gebhart/patrepeval huggingface dataset:
Continuous representations in linear predictive coding (1991)

A major source of audible distortion in current low-bit-rate speech coding algorithms is an inaccurate degree of periodicity of the voiced speech signal. If the correlations between neighboring pitch cycles are accurately reproduced, these audible distortions can be reduced significantly. To this purpose, a novel method of coding voiced speech is introduced, which transmits an encoded prototype waveform at 20-30 ms intervals. The prototype waveform describes a pitch cycle representative for the interval, and is quantized using analysis-by-synthesis methods. The speech signal is reconstructed by concatenation of interpolated prototype waveforms. The short-term and the long-term correlations between pitch cycles can be controlled explicitly. Unquantized reconstructed speech is virtually indistinguishable from the original signal. The method results in excellent speech quality at rates between 3.0 and 4.0 kb/s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Protein dynamics and imidazole binding in cytochrome P450 enzymes (2006)

P450 (cytochrome P450) enzymes have major roles in the biosynthesis of endogenous factors such as steroids and eicosanoids, in the termination of the action of endogenous factors such as retinoic acid, in the metabolism of most drugs and xenobiotics and in the generation of toxic and carcinogenic products. Understanding the determinants of the substrate and inhibitor specificities of these enzymes is important for drug design. The crystallographic analysis of the deformability of two bacterial P450 active sites associated with the binding of azole (a class of inhibitors with an imidazole or triazole ring that co-ordinates to the haem iron) inhibitors described in the present study illustrates the importance of protein conformational malleability in the binding of imidazole derivatives.
Stage-Specific Expression of Polycomb Group Genes in Human Bone Marrow Cells (1998)

Mammalian Polycomb group (Pc-G) genes, constituting some 5 subfamilies based on their identity to the Drosophila genes Pc, Psc, ph, esc, and E(z), appear to play critical roles in maintaining the transcriptional repression state of Hox/HOM-C genes during development. Despite increasing evidence of the important role of Hox genes in both normal hematopoiesis and leukemic transformation, little is known about the expression and possible function played by Pc-G genes in hematopoietic cells. To address this, we first examined the expression of Pc genes in purified CD34(+) human bone marrow cells by reverse transcriptase-polymerase chain reaction (RT-PCR), using degenerate primers that specifically amplify the majority of Pc genes. This analysis showed the expression of 8 different Pc genes in CD34(+) bone marrow cells, including HP1(Hsalpha), HP1(Hsgamma), the heterochromatin p25 protein, the human homologue of the murine M32 gene, and 4 novel members of this family. To assess whether Pc-G mRNA levels change during differentiation of bone marrow cells, a quantitative RT-PCR method was used to amplify the total cDNA originating from three purified subpopulations of CD34(+) bone marrow cells known to differ in their ability to grow in long-term or semisolid cultures. In sharp contrast to Hox gene expression, which is highest in the most primitive bone marrow cells, these studies show that the expression level of 8 of the 9 Pc-G genes studied (ie, HP1(Hsalpha), HP1(Hsgamma), M31, M32, M33, Mel-18, Mph1/Rae-28, and ENX-1) markedly increases with differentiation of bone marrow cells. Interestingly, BMI-1 exhibits a strikingly different pattern of expression, with high expression levels in primitive cells and very little expression in mature CD34(-) cells. Together, these results document for the first time that differentiation of human bone marrow cells is accompanied by profound changes in Pc-G gene expression levels.
[Effect of surgery on the level of total and free thyroid hormones, reverse T3 and TSH]. (1983)

Changes in total and free thyroid hormones, reverse triiodothyronine (rT3) and TSH were followed in 64 patients undergoing surgery and divided into three groups according to nature of surgery. Group I patients underwent extraperitoneal surgery, group II mild and group III heavy intraperitoneal surgery. A significant fall in total and free triiodothyronine (T3), a rise in rT3, free thyroxine (FT4) and in TSH were noted in each group after surgery, while total T4 levels remained unchanged. There was no correlation between the change in thyroid hormones and TSH. These changes are more marked in groups II and III than in group I. The rT3/T3 ratio was more elevated after surgery in group III than in group II. Thus the severity of the stress induced by surgery may interact with the mechanism of peripheral T4 conversion. The rise in FT4 may be interpreted as a consequence of the presence of an inhibitor of thyroid-hormonal binding to serum proteins. The slight increase in TSH levels seems rather due to stress than to a feed-back adaptation. The ratio rT3/T3 appears as an index of severity and prognosis.
Efficacy of infliximab in refractory ankylosing spondylitis: results of a six-month open-label study (2002)

