gebhart/patrepeval huggingface dataset:
Experimental and clinical pharmacology of glycosaminoglycans (GAGs). (1991)

The experimental and clinical pharmacology of glycosaminoglycans (GAGs) is discussed, including that of heparin and related compounds, hyaluronic acid and chondroitin sulfates.
Cytokine dysregulation in AIDS: in vivo overexpression of mRNA of tumor necrosis factor-alpha and its correlation with that of the inflammatory cytokine GRO. (1992)

The human immunodeficiency virus establishes an intimate interaction with the immune system. The virus can use cytokines, such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 (Il-1), to regulate its own expression by modifying the normal immunoregulatory network. We demonstrate that mRNA of the cytokine TNF-alpha from peripheral blood mononuclear cells is overexpressed in virtually all patients with AIDS who do not have active opportunistic infections compared with uninfected volunteers (p < 0.0001). This overexpression correlates with elevated mRNA levels of the recently discovered GRO (p < 0.05), a cytokine involved in the inflammatory response.
Major heat shock protein Hsp72 controls oncogene‐induced senescence (2010)

Various heat shock proteins, including Hsp72, are strongly upregulated in cancers, but their significance for tumor emergence and growth is poorly understood. Here we review recent data from several labs to indicate that Hsps, including Hsp72, are critical for growth of transformed but not normal cells. By manipulating expression and activity of Hsp72 and several oncogenes, it was shown that Hsp72 suppresses oncogene-induced senescence, thus allowing proliferation of cancer cells. Importantly, Hsp72 is able to suppress both p53-dependent and p53-independent senescence pathways. We propose that targeting Hsp72 may be a promising approach toward development of novel cancer therapies.
Amino Acid, Peptide, and Protein Volume in Solution (1984)

Modern physicochemical biology steadily enriches our knowledge of the functional role of proteins and their elements-amino acids and peptides. These substances are involved in all essential molecular processes occurring in the living cell and perform key regulatory functions at the cellular and organismic levels. Their functional specificity arises from their unique physicochemical properties, specific chemical composition, and the variety of intraand intermolecular interactions of protein residues with each other and with neighboring molecules. As a result, the protein assumes a particular form and volume. Spatial coordinates of the atoms of all macromolecules completely characterize the macromolecule structure. It is difficult to define a portion of space filled by a macromolecule, i.e. the volume. To do so, one must estimate the surface surrounding the macromolecule or the volume of all its atoms and all intramolecular cavities. Nevertheless, there are a number of definitions of macromolecule volume. For example, the concept of hydrodynamic volume is used to characterize a space occupied by the macromolecule together with its impregnating solvent. Or the volume may be defined by measuring the structures observed with the electron microscope, using X-ray small-angle scattering, etc. Of special interest are the macromolecule volume values obtained under conditions approaching natural ones, i.e. without electron beams or X rays, without applying great hydrodynamic fields and hydrostatic pressure, and
Indoor location with Wi-Fi fingerprinting (2013)

There are many applications for indoor location determination, from the navigation of hospitals, airports, parking garages and shopping malls, for example, to navigational aids for the blind and visually impaired, targeted advertising, mining, and disaster response. GPS signals are too weak for indoor use, however, making it necessary to investigate other means of navigation. Most approaches such as ultrasound and RFID tags require special hardware to be installed and remain expensive and inconvenient. The solution proposed in this paper makes use of commonly available Wi-Fi networks and runs on ordinary smart phones and tablets without the need to install special hardware. It comprises a calibration stage and a navigation stage. The calibration stage creates a “Wi-Fi fingerprint” for each room of a building. It minimizes the calibration time through the use of waypoints. The navigation stage matches Wi-Fi signals to the fingerprints to determine the user's most likely location. It uses maximum likelihood classification for this matching and takes the building's topology into account through the use of Bayes' Theorem. The system is implemented as a mobile Android app and is easy to use. In testing, it took only an hour to calibrate a home or shopping mall, and the navigation stage yielded the correct location 97.5% of the time in a home and 100% of the time in a mall.
Pilot design for OFDM systems in the presence of phase noise (2010)

The bit error rate performance of orthogonal frequency division multiplexing (OFDM) systems is severely degraded in the presence of phase noise. The effect of phase noise on an OFDM signal has been studied in the literature. The OFDM signal sub-carriers are distorted due to phase noise in two ways. First is the constant phase shift of all the sub-carriers, and second is the inter-carrier interference. A pilot structure is proposed to estimate the phase noise spectral components in every data OFDM symbol. The pilot design parameters are specifically optimized for an OFDM system in the presence of phase noise.
Relationship Between Sperm Viability as Determined by Flow Cytometry and Nonreturn Rate of Dairy Bulls (2005)

