gebhart/patrepeval huggingface dataset:
Expression of Two Different Antiphagocytic M Proteins by Streptococcus pyogenes of the OF+ Lineage (1998)

All clinical isolates of Streptococcus pyogenes (group A streptococcus) share the ability to resist phagocytosis and grow in human blood. In many strains, this property is due to the expression of a single antiphagocytic M protein, while other strains express more than one M-like molecule, of which the role in phagocytosis resistance is unclear. In particular, all S. pyogenes strains of the OF+ lineage, representing approximately half of all isolates, express two M-like proteins, Mrp and Emm, which are immunologically unrelated. These two proteins bind different ligands that have been implicated in phagocytosis resistance: Mrp binds fibrinogen and Emm binds the complement inhibitor C4BP. Using a clinical isolate of the common serotype 22, we created mutants affected in the mrp and emm genes and characterized them in phagocytosis experiments and by electron microscopy. A double mutant mrp-emm- showed strongly decreased resistance to phagocytosis, while mrp- and emm- single mutants grew well in blood. However, optimal growth required the expression of both Mrp and Emm. Experiments in which coagulation was inhibited using the specific thrombin inhibitor, hirudin, rather than heparin, indicated that Emm is more important than Mrp for resistance to phagocytosis. Tuftlike surface structures typical for S. pyogenes were still present in the mrp-emm- double mutant, but not in a mutant affected in the regulatory gene mga, indicating that the presence of these surface structures is not directly correlated to phagocytosis resistance. Our data imply that OF+ strains of S. pyogenes express two antiphagocytic M proteins with different ligand-binding properties.
Quasi-cyclic low-density parity check codes (2004)

This paper introduces a combinatorial construction of regular low-density parity check (LDPC) codes based on balanced incomplete block designs, or more specifically on cyclic difference families of Abelian groups and affine geometries. Several constructions are presented, and the bounds on minimal distance are derived by using the concept of Pasch configurations.
The Wilms' tumor gene product, WT1, represses transcription of the platelet-derived growth factor A-chain gene. (1992)

The Wilms' tumor locus on chromosome 11p13 contains a tumor suppressor gene, wt1, which encodes a DNA binding protein (WT1) with four zinc fingers and a glutamine-proline-rich N terminus and which functions as a repressor of transcription. The platelet-derived growth factor (PDGF) A-chain gene encodes a potent growth factor, which is expressed in high levels in a number of tumor cell lines. We initiated a search for WT1 target genes and now report that WT1 strikingly represses transcription of the PDGF A-chain gene in transient transfection assays and that the WT1 protein interacts directly with a highly G+C-rich region of the PDGF A-chain promoter in gel mobility shift assays. The results suggest that WT1 may function to repress expression of the PDGF A-chain gene and that loss of this or related repressor activities may contribute to the abnormal growth of Wilms' tumors.
Effects of fatty acids and eicosanoid synthesis inhibitors on the growth of two human prostate cancer cell lines (1991)

Abstract Dietary Fatty acids (FAs) may be involved in the carcinogenic process within the prostate gland and progression to clinically manifest disease. We have shown that growth of the androgen‐unresponsive PC‐3 human prostate cancer cell line is stimulated in vitro by the presence of linoleic acid (LA), an omega‐6 polyunsaturated FA. The response was positively related to the FA concentration over the entire range examined (5–750 ng/ml). Conversely, docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), two omega‐3 FAs present in fish oils, inhibited PC‐3 cell growth in a dose‐dependent manner; both were equally effective, with an approximately 65% reduction in growth occurring at a concentration of 2.0 μg/ml ( P &lt; 0.001). The DU 145 human prostate cancer cell line, which is also androgen‐unresponsive, showed no growth response to LA and was less susceptible to growth inhibition when cultured in the presence of omega‐3 FAs. Growth experiments with indomethacin, esculetin, and piroxicam, pharmacological inhibitors of eicosanoid biosynthesis with differing sites of action, indicated that human prostate cancer cell growth requires intact metabolic pathways for both leukotriene and prostaglandin production.
CaSPredictor: a new computer-based tool for caspase substrate prediction (2005)

Supplementary information is available for academic users at site http://icb.usp.br/~farmaco/Jose/CaSpredictorfiles.
Elastic-Vt CMOS circuits for multiple on-chip power control (2002)

