gebhart/patrepeval huggingface dataset:
Correction: Effective Detection of Human Leukocyte Antigen Risk Alleles in Celiac Disease Using Tag Single Nucleotide Polymorphisms (2009)

The HLA genes, located in the MHC region on chromosome 6p21.3, play an important role in many autoimmune disorders, such as celiac disease (CD), type 1 diabetes (T1D), rheumatoid arthritis, multiple sclerosis, psoriasis and others. Known HLA variants that confer risk to CD, for example, include DQA1*05/DQB1*02 (DQ2.5) and DQA1*03/ DQB1*0302 (DQ8). To diagnose the majority of CD patients and to study disease susceptibility and progression, typing these strongly associated HLA risk factors is of utmost importance. However, current genotyping methods for HLA risk factors involve many reactions, and are complicated and expensive. We sought a simple experimental approach using tagging SNPs that predict the CD-associated HLA risk factors.
A carbonic anhydrase from the archaeon Methanosarcina thermophila. (1994)

Carbonic anhydrase (CA) from acetate-grown Methanosarcina thermophila was purified > 10,000-fold (22% recovery) to apparent homogeneity with a specific activity of 4872 units/mg. The estimated native molecular mass of the enzyme is 84 kDa based on gel filtration chromatography. SDS/PAGE revealed one protein band with an apparent molecular mass of 40 kDa. The M. thermophila CA is less sensitive than human CA isozyme II toward inhibition by sulfonamides and monovalent ions. The gene encoding this CA was cloned into pUC18 and sequenced. Escherichia coli harboring the recombinant plasmid expresses CA activity (2.3 units/mg of cell extract protein). Comparison of the deduced amino acid sequence with the N-terminal sequence of the purified protein shows that the gene encodes an additional 34 N-terminal residues with properties characteristic of signal peptides in secretory proteins. The calculated molecular mass (22.9 kDa) and pI (4.0) suggest that SDS/PAGE overestimates the subunit size and that the native enzyme is a tetramer. To our knowledge, the deduced amino acid sequence has no significant identity to any known CA but has 35% sequence identity to the first 197 deduced N-terminal amino acids of a proposed CO2-concentrating-mechanism protein from Synechococcus PCC7942 and 28% sequence identity to the deduced sequence of ferripyochelin binding protein from Pseudomonas aeruginosa. Thus, our results indicate that this archaeal CA represents a distinct class of CAs and provide a basis to determine physiological roles for CA in acetotrophic anaerobes.
Hyaluronan Binding Properties of a CD44 Chimera Containing the Link Module of TSG-6 (2002)

CD44, a cell-surface receptor for the extracellular matrix glycosaminoglycan hyaluronan, can mediate leukocyte rolling on hyaluronan substrates and has been implicated in leukocyte migration to sites of inflammation. CD44-mediated binding to hyaluronan is of low affinity, and effective cell/matrix interaction depends on multiple interactions with the multivalent ligand. We replaced the Link module of CD44 with the homologous region of TSG-6, a hyaluronan-binding protein secreted in response to inflammation whose Link module has a higher affinity for ligand. Monoclonal antibodies raised against the CD44/TSG-6 chimera recognized recombinant human TSG-6 and native mouse TSG-6 and blocked hyaluronan binding to these proteins. Cells expressing the CD44/TSG-6 molecule bound hyaluronan with higher avidity than cells expressing CD44. This resulted in changes in the hyaluronan binding properties characteristic of cells expressing CD44 such as requirements for threshold levels of receptor expression and for hyaluronan of high molecular mass. In parallel plate flow assays used to model leukocyte rolling, cells expressing CD44/TSG-6 failed to roll on hyaluronan. Instead, they stuck and remained "tethered" to the substrate under fluid flow. This result argues that the low affinity of CD44 for its ligand is important for rolling, an early phase of leukocyte extravasation from the blood.
Ionic selectivity of Ih channels of rod photoreceptors in tiger salamanders. (1992)