This study confirms, in a large group of severely affected AS patients, the remarkable efficacy of infliximab. Relapse usually occurred after discontinuation of the drug, but almost one-third of completers were still free of relapse 4 months after the last infusion.
Retroviral Delivery and Anti-HIV Testing of Hammerhead Ribozymes (2003)

Successful ribozyme-mediated gene therapy for HIV infection has to take into account several factors: 1. The therapeutic gene must interfere with or shut down the expression of essential viral genes. 2. This requires a vector system for gene delivery and expression in HIV-sensitive cells. 3. To bypass the high genetic variability of the HIV-1 replication process, the target sequence should be chosen in highly conserved sequences of HIV-1. These fortunately are mostly present in the essential regulatory genes (tat, rev) or sequences (PBS, U5), which are required to produce infectious viral particles ().
Transformation of Glassy Palladium‐Zirconium Alloys to Highly Active CO‐Oxidation Catalysts During In Situ Activation Studied by Thermoanalytical Methods and X‐Ray Diffraction (1993)

Abstract Palladium/zirconia catalysts highly active for the oxidation of CO can be prepared by exposing amorphous Pd‐Zr alloys to CO oxidation conditions at 280°C. The bulk chemical and structural changes occuring under these conditions have been studied using thermoanalytical methods (TG, DTA) combined with mass spectrometry and in‐situ powder XRD. Amorphous PdZr 2 and PdZr 3 alloys exhibit virtually no activity when exposed to CO oxidation conditions, mainly due to their low specific surface area (˜ 0.01 m 2 /g). The activity develops with time on stream, passes through a maximum and reaches a stable state only after several hours. The maximum in the activity is observed when about 50–70% of the amount of oxygen necessary for complete oxidation of the precursor to PdO and ZrO 2 has been consumed. The oxidation of the amorphous Pd‐Zr alloys, which results in a drastic increase of the specific surface area of the samples, starts at significantly lower temperature than the crystallization temperatures of the alloys. The stable catalysts contain poorly crystalline monoclinic and tetragonal ZrO 2 , metallic palladium and PdO as bulk phases. The concentration of these phases is influenced by a series of simultaneously occurring reactions, including: the oxidation of the alloy constituents by O 2 which results in PdO and ZrO 2 , the oxidation by CO 2 resulting in Pd and ZrO 2 , and the reduction of the PdO formed by CO and by metallic Zr present in the unreacted part of the alloy. The solid state reduction 2 PdO + Zr → Pd + ZrO 2 contributes significantly to the reduction of the PdO as long as metallic Zr is abundant in the alloys.
Vaccine-Induced Cellular Responses Control Simian Immunodeficiency Virus Replication after Heterologous Challenge (2009)

All human immunodeficiency virus (HIV) vaccine efficacy trials to date have ended in failure. Structural features of the Env glycoprotein and its enormous variability have frustrated efforts to induce broadly reactive neutralizing antibodies. To explore the extent to which vaccine-induced cellular immune responses, in the absence of neutralizing antibodies, can control replication of a heterologous, mucosal viral challenge, we vaccinated eight macaques with a DNA/Ad5 regimen expressing all of the proteins of SIVmac239 except Env. Vaccinees mounted high-frequency T-cell responses against 11 to 34 epitopes. We challenged the vaccinees and eight naïve animals with the heterologous biological isolate SIVsmE660, using a regimen intended to mimic typical HIV exposures resulting in infection. Viral loads in the vaccinees were significantly less at both the peak (1.9-log reduction; P < 0.03) and at the set point (2.6-log reduction; P < 0.006) than those in control naïve animals. Five of eight vaccinated macaques controlled acute peak viral replication to less than 80,000 viral RNA (vRNA) copy eq/ml and to less than 100 vRNA copy eq/ml in the chronic phase. Our results demonstrate that broad vaccine-induced cellular immune responses can effectively control replication of a pathogenic, heterologous AIDS virus, suggesting that T-cell-based vaccines may have greater potential than previously appreciated.
Of circles, forks and humanity: Topological organisation and replication of mammalian mitochondrial DNA (2011)

