVHD cohort. We aimed to verify the diagnostic accuracy of previously reported markers of cGVHD in a multi-centre Chronic GVHD Consortium. A total of 42 RNA and 18 protein candidate biomarkers were assessed amongst 59 cGVHD cases and 33 matched non-GVHD controls. Total RNA was isolated from PBMC, and RNA markers were quantified using PCR. Serum protein markers were quantified using ELISA. A combined 3 RNA biomarker (IRS2, PLEKHF1 and IL1R2) and 2 clinical variables (recipient CMV serostatus and conditioning regimen intensity) panel accurately (AUC 0.81) segregated cGVHD cases from controls. Other studied RNA and protein markers were not confirmed as accurate cGVHD diagnostic biomarkers. The studied markers failed to segregate higher risk cGVHD (per overall NIH 0-3 score, and overlap versus classic cGVHD status). These data support the need for multiple independent verification studies for the ultimate clinical application of cGVHD diagnostic biomarkers.
Recent advances in RF integrated circuits (1997)

This article describes recent activities in the area of RF integrated circuits. First, transceiver architectures developed for cellular and cordless telephone standards are presented. Next, the choice of device technology is discussed, and the design of building blocks such as low-noise amplifiers and mixers, oscillators, and power amplifiers is described. Last, some of the emerging applications of RF circuits and their implications for the design are considered.
Martorell hypertensive ischaemic leg ulcer The ulcer nobody is talking about……but should (2020)

Wound healing refers to a person’s ability to restore tissue that has been compromised. In chronic wounds, there is a significant delay in this restoration process and this delay can be due to various intrinsic (underlying comorbidities) or extrinsic (environment, positioning) factors found in a patient. The first step in the assessment of a clinical wound is to distinguish between chronic and acute wounds; this is easily done by taking a comprehensive history during consultation. A comprehensive medical history will include:
• current wound history (onset, causal factors, pain, size, drainage, current wound care),
• prior wound history (similar wounds in the past, how long did they take to heal),
• medical history (comorbidities such as hypertension, diabetes, kidney disease, nerve involvement),
• social history (cigarette smoking, alcohol use, nutritional status, obesity, age), and
• surgical history (previous wounds with delayed healing, surgery to manage non-healing, grafting, ablation of veins, vascular surgery).
Morphological study of cysts of Pelomyxa palustris Greeff, 1874 (2007)

Pelomyxa palustris Greeff, 1874, is the only representative of pelomyxoid amoebae with rest cysts in its life cycle. The morphology of the P. palustris cysts was studied using light and electron microscopy. The encystation of P. palustris under the climatic conditions of northwestern Russia occurs in August through September. The rest of the cysts have complex, trilaminar walls. The most developed are the two inner layers, i.e., the electron-dense structureless endocyst and the laminated mesocyst; the thickness of each layer can reach 0.6–0.7 μm. The thickness of the superficial electron-dense ectocyst lamina usually does not exceed 0.1–0.2 μm. The encysted cell of P. palustris has a unique structure. About 60% of its cell volume is occupied by a giant central vacuole filled with prokaryotic cytobionts. This vacuole has also been found to contain vacuoles and vesicles of different natures, restricted by vacuole membranes, autophagosomes, and lipid droplets. The amoeba cytoplasm occupies the space between the endocyst inner surface and the central vacuole. It contains no inclusions, prokaryotic cytobionts and most of cell organelles. In the cytoplasm there are 4 large nuclei filled with relatively homogeneous karyoplasm. The nuclear envelope forms numerous long tubular outgrowths, piercing the cytoplasm and underlining the central vacuole membrane. In this state the encysted pelomyxoids survive until the beginning of excystation. The excystation of P. palustris in the studied region occurs in spring, during the second half of April through the beginning of May. The cysts undergo complex morphofunctional changes due to reorganization of the wall and formation of young multinucleate amoebae. Out of the three initial lamina of the wall, only one persists until the moment of encystation. The central vacuole is destroyed and its content penetrates into the cytoplasm. Pelomyxoid nuclei divide twice. Prokaryotic cytobionts are localized in the cytoplasm and in the perinuclear area. Young multinuclear P. palustris individuals exiting cysts do not differ from the adult forms by their organization.
CrySL: An Extensible Approach to Validating the Correct Usage of Cryptographic APIs (2018)