Ionic selectivity of Ih channels of tiger salamander rod photoreceptors was investigated using whole-cell voltage clamp. Measured reversal potentials and the Goldman-Hodgkin-Katz voltage equation were used to calculate permeability ratios with 20 mM K+ as a reference. In the absence of external K+, Ih is small and hard to discern. Hence, we defined Ih as the current blocked by 2 mM external Cs+. Some small amines permeate Ih channels, with the following permeability ratios (PX/PK):NH4+, 0.17; methylammonium, 0.06; and hydrazine, 0.04. Other amines are tially impermeant: dimethylammonium (< 0.02), ethylammonium (< 0.01), and tetramethylammonium (< 0.01). When K+ is the only external permeant ion and its concentration is varied, the reversal potential of Ih follows the Nernst potential for a K+ electrode. Ih channels are also permeable to other alkali metal cations (PX/PK): T1+, > 1.55; K+, 1; Rb+, > 0.55; Na+, 0.33; Li+, 0.02. Except for Na+, the relative slope conductance had a similar sequence (GX/GK): T1+, 1.07; K+, 1; Rb+, 0.37; NH4+, 0.07; Na+, 0.02. Based on permeabilities to organic cations, the narrowest part of the pore has a diameter between 4.0 and 4.6 A. Some permeant cations have large effects on the gating kinetics of Ih channels; however, permeant cations appear to have little effect on the steady-state activation curve of Ih channels. Lowering K+ or replacing K+ with Na+ reduces the maximal conductance of Ih but does not shift or change the steepness of its voltage dependence. With ammonium or methylammonium replacing K+ a similar pattern is seen, except that there is a small positive shift of approximately 10 mV in the voltage dependence.
Androgen-dependent and -independent human prostate xenograft tumors as models for drug activity evaluation. (1998)

The present study evaluated three human prostate xenograft tumors (CWR22, CWR22R, and CWR91) as models for drug activity evaluation. The chemosensitivity and the expression of several proteins (i.e., p-glycoprotein or Pgp, prostate specific antigen or PSA, p53, and Bcl-2) in xenograft tumors were compared with those in patient tumors obtained through radical prostatectomy (n = 26). CWR22 is androgen-dependent, CWR22R is the androgen-independent subline of CWR22, and CWR91 is a separately derived androgen-independent tumor. The results of immunohistochemical and/or Western blot analysis indicate that the expression of PSA, Pgp, p53, and Bcl-2 in the three CWR xenograft tumors are representative of their expression in 100, 85, 90, and 60%, respectively, of patient tumors. The responses of histocultures of xenograft tumors to doxorubicin and paclitaxel, including inhibition of DNA precursor incorporation and cell death induction, were qualitatively similar to the responses of patient tumors. For example, in all three xenograft and patient tumors, doxorubicin produced complete antiproliferation and cytotoxicity (ie., cell kill) whereas paclitaxel produced incomplete effects. A comparison of the concentration-effect relationships in xenograft and patient tumors (population median values) indicates that the chemosensitivity observed in patient tumors is represented by the chemosensitivity of one or more of the three xenograft tumors, as follows: (a) the three xenograft tumors and patient tumors responded equally to doxorubicin-induced antiproliferation; (b) CWR22R, CWR91 and patient tumors responded equally to doxorubicin-induced cytotoxicity, whereas CWR22 was 2-3-fold less sensitive; (c) CWR22 and CWR22R tumors were less sensitive to paclitaxel-induced antiproliferation compared with patient tumors, whereas CWR91 was several-fold more sensitive; and (d) CWR22, CWR22R and patient tumors responded equally to paclitaxel-induced cytotoxicity, whereas CWR91 was 2-3-fold more sensitive. The results of this study indicate that the three xenograft tumors, which show chemosensitivity comparable with the results of > or =50% patient tumors and encompass the majority of the heterogeneous patient prostate tumors in the expression of Pgp, PSA, p53 and Bcl-2 proteins, are useful models for drug activity evaluation.
D3 Phosphoinositides and Outside-in integrin Signaling by Glycoprotein IIb-IIIa Mediate Platelet Actin Assembly and Filopodial Extension Induced by Phorbol 12-Myristate 13-Acetate (1996)

