gebhart/patrepeval huggingface dataset:
T-cell receptor peptides as immunotherapy for autoimmune disease. (1997)

The observations in both mouse and rat models of experimental allergic encephalomyelitis (EAE) demonstrating restricted T-cell receptor (TCR) usage among pathogenic T cells has led to the generation of a new class of therapeutic vaccines composed of TCR V region peptides. Whether a similar approach will be of use in the treatment of human autoimmune disorders is still unclear. The experiments performed in our laboratory over the past several years have focused on two aspects of TCR peptide immunoregulation, namely, (1) how to identify the critical T-cell populations involved in the pathology of autoimmune disease, and (2) how to identify biologically relevant TCR peptides--those endogenous TCR peptides presented in association with MHC molecules on the surface of pathogenic T cells that are recognized by immunoregulatory T-cell populations. Results of our recently completed clinical studies regarding TCR V beta expression among CD4+ T cells in the cerebral spinal fluid (CSF) of patients with multiple sclerosis suggests that these cells may be an appropriate T-cell population to be targeted for TCR peptide therapy. In addition, our studies on the immune response to autologous, soluble TCR heterodimers may provide a strategy for the identification of new TCR peptide candidate vaccines.
Sulphated proteoglycan is required for collecting duct growth and branching but not nephron formation during kidney development (1995)

Kidney epithelia have separate origins; collecting ducts develop by ureteric bud growth and arborisation, nephrons by induced mesenchyme-epithelium transition. Both express sulphated glycosaminoglycans (GAGs) which are strikingly upregulated during nephron differentiation. However, sodium chlorate, an inhibitor of GAG sulphation, and the GAG-degrading enzymes heparitinase plus chondroitinase, did not prevent nephron development. In contrast, ureteric bud growth and branching were reversibly inhibited by the above reagents, the inhibition correlating quantitatively with sulphated GAG deprivation caused by a range of chlorate concentrations. Growth and branching could be independently restored during GAG deprivation by hepatocyte growth factor and phorbol-12-myristate acetate (PMA) respectively. Together these signalling effectors stimulated both branch initiation and growth. Thus growth and morphogenesis of ureteric bud involve distinct signalling pathways both regulated by GAGs.
International Approaches for Nuclear Waste Disposal in Geological Formations: Geological Challenges in Radioactive Waste Isolation—Fifth Worldwide Review (2017)

The overall objective of the Fifth Worldwide Review (WWR-5) is to document the current state-of-the-art of major developments in a number of nations throughout the World pursuing geological disposal programs, and to summarize challenging problems and experience that have been obtained in siting, preparing and reviewing cases for the operational and long-term safety of proposed and operating nuclear waste repositories. The scope of the Review is to address current specific technical issues and challenges in safety case development along with the interplay of technical feasibility, siting, engineering design issues, and operational and post-closure safety. In particular, the chapters included in the report present the following types of information: the current status of the deep geological repository programs for high level nuclear waste and low- and intermediate level nuclear waste in each country, concepts of siting and radioactive waste and spent nuclear fuel management in different countries (with the emphasis of nuclear waste disposal under different climatic conditions and different geological formations), progress in repository site selection and site characterization, technology development, buffer/backfill materials studies and testing, support activities, programs, and projects, international cooperation, and future plans, as well as regulatory issues and transboundary problems.
A QoS Architecture for IDMA-Based Multi-Service Wireless Networks (2007)

The recent investigations on interleave-division multiple-access (IDMA) have demonstrated its advantage in supporting high-data-rate and multi-rate services over wireless fading channels. This paper focuses on quality of service (QoS) guarantee in IDMA-based multi-service wireless networks. We propose a QoS architecture which addresses the key issues of QoS guarantee for multi-service in IDMA, including medium access control (MAC), admission control, power control, and rate allocation. The proposed IDMA QoS architecture avoids complex packet scheduling at the MAC layer which is however required in other existing multiple access systems. Data packets can be transmitted in IDMA without scheduling delay. Additionally, to improve the efficiency of random access, an interleave- division slotted-ALOHA (IDSA) access method is proposed for the IDMA MAC protocol. We derive the relationship between the arrival rate of access requests and the number of access interleavers allocated to an IDMA system for a given access success probability. Based on this relationship, we can adaptively adjust the number of access interleavers according to the traffic load of access requests, so as to ensure a satisfactory probability of successful access as well as low complexity of request detection at the receiver.
Iron in East Antarctic snow: Implications for atmospheric iron deposition and algal production in Antarctic waters (2001)

