gebhart/patrepeval huggingface dataset:
Development of Highly Potent and Selective Phosphinic Peptide Inhibitors of Zinc Endopeptidase 24-15 Using Combinatorial Chemistry (1995)

Several hundred phosphinic peptides having the general formula Z-(L,D)Phe psi (PO2CH2)(L,D)Xaa'-Yaa'-Zaa', where Xaa' = Gly or Ala and Yaa' and Zaa' represent 20 different amino acids, have been synthesized by the combinatorial chemistry approach. Peptide mixtures or individual peptides were evaluated for their ability to inhibit the rat brain zinc endopeptidases 24-15 and 24-16. Numerous phosphinic peptides of this series act as potent (Ki in the nanomolar range) mixed inhibitors of these two peptidases. However, our systematic and comparative strategy led us to delineate the residues located in P2' and P3' positions of the inhibitors that are preferred by these two peptidases. Thus, endopeptidase 24-15 exhibits a marked preference for inhibitors containing a basic residue (Arg or Lys) in the P2' position, while 24-16 prefers a proline in this position. The P3' position has less influence on the inhibitory potency and selectivity, both peptidases preferring a hydrophobic residue at this position. On the basis of these observations, we have prepared highly potent and selective inhibitors of endopeptidase 24-15. The Z-(L,D)Phe psi-(PO2CH2)(L,D)Ala-Arg-Met compound (mixture of the four diastereoisomers) displays a Ki value of 70 pM for endopeptidase 24-15. The most selective inhibitor of endopeptidase 24-15 in this series, Z-(L,D)Phe psi (PO2-CH2)(L,D)Ala-Arg-Phe, exhibits a Ki value of 0.160 nM and is more than 3 orders of magnitude less potent toward endopeptidase 24-16 (Ki = 530 nM). Furthermore, at 1 microM this selective inhibitor is unable to affect the activity of several other zinc peptidases, namely endopeptidase 24-11, angiotensin-converting enzyme, aminopeptidase M, leucine aminopeptidase, and carboxypeptidases A and B. Therefore, Z-(L,D)Phe psi (PO2CH2)(L,D)Ala-Arg-Phe can be considered as the most potent and specific inhibitor of endopeptidase 24-15 developed to date. This new inhibitor should be useful in assessing the contribution of this proteolytic activity in the physiological inactivation of neuropeptides known to be hydrolyzed, at least in vitro, by endopeptidase 24-15. Our study also demonstrates that the combinatorial chemistry approach leading to the development of phosphinic peptide libraries is a powerful strategy for discovering highly potent and selective inhibitors of zinc metalloproteases and should find a broader application in studies of this important class of enzymes.
On the design of optimal TDM schedules for broadcast WDM networks with arbitrary transceiver tuning latencies (2002)

We consider the problem of scheduling packet transmissions in single-hop WDM networks, with tunability provided only at one end. Our objective is to design schedules of minimum length for a given traffic demand matrix. The contribution of our work is twofold. First we define a special class of schedules which permit an intuitive formulation of the scheduling problem. We then present algorithms which construct schedules of length equal to the lower bound provided that certain optimality conditions are satisfied. We also develop heuristics which, in the general case, give schedules of length equal or very close to the lower bound. Secondly, we identify two distinct regions of network operation. In the first region the schedule length is determined by the tuning requirements, while in the second it is determined by the traffic demands. The point at which the network switches between the two regions is identified in terms of the number of nodes and channels, and the tuning latency. Accordingly, we show that it is possible to appropriately dimension the network to offset the effects of even large values of tuning latency.
Predicting arthritis outcomes--what can be learned from the Leiden Early Arthritis Clinic? (2010)

Predictors for RA development, previously used to develop a prediction rule in UA patients, are largely similar to predictors for arthritis persistency. Only part of the joint destruction level in RA is explained by the currently known risk factors. New factors need to be identified in order to guide pharmaceutical intervention at the level of individual RA patients.
Hole Free Phase Plate Electron Tomography in Material Sciences (2018)