A newly developed flow cytometric method for determination of sperm concentration and viability was tested in an insemination trial with cryopreserved bull sperm to establish the relationship between sperm viability and nonreturn rates. Semen for experimental inseminations was produced from 157 young sires (114 Holstein and 43 Jersey), each contributing 4 experimental semen collections. Straws containing approximately 15 x 10(6) motile sperm before freezing were used in 118,680 experimental inseminations performed by 254 artificial insemination technicians in 6352 Danish herds. Statistical analysis based on 44,946 experimental first inseminations showed that the major part (95.4%) of variation in the 56-day nonreturn rate (NRR56) was residual. Only 0.38% of the total variation in NRR56 was due to bulls and differences between ejaculate within bull. However, bulls were preselected, and a relatively high insemination dose was used. Correlations between sperm viability as assessed by flow cytometry and NRR56 was slightly lower than observed for microscopic assessment of sperm motility. However, flow cytometry makes it possible to achieve an objective and precise determination of sperm viability. It was therefore possible to calculate the effect on NRR56 provided selection of semen is based on the flow cytometric method. Three freezing extenders were used in this experiment, but a significant difference in NRR56 was not observed. Flow cytometric results for 1 extender (Biociphos Plus) indicated poorer sperm survival during postthaw incubation compared with Triladyl extender with whole and with clarified egg yolk.
A general sampling theory for nonideal acquisition devices (1994)

The authors first describe the general class of approximation spaces generated by translation of a function /spl psi/(x), and provide a full characterization of their basis functions. They then present a general sampling theorem for computing the approximation of signals in these subspaces based on a simple consistency principle. The theory puts no restrictions on the system input which can be an arbitrary finite energy signal; bandlimitedness is not required. In contrast to previous approaches, this formulation allows for an independent specification of the sampling (analysis) and approximation (synthesis) spaces. In particular, when both spaces are identical, the theorem provides a simple procedure for obtaining the least squares approximation of a signal. They discuss the properties of this new sampling procedure and present some examples of applications involving bandlimited, and polynomial spline signal representations. They also define a spectral coherence function that measures the "similarity" between the sampling and approximation spaces, and derive a relative performance bound for the comparison with the least squares solution.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The K101P and K103R/V179D Mutations in Human Immunodeficiency Virus Type 1 Reverse Transcriptase Confer Resistance to Nonnucleoside Reverse Transcriptase Inhibitors (2005)

Genotypic patterns associated with nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance in the absence of well-characterized resistance mutations were identified using a database (n > 47,000) of phenotype-genotype data. Among samples with no known NNRTI mutations, the most resistant samples contained K101P (n = 35) or a combination of K103R and V179D (n = 41). Site-directed mutagenesis confirmed the importance of these mutations.
COPOLYMER 1 INHIBITS MANIFESTATIONS OF GRAFT REJECTION1 (2001)

Cop 1 treatment inhibited the Th1 response to graft and induced a Th2 cytokines secretion in response to both Cop 1 and graft cells, leading to improved survival and function of the transplanted grafts.
An Ion Trap Interface for ESI−Ion Mobility Experiments (1997)

A method for improving the sensitivity of ion mobility measurements of ions generated from continuous ionization sources such as electrospray ionization is described. The method involves an ion trap interface between the continuous source and the pulsed experiment. The trap allows the electrosprayed ion beam to be accumulated between pulses of the mobility experiment and provides tightly focused (both spatially and temporally) ion pulses for initiating experiments. Using this method, we have improved signal-to-noise ratios by factors of ∼10−30 compared with those of existing approaches and achieved experimental duty cycles of nearly 100%. With these improvements, it is possible to record complex ion mobility distributions in less than 10 s, and we have obtained detection limits of 1.3 pmol for the oligosaccharide maltotetraose. A detailed description of the experimental arrangement is given. An application of the improved methods in which collision-induced fragmentation of biomolecules is monitored by ion mobility spectrometry is described.
The human DNA-activated protein kinase, DNA-PK: Substrate specificity (1994)

Although much has been learned about the structure and function of p53 and the probable sequence of subsequent events that lead to cell cycle arrest, little is known about how DNA damage is detected and the nature of the signal that is generated by DNA damage. Circumstantial evidence suggests that protein kinases may be involved. In vitro, human DNA-PK phosphorylates a variety of nuclear DNA-binding, regulatory proteins including the tumor suppressor protein p53, the single-stranded DNA binding protein RPA, the heat shock protein hsp90, the large tumor antigen (TAg) of simian virus 40, a variety of transcription factors including Fos, Jun, serum response factor (SRF), Myc, Sp1, Oct-1, TFIID, E2F, the estrogen receptor, and the large subunit of RNA polymerase II (reviewed in Anderson, 1993; Jackson et al., 1993). However, for most of these proteins, the sites that are phosphorylated by DNA-PK are not known. To determine if the sites that were phosphorylated in vitro also were phosphorylated in vivo and if DNA-PK recognized a preferred protein sequence, the authors identified the sites phosphorylated by DNA-PK in several substrates by direct protein sequence analysis. Each phosphorylated serine or threonine is followed immediately by glutamine in the polypeptide chain; at no other positions are the amino acid residues obviously constrained.
Lignin Characterization of Waste Liquor by Modified Pulping Process (1995)