To evaluate the deposition and solubility of aerosol iron in the Antarctic seasonal sea ice zone (SSIZ), iron was measured in snow samples collected from three areas in the SSIZ (Prydz Bay, Dumont d'Urville Sea and Ross Sea) and one continental area (Princess Elizabeth Land) of East Antarctica. Concentrations of total‐dissolvable iron (that soluble at pH ∼2) ranged from 20–2950 pg g −1 , with the lowest concentrations measured in snow from the Dumont d'Urville Sea. Using estimates of snow accumulation rates, we calculate atmospheric iron deposition fluxes of 0.017–0.11 mg m −2 yr −1 (0.30–2.0 µmol m −2 yr −1 ), which are generally lower than previously published estimates. Measurements of iron in filtered meltwaters of snow samples from Prydz Bay and Princess Elizabeth Land suggest that ∼10–90% of the total atmospheric iron is readily soluble. Assuming our results to be broadly representative of atmospheric deposition over seasonally ice‐covered, high‐nutrient Antarctic waters, we use our mean estimates of atmospheric iron deposition (1.1 µmol m −2 yr −1 ) and solubility (32%) to calculate that atmospheric iron potentially supports annual phytoplankton production of 1.1 × 10 12 mole C in the Antarctic SSIZ, which is less than 5% of the estimated total annual primary production in this ocean region.
Intraarticular expression of biologically active interleukin 1-receptor-antagonist protein by ex vivo gene transfer. (1993)

Gene therapy offers a radical different approach to the treatment of arthritis. Here we have demonstrated that two marker genes (lacZ and neo) and cDNA coding for a potentially therapeutic protein (human interleukin 1-receptor-antagonist protein; IRAP or IL-1ra) can be delivered, by ex vivo techniques, to the synovial lining of joints; intraarticular expression of IRAP inhibited intraarticular responses to interleukin 1. To achieve this, lapine synoviocytes were first transduced in culture by retroviral infection. The genetically modified synovial cells were then transplanted by intraarticular injection into the knee joints of rabbits, where they efficiently colonized the synovium. Assay of joint lavages confirmed the in vivo expression of biologically active human IRAP. With allografted cells, IRAP expression was lost by 12 days after transfer. In contrast, autografted synoviocytes continued to express IRAP for approximately 5 weeks. Knee joints expressing human IRAP were protected from the leukocytosis that otherwise follows the intraarticular injection of recombinant human interleukin 1 beta. Thus, we report the intraarticular expression and activity of a potentially therapeutic protein by gene-transfer technology; these experiments demonstrate the feasibility of treating arthritis and other joint disorders with gene therapy.
Rumen bacterial communities can be acclimated faster to high concentrate diets than currently implemented feedlot programs (2016)

These findings may have implications for beef producers to reduce feedlot costs, as less time adapting animals would result in lower feed costs. However, animal feeding behavior patterns and other factors must be considered.
Photonic Crystals That Can Be Addressed with an External Magnetic Field (2001)

Photonic crystals whose properties can be manipulated with an external magnetic field have been made by self-assembly of magnetic nanoparticles around larger polystyrene spheres into opaline, long-range-ordered lattices (see Figure for details of a sample after calcination). Optical properties of such crystals (e.g., wavelength of diffracted light) can be tuned by magnetically rotating the crystals relative to the incident light (see also images on the front cover).
Accumulation of Glucosylceramide and Glucosylsphingosine (Psychosine) in Cerebrum and Cerebellum in Infantile and Juvenile Gaucher Disease (1982)