To visualize the internal components of electronic devices in three dimensions (3D), it is necessary to use an imaging method that provides high contrast difference between the materials the device is composed of. Often the contrast of bright field transmission electron microscope (BFTEM) or scanning transmission electron microscope (STEM) is too low resulting in high irradiation dose to obtain adequate signal to noise ratio (SNR) for reliable 3D reconstruction. The low contrast is of concern especially when the sample of interest is composed of light elements [1]. The high irradiation dose implies extensive radiation damage [2] and thus unreliable 3D volume reconstruction. High angle annular dark field (HAADF) STEM is not applicable as it relies on large difference of atomic number of the components. Core loss electron energy loss spectroscopy (EELS) typically requires high irradiation dose due to small core loss cross sections while low loss EELS signal delocalization is often of the same order as the lateral dimensions of the examined layers.
Nucleolytic processing of a tRNAArg-tRNAAsp dimeric precursor by a homologous component from Saccharomyces cerevisiae. (1985)

A subcellular extract from Saccharomyces cerevisiae has been used to transcribe cloned yeast tRNA genes in vitro and to process the primary transcripts at the 5' and 3' termini. Chromatographic fractionation of the extract has separated the transcription components from two distinct nucleolytic activities: an endonuclease that cleaves the precursors to produce mature 5' termini; and a 3'-5' exonuclease. These fractions have been used to elaborate a processing pathway for the dimeric primary transcript of the yeast tRNAArg-tRNAAsp gene pair. Under optimal conditions in vitro this gene is expressed at a rate of 200 transcripts/gene/hour, initiating at position -10 with respect to the mature 5' terminus of tRNAArg and terminating near position +160. The primary transcripts are cleaved by an endonuclease to give tRNAAsp with a mature 5' terminus, and a pre-tRNAArg monomer with a 5' leader and 3' trailer sequences. A second endonuclease cleavage of pre-tRNAArg generates the mature 5' terminus of tRNAArg. The endonuclease cleavages are not ordered. Exonuclease activity(ies) remove the spacer sequences from the 5' mature tRNAArg, and trim the 3' trailer portion from tRNAAsp. Exonucleolytic removal of the 3' trailer does not require prior endonuclease action, but removal of the spacer sequences from pre-tRNAArg is incomplete without prior removal of the 5' leader sequences.
[S1.4]: Recovery from amblyopia in adulthood (2010)

Heightened cortical plasticity during postnatal critical periods wanes with age to consolidate neural circuits and behavior. Such rigidity in turn limits recovery from injury or developmental disorders. Identifying these mechanisms carries a broad impact for therapeutic approaches, but is often hampered by complex etiologies and distributed networks. An approachable model is the permanent loss of visual acuity (amblyopia) following sensory deprivation within primary visual cortex, which does not readily recover later in life. Here, we identify two classes of “molecular brakes” on (1) structural growth (acute myelin-related Nogo receptor signaling), and (2) neuromodulation (Lynx1 suppression of nicotinic cholinergic receptor signaling) that actively limit plasticity in adulthood. Removal of these brakes notably restores visual acuity to normal levels simply upon reopening the eye rendered amblyopic earlier in life. Given the widespread distribution of these factors, they may offer a more general model for understanding cognitive development and for treating disorders of similar origin in early postnatal life.
IL-7 Restores Lymphocyte Functions in Septic Patients (2012)

Septic syndrome is the leading cause of mortality for critically ill patients worldwide. Patients develop lymphocyte dysfunctions associated with increased risk of death and nosocomial infections. In this study, we performed preclinical experiments testing the potential of recombinant human IL-7 (rhIL-7) as a lymphostimulating therapy in sepsis. Circulating IL-7 and soluble IL-7 receptor α-chain (soluble CD127) concentrations were measured in plasma, whereas cellular CD127 expression was evaluated on circulating CD4(+) and CD8(+) lymphocytes from septic shock patients and healthy volunteers. Lymphocyte proliferation, IFN-γ production, STAT5 phosphorylation, and B cell lymphoma 2 induction were measured ex vivo in response to T cell stimulation in the presence or not of rhIL-7. We show that IL-7 pathway (plasmatic IL-7 concentration and cellular and soluble CD127 expressions) is not overtly altered and remains activable in septic patients. Most importantly ex vivo treatment of patients' cells with rhIL-7 significantly improves lymphocyte functionality (CD4(+) and CD8(+) lymphocyte proliferations, IFN-γ production, STAT5 phosphorylation, and B cell lymphoma 2 induction after stimulation). To our knowledge, this constitutes the first report of rhIL-7 ability to restore normal lymphocyte functions in septic patients. These results support the rational for initiating a clinical trial testing rhIL-7 in septic shock.
ANTIBODIES TO CANINE AND FELINE VIRUSES IN SPOTTED HYENAS (CROCUTA CROCUTA) IN THE MASAI MARA NATIONAL RESERVE (2004)