The elastic-Vt CMOS (EVTCMOS) circuit design controls MOS transistor source (not substrate) voltages, so fabrication requires no special steps. The post-fabrication threshold voltages can be switched back and forth between high Vt (sleep mode) and low Vt (active mode), and can be also controlled as a means of reducing the sensitivity to device-parameter deviations and operating-environment variations. This results in reduction of switching time between sleep and active modes, and in reduced static power consumption in sleep mode.
Unraveling the hemolytic subphenotype of sickle cell disease (2005)

Comment on Nolan et al, page [3264][1] 

Hemolytic anemia, while silent from a vaso-occlusive pain crisis standpoint, leads to sustained nitric oxide depletion, oxidant stress, vasoconstriction and proliferative vasculopathy in a number of organ systems, ultimately contributing to the development of
Sequence of rat RL/IF-1 encoding IKBβ-like activity and comparison with related proteins containing notch-like repeats (1992)

The title of this paper should be revised to read: ‘Sequence of rat RL/IF-1 encoding an IχB, and comparison with related proteins containing notch-like repeats’. Although we found (Tewari et al., Mol. Cell Biol., in press) that RL/IF-1 has IχBβ-like activity as defined by Kerr et al., Genes and Development, 5, 1464–1476, 1991, we also found Tewari et al., Mol. Cell Biol., in press) that the sequence of RL/IF-1 and molecular weight of cellular RL/IF-1 are identical with IχBα as defined by Davis et al., Science, 253, 1268–1271, 1991.
Therapeutic anti‐integrin (α4 and αL) monoclonal antibodies: two‐edged swords? (2005)

Anti-alpha4 and anti-alphaL integrin chain monoclonal antibodies have shown a clear-cut beneficial effect in different animal models of autoimmune and inflammatory disorders as well as in human diseases, including multiple sclerosis, inflammatory bowel disease, and psoriasis. It has been widely assumed that this therapeutic effect is mainly consequence of the blockade of leucocyte adhesion to endothelium, inhibiting thus their extravasation and the inflammatory phenomenon. However, it is evident that both alpha4beta1 (very late antigen-4) and alphaLbeta2 (leucocyte function-associated antigen-1) integrins have additional important roles in other immune phenomena, including the formation of the immune synapse and the differentiation of T helper 1 lymphocytes. Therefore, it is very feasible that the long-term administration of blocking agents directed against these integrins to patients with inflammatory/autoimmune conditions may have undesirable or unexpected effects.
Protection of Sensors for Biological Applications by Photoinitiated Chemical Vapor Deposition of Hydrogel Thin Films (2008)

We report photoinitiated chemical vapor deposition (piCVD), a gentle synthetic method for the preparation of ultrathin films (approximately 100 nm) of the hydrogel poly(hydroxyethyl methacrylate) (pHEMA). piCVD occurs near room temperature and requires only mild vacuum conditions. The deposited films swell rapidly and reversibly in buffer solution, and the swelling properties can be controlled via the deposition conditions. Analysis of the swelling data indicates that the mesh size of the hydrogel creates a selectively permeable coating. The mesh is large enough to allow small molecule analytes to permeate the film but small enough to prevent the transport of large biomolecules such as proteins. X-ray photoelectron spectroscopy (XPS) shows that the films decrease nonspecific adhesion of the protein albumin by nearly 8-fold over bare silicon. A dry process, piCVD is suitable for coating particles with diameters as small as 5 microm. The absence of solvents and plasmas in piCVD allows films to be directly synthesized on optode sensors without degradation of sensitivity or response time.
The Effect of Menthol on the Thermoreceptors (1951)

Summary. The discharge of specific cold and warm fibres in the lingual nerve of the cat has been studied in response to the application of menthol solutions and to exactly defined thermal stimuli on the tongue. Aqueous menthol solutions of 1: 10,000 lead to strong stationary discharge of the tongue's cold receptors at constant warm temperatures at which there without menthol is no discharge. At lower temperatures at which the cold receptors are stationary discharging without menthol, this substance produces a great increase of the stationary cold impulse frequency. The effect of menthol can be completely compensated for by sudden heating or by keeping the tongue at a constant higher temperature as these measures can cause the cold impulses elicited by menthol to disappear entirely. Thus it is not simply the question of a chemical “inadequate” stimulation of the cold receptors but of a sensitization of the thermal effect. Our experiments have not given any evidence that menthol exerts any corresponding action on the warm receptors. The threshold of the menthol effect lies between a concentration 1: 1,000,000 and 1: 500,000. It is thus likely that the action of menthol concerns some enzymatic process in the cold receptors.
The leader sequence of the Escherichia coli lysC gene is involved in the regulation of LysC synthesis (1998)

In Escherichia coli and Bacillus subtilis, long leader sequences are found upstream of the lysC coding sequences which encode lysine-sensitive aspartokinase. Highly conserved regions exist between these sequences. Mutations leading to constitutive expression of the E. coli lysC gene have been localised within these conserved regions, indicating that they participate in the lysine-mediated repression mechanism of lysC expression.
Purification and Characterization of Angiotensin I-Converting Enzyme Inhibitors from Sour Milk (1995)

The inhibitory activity of angiotensin I-converting enzyme in milk increased during fermentation with the Calpis sour milk starter containing Lactobacillus helveticus and Saccharomyces cerevisiae. Two kinds of peptides inhibitory to angiotensin I-converting enzyme were purified from the sour milk by using four-step HPLC. The amino acid sequences of these inhibitors were identified as Val-Pro-Pro and Ile-Pro-Pro. The concentrations of peptides providing 50% inhibition of angiotensin I-converting enzyme were 9 and 5 microM, respectively. Most of the inhibitory activity in sour milk was attributed to these two peptides.
Automating the design of a generic modular power system for the global market (1999)

The concept of automating the design of a modular power system built from generic blocks and suitable for use in any country or application may be considered by many to be unrealistic. However as a result of the removal of the national telephone monopolies in many countries and the inevitable staff reductions, the nonrevenue positions such as power engineers have been in most cases greatly reduced or eliminated. This has resulted in the perception that power is a commodity which can be procured against a generic or nonexistent specification, placing the responsibility for ensuring that the system design is correct on the power equipment vendor. Under this scenario the potential for a rule based design system and the associated products becomes very important. Not only as a means of rapidly configuring standard systems, but as a tool to validate the design of nonstandard concepts.
Expression of the Chemokine Receptor CXCR2 in Normal and Neoplastic Neuroendocrine Cells (2000)

The expression of CXCR2 by normal neuroendocrine cells and neoplastic counterparts that have retained phenotypic features of this differentiation program suggests that chemokines may play an important role in functions that are characteristic of this cell type. In addition, this raises the possibility that chemokines may modulate secretion of biologically active products of these cells and their neoplastic counterparts.
Direct actions of angiopoietin-1 on human endothelium: evidence for network stabilization, cell survival, and interaction with other angiogenic growth factors. (1999)

Angiopoietin-1 (Ang-1) is a recently described angiogenic protein that activates the endothelial Tie 2 receptor. Disruption of the Ang-1 gene shows that it has an indispensable role in blood vessel development, but it is not clear what specific effects, if any, Ang-1 has on endothelial cell (EC) phenotypes. Here, we show that Ang-1 dose-dependently stabilizes HUVEC network organization for up to 48 hours; this action of Ang-1 is dependent on Tie-2 receptor activation, because a soluble form of the Tie2-, but not the Tie1-receptor, completely blocks the effects of Ang-1. Moreover, we show that Ang-1 potentiates the actions of other angiogenic growth factors. Ang-1 markedly increases the survival of vascular networks (up to 96 hours) exposed to either vascular endothelial growth factor or endothelial cell growth supplement, a form of acidic fibroblast growth factor. In addition, Ang-1 prevents apoptotic death in HUVEC triggered by withdrawal of endothelial cell growth supplement. Collectively, these data are consistent with the idea that Ang-1 directly acts on human EC and interacts with other angiogenic molecules to stabilize vascular structures by promoting the survival of differentiated ECs.
Large-scale analysis of human heavy chain V(D)J recombination patterns (2008)

We present here the most precise estimates of gene segment usage frequencies currently available along with analyses regarding n-nucleotide distributions and D-J segment pair preferences. Additionally, we provide the first statistical evidence that sequential D-J recombinations occur at the human heavy chain locus during B-cell ontogeny with an approximate frequency of 20%.
Modulation of auditory evoked responses to spectral and temporal changes by behavioral discrimination training (2009)

We found that discrimination training differentially modulates the cortical responses to pitch changes and to envelope fluctuation changes of AM tones. This suggests that discrimination between AM tones requires additional neuronal mechanisms compared to discrimination process between pure tones. After the training, the subjects demonstrated an involuntary attention switch to the deviant stimulus (represented by the P3a-component in the MEG) even though attention was not prerequisite.
Inhibition of Vascular Permeability by Antisense-Mediated Inhibition of Plasma Kallikrein and Coagulation Factor 12 (2013)

Hereditary angioedema (HAE) is a rare disorder characterized by recurrent, acute, and painful episodes of swelling involving multiple tissues. Deficiency or malfunction of the serine protease inhibitor C1 esterase inhibitor (C1-INH) results in HAE types 1 and 2, respectively, whereas mutations in coagulation factor 12 (f12) have been associated with HAE type 3. C1-INH is the primary inhibitor of multiple plasma cascade pathways known to be altered in HAE patients, including the complement, fibrinolytic, coagulation, and kinin-kallikrein pathways. We have selectively inhibited several components of both the kinin-kallikrein system and the coagulation cascades with potent and selective antisense oligonucleotides (ASOs) to investigate their relative contributions to vascular permeability. We have also developed ASO inhibitors of C1-INH and characterized their effects on vascular permeability in mice as an inducible model of HAE. Our studies demonstrate that ASO-mediated reduction in C1-INH plasma levels results in increased vascular permeability and that inhibition of proteases of the kinin-kallikrein system, either f12 or prekallikrein (PKK) reverse the effects of C1-INH depletion with similar effects on both basal and angiotensin converting enzyme (ACE) inhibitor-induced permeability. In contrast, inhibition of coagulation factors 11 (f11) or 7 (f7) had no effect. These results suggest that the vascular defects observed in C1-INH deficiency are dependent on the kinin-kallikrein system proteases f12 and PKK, and not mediated through the coagulation pathways. In addition, our results highlight a novel therapeutic modality that can potentially be employed prophylactically to prevent attacks in HAE patients.
Highly Chemo‐ and Regioselective Reduction of Aromatic Nitro Compounds Catalyzed by Recyclable Copper(II) as well as Cobalt(II) Phthalocyanines (2010)

Abstract Copper/cobalt phthalocyanines were established for the first time as catalysts for the very efficient chemo‐ and regioselective reduction of aromatic nitro compounds to generate the corresponding amines. The selective reduction of nitro compounds was observed in the presence of a large range of functional groups such as aldehyde, keto, acid, amide, ester, halogen, lactone, nitrile and heterocyclic functional groups. Furthermore, the present method was found to be highly regioselective towards the reduction of aromatic dinitro compounds in a short time with high yields. In most of the cases the conversion and selectivity were &gt;99% as monitored by GC‐MS. The reduction mechanism was elucidated by UV‐vis and electrospray ionization quadrupole time‐of‐flight tandem mass spectrometry.
Establishment of the novel B acute lymphoblastic leukemia (FAB L3) cell line KHM-10B with a 13q34 abnormality and constitutive expression of c-myc and max during cell cycle. (1995)

We established and characterized a new acute lymphoblastic leukemia (ALL-L3 according to FAB classification, or Burkitt's type) cell line, KHM-10B. The morphology of the patient's lymphoblasts and KHM-10B cells corresponded to that of ALL-L3 cells. The cells were positive for HLA-DR, CD19 and surface immunoglobulin (mu, lambda). Southern blot analysis revealed that the fresh lymphoblasts and KHM-10B shared the same immunoglobulin gene rearrangement. Conventional cytogenetic analysis of fresh lymphoblasts from the patient and KHM-10B cells revealed the 13q34 abnormality, the second most common additional abnormality in Burkitt's lymphoma, but no detectable 8q24 involvement. Rearrangement of the c-myc oncogene was not detected by Southern blot analysis. However, a fluorescence in situ hybridization (FISH) assay identified a t(8;22)(q24;q11). The KHM-10B cells were arrested at S phase with hydroxyurea and thymidine, and the synchronized cells progressed through the cell cycle in drug-free medium. The expression of c-myc and max was observed throughout the cell cycle, as was found in the Burkitt's lymphoma cell in Raji. Our findings indicate that FISH analysis is of diagnostic value in detecting obscure chromosomal translocations and that max, as well as c-myc, is expressed constitutively in ALL-L3 and Burkitt's lymphoma cell lines.
Optically transparent high temperature shape memory polymers (2015)