The organisation of mammalian mitochondrial DNA (mtDNA) is more complex than usually assumed. Despite often being depicted as a simple circle, the topology of mtDNA can vary from supercoiled monomeric circles over catenanes and oligomers to complex multimeric networks. Replication of mtDNA is also not clear cut. Two different mechanisms of replication have been found in cultured cells and in most tissues: a strand-asynchronous mode involving temporary RNA coverage of one strand, and a strand-coupled mode rather resembling conventional nuclear DNA replication. In addition, a recombination-initiated replication mechanism is likely to be associated with the multimeric mtDNA networks found in human heart. Although an insight into the general principles and key factors of mtDNA organisation and maintenance has been gained over the last few years, there are many open questions regarding replication initiation, termination and physiological factors determining mtDNA organisation and replication mode. However, common themes in mtDNA maintenance across eukaryotic kingdoms can provide valuable lessons for future work.
A graph-theoretic approach to extract storylines from search results (2004)

We present a graph-theoretic approach to discover storylines from search results. Storylines are windows that offer glimpses into interesting themes latent among the top search results for a query; they are different from, and complementary to, clusters obtained through traditional approaches. Our framework is axiomatically developed and combinatorial in nature, based on generalizations of the maximum induced matching problem on bipartite graphs. The core algorithmic task involved is to mine for signature structures in a robust graph representation of the search results. We present a very fast algorithm for this task based on local search. Experiments show that the collection of storylines extracted through our algorithm offers a concise organization of the wealth of information hidden beyond the first page of search results.
Analysis of cell‐free DNA in maternal blood in screening for fetal aneuploidies: updated meta‐analysis (2015)

Screening by analysis of cfDNA in maternal blood in singleton pregnancies could detect > 99% of fetuses with trisomy 21, 98% of trisomy 18 and 99% of trisomy 13 at a combined FPR of 0.13%. The number of reported cases of SCA is too small for accurate assessment of performance of screening. In twin pregnancies, performance of screening for trisomy 21 is encouraging but the number of cases reported is small. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
Characterization of Antibody and Cytotoxic T Lymphocyte Responses to Human Influenza Virus H3 Haemagglutinin Expressed from the Haemagglutinin Locus of Vaccinia Virus (1990)

Antibody and cytotoxic T lymphocyte (CTL) responses to the haemagglutinin (HA) of human H3N2 influenza virus were analysed, using recombinant vaccinia viruses containing the influenza HA gene inserted into the HA gene locus of vaccinia virus. The recombinant vaccinia viruses elicited a high haemagglutination inhibiting (HI) antibody response to the homologous influenza virus in mice. In addition, HI antibody generated by the recombinant vaccinia virus reacted with antigenic variants of human H3N2 influenza virus in a manner similar to that elicited by the HA vaccine. Mice with a high response to influenza virus HA vaccine were highly responsive to the HA expressed from the recombinant vaccinia virus, as measured by HI antibody production. The immunogenicity of the influenza virus HA expressed by the recombinant seems to be attributable to the intrinsic immunogenicity of the HA molecule. The recombinants primed mice for an influenza virus H3-specific CTL response and primed CTLs recognized the target cells in a subtype-specific manner. The results indicate that a recombinant vaccinia virus derived by the insertion of a foreign gene into its HA gene locus is a potent live vaccine not only for eliciting a high antibody response but also for priming a specific CTL response.
Diamond emitters fabrication and theory (1996)

The fabrication of gated diamond field-emission cathodes is described and a theory of their operation is discussed. These cathodes are made using commercial diamond grit with the addition of Ni and Cs salts to enhance emission. The resulting structure resembles a field-emission Spindt cathode with the internal metal cone replaced by a ∼100 nm layer of diamond grit. Emission from these cathodes occurs at the lowest reported gate voltage of any field emission device and is unaffected by operation at pressures of over 100 Pa of N2. Operation in oxygen and H2S at pressures of 6×10−4 Pa degrades emission, but the cathodes recover once the ambient pressure is reduced to below 1×10−4 Pa. The emission current noise is 2.5% rms over an 8 h period and 1% rms over 3 ms. These cathodes suffer from high gate current that varies from 0.2 to 1000 times the emitted current. The high gate current is known to be process dependent and not inherent to the cathodes. The emission performance is explained by the stable negative electron affinity of diamond, which allows for injection of electrons from diamond into vacuum with little to no electric field, 0–1 V μm−1. Cathode operation is limited by the injection of electrons into the diamond at the back metal–diamond interface, which depends upon the doping of the diamond and the roughness of that interface.
Seasonal increase of carbachol airway responsiveness in patients allergic to grass pollen. Reversal by corticosteroids. (1984)

By measuring airway resistance (Raw) as an index of response, dose-response curves to aerosolized carbachol were constructed in 10 patients suffering from grass pollen allergy. The subjects were first tested before the pollen season (March). During the pollen season (May and June), another control test was performed; the patients were then treated (double blind and at random) with placebo or methylprednisolone (16 mg/day given orally) for 7 days and then retested. After a 10-day interval devoid of treatment, the 2 treatments were crossed over and a fourth carbachol test was performed. Baseline function values were comparable for all 4 tests. In all but one subject (who was a smoker), carbachol increased Raw by more than 150% over baseline for each of the 4 tests. In these 9 patients, carbachol responsiveness significantly increased during the pollen season and returned to its preseason level after corticosteroid treatment. The data suggest that airway inflammation was responsible for the seasonal increase in airway reactivity.
The Role of Tumor Size in the Radiosurgical Management of Patients with Ambiguous Brain Metastases (2003)

A convincing brain metastasis measuring less than 1 cm should be pursued aggressively. If the suspected brain metastasis is ambiguous, observation is proposed up to a diameter of 1 cm. This is the first study in the literature to identify a 1-cm cutoff for radiosurgical control of small brain metastases, and validation by additional studies is required.
Repetitive‐Synthesis of Bulky Dendrimers – A Reversibly Photoactive Dendrimer with Six Azobenzene Side Chains (1993)

Abstract Dendrimers with bulky repeating units containing up to 43 benzene rings (in 9 ) have been obtained by using a repetitive divergent synthetic strategy (three generations). The new functional dendrimer 13 containing six azobenzene units at the periphery was synthesized allowing a reversible switching of the shape and size of the molecule upon irradiation. An X‐ray structure analysis of the dendritic molecule 3a shows the inclusion of acetonitrile.
Improved workflows for high throughput library preparation using the transposome-based nextera system (2013)

We addressed the bottlenecks of Nextera library construction to produce a modified protocol which harnesses the full power of the Nextera kit and allows the reproducible construction of libraries on a high-throughput scale reducing the associated cost of the kit.
Whole blood cytokine attenuation by cholinergic agonists ex vivo and relationship to vagus nerve activity in rheumatoid arthritis (2010)

These findings suggest that it is possible to pharmacologically target the alpha7nAChR dependent control of cytokine release in RA patients with suppressed vagus nerve activity. As alpha7nAChR agonists ameliorate the clinical course of collagen induced arthritis in animals, it may be possible in the future to explore whether alpha7nAChR agonists can improve clinical activity in RA patients.
Molecular analysis of anti‐DNA antibodies (1994)