Spotted hyenas (Crocuta crocuta) are abundant predators in the Serengeti ecosystem and interact with other species of wild carnivores and domestic animals in ways that could encourage disease transmission. Hyenas also have a unique hierarchical social system that might affect the flow of pathogens. Antibodies to canine distemper virus (CDV), feline immunodeficiency virus (FIV), feline panleukopenia virus/canine parvovirus (FPLV/CPV), feline coronavirus/ feline infectious peritonitis virus (FECV/IPV), feline calicivirus (FCV), and feline herpesvirus 1 (FHV1) have been detected in other Serengeti predators, indicating that these viruses are present in the ecosystem. The purpose of this study was to determine whether spotted hyenas also had been infected with these viruses and to assess risk factors for infection. Serum samples were collected between 1993 and 2001 from 119 animals in a single clan for which behavioral data on social structure were available and from 121 hyenas ill several other clans. All animals resided in the Masai Mara National Reserve. Antibodies to CDV, FIV, FPLV/CPV, FECV/FIPV, FCV, and FHV1 were present in 47%, 3.5%, 81%, 36%, 72%, and 0.5% of study hyenas, respectively. Antibody prevalence was greater in adults for FIV and FECV/FIPV, and being a female of high social rank was a risk factor for FIV. Hyenas near human habitation appeared to be at lower risk to have CDV, FIV, and FECV/FIPV antibodies, whereas being near human habitation increased the risk for FPLV/CPV antibodies. Canine (distemper virus and FECV/FIPV antibody prevalence varied considerably over time, whereas FIV, FPLV/CPV, and FCV had a stable, apparently endemic temporal pattern. These results indicate that hyenas might play a role in the ecology of these viruses in the Serengeti ecosystem. The effect of these viruses on hyena health should be further investigated. The lower prevalence of CDV antibody-positive hyenas near human habitation suggests that reservoirs for CDV other than domestic dogs are present in the Serengeti ecosystem.
Oligomeric azodinitrile compounds with epoxy groups on the basis of 4,4'-azo-bis-(4-cyanopentanoic) acid (2003)

Oligomeric azodinitrile compounds with epoxy groups were synthesized by interaction between 4,4'-azo-bis-(4-cyanopentanoic) acid and diglycydyl ethers of diphenylpropane, ethylene glycol and resorcine in the presence of benzyltriethylammmonium chloride as the catalyst. Effects of temperature, reaction medium, initial components ratio and catalyst concentration on oligomer yields have been studied. Styrene polymerization is an example demonstrating the possibility of using such compounds for obtaining oligomers with epoxy end groups.
Predicting antigen specificity of single T cells based on TCR CDR 3 regions (2020)

It has recently become possible to simultaneously assay T-cell specificity with respect to large sets of antigens and the T-cell receptor sequence in high-throughput single-cell experiments. Leveraging this new type of data, we propose and benchmark a collection of deep learning architectures to model T-cell specificity in single cells. In agreement with previous results, we found that models that treat antigens as categorical outcome variables outperform those that model the TCR and antigen sequence jointly. Moreover, we show that variability in single-cell immune repertoire screens can be mitigated by modeling cell-specific covariates. Lastly, we demonstrate that the number of bound pMHC complexes can be predicted in a continuous fashion providing a gateway to disentangle cell-to-dextramer binding strength and receptor-to-pMHC affinity. We provide these models in the Python package TcellMatch to allow imputation of antigen specificities in single-cell RNA-seq studies on T cells without the need for MHC staining.
Comparative analysis of fabrication methods for achieving rounded microchannels in PDMS (2016)

Many microfluidic applications demand control over channel cross-sectional geometry. In particular, rounded microchannels are essential to the function of microfluidic valves, which have played an integral part in the success of microfluidics over the past fifteen years. Here we investigate the relative strengths and weaknesses of different strategies for fabricating rounded microchannels in PDMS, systematically examining five common strategies. We consider the appropriateness of the fabrication strategies for microchannels of differing sizes and aspect ratios, and evaluate these various strategies on a number of metrics ranging from microchannel resolution to fabrication difficulty. We discuss the merits of the different strategies for a range of applications, and make recommendations on which strategy to use based on the driving constraints of the device.
TH‐EF‐BRD‐04: A Fast 4D IMRT/VMAT Planning Method Based On Segment Aperture Morphing (2015)