Various studies have empirically shown that the majority of Java and Android apps misuse cryptographic libraries, causing devastating breaches of data security. It is crucial to detect such misuses early in the development process. To detect cryptography misuses, one must first define secure uses, a process mastered primarily by cryptography experts, and not by developers. In this paper, we present CrySL, a definition language for bridging the cognitive gap between cryptography experts and developers. CrySL enables cryptography experts to specify the secure usage of the cryptographic libraries that they provide. We have implemented a compiler that translates such CrySL specification into a context-sensitive and flow-sensitive demand-driven static analysis. The analysis then helps developers by automatically checking a given Java or Android app for compliance with the CrySL-encoded rules. We have designed an extensive CrySL rule set for the Java Cryptography Architecture (JCA), and empirically evaluated it by analyzing 10,000 current Android apps. Our results show that misuse of cryptographic APIs is still widespread, with 95% of apps containing at least one misuse. Our easily extensible CrySL rule set covers more violations than previous special-purpose tools with hard-coded rules, with our tooling offering a more precise analysis.
Backcross Introgression of the Cucumis hystrix Genome Increases Genetic Diversity in U.S. Processing Cucumber (2010)

The genetic base of commercial cucumber ( Cucumis sativus L.) is extremely narrow (about 3%–8% polymorphism). Wide-based crosses within C. sativus [i.e., C. sativus var. sativus × C. sativus var. hardwickii (R.) Alef.] and interspecific hybridization attempts before 1995 have not substantially increased genetic diversity for plant improvement. However, in 1995, an amphidiploid ( Cucumis hytivus Chen and Kirkbride) was derived from a C. sativus × Cucumis hystrix Chakr. mating. A derivative of this amphidiploid was used herein to broaden the genetic base of cucumber through backcross introgression [( C. sativus × C. hytivus ) × C. sativus ]. Initially, the combining ability of eight genetically diverse lines was investigated for days to anthesis (DA), sex expression (SEX), lateral branch number (LBN), fruit per plant (FP), fruit length:diameter ratio (L:D), and salt-processing ability [i.e., processed fruit color (exterior and interior), shape, and seed cavity characteristics]. Based on the combining ability, inbred backcross lines [IBL (BC 2 S 3 )] were developed from an original gynoecious determinate line WI 7023A [ C. sativus (recurrent parent)] × monoecious indeterminate line WI 7012A ( C. sativus × C. hytivus derived) mating, where 30 of 392 (8%) BC 1 progeny were selected based on their diversity at 16 mapped marker loci. These progeny were used to develop BC 2 progeny, which were then self-pollinated without further selection to produce 94 IBL. These IBL were genotyped and evaluated in the open field in two plantings in 2008 for DA, SEX, LBN, leaf size, FP, and L:D. The genetic distance (GD) between parental lines was 0.85, and the GD among IBL ranged between 0.16 and 0.75. Multivariate analyses indicated that IBL differed from parental lines and possessed considerable morphological and genotypic diversity that could be used to broaden the genetic base of commercial U.S. processing cucumber.
Role of platelet age in assessment of coagulation. (1995)