Three major clinical variants of Gaucher disease have been defined: Type I, chronic nonneuronopathic; Type II, acute neuronopathic; and Type III, subacute neuronopathic. In a search for the underlying molecular basis of the neurological manifestations, the concentration and composition of cholesterol, phospholipids, neutral glycosphingolipids, and gangliosides were examined in cerebral and cerebellar cortices of five cases of Type II, eight cases of Type III, and one case of presumed Type I/III. In Type II the concentration of glucosylceramide was 140-530 mumol/kg in cerebral cortex and 51-450 mumol/kg in cerebellar cortex, the highest values found in the most fulminant cases. These concentrations were 20-80 times greater than normal in cerebral cortex and 5-40 times normal in cerebellar cortex. In type III the concentration of glucosylceramide was 37-65 and 59-1750 mumol/kg in cerebral and cerebellar cortex, respectively. The highest concentrations were found in the cerebellum of patients who had survived splenectomy for several years. The ceramide composition of the accumulated glucosylceramide suggested that brain gangliosides were the major precursors of the glucosylceramide in brains of Type II but in cerebellar cortex in Type III was partly of extracerebral origin. The levels of lactosylceramide and oligohexaosylceramides were slightly raised in all brain specimens from the Gaucher cases. The ganglioside concentration was normal, whereas there was a certain increase in the proportion of GM2 and GM3 gangliosides. The brain glycosphingolipid changes in the Type I/III case were similar but slightly less than those in Type III cases of corresponding age. Glucosylsphingosine (psychosine), never detected in normal human brain, was demonstrated in brains from all the Gaucher cases. The psychosine concentration was highest in Type II cases, 3.8-8.8 and 3.9-12.3 mumol/kg in cerebral and cerebellar cortex, respectively, with the highest values found in the most fulminant cases. In type III the psychosine concentration varied more widely, 0.8-4.6 and 1.4-6.3 mumol/kg in cerebral and cerebellar cortex, respectively. The lowest value, 0.7 mumol/kg, was found in the Type I/III case. Our method detected psychosine down to 0.01 mumol/kg, which means that the concentration of psychosine was increased at least 100- to 1000-fold in Gaucher grey matter. We suggest that the accumulation of the cell-toxic substance psychosine is the basis for the extensive neuronal cell loss in Gaucher disease, which is most striking in Type II disease.
β-adrenergic receptor blockade as a therapeutic approach for suppressing the renin-angiotensin-aldosterone system in normotensive and hypertensive subjects (1999)

Although beta-adrenergic-blocking drugs suppress the renin system (RAAS), plasma angiotensin II (Ang II) responses during beta-blockade have not been defined. This study quantifies the effects of beta-blockade on the RAAS and examines its impact on prorenin processing by measuring changes in the ratio of plasma renin activity (PRA) to total renin. In normotensive (N = 14) and hypertensive (N = 16) subjects, blood pressure (BP), heart rate, PRA, plasma prorenin, plasma total renin (prorenin + PRA), ratio of PRA to total renin (%PRA), plasma Ang II, and urinary aldosterone were measured before and after 1 week of beta-blockade. Plasma renin activity, Ang II, and urinary aldosterone levels were similar for normotensive and hypertensive subjects. Plasma renin activity correlated with Ang II. Total renin, which is proportional to (pro)renin gene expression, was lower in hypertensive subjects and was inversely related to BP. Beta-blockade decreased BP and heart rate in both groups, with medium- and high-renin hypertensive subjects responding more frequently than those with low renin. Beta-blockade consistently suppressed PRA, Ang II, and aldosterone. Total renin was unchanged, thus, %PRA fell. These results indicate that beta-blockers suppress plasma angiotensin II levels, in parallel with the marked reductions in PRA and urinary aldosterone levels in normotensive and hypertensive subjects. The suppression of Ang II levels was comparable to that produced during angiotensin converting enzyme (ACE) inhibition. However, by reducing prorenin processing to renin, beta-blockers do not stimulate renin secretion, unlike ACE inhibitors and Ang II receptor antagonists. This unique action of beta-blockers has important implications for the treatment of cardiovascular disease.
CpG island hypermethylation in human colorectal tumors is not associated with DNA methyltransferase overexpression. (1999)

The molecular basis of aberrant hypermethylation of CpG islands observed in a subset of human colorectal tumors is unknown. One potential mechanism is the up-regulation of DNA (cytosine-5)-methyltransferases. Recently, two new mammalian DNA methyltransferase genes have been identified, which are referred to as DNMT3A and DNMT3B. The encoded proteins differ from the predominant mammalian DNA methyltransferase DNMT1 in that they have a substantially higher ratio of de novo to maintenance methyltransferase activity. We have used a highly quantitative 5' nuclease fluorogenic reverse transcription-PCR method (TaqMan) to analyze the expression of all three DNA methyltransferase genes in 25 individual colorectal adenocarcinoma specimens and matched normal mucosa samples. In addition, we examined the methylation patterns of four CpG islands [APC, ESR1 (estrogen receptor), CDKN2A (p16), and MLH1] to determine whether individual tumors show a positive correlation between the level of DNA methyltransferase expression and the frequency of CpG island hypermethylation. All three methyltransferases appear to be up-regulated in tumors when RNA levels are normalized using either ACTB (beta-actin) or POLR2A (RNA pol II large subunit), but not when RNA levels are normalized with proliferation-associated genes, such as H4F2 (histone H4) or PCNA. The frequency or extent of CpG island hypermethylation in individual tumors did not correlate with the expression of any of the three DNA methyltransferases. Our results suggest that deregulation of DNA methyltransferase gene expression does not play a role in establishing tumor-specific abnormal DNA methylation patterns in human colorectal cancer.
A one-step cloning method for the construction of somatic cell gene targeting vectors: application to production of human knockout cell lines (2012)

Our method is a fast, simple, and efficient technique for cloning, and has great potential for high-throughput construction of KO vectors.
The Palladium-Catalyzed Cross-Coupling Reaction of Phenylboronic Acid with Haloarenes in the Presence of Bases (1981)

Abstract The transition metal-catalyzed reactions of organometallics with organic halides have been extensively studied to prove a new approach to selective formation of carbon-carbon bonds. Recently, such coupling reactions of haloarenes with aryl magnesium1–3 and zinc4 compounds in the presence of palladium or nickel complexes have been reported for the synthesis of biaryls. Davidson and Triggs5 have previously reported that arylboronic acids react with sodium palladate to give the corresponding biaryls in good yields. The synthetic utility of the dimerization reaction is, however, limited because it requires stoichiometric amounts of the palladium compound. On the other hand, we have recently reported that cross-coupling reactions between alkenylboranes and organic halides such as alkenyl,6 alkynyl,6 aryl,7 allyl,8 and benzyl8 halides are effectively catalyzed by a catalytic amount of tetrakis(triphenylphosphine)palladium, Pd(PPh3)4 in the presence of suitable bases as indicated in Scheme 1. Although the detailed mechanistic pathway is not clear at present, the reaction should involve a transmetallation step from alkenylboranes to alkenylpalladiums.
Advance Database Aggregation Query Processing. (2002)

The aggregation query is an important but costly operation in database management systems. In the worst case, to compute an aggregate, all tuples in a database needs to be examined. However, in many applications (on-line analysis, etc.), we need to compute the aggregates very fast. In the Ph.D. research, we focus on devising specialized indices for the box-aggregation query and its relatives. Our research shows that the newly designed structures have much better query performance than the existing solutions, sometimes over a hundred times faster. In this paper, we summarize our findings.
Calculating input impedance of electrically small insulated antennas for microwave hyperthermia (1993)

Two analytical methods for approximating the input impedance of insulated monopole or dipole antennas embedded within an electrically dense medium, which have been reported in the literature, are considered. The methods differ by the degree of approximation applied in solving the integral equation for the current in the insulated conductor. These methods directly affect the calculation of the wavenumber and the characteristic impedance of an antenna treated as a lossy coaxial line. In the more complex approach the resulting formulas contain an additional term which improves the correlation with measured and numerically modeled results for electrically longer antennas. When applied to electrically small antennas (i.e. <1/8 wavelength in the medium), this term introduces a significant error into the calculation of the real part of the complex input impedance. Special care must be taken if these formulas are used to design multisectional antennas in order to avoid impedance mismatch. Methods for correcting this error are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
On-Chip Inductors with Self-Rolled-Up SiNxNanomembrane Tubes: A Novel Design Platform for Extreme Miniaturization (2012)

Inductors are essential components of radio frequency integrated circuits (RFICs). While the active devices in RF systems downscale steadily, inductors have not been able to keep up with the pace of continual miniaturization because of the trade-off between size and performance as well as fabrication complexity. Strain-induced self-rolled-up nanotechnology allows the formation of three-dimensional (3D) architectures, such as multiple-turn spiral tubes, through planar processing. Here, we report on using 3D SiN(x) tubular structures with accompanying prepatterned metal layers, as a novel on-chip tube inductor design platform. We found, by an equivalent lumped circuit and electromagnetic modeling, that the 3D metal spiral structure has the ability to significantly better confine magnetic field compared to conventional planar spiral on-chip inductors. More than 100× reduction in footprint can be realized using this platform while achieving excellent electrical performance, including large inductance, high quality (Q) factor, and high self-resonance frequency (f(0)).
Expression of the RNA genome of an animal virus in Saccharomyces cerevisiae. (1986)

The nucleocapsid of vesicular stomatitis virus (VSV) was introduced into the cytoplasm of Saccharomyces cerevisiae by low pH-dependent fusion of the viral envelope with the spheroplast plasma membrane. This led to de novo synthesis of the three major structural proteins of the virus--the G, N, and M proteins--as shown by immunoprecipitation of [35S]methionine-labeled spheroplast lysates. In NaDodSO4/polyacrylamide gel electrophoresis, M and N proteins comigrated with those of the virion, whereas the yeast-made G protein migrated as two bands with apparent molecular sizes of 60 and 70 kDa. Both polypeptides appeared to be N-glycosylated, since only one polypeptide with the apparent molecular mass of approximately equal to 55 kDa was produced in the presence of tunicamycin. Phase separation into Triton X-114 suggested that the unglycosylated G protein was membrane bound. According to immunofluorescent surface staining of live spheroplasts, at least part of the G protein was transported to the plasma membrane. Spheroplasts expressing the VSV genes could be fused together by low pH to form polykaryons, indicating that G protein synthetized by yeast was fusogenic--i.e., biologically active.
Use of Levetiracetam in Special Populations (2001)

A subset of the 27 safety and pharmacokinetic studies of levetiracetam has been conducted in selected special populations: children, the elderly, and people with renal or hepatic impairment. The results of these studies indicate that higher doses need to be used for children (on a per-weight basis), and individuals with renal dysfunction require dosage modifications related to creatinine clearance. Individuals with hepatic impairment do not require modifications from standard doses. Little information is available on the effect of levetiracetam on the developing fetus, so cautious use during pregnancy is recommended until more information is available. Additional studies will refine the recommendations for use of levetiracetam in these special populations.
Active semi-supervised fuzzy clustering for image database categorization (2005)

We consider data clustering problems where a limited amount of high-level semantic information, in the form of pairwise must-link and cannot-link constraints, can be acquired from the user. This form of supervision will guide the categorization of image databases in order to provide overviews that fit better user expectations. We propose here an effective semi-supervised clustering algorithm, Active Fuzzy Constrained Clustering (AFCC), that minimizes a competitive agglomeration-based cost function with fuzzy terms corresponding to pairwise constraints provided by the user. In order to minimize the amount of constraints required, we define an active mechanism for the selection of candidates for constraints. The comparisons performed on a simple benchmark and on a ground truth image database show that with AFCC the results of clustering can be significantly improved with few constraints, making this semi-supervised approach an attractive alternative in the categorization of image databases.