Phorbol 12-myristate 13-acetate (PMA) uncaps a small number of the fast-growing (barbed) ends of actin filaments, thereby eliciting slow actin assembly and extension of filopodia in human blood platelets. These reactions, which also occur in response to immunologic perturbation of the integrin glycoprotein (GP) IIb-IIIa, are sensitive to the phosphoinositide 3-kinase inhibitor wortmannin. Platelets deficient in GPIIb-IIIa integrins or with GPIIb-IIIa function inhibited by calcium chelation or the peptide RGDS have diminished PMA responsiveness. The effects of PMA contrast with thrombin receptor stimulation by >/=5 microM thrombin receptor-activating peptide (TRAP), which causes rapid and massive wortmannin-insensitive actin assembly and lamellar and filopodial extension. However, we show here that wortmannin can inhibit filopod formation if the thrombin receptor is ligated using suboptimal doses (<1 microM) of TRAP. Phosphatidylinositol 3,4-bisphosphate inhibits actin filament severing and capping by human gelsolin in vitro. The findings implicate D3 polyphosphoinositides and integrin signaling in PMA-mediated platelet stimulation and implicate D3 containing phosphoinositides generated in response to protein kinase C activation and GPIIb-IIIa signaling as late-acting intermediates leading to filopodial actin assembly.
A scaled floating body cell (FBC) memory with high-k+metal gate on thin-silicon and thin-BOX for 16-nm technology node and beyond (2008)

A scaled, undoped, thin-BOX, planar FBC technology is demonstrated for the first time, featuring 10-nm BOX, 25-nm SOI, high-k, metal gate, separate back-gate (BG) doping, and raised source-drain epitaxy. Retention of a minimum 3-muA sensing window for 100 ms, in devices with 60-nm gate-length (L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> ) and 70-nm diffusion width (W), represents the best retention time of all sub-100-nm FBC devices. FBC scaling is predicted to be feasible at least to 40-nm L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> , enabling memory cell sizes much smaller than 6T-SRAM at 16-nm technology node. Functional 32-nm L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> devices suggest the feasibility at the 11-nm technology node.
Genetic findings in congenital bilateral aplasia of vas deferens patients and identification of six novel mutations (1998)

Congenital bilateral aplasia of vas deferens (CBAVD), a form of male sterility, has been suggested to represent a "genital" form of cystic fibrosis (CF), as mutations in the CFTR gene have been identified in most patients with this condition. Interestingly, the 5T allele in intron 8 appeared to be the most frequent mutation associated with CBAVD. However, the molecular basis of CBAVD is not completely understood. We have analysed the complete coding and flanking CFTR sequences by PCR-DGGE in 64 men with CBAVD from southern France with the aim to list any sequence alteration. Fourty-two of the 64 patients (65.6%) had mutations on both copies of the CFTR gene, including one patient with two mutations in the same copy (DF508 + A1067T). The 5T allele was present in 21/64 cases (33%). Six of the 28 different mutations identified in this study had never been described previously, and appeared to be specific to CBAVD (P111L, M244K, A1364V, G544V, 2896insAG, -33G→A). Hum Mutat 11:480, 1998. © 1998 Wiley-Liss, Inc.
The Effect of Trunk-Flexed Postures on Balance and Metabolic Energy Expenditure During Standing (2007)

Compensatory actions, such as ankle plantarflexion and hip flexion, allowed the mean position of the net COP to remain within a narrowly defined region irrespective of trunk posture. Changes in muscle activity associated with a trunk-flexed posture and the associated compensations likely contributed to the increased energy expenditure.
Potentiation of Gene Transfer to the Mouse Lung by Complexes of Adenovirus Vector and Polycations Improves Therapeutic Potential (1998)

Recombinant adenovirus (Ad) vectors are being considered for in vivo delivery of various therapeutic genes. One limiting factor in the development of Ad-based gene therapy is the low efficiency of gene transfer to target tissues such as vascular endothelium, smooth muscle, and airway epithelium. Complexing Ad vector with various polycations has been shown to enhance transduction of cell lines otherwise resistant to Ad infection in vitro. On the basis of this observation, the activity of Ad/polycation complexes was tested in vivo in the mouse lung. The results indicated that several polycations were capable of enhancing transduction of mouse respiratory epithelium, leading to a 1-2 log increase in levels of transgene expression. Poly-L-lysine (PLL) and DEAE-dextran were examined further and were found to increase Ad-mediated gene transfer without any additional toxicity as assessed histologically or through the measurement of inflammatory cytokines in bronchoalveolar lavages. The two polycations also failed to affect the humoral response against Ad vector and were themselves nonimmunogenic under conditions leading to enhanced gene transfer. Moreover, the ability to use reduced doses of vector complexed with polycations resulted in lower levels of Ad-specific antibodies and, thereby, improved readministration of vector. These results suggest that complexing Ad vectors with polycations has the potential to improve the therapeutic index by increasing transgene expression while reducing unwanted responses associated with high doses of vector.
Interface formation and thermal stability of advanced metal gate and ultrathin gate dielectric layers (1998)

The compatibility of metallic titanium nitride (TiNx) films for advanced gate electrodes and remote plasma enhanced chemical vapor deposited silicon oxide (SiO2) or silicon oxide/silicon nitride (Si3N4) advanced gate dielectric layers is investigated by interrupted growth and on-line rapid thermal annealing using on-line Auger electron spectroscopy. Growth of TiNx on SiO2 and Si3N4 occurs uniformly without a titanium seed layer. TiNx/SiO2 and TiNx/Si3N4 interfaces are chemically stable against reaction for rapid thermal annealing treatments below 850 °C. Metal–oxide–semiconductor capacitors using TiNx gate contacts and SiO2 or SiO2/Si3N4 gate dielectrics exhibit excellent C–V characteristics. The measured TiNx/SiO2 barrier height in these devices is Φb=3.7±0.1 eV. The observed difference in fixed charge for SiO2 and SiO2/Si3N4 dielectrics is briefly discussed in terms of a new interface dipole model.
Interleukin 2 activation of cytotoxic T-lymphocytes infiltrating into human metastatic melanomas. (1986)

Tumor infiltrating lymphocytes (TIL) were isolated from 22 tumors obtained from 15 patients with metastatic melanoma. In 18 of the 22 tumors, a substantial number of lymphocytes was isolated with an average lymphoid cell:tumor cell ratio of 1.26. The TIL were predominantly cytotoxic/suppressor T-lymphocytes with an average of 87% Leu4+, 61% Leu2a+, and 18% Leu3a+ cells. There were less than 2% natural killer cells, B-cells, or macrophages. An average of 3.8% (range, less than 0.1 to 8.6%) of freshly isolated TIL bound to autologous tumor cells. Prior to culture, none of the tumor-binding cells (TBC) was cytotoxic as judged by trypan blue exclusion. The frequency of TBC increased to 11.6% after 2 days of culture, and 10% of these TBC developed cytotoxic activity. When interleukin 2 was added to cultures, the frequency of TBC increased, and the frequency of cytotoxic TBC was 2-fold higher compared to control cultures. After 10 days of culture with interleukin 2, TIL increased in number with a concomitant disappearance of tumor cells, whereas there were severe decreases of lymphocytes and no decrease of tumor cells in control cultures. TIL were cultured for 8 to 10 days with recombinant interleukin 2 and tested for cytotoxicity against autologous and allogenic tumor cells and K562 targets in a 4-h 51Cr release assay. rIL2-cultured TIL from all nine patients tested exhibited the highest levels of lysis against autologous tumor cells. Of the nine TIL samples, five exhibited an apparent specificity for autologous melanoma, while four specimens killed both allogenic and autologous melanoma. The ability of TIL to kill K562 targets appeared to parallel the ability to kill allogenic targets. For comparison, recombinant interleukin 2-cultured peripheral blood mononuclear cells from the same patients were assayed for cytotoxic activity against autologous and allogenic melanomas. Unlike some TIL, none of the peripheral blood mononuclear cells exhibited specificity for autologous tumor cells. In summary, TIL isolated from metastatic melanoma patients were predominantly cytotoxic T-lymphocytes with the ability to recognize and kill autologous tumor cells after in vitro culture; interleukin 2 induced proliferation of TIL and augmented their cytotoxic activity such that they eliminated autologous tumor cells.
Serum tumor markers for detection of hepatocellular carcinoma (2006)