This study was carried out to investigate the characterization of lignins from waste liquors in SP, KP, ASAM, and AS from Pinus densiflora, Quercus mongolica, and Betula ermanii. Spectroscopic study was applied to examine the lignins separated from different pulping process. Lignin contents in waste liqours increased in order of AS, ASAM, KP, and SP. UV spectra of three types of lignin except AS lignin showed similar pattern. IR spectra of AS lignin showed strong C=O absorptions in the range from 1730 to 1750, where as those of KP, SP, and ASAM showed weak stretch in this region. NMR spectra of AS lignin showed strong characteristic chemical shifts of acetoxyl groups of acetylated aliphatic and aromatic hydroxyl groups at 2.0~2.5 ppm. Molecular weight of ASAM lignin from Pinus densiflora determined and found number average molecular weight 1,199, weight average molecular weight 5,458. z average molecular weight 17,242, and viscosity average molecular weight 5,457. It is considered from the results based on spectroscopic study of lignin that waste liquors (in SP, KP, ASAM and AS) from Pinus densiflora, Quercus mongolica, and Betula ermanii can be used for lignin utilization.
Image and video compression (1998)

The authors discuss the underlying principles of image and video compression. The network model they use for image compression is the random neural network (RNN). This pulsed network model provides a somewhat more accurate representation of what occurs in "real" neurons. Signals in the form of pulse trains travel between neurons. These pulses can be either excitatory (we call these "positive" pulses), or they can be inhibitory or "negative". Just like many naturally occurring neural nets, these pulses all have the same magnitude which is normalized as 1. A neuron in the RNN emits pulses at an instantaneous rate proportional to its degree of excitation and to its rate of firing. Besides being more accurate, the RNN is also useful because an algorithm, which allows for the training of a fully recurrent RNN, has been designed. This means it is possible to find good weights between neurons even if every neuron has a connection to every other neuron. This full recurrence is not easily allowed in standard back propagation networks.
A scalable complex event processing framework for combination of SQL-based continuous queries and C/C++ functions (2012)

SQL-based languages are widely used for Software-based Complex Event Processing (CEP) systems. This paper proposes a FPGA acceleration framework to compile a SQL-based event processing language, which is based on the ANSI standard proposal to support event processing, into a high-performance CEP engine on FPGAs. Besides the SQL's primitives such as partitioning, windowing, aggregation and pattern matching, the proposed framework allows C/C++ functions to implement complex algorithms required by real-world applications. The CEP engine also scales very efficiently processing multiple streams in parallel by making use of inexpensive block memories. Experimental results show that our proposed CEP engine, which is compiled for a financial analysis application calculating a popular trading benchmark to capture meaningful market trends, achieves 150M events/sec (20Gbps) processing performance for over 16,000 streams.
Comparison of two quantitative hepatitis C virus reverse transcriptase PCR assays (1996)

A quantitative hepatitis C virus reverse transcriptase PCR (HCV RT-PCR) assay established in our laboratory was compared with the Roche Amplicor HCV Monitor test kit for agreement of test results and intra-assay variability. Both assays rely on reverse transcription and amplification of extracted RNA from patients' sera together with an internal RNA standard derived from the 5'-noncoding region of HCV. A panel of clinical serum samples (n = 33) was quantitatively analyzed in parallel by both test systems. The methods demonstrated substantial agreement between 1 x 10(3) and 5 x 10(5) HCV RNA molecules per ml of serum. However, with sera containing more than 5 x 10(5) copies per ml, according to our in-house assay, the results diverged on average in a nonacceptable range of 2 orders of magnitude. Our in-house HCV RT-PCR assay measured up to 5 x 10(7) HCV-RNA molecules per ml in some serum samples. However, the Roche Amplicor HCV Monitor test kit did not detect more than 2 x 10(6) molecules in any of the serum samples tested. After dilution of serum samples prior to testing, an approximately 0.5 order of magnitude more HCV RNA molecules was detected by the Roche HCV test kit in sera containing high copy numbers (> 5 x 10(5) RNA copies according to the in-house assay). The in-house PCR and the Roche Amplicor HCV Monitor test kit revealed coefficients of variation of 6.2 and 7.5%, respectively.
Inhibition of coronary thrombosis and local inflammation by a noncarbohydrate selectin inhibitor (2000)