There are two major reasons for interest in antibodies to DNA: autoantibodies to DNA are characteristic of the autoimmune disease systemic lupus erythematosus and contribute to its pathology; and both autoantibodies and experimentally induced antibodies to nucleic acids serve as useful biochemical reagents. Physical biochemistry and molecular biology are applied increasingly to questions of the structure and origin of antibodies to DNA and how antibodies recognize specific structures in DNA. Cloning of cDNA for Ig V regions of anti-DNA antibodies reveals that some cells making IgG disease-related autoantibodies are derived from precursor cells that produce natural autoantibodies unrelated to disease. In addition, some immunization-induced antibodies to DNA use gene segments similar to those found in autoantibodies. Cloning and expression of recombinant V regions allow detailed analysis of antibody structures required for DNA binding. Domain swapping and mutagenesis with vectors for bacterial expression of single chain Fv molecules revealed the importance of CDR3 sites of both H and L chain V regions for specific antigen binding by antibody to Z-DNA. In certain autoantibodies, the H chain plays a dominant role in determining DNA binding. Molecular analysis opens doors to studies of normal immune tolerance and its loss in autoimmune disease as well as to development of antibodies with modified specificity.
Element partition ratios in some sedimentary environments. I. Statistical treatments (1975)

Partitioning or assigning trace elements to different minerals in a rock has long been a major problem in sedimentary geochemistry. A combination of factor and regression analysis appears to be applicable to solve a part of this problem. Although the statistical theory has been developed for some time, there are some practical conditions or limitations that should always be considered when analyzing geochemical data. These include geochemical independence of the variables and the interpretation of the regression constant. Both, created data simulating simplified rock compositions, and real data of a 29 core, samples set of Pennsylyanian black shales were used to illustrate the application of factor analysis and multiple regression analysis to the partitioning of trace elements among minerals.
GGTI-298 induces G0-G1 block and apoptosis whereas FTI-277 causes G2-M enrichment in A549 cells. (1997)

The mechanism by which the geranylgeranyltransferase I inhibitor GGTI-298 and the farnesyltransferase inhibitor FTI-277 inhibit human tumor growth is not known. Herein, we demonstrate that in the human lung adenocarcinoma A549 cells, GGTI-298 induced a G1-G0 block whereas FTI-277 induced an enrichment in the G2-M phase of the cell cycle. Although FTI-277, GGTI-298, and compactin inhibited A549 cell growth, only GGTI-298 and compactin induced apoptosis as demonstrated by four criteria: 4',6-diamidine-2-phenylindoledihydrochloride staining, terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling, DNA fragmentation assay, and flow cytometry. Furthermore, the involvement of geranylgeranylated proteins in apoptotic pathways was confirmed by demonstrating that geranylgeraniol was able to block the ability of compactin to induce apoptosis. These results suggest that protein geranylgeranylation is critical for the control of programmed cell death and that, in A549 cells, farnesylated and geranylgeranylated proteins are involved in G2-M and G0-G1, respectively.
Rapid uptake of tyrphostin into A431 human epidermoid cells is followed by delayed inhibition of epidermal growth factor (EGF)-stimulated EGF receptor tyrosine kinase activity. (1991)

Treatment of A431 human epidermoid cells with epidermal growth factor (EGF; 20 nM) results in decreased proliferation. This is associated with blockage of the cells in the S and/or G2 phases of the cell cycle. We found that tyrphostin, a putative tyrosine kinase inhibitor, in the range of 50 to 100 microM, partially reversed the growth-inhibitory and cell cycle changes induced by EGF. By using high-pressure liquid chromatography with electrochemical detection, we found that tyrphostin was readily incorporated into A431 cells, reaching maximal levels within 1 h. Although tyrphostin (50 to 100 microM) had no effect on high-affinity binding of EGF to its receptor in A431 cells for up to 24 h, the compound partially inhibited EGF-stimulated EGF receptor tyrosine kinase activity. However, this effect was evident only after prolonged treatment of the cells (4 to 24 h) with the drug. When the peak intracellular concentration of tyrphostin occurred (1 h), no inhibition of tyrosine kinase activity was observed. After both 1 and 24 h, tyrphostin was a less effective inhibitor of tyrosine kinase activity than the potent tumor promoter 12-O-tetradecanoyl phorbol-13-acetate, which almost completely blocked EGF receptor autophosphorylation. On the basis of our data, we hypothesize that tyrphostin is not a competitive inhibitor of the EGF receptor tyrosine kinase in intact cells and that it functions by an indirect mechanism.