Optically transparent shape memory polymers (SMPs) have potential in advanced optoelectronic and other common shape memory applications, and here optically transparent shape memory polyimide is reported for the first time. The polyimide possesses a glass transition temperature (Tg) of 171 °C, higher than the Tg of other transparent SMPs reported, and the influence of molecular structure on Tg is discussed. The 120 μm thick polyimide film exhibits transmittance higher than 81% in 450-800 nm, and the possible mechanism of its high transparency is analyzed, which will benefit further research on other transparent high temperature SMPs. The transparent polyimide showed excellent thermomechanical properties and shape memory performances, and retained high optical transparency after many shape memory cycles.
Further Characterization of Cells Expressing STRO-1 in Cultures of Adult Human Bone Marrow Stromal Cells (1999)

Primitive cells of the osteoblast lineage are not well characterized but are known to be present within the STRO-1+ fraction of adult human bone and marrow. A survey of human osteosarcoma cell lines revealed that STRO-1 is expressed by MG-63 but not SaOS-2. Among murine cell lines tested, expression of STRO-1 was detected in the bipotential (adipocyte/osteoblast) line BMS-2 but not the committed osteoblast precursor MC3T3-E1. A proportion of cultured adult human bone marrow stromal cells (BMSCs) consistently expressed the STRO-1 antigen. The expression of a range of cell surface antigens was studied in relation to STRO-1 by flow cytometry and several, including the bone/liver/kidney isoform of alkaline phosphatase (ALP), were found to subtype the STRO-1+ population of BMSCs. Further, BMSCs dual-labeled with antibodies recognizing STRO-1 and ALP could be assigned to one of four fractions: STRO-1-/ALP-, STRO-1+/ALP-, STRO-1+/ALP+, and STRO-1-/ALP+. Cells from each fraction could be isolated in high purity and, when recultured, remained viable and exhibited a limited degree of phenotypic stability. Using reverse transcriptase-polymerase chain reaction, cells in the four fractions were found to express different levels of transcripts for the parathyroid hormone receptor (PTHr) and bone sialoprotein (BSP). The expression of transcripts for the nuclear transcription factor core-binding factor alpha 1/osteoblast-specific factor-2 (CBFA1/OSF2) was restricted to those fractions expressing STRO-1 and/or ALP. Treatment with 10 nM dexamethasone consistently increased the proportion of cells present in those fractions which expressed the highest levels of transcripts for PTHr and BSP (STRO-1+/ALP+ and STRO-1-/ALP+) while simultaneously decreasing the proportion present in the STRO-1+/ALP- fraction. In conclusion, the expression of STRO-1 in vitro remains a characteristic of less well differentiated cells of the osteoblast lineage; in cultures of BMSCs and in established human osteosarcoma cell lines, there is an inverse association between the expression of STRO-1 and ALP; dual labeling of BMSCs with monoclonal antibodies recognizing STRO-1 and ALP permits the identification and isolation of cells of the osteoblast lineage at different stages of differentiation.
Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole-Exome Sequencing (2013)

In humans, exposure to aristolochic acid (AA) is associated with urothelial carcinoma of the upper urinary tract (UTUC). Exome sequencing of UTUCs from 19 individuals with documented exposure to AA revealed a remarkably large number of somatic mutations and an unusual mutational signature attributable to AA. Most of the mutations (72%) in these tumors were A:T-to-T:A transversions, located predominantly on the nontranscribed strand, with a strong preference for deoxyadenosine in a consensus sequence (T/CAG). This trinucleotide motif overlaps the canonical splice acceptor site, possibly accounting for the excess of splice site mutations observed in these tumors. The AA mutational fingerprint was found frequently in oncogenes and tumor suppressor genes in AA-associated UTUC. The AA mutational signature was observed in one patient's tumor from a UTUC cohort without previous indication of AA exposure. Together, these results directly link an established environmental mutagen to cancer through genome-wide sequencing and highlight its power to reveal individual exposure to carcinogens.