gebhart/patrepeval huggingface dataset:
SELECTION OF THE T CELL REPERTOIRE (1999)

Advances in gene technology have allowed the manipulation of molecular interactions that shape the T cell repertoire. Although recognized as fundamental aspects of T lymphocyte development, only recently have the mechanisms governing positive and negative selection been examined at a molecular level. Positive selection refers to the active process of rescuing MHC-restricted thymocytes from programmed cell death. Negative selection refers to the deletion or inactivation of potentially autoreactive thymocytes. This review focuses on interactions during thymocyte maturation that define the T cell repertoire, with an emphasis placed on current literature within this field.
Isolation of a novel chick homolog of Serrate and its coexpression with C-Notch-1 in chick development (1996)

Intercellular signaling mediated by the transmembrane proteins, Notch as receptor and its ligands, Delta and Serrate, plays essential roles in the developmental fate decision of many cell types in Drosophila. The Notch genes are highly conserved both in invertebrates and in vertebrates, suggesting that Notch pathway regulates cell fate decisions during vertebrates development. Notch, Delta and Serrate homologs in chicken have been cloned (Henrique et al., Nature 375: 787-790, 1995; Myat et al., Dev. Biol. 174: 233-247, 1996). We isolated a novel chick homolog of Drosophila Serrate, named C-Serrate-2, and examined its expression patterns during the early chick development using whole-mount in situ hybridization. C-Serrate-2 transcripts were detected in several tissues including the forebrain, the myotome and the apical ectodermal ridge (AER) of the limb bud of a 4-day-old chick embryo. In most of the regions where C-Serrate-2 was expressed, C-Notch-1 was also expressed. Our observations suggest that Serrate-2-Notch-1 signaling plays a role in a variety of morphogeneses during the chick development.
Multidimensional-signal sample dependency at Nyquist densities (1986)

When a multidimensional signal is uniformly sampled, its spectrum is replicated. If the signal is band limited and the replications (1) contain regions that are identically zero and (2) are not aliased, then the samples are dependent. Indeed, lost samples can be regained from those remaining. In dimensions greater than one, there are spectral regions of support for which this is the case even when sampling is performed at the Nyquist (minimum) density (e.g., a circular spectral region of support in two dimensions). When the known samples are perturbed by additive noise, lost-sample restoration noise levels in certain cases can be obtained by simple geometrical observations in the frequency domain. The results are specifically applied to coherent and incoherent optical images of objects of finite extent obtained from imaging systems with circular pupils.
Interactions between the non-seed region of siRNA and RNA-binding RLC/RISC proteins, Ago and TRBP, in mammalian cells (2014)

Small interfering RNA (siRNA)-based RNA interference (RNAi) is widely used for target gene silencing in various organisms. We previously showed that 8-nt-long 5' proximal nucleotides, which include seed sequence (positions 2-8 from the 5' end of guide strand), and the complementary sequence of the passenger strand are capable of being simultaneously replaced with cognate deoxyribonucleotides without any substantial loss of gene silencing. In the present study, examination was made of RNA requirements in the non-seed region of siRNA. The non-seed region of siRNA was found to be subdivided into four domains, in which two nucleotide pairs (positions 13 and 14) were replaceable with cognate deoxyribonucleotides without reducing RNAi activity. However, RNA sequences at positions 9-12 and 15-18 were essential for effective gene silencing, and these two double-stranded RNA cores are required for binding of the trans-activation response RNA-binding protein (TRBP). The terminal RNA (positions 19-21) provided Argonaute protein binding sites. Argonaute binding was enhanced by the presence of RNAs at positions 15-18. Knockdown experiments showed that, unlike Argonaute and TRBP, Dicer was dispensable for RNAi. Based on these observations, we discuss possible RNA/protein and protein/protein interactions in RNA-induced silencing complex formation.
Effects of Caloric Restriction and Exercise on Age-Related, Chronic Inflammation Assessed by C-Reactive Protein and Interleukin-6 (2006)

Chronic inflammation is associated with the aging process and numerous age-related pathologies. We evaluated the effects of age, caloric restriction (CR), and exercise on plasma C-reactive protein (CRP), interleukin-6, and total antioxidant capacity in Fisher 344 rats. The inflammatory markers were analyzed using enzyme-linked immunosorbent assays (ELISA), while total antioxidant potential was determined by a spectrophotometric method. An increase in circulating levels of CRP with age was attenuated with long-term 40% CR; short-term 40% CR in young animals also reduced CRP concentration compared to age-matched controls. Lifelong exercise with 8% CR showed a marked decrease in CRP levels compared to 8% CR controls and an even greater reduction compared to ad libitum-fed rats. Plasma interleukin-6 levels remained unchanged with age, CR, and exercise, whereas inflammation levels showed an inverse association with plasma antioxidant status. These studies highlight the anti-inflammatory effects of CR and exercise.
Enzymatic switching for efficient and accurate translesion DNA replication (2004)

When cyclobutane pyrimidine dimers stall DNA replication by DNA polymerase (Pol) delta or epsilon, a switch occurs to allow translesion synthesis by DNA polymerase eta, followed by another switch that allows normal replication to resume. In the present study, we investigate these switches using Saccharomyces cerevisiae Pol delta, Pol epsilon and Pol eta and a series of matched and mismatched primer templates that mimic each incorporation needed to completely bypass a cis-syn thymine-thymine (TT) dimer. We report a complementary pattern of substrate use indicating that enzymatic switching involving localized translesion synthesis by Pol eta and mismatch excision and polymerization by a major replicative polymerase can account for the efficient and accurate dimer bypass known to suppress sunlight-induced mutagenesis and skin cancer.
Human von Willebrand Factor (vWF): Isolation of Complementary DNA (cDNA) Clones and Chromosomal Localization (1985)

Human factor VIII--von Willebrand factor (vWF) is a large, multimeric glycoprotein that plays a central role in the blood coagulation system, serving both as a carrier for factor VIIIC (antihemophilic factor) and as a major mediator of platelet-vessel wall interaction. Diminished or abnormal vWF activity results in von Willebrand's disease (vWD), a common and complex hereditary bleeding disorder. Overlapping vWF cDNA clones that span 8.2 kilobases of the vWF messenger RNA have been obtained. vWF accounts for approximately 0.3 percent of endothelial cell messenger RNA and was undetectable in several other tissues examined. A large single copy gene for vWF is located on the short arm of chromosome 12 (12p12----12pter). No gross gene rearrangement or deletion was detected in the DNA of two patients with severe vWD.
TGF-β impairs renal autoregulation via generation of ROS (2005)

Impaired autoregulation in chronic kidney disease can result in elevation of glomerular capillary pressure and progressive glomerular damage; however, the factors linking chronic glomerular disorders to impaired autoregulation have not been identified. We tested the hypothesis that the cytokine most closely associated with progressive glomerular disease, transforming growth factor (TGF)-beta, may also attenuate autoregulation. Kidneys from normal rats were prepared for videomicroscopy, using the blood-perfused juxtamedullary nephron technique. Autoregulatory responses were measured under control conditions and during superfusion with TGF-beta1 (10 ng/ml). Control afferent arteriolar diameter averaged 18.4 +/- 1 microm and significantly decreased to 16.3 +/- 0.9 and 13.2 +/- 0.8 microm at perfusion pressures of 130 and 160 mmHg, respectively. In the presence of TGF-beta1, autoregulatory responses were completely blocked. In similar experiments performed using PDGF-BB (10 ng/ml) and HGF (25 ng/ml), the normal autoregulatory response was not affected. In vitro studies, using isolated preglomerular vascular smooth muscle cells, revealed that exposure to TGF-beta1 stimulated a rapid increase in reactive oxygen species (ROS) that was inhibited by NADPH oxidase inhibitors. In situ studies, with dihydroethidium staining, revealed a marked increase in renal vessel ROS production on exposure to TGF-beta1. Pretreatment of the juxtamedullary afferent arterioles with tempol, a ROS scavenger, or with apocynin, a NADPH oxidase inhibitor, prevented the impaired autoregulation induced by TGF-beta1. These data reveal a novel hemodynamic pathway by which TGF-beta could lead to progressive glomerular injury by impairing normal renal microvascular function.
Activated monocytes and granulocytes, capillary nonperfusion, and neovascularization in diabetic retinopathy. (1991)

Capillary occlusions are characteristic features of the early diabetic retinopathy and are presumed to initiate neovascularization. Activated leukocytes can cause microvascular occlusions and cell damage by release of cytotoxic products. To explore the role of leukocytes in capillary occlusion, nonperfusion, and neovascularization of diabetic retinopathy, a rat model was used, in which a diabetic state was induced by alloxan. Retina flat preparations were differentially stained for monocytes and granulocytes. Capillary occlusion, nonperfusion, and neovascularization were assessed microscopically in the center, midperiphery, and periphery of the retina. In contrast to control retinas, 2- to 9-month diabetic rats showed many capillary occlusions by leukocytes, especially monocytes, endothelial cell damage, extravascular macrophage accumulation, and tissue damage. The percentage of activated monocytes and granulocytes in the circulating blood of diabetic rats was greatly increased, and areas of capillary 'loss' and neovascularization in the retina coincided with sites of extravascular leukocytes. The authors' results suggest a potential role of monocytes and macrophages in the pathogenesis of diabetic retinopathy.
호텔 조직문화유형이 조직구조특성에 미치는 영향에 대한 호텔구성원 지각에 관한 연구 (2002)

This study will be conducted in the, following three stages: First, characteristic variables of hotels culture and its structure will be examined in a preceding study. Second, employees of hotels in Seoul area, primarily of extraordinary A- and B-class hotels in north and south of the Han River, will be surveyed by means of questionnaires with 5-point scales in a try to make an empirical study by determining their service quality and organizational system. Third, countermeasures will be presented from the analysis into the causes of impact and difference in the organizational culture and structural characters of hotel corporations. From the study based on the assumption that the hotel culture may exercise a positive influence upon the structural characters of hotel (leadership style, incentive system, formalization, and decentralization), it became evident that the hotel culture of goal-, control- and unity-oriented types, except of client-oriented one, have positively affected the organizational characters of hotels.
Time-Resolved Fluorescence Investigations of the Interaction of the Voltage-Sensitive Probe RH421 with Lipid Membranes and Proteins (1995)

Fluorescence lifetimes and fluorescence anisotropy decays of the voltage-sensitive styryl-pyridinium dye RH421 have been measured in the presence of dimyristoylphosphatidylcholine vesicles, the water soluble enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco), and Na+,K(+)-ATPase-containing membrane fragments. The effect of an intramembrane electric field on the photophysical properties of the dye was investigated by the binding of the hydrophobic ion tetraphenylborate (TPB) to the membrane. TPB was found to significantly increase the average fluorescence lifetime and the order of membrane-bound dye. The increase in fluorescence lifetime is consistent with reorientation of the dye further into the membrane interior. The increase in order may be attributed to an electric field-induced alignment of the dye molecules. From the values of the rotational diffusion constant experimentally determined, the expected response time of the dye to an applied electric field can be calculated for a reorientational mechanism to be on the order of tens of nanoseconds. Experiments with rubisco showed that the dye interacts strongly with the protein. In this case, the dye is so tightly bound that it has almost no independent motion and rotates virtually solely with the protein. The rate of rotational motion of the dye in the presence of Na+,K(+)-ATPase-containing membrane fragments is similar to that in pure lipid membranes. The order parameter of the dye in the Na+,K(+)-ATPase membrane fragments is close to the maximum value. This is most probably due to the high density of protein molecules, which restricts the range of motion of the dye.
Epidermal growth factor receptor inhibitors in the treatment of lung cancer: reality and hopes (2008)

EGFR inhibition, by a range of strategies, remains a central node in the treatment of nonsmall cell lung cancer.
[Establishment of the model of oxygen-glucose deprivation in vitro rat hippocampal neurons]. (2003)

The model of oxygen-glucose deprivation in vitro rat hippocampal neurons is established successfully by using the modified ACSF (artificial cerebral spinal fluid) with serum and glucose free.
Cascaded convolutional neural networks for spine chordoma tumor segmentation from MRI (2019)

Chordoma is a rare type of tumor that usually appears in the bone near the spinal cord and skull base. Due to their location in the skull base and diverse appearance in size and shape, automatic segmentation of chordoma tumors from magnetic resonance images (MRI) is a challenging task. In addition, similar MR intensity distributions of different anatomical regions, specifically sinuses, make the segmentation task from MRI more challenging. In comparison, most of the state-of-the-art lesion segmentation methods are designed to segment pathologies inside the brain. In this work, we propose an automatic chordoma segmentation framework using two cascaded 3D convolutional neural networks (CNN) via an auto-context model. While the first network learns to detect all potential tumor voxels, the second network fine-tunes the classifier to distinguish true tumor voxels from the false positives detected by the first network. The proposed method is evaluated using multi-contrast MR images of 22 longitudinal scans from 8 patients. Preliminary results showed a linear correlation of 0.71 between the detected and manually outlined tumor volumes, compared to 0.40 for a random forest (RF) based method. Furthermore, the response of tumor growth over time, i.e. increasing, decreasing, or stable, is evaluated according to the response evaluation criteria in solid tumors with an outcome of 0.26 kappa coefficient, compared to 0.13 for the RF based method.
Neuronal protection by sirtuins in Alzheimer's disease (2005)

Silent information regulator 2, a member of NAD+-dependent histone deacetylase in yeast, and its homologs in mice and humans, participate in numerous important cell functions, including cell protection and cell cycle regulation. The sirtuin family members are highly conserved evolutionarily, and are predicted to have a role in cell survival. The science of sirtuins is an emerging field and is expected to contribute significantly to the role of sirtuins in healthy aging in humans. The role of sirtuins in neuronal protection has been studied in lower organisms, such as yeast, worms, flies and rodents. Both yeast Sir2 and mammalian sirtuin proteins are up-regulated under calorie-restricted and resveratrol treatments. Increased sirtuin expression protects cells from various insults. Caloric restriction and antioxidant treatments have shown useful effects in mouse models of aging and Alzheimer's disease (AD) and in limited human AD clinical trials. The role sirtuins may play in modifying and protecting neurons in patients with neurodegenerative diseases is still unknown. However, a recent report of Huntington's disease revealed that Sirtuin protects neurons in a Huntington's disease mouse model, suggesting that sirtuins may protect neurons in patients with neurodegenerative diseases, such as AD. In this review, we discuss the possible mechanisms of sirtuins involved in neuronal protection and the potential therapeutic value of sirtuins in healthy aging and AD.
Searching sequence space for ATP-binding proteins (2001)

A library of random protein sequences has yielded novel, ATP-binding proteins not found in any organism.
The cloned avirulence gene avrPto induces disease resistance in tomato cultivars containing the Pto resistance gene (1992)

Resistance of tomato plants to the bacterial pathogen Pseudomonas syringae pv. tomato race 0 is controlled by the locus Pto. A bacterial avirulence gene was cloned by constructing a cosmid library from an avirulent P. syringae pv. tomato race, conjugating the recombinants into a strain of P. syringae pv. maculicola virulent on a tomato cultivar containing Pto, and screening for those clones that converted the normally virulent phenotype to avirulence. The cloned gene, designated avrPto, reduced multiplication of P. syringae pv. tomato transconjugants specifically on Pto tomato lines, as demonstrated by bacterial growth curve analyses. Analysis of F2 populations revealed cosegregation of resistance to P. syringae pv. tomato transconjugants carrying avrPto with resistance to P. syringae pv. tomato race 0. Surprisingly, mutation of avrPto in P. syringae pv. tomato race 0 does not eliminate the avirulent phenotype of race 0, suggesting that additional, as yet uncharacterized, avirulence genes and/or resistance genes may contribute to specificity in the avrPto-Pto interaction. Genetic analysis indicates that this resistance gene(s) would be tightly linked to Pto. Interestingly, P. syringae pv. glycinea transconjugants carrying avrPto elicit a typical hypersensitive resistant response in the soybean cultivar Centennial, suggesting conservation of Pto function between two crop plants, tomato and soybean.
Theory of line-source radiation from a metal-strip grating dielectric-slab structure (2000)

This paper describes the fundamental theory of line source radiation from a source on a dielectric slab backed by a metal-strip grating. A continuous phased-array (CPA) method is applied to treat the analytic and numerical problems of antenna interaction with periodic structures. Both TE and TM mode cases for a one-dimensional strip grating are investigated. It is found that the strip grating on the dielectric surface may result in surface wave elimination and may also be used to support leaky waves. It is shown that high-efficiency and high-gain antennas on a dielectric substrate are possible with such metal-strip gratings.
Bioactive Coatings Based on a Polyelectrolyte Multilayer Architecture Functionalized by Embedded Proteins (2003)

Does a signal protein imbedded in a polyelectrolyte layer keep its activity? The study reported here demonstrates that cells can indeed interact with proteins incorporated in poly( L ‐lysine/glutamic acid) multilayer films. In contrast, poly( D ‐lysine) acts as a barrier to cell communication. For the case of monocytic cells the mechanism of contact with the active protein is elucidated. It is believed that such functionalized coatings could be useful tools for the modification of biomaterial surfaces with applications in, e.g., implants or tissue engineering.
Feature selection: evaluation, application, and small sample performance (1997)

A large number of algorithms have been proposed for feature subset selection. Our experimental results show that the sequential forward floating selection algorithm, proposed by Pudil et al. (1994), dominates the other algorithms tested. We study the problem of choosing an optimal feature set for land use classification based on SAR satellite images using four different texture models. Pooling features derived from different texture models, followed by a feature selection results in a substantial improvement in the classification accuracy. We also illustrate the dangers of using feature selection in small sample size situations.
Involvement of Cellular Double-Stranded DNA Break Binding Proteins in Processing of the Recombinant Adeno-Associated Virus Genome (2001)

Unlike postmitotic tissues in vivo, transduction of cultured cells is poor with recombinant adeno-associated virus (rAAV). The ability of rAAV to transduce cells is greatly enhanced by a variety of agents that induce DNA damage and is elevated in cells defective in the ataxia telangiectasia gene product (ATM), showing increased genomic instability. Here we show that DNA double-stranded break (DSB) repair pathways are involved in the regulation of rAAV transduction efficiency. By quantitative chromatin immunoprecipitation, we found that Ku86 and Rad52 proteins associate with viral DNA inside transduced cells. Both proteins are known to competitively recognize hairpin structures and DNA termini and to promote repair of DSBs, the former by facilitating nonhomologous end joining and the latter by initiating homologous recombination. We found that rAAV transduction is increased in Ku86-defective cells while it is inhibited in Rad52 knockout cells. These results suggest that binding of Rad52 to the rAAV genome might be involved in processing of the vector genome through a homologous recombination pathway.
Aqueous Colloidal Acene Nanoparticles: A New Platform for Studying Singlet Fission (2013)

Singlet fission is a process that occurs in select molecular systems wherein a singlet excited state divides its energy to form two triplet excitations on neighboring chromophores. While singlet fission has been largely studied in molecular crystals, colloidal nanoparticles offer the ability to investigate fission using liquid suspensions, allowing questions regarding the importance of molecular arrangement and charge transfer to be assessed. Herein, we report the synthesis of aqueous colloidal nanoparticles of 5,12-diphenyltetracene (DPT), a material recently demonstrated to undergo singlet fission in disordered films. Upon synthesis, nanoparticles display absorption features that lie between those of monomeric DPT and disordered DPT films. These features evolve over a few days in a manner that suggests an increase in the degree of association between neighboring molecules within the nanoparticles. Transient absorption and time-resolved emission experiments indicate that photoexcited DPT nanoparticles undergo fission, but produce a lower triplet yield than disordered films.
[Hydrogen sulfide: a novel cardiovascular functional regulatory gas factor]. (2004)

Hydrogen sulfide (H(2)S) may be endogenously produced by cystathionine beta-lyase (CBS) and cystathionine gamma-lyase (CSE) as a cardiovascular physiological functional factor. On the hypoxic pulmonary hypertension (HPH) animal model, the plasma H(2)S concentration, the gene expression and the activity (CSE) were decreased in lung tissues In L-NAME induced hypertension and spontaneous hypertension rats (SHR) models, the plasma H(2)S concentration, vascular CSE activity and mRNA expression were obviously decreased. When H(2)S was exogenously supplied, systolic pressure obviously decrease. These studies suggested that CSE/H(2)S pathway participated in the pathophysiological development of hypertension. The endogenous level of H(2)S produced by some arterial tissues increased in both septic and endotoxic shock rats. The level of H(2)S highly correlated with the endogenous level of NO. These results suggest that H(2)S may be a novel cardiovascular functional regulator.