Purpose: To investigate dosimetric advantages of a 4D IMRT/VMAT planning method employing a segment aperture morphing (SAM) algorithm accounting for respiration‐induced target motion and deformation. The minimal required number of calculated SAM phases was tested to minimize plan creation time. Methods: The new technique involves generating 4D step‐and‐shoot IMRT or VMAT plans based on 10‐phase 4DCT in the following steps: (1) optimizing a flattening‐filter‐free IMRT/VMAT plan based on the 50% phase CT dataset (2) warping contours from the 50%‐phase CT to the remaining phases via deformable image registration (DIR) and manual editing (3) morphing segment apertures of the 50%‐phase plan to each phase CT using SAM that adjusts each aperture shape based on the change of the beam's‐eye‐view of the target contour between the two phases (4) calculating the dose distribution for each phase with the morphed apertures and same MUs as in the 50%‐phase plan, and (5) generating the 4D plan by accumulating the dose from all nine SAM‐corrected phases and the original 50% optimized phase using DIR. 4D plans based on 10, 7, 5 and 3 SAM‐corrected phases were generated for representative lung and pancreatic cancer cases, and were compared using DVH analysis against the gold‐standard 4D plan where all 10 phases are individually planned and optimized. A SAM‐corrected 4D plan was also compared to a simpler phase‐by‐phase isocenter‐shifted plan to assess accounting for tumor deformation and translation opposed to only tumor translation. Results: Plan DVH quality for the 10‐phase and 7‐phase 4D SAM plans were comparable with the fully‐optimized 4D plans (PTV‐D95's within 3% of fully‐optimized plans). SAM based algorithms out‐performed simpler isocenter‐shifted‐only approaches (∼1.5% PTV‐D95 improvement). SAM‐based 4D planning greatly reduces planning time verses individually optimized phase planning techniques. Conclusion: SAM with DIR provides a fast and accurate way to create 4D IMRT/VMAT plans.
Kvalitetsavvik sildefilet. Spektroskopisk karakterisering av blodinnhold (2013)

Gjennom spektrofotometriske målinger av hemoglobin i fiskemuskel og avbildende spektroskopi er tre ulike grupper med flekket sild studert for å avdekke hvordan pumpetrykk påvirker mengde restblod i silden. Effekten på mengde restblod ble studert for tre ulike pumpetrykk, 80, 120 og 160 bar. Resultatene viste at det var signifikant mer restblod i filetene hvor pumpetrykket var 160 bar og at variasjonen innad i hver gruppe var veldig stor.
High Performance Tunable Catalysts Prepared by Using 3D Printing (2021)

Honeycomb monoliths are the preferred supports in many industrial heterogeneous catalysis reactions, but current extrusion synthesis only allows obtaining parallel channels. Here, we demonstrate that 3D printing opens new design possibilities that outperform conventional catalysts. High performance carbon integral monoliths have been prepared with a complex network of interconnected channels and have been tested for carbon dioxide hydrogenation to methane after loading a Ni/CeO<sub>2</sub> active phase. CO<sub>2</sub> methanation rate is enhanced by 25% at 300 °C because the novel design forces turbulent flow into the channels network. The methodology and monoliths developed can be applied to other heterogeneous catalysis reactions, and open new synthesis options based on 3D printing to manufacture tailored heterogeneous catalysts.
Two edge type LDPC codes for the wiretap channel (2009)

We consider transmission over a wiretap channel where both the main channel and the wiretapper's channel are Binary Erasure Channels (BEC). We propose a code construction using two edge type LDPC codes based on the method of Thangaraj, Dihidar, Calderbank, McLaughlin and Merolla. The advantage of our construction is that we can easily calculate the threshold over the main channel. Using standard LDPC codes with a given threshold over the BEC we give a construction for a two edge type LDPC code with the same threshold. Since this construction gives a code for the main channel with threshold zero we also give numerical methods to find two edge type LDPC codes with non-zero threshold for the main channel.
DNA nanotechnology &#x2014; Nanophotonic device &amp; medical applications (2012)