Hepatocellular carcinoma (HCC) is one of the most frequent malignant tumors and is the second most common cause of cancer death in China. Therefore, it is very important to detect this disease and the recurrence at its earlier period. Serum tumor markers, as the effective method for detecting hepatocellular carcinoma for a long time, could be divided into 4 categories: oncofetal antigens and glycoprotein antigens; enzymes and isoenzymes; genes; and cytokines. Serum alpha fetoprotein (AFP) is the most widely used tumor marker in detecting patients with hepatocellular carcinoma, and has been proven to have capability of prefiguring the prognosis. However, it has been indicated that AFP-L3 and DCP excel AFP in differentiating hepatocellular carcinoma from nonmalignant hepatopathy and detecting small hepatocellular carcinoma. Some tumor markers, such as human cervical cancer oncogene and human telomerase reverse transcriptase mRNA, have also been indicated to have higher accuracies than AFP. Furthermore, some other tumor markers, such as glypican-3, gamma-glutamyl transferase II, alpha-l-fucosidase, transforming growth factor-beta1, tumor-specific growth factor, have been indicated to be available supplementaries to AFP in the detection. AFP mRNA has been shown to correlate with the metastasis and recurrence of HCC, and it may be the most useful marker to prefigure the prognosis. Some other markers, such as gamma-glutamyl transferase mRNA, vascular endothelial growth factor, and interleukin-8, could also be used as available prognostic indicators, and the simultaneous determination of AFP and these markers may detect the recurrence of HCC at its earlier period.
Induction of T-cell development from human cord blood hematopoietic stem cells by Delta-like 1 in vitro (2004)

The Notch signaling pathway plays a key role at several stages of T-lymphocyte differentiation. However, it remained unclear whether signals induced by the Notch ligand Delta-like 1 could support full T-cell differentiation from a defined source of human hematopoietic stem cells (HSCs) in vitro. Here, we show that human cord blood-derived HSCs cultured on Delta-like 1-expressing OP9 stromal cells undergo efficient T-cell lineage commitment and sustained T-cell differentiation. A normal stage-specific program of T-cell development was observed, including the generation of CD4 and CD8 alpha beta-T-cell receptor (TCR)-bearing cells. Induction of T-cell differentiation was dependent on the expression of Delta-like 1 by the OP9 cells. Stimulation of the in vitro-differentiated T cells by TCR engagement induced the expression of T-cell activation markers and costimulatory receptors. These results establish an efficient in vitro coculture system for the generation of T cells from human HSCs, providing a new avenue for the study of early T-cell differentiation and function.
The LPS receptor (CD14) links innate immunity with Alzheimer's disease (2003)

To rapidly respond to invading microorganisms, humans call on their innate immune system. This occurs by microbe-detecting receptors, such as CD14, that activate immune cells to eliminate the pathogens. Here, we link the lipopolysaccharide receptor CD14 with Alzheimer's disease, a severe neurodegenerative disease resulting in dementia. We demonstrate that this key innate immunity receptor interacts with fibrils of Alzheimer amyloid peptide. Neutralization with antibodies against CD14 and genetic deficiency for this receptor significantly reduced amyloid peptide induced microglial activation and microglial toxicity. The observation of strongly enhanced microglial expression of the LPS receptor in brains of animal models of Alzheimer's disease indicates a clinical relevance of these findings. These data suggest that CD14 may significantly contribute to the overall neuroinflammatory response to amyloid peptide, highlighting the possibility that the enormous progress currently being made in the field of innate immunity could be extended to research on Alzheimer's disease.
Live, attenuated strains of Listeria and Salmonella as vaccine vectors in cancer treatment (2010)

Live, attenuated strains of many bacteria that synthesize and secrete foreign antigens are being developed as vaccines for a number of infectious diseases and cancer. Bacterial-based vaccines provide a number of advantages over other antigen delivery strategies including low cost of production, the absence of animal products, genetic stability and safety. In addition, bacterial vaccines delivering a tumor-associated antigen (TAA) stimulate innate immunity and also activate both arms of the adaptive immune system by which they exert efficacious anti-tumor effects. Listeria monocytogenes and several strains of Salmonella have been most extensively studied for this purpose. A number of attenuated strains have been generated and used to deliver antigens associated with infectious diseases and cancer. Although both bacteria are intracellular, the immune responses invoked by Listeria and Salmonella are different due to their sub-cellular locations. Upon entering antigen-presenting cells by phagocytosis, Listeria is capable of escaping from the phagosomal compartment and thus has direct access to the cell cytosol. Proteins delivered by this vector behave as endogenous antigens, are presented on the cell surface in the context of MHC class I molecules, and generate strong cell-mediated immune responses. In contrast, proteins delivered by Salmonella, which lacks a phagosomal escape mechanism, are treated as exogenous antigens and presented by MHC class II molecules resulting predominantly in Th2 type immune responses. This fundamental disparity between the life cycles of the two vectors accounts for their differential application as antigen delivery vehicles. The present paper includes a review of the most recent advances in the development of these two bacterial vectors for treatment of cancer. Similarities and differences between the two vectors are discussed.