There are two important reasons why most platelet function studies can be inaccurate. First, platelet function deteriorates when blood is taken out of the vascular tree. Second, tests performed on platelets removed from the blood do not incorporate the role of other cellular and chemical components that may alter platelet activity. This article demonstrates that a coagulation test developed in our laboratory can accurately assess the role of platelet age on the speed of the coagulation of blood. Samples (5.0 mL) of citrated venous blood from 15 volunteers were divided into two groups. One group (n = 6), comprised of subgroups A, B, C, and D of 950 microL aliquots each, was tested within 3 hours. The second group (n = 9), comprised of subgroups E, F, G, and H of 950 microL aliquots each, was tested at 24 hours. The aliquots were added to 50 microL saline without collagen (subgroups A and E), 50 microL saline with 10 micrograms collagen (subgroups B and F), 50 microL saline with 50 micrograms collagen (subgroups C and G), and 50 microL saline with 100 micrograms collagen (subgroups D and H). All collagen-incubated fresh blood samples were significantly more hypercoagulable (shorter recalcification times) compared with the control (no collagen) blood. In the 24-hour-old blood, changes were significant only in the sample with 50 micrograms/mL collagen. We conclude that these data authenticate the role of platelet age in the assessment of the coagulation process.
Antioxidant Properties of Alpha-Lipoic (Thioctic) Acid Treatment on Renal and Heart Parenchyma in a Rat Model of Hypertension (2021)

Renal and cardiac impairments are frequent events in the presence of hypertension. Organ damage is mainly linked to oxidative stress due to high blood pressure and may be reduced by antioxidant supplementation. Alpha-lipoic acid (ALA) is one of most effective antioxidants. It is widely used as a nutritional supplement in a racemic mixture (+/-), even though the (+)-enantiomer is biologically active. This study was designed to investigate the effect of treatment with (+/-)-ALA and its enantiomers on renal and heart parenchyma in spontaneously hypertensive rats (SHR), using immunochemical and immunohistochemical techniques. The results confirmed that the oxidative mechanisms of organ alterations, due to hypertension, and characterized by glomerular and tubular lesions, left ventricular hypertrophy, and fibrosis but not by apoptosis were accompanied by proteins' and nucleic acids' oxidation. We found greater effectiveness of (+)-ALA compared to (+/-)-ALA in reducing oxidative stress, cardiac and renal damages in SHR. To conclude, these data propose (+)-ALA as one of the more appropriate antioxidant molecules to prevent renal and cardiac alterations associated with hypertension.
Ameliorating Patient-Caregiver Stigma in Early-Stage Parkinson's Disease using Robot co-Mediators (2014)

Abstract. Facial masking in early stage Parkinson’s disease leads to a well-documented deterioration (stigmatization) in the patient-caregiver relationship. This research described in this paper is concerned with preserving dignity in that bond where otherwise it might be lost, through the use of a robot co-mediator that will be capable of monitoring the human-human relationship for lack of congruence in the perceived emotional states of the parties concerned. This paper describes the component architectural modules that are being used in support of this 5-year effort, including an ethical architecture developed earlier for the military and previous research on affective companion robots for Sony and Samsung that are able to express affective state through kinesics and proxemics. 1
A Model for the Enzyme−Substrate Complex of DNA Photolyase and Photodamaged DNA (1999)

The three-dimensional structure of Escherichia coli DNA photolyase and molecular dynamics simulations using the AMBER force field were used to construct a model of the enzyme−substrate complex. Three different dinucleotides with cyclobutane pyrimidine dimers (T<>T, T<>U, and U<>T), two conformations of a single-stranded DNA nonamer, and a duplex DNA dodecamer containing the T<>T lesion were studied. The results are in good agreement with available experimental data and provide a structural rationalization for the results of ethylation studies, the measurement of the relative rates of electron transfer for different dinucleotides complexed to the enzyme, and the similar binding constants for T<>T containing single stranded and duplex DNA. The results support the base-flipping mechanism suggested earlier. The proposed active-site model reveals three types of interactions: (i) ion-pair interactions at the rim of the active site between the positively charged residues on the enzyme surface (Arg226, Arg342, Arg397, and Lys154) and the deoxyribophosphate immediately 5‘ to the dimer as well as the three deoxyribophosphates on the 3‘ side, (ii) polar interactions between Glu274 and the NH function of the 3‘ base of the dimer as well as a hydrogen bond between the C-4 carbonyl on the 5‘ base of the dimer with Trp384, and (iii) hydrophobic interactions between Trp277 and Trp384 and the nonpolar cyclobutane moiety of the dimer, thus shielding the radical anion intermediate of the DNA repair from electrophilic attack. In this model, the distance between the redox active FADH cofactor and the dimer is too large to account for the observed rates of electron transfer. Rather, the results suggest an electron transfer mediated by the π-systems of the aromatic residues Trp277 and Trp384.
Gene expression profiling of the nervous system in murine experimental autoimmune encephalomyelitis (2001)

Multiple sclerosis is thought to be a polygenic disease driven by dysregulation of the immune system leading to an autoimmune response against one or several antigens of cerebral white matter tissue. Experimental autoimmune encephalomyelitis (EAE) is a mouse model that is used to study the aetiology and pathogenesis of multiple sclerosis and new therapeutic approaches. We used oligonucleotide microarrays to determine gene expression profiles of the inflamed spinal cords of EAE mice at the onset and at the peak of the disease. Of the approximately 11 000 genes studied, 213 were regulated differentially and 100 showed consistent differential regulation throughout the disease. Inflammation resulted in a profile of increased gene expression of immune-related molecules, extracellular matrix and cell adhesion molecules and molecules involved in cell division and transcription, and differential regulation of molecules involved in signal transduction, protein synthesis and metabolism. Of the 104 genes with defined chromosomal locations, 51 mapped to known EAE-linked quantitative trait loci and as such are putative candidate genes for susceptibility to EAE.
Phosphorylation-mediated 14-3-3 Protein Binding Regulates the Function of the Rho-specific Guanine Nucleotide Exchange Factor (RhoGEF) Syx* (2013)

Syx is a Rho-specific guanine nucleotide exchange factor (GEF) that localizes at cell-cell junctions and promotes junction stability by activating RhoA and the downstream effector Diaphanous homolog 1 (Dia1). Previously, we identified several molecules, including 14-3-3 proteins, as Syx-interacting partners. In the present study, we show that 14-3-3 isoforms interact with Syx at both its N- and C-terminal regions in a phosphorylation-dependent manner. We identify the protein kinase D-mediated phosphorylation of serine 92 on Syx, and additional phosphorylation at serine 938, as critical sites for 14-3-3 association. Our data indicate that the binding of 14-3-3 proteins inhibits the GEF activity of Syx. Furthermore, we show that phosphorylation-deficient, 14-3-3-uncoupled Syx exhibits increased junctional targeting and increased GEF activity, resulting in the strengthening of the circumferential junctional actin ring in Madin-Darby canine kidney cells. These findings reveal a novel means of regulating junctional Syx localization and function by phosphorylation-induced 14-3-3 binding and further support the importance of Syx function in maintaining stable cell-cell contacts.
Conductance of single thiolated poly(GC)-poly(GC) DNA molecules (2005)

We use ultrahigh vacuum scanning tunneling microscopy∕spectroscopy (UHV-STM∕STS) to investigate the electronic properties of single thiolated 12-base-pair poly(GC)-poly(GC) DNA molecules on a Au(111) surface at room temperature. Reproducible current-voltage curves of the DNA are obtained at variable sample-tip separations. The normalized conductance, which can be interpreted as the density of states, shows a well-defined wide band gap. UHV-STM∕STS opens up a novel technique to probe the electronic properties of biomolecules on surfaces at the atomic level.
Taxus baccata culture: initiation, growth, maintenance, characterization and taxoids production (1995)

info:eu-repo/semantics/published
Development of a back-contact, scalable silicon photomultiplier array for PET (2008)

The long term goal of the work described in this paper is to develop a scalable silicon photomultiplier (SiPM) array technology with back-side contacts to facilitate integration with scintillating crystals used in positron emission tomography (PET) imaging applications. We refer to the proposed device back-side contact, scalable SiPM (BCS_SiPM) array.
New reagents, reactions, and peptidomimetics for drug design (2001)

It has been a major focus in our laboratories to prepare novel reagents and peptidomimetic structures for drug design. We have designed and prepared novel guanidinylation reagents that can be employed in solution or as solid phase reagents. We and others have utilized the reagent 3-(diethoxyphosphoryloxy)-1,2,3-benzotriazin-4(3H)-one (DEPBT) for amide bond formation to couple sterically hindered structures. These couplings proceed with remarkably strong resistance to racemization. In the area of peptidomimetics, we have incorporated novel building blocks to create biologically active compounds. These building blocks include thioether and alkylamine bridges, beta-methylated, and beta,beta-dimethylated amino acid residues. These mimetic structures have been incorporated into specific target molecules such as opioids to obtain cyclic peptidomimetics with potent and selective biological activity.
Residues Throughout the Cytoplasmic Domain Affect the Internalization Efficiency of P-selectin (1995)

The cytoplasmic domains of many membrane proteins have short sequences, usually including a tyrosine or a di-leucine, that function as sorting signals. P-selectin is an adhesion receptor for leukocytes that is expressed on activated platelets and endothelial cells. Its 35-residue cytoplasmic domain contains signals for sorting into regulated secretory granules, for endocytosis, and for movement from endosomes to lysosomes. The domain has a membrane-distal sequence, YGVFTNAAF, that resembles some tyrosine-based signals. We studied the effects of deletions and mutations in the cytoplasmic tail of human P-selectin on its internalization in clathrin-coated pits of transfected Chinese hamster ovary cells. Mutations and deletions in the putative tyrosine-based motif did not clearly implicate these residues as critical components of a short internalization signal. Indeed, a construct containing a truncated 18-residue cytoplasmic domain with a single substitution (K761A/H773Stop) was internalized nearly three times as fast as wild-type P-selectin; this construct contained no di-leucine, tyrosine, or other known sorting motif. Substitution of residues throughout the cytoplasmic domain affected the internalization rate of P-selectin. Furthermore, the cytoplasmic domain of P-selectin mediated faster internalization when attached to the extracellular and transmembrane domains of the low density lipoprotein receptor than when attached to the corresponding domains of P-selectin. Thus, we were unable to identify a short internalization signal in the cytoplasmic tail of P-selectin. Residues throughout the cytoplasmic domain, and perhaps the transmembrane sequence to which the domain is attached, affect the efficiency of internalization.
Development of a simple driving simulator and determination of the reference range of normative performance (2018)

We provide evidence that impaired performance on ≤2 items of the SiDS provides a sensitive criterion of 'driving fitness' in young adults after a TBI.
In vitro expression of human cannabinoid 1 receptor for ligand-assisted binding site characterization (2012)

The Cannabinoid 1 receptor (CB1) is a type A G-protein coupled receptor (GPCR) expressed most widely in the human brain and has been identified as a key receptor in modulating a number of physiological functions of the human body. Therefore, drugs acting on the CB1 have an enormous pharmacotherapeutic potential in disease conditions such as chronic neuropathic pain, cardio-metabolic diseases, obesity, and even in neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. In order to develop CB1-specific, high-affinity ligands, a better understanding of the structural aspects of the receptor in its native state is essential. Using an E. coli-based cell-free (in vitro) expression system in addition with nanolipid bilayers (Nanodiscs), we developed a convenient method for efficient production of the re-engineered human cannabinoid receptor and showed proof of functionality of the expressed receptor using a radioligand-binding assay. The saturation binding curve with CP55,940, a non-classical bicyclic analog of Δ9-tetrahydrocannabinol (Δ9-THC), showed Bmax of 1358 pmoles/g and a Kd of 8.57 nM. The total amount of functional receptor was calculated to be 500 ng/ml of expression reaction.