Summary form only given. DNA nanotechnology is a versatile self-assembly process whereby a variety of complex nanostructures can be fabricated with sub-lithographic features [1]. Adopting this technology, 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sup> identical devices having hundreds of components with nanometer resolution can be synthesized simultaneously. Example nanostructures include DNA motifs [2], two-dimensional DNA crystals [3], and DNA origami [4]. Currently, DNA nanotechnology is being adopted towards excitonic and plasmonic devices [5] and medical applications[6]. This presentation will examine examples of both and discuss several the approaches being used at Boise State University.
Systematic, Genome-Wide, Sex-Specific Linkage of Cardiovascular Traits in French Canadians (2008)

The sexual dimorphism of cardiovascular traits, as well as susceptibility to a variety of related diseases, has long been recognized, yet their sex-specific genomic determinants are largely unknown. We systematically assessed the sex-specific heritability and linkage of 539 hemodynamic, metabolic, anthropometric, and humoral traits in 120 French-Canadian families from the Saguenay-Lac-St-Jean region of Quebec, Canada. We performed multipoint linkage analysis using microsatellite markers followed by peak-wide linkage scan based on Affymetrix Human Mapping 50K Array Xba240 single nucleotide polymorphism genotypes in 3 settings, including the entire sample and then separately in men and women. Nearly one half of the traits were age and sex independent, one quarter were both age and sex dependent, and one eighth were exclusively age or sex dependent. Sex-specific phenotypes are most frequent in heart rate and blood pressure categories, whereas sex- and age-independent determinants are predominant among humoral and biochemical parameters. Twenty sex-specific loci passing multiple testing criteria were corroborated by 2-point single nucleotide polymorphism linkage. Several resting systolic blood pressure measurements showed significant genotype-by-sex interaction, eg, male-specific locus at chromosome 12 (male-female logarithm of odds difference: 4.16; interaction P=0.0002), which was undetectable in the entire population, even after adjustment for sex. Detailed interrogation of this locus revealed a 220-kb block overlapping parts of TAO-kinase 3 and SUDS3 genes. In summary, a large number of complex cardiovascular traits display significant sexual dimorphism, for which we have demonstrated genomic determinants at the haplotype level. Many of these would have been missed in a traditional, sex-adjusted setting.
Catheter ablation of monomorphic ventricular tachycardia. (2005)

Ablation is a reasonable alternative to antiarrhythmic drug therapy for controlling frequent ventricular tachycardia episodes in many patients. Further technological advances can be anticipated.
Insulin‐Like Growth Factor‐I Enhances Immune Response in Dexamethasone‐Treated or Surgically Stressed Rats Maintained With Total Parenteral Nutrition (1995)

our data demonstrate that IGF-1 enhances immune response during TPN in rats.
p38 MAPK phosphorylation and NF-kappaB activation in human crescentic glomerulonephritis (2002)

We conclude that the phosphorylation of p38 MAPK associated with the activation of NF-kappa B may be involved in the upregulation of intrarenal MIP-1 alpha and the utilization of CCR5 signalling, which may result in human crescentic glomerulonephritis.
Data from Tie2 Expression on Macrophages Is Required for Blood Vessel Reconstruction and Tumor Relapse after Chemotherapy (2023)

&lt;div&gt;Abstract&lt;p&gt;Tumor relapse after chemotherapy is a major hurdle for successful cancer therapy. Chemotherapeutic drugs select for resistant tumor cells and reshape tumor microenvironment, including the blood supply system. Using animal models, we observed on macrophages in tumor tissue a close correlation between upregulated Tie2 expression and tumor relapse upon chemotherapy. Conditional deletion of Tie2 expression in macrophages significantly prohibited blood supply and regrowth of tumors. Tie2&lt;sup&gt;+&lt;/sup&gt; macrophages were derived from tumor-infiltrating Tie2&lt;sup&gt;−&lt;/sup&gt;CD11b&lt;sup&gt;+&lt;/sup&gt; cells and hypoxia-induced Tie2 expression on these cells. Mechanistically, expression of Tie2 prevented macrophages from apoptosis in stress conditions via the AKT-dependent signaling pathway. Together, these results demonstrate that Tie2 expression by macrophages is necessary and sufficient to promote the reconstruction of blood vessels after chemotherapy, shedding new light on developing novel strategies to inhibit tumor relapse. &lt;i&gt;Cancer Res; 76(23); 6828–38. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;