We tested the hypothesis that selectin inhibition with blocking antibodies or a small-molecular-weight inhibitor of L-, P-, and E-selectin, methoxybenzoylpropionic acid (MBPA), prevents thrombus formation in a canine coronary Folts' model. Cyclic flow variations (CFVs) were induced by crush injury and constriction of the left anterior descending coronary artery in dogs. Systemic infusion of antibodies to P- and L-selectin abolished CFVs, respectively, in 50% and 17% of treated dogs [P = not significant (NS)]. The combination of P- and L-selectin antibodies suppressed CFVs in 60% of treated dogs (P = NS). In contrast, systemic selectin blockade by intravenous infusion or local adventitial application of MBPA markedly reduced CFVs and, in addition, reduced myocardial myeloperoxidase (MPO) activity. We conclude that inhibition of L-, P-, and E-selectin binding by a small-molecular-weight, noncarbohydrate compound markedly reduces arterial thrombosis, whereas systemic administration of antibodies to L- and P-selectin fail to reproduce this antithrombotic effect. These results underscore the role of selectins in the pathogenesis of arterial thrombosis under high shear stress and suggest that inhibition of P- and L- selectin may not suffice to prevent thrombus formation in this model. The role of E-selectin in thrombus formation in this model awaits further testing.
Efficacy of Memantine in Acute Non-Arteritic Ischemic Optic Neuropathy (2008)

Purpose: Evaluation of efficacy of Memantine (N-Methyl-D-Aspartate Receptor Antagonist) on visual function of patients with acute non-arteritic ischemic optic neuropathy (NAION). Methods: The study was conducted as interventional case series from November 2005 through November 2006 in Farabi Eye Hospital. Twenty-two patients with acute NAION of less than 8 weeks duration entered the study. Memantine was prescribed with a dose of 5 mg per day for the first week and 10 mg per day for the following two weeks. Baseline best corrected visual acuity (BCVA); visual evoked potential (VEP) and visual field was done for all patients. BCVA recording repeated 3 weeks, 3 and 6 months later. VEP and perimetry repeated 3 months after treatment. Results: After 3 weeks, 3 and 6 months, BCVA improved -0.32±0.40 LogMAR, -0.51±0.49 and -0.51±0.49, respectively (P=0.005, P=0.001 and P=0.001, respectively). VEP recordings after 3 months, demonstrated -8.61±14.51 db mean decrease in implicit time (P=0.019). Amplitude of voltage did not show significant difference with baseline (P=0.10). Perimetry results after 3 months showed that mean deviation (MD) improved 2.77± 3.94 db (P=0.016). Conclusion: Memantine resulted in significant improvement of BCVA 3 weeks, 3 and 6 months after treatment of acute NAION. Memantine also resulted in significant decrease of implicit time and significant improvement of mean deviation in VEP and perimetry after 3 months.
Detection of Large COOH-Terminal Domains Processed from the Precursor of Serratia marcescens Serine Protease in the Outer Membrane of Escherichia coli (1992)

The Serratia marcescens serine protease gene encoding a 1,045-amino-acid precursor protein of 112 kDa directs excretion of the mature protease of ca. 58 kDa through the outer membrane of Escherichia coli. A typical signal peptide of 27 amino acids and a large COOH-terminal domain of the precursor are both functionally essential for the excretion of the mature protease into the medium. Sequence analysis of the fragment peptides of the mature protease as well as site-directed mutagenesis indicated that the COOH-terminus of the mature enzyme was Asp645. By using the polyclonal antibody against the 112-kDa precursor protein, not only the intact precursor but also two proteins, C-1 (40 kDa) and C-2 (38 kDa), corresponding to the processed COOH-terminal domains were detected in the insoluble fraction of E. coli cells. Further fractionation by sucrose density gradient centrifugation showed that C-1 and C-2 were localized in the outer membrane. The NH2-terminal residues of C-1 and C-2 were determined to be Ala702 and Phe717, respectively. All these data suggest that the precursor is cleaved at three positions, between Asp645-Ser646, Glu701-Ala702, and Gly716-Phe717, probably by the self-processing activity in the normal excretion pathway through the outer membrane.
Cold-Active Winter Rye Glucanases with Ice-Binding Capacity (2006)

Extracellular pathogenesis-related proteins, including glucanases, are expressed at cold temperatures in winter rye (Secale cereale) and display antifreeze activity. We have characterized recombinant cold-induced glucanases from winter rye to further examine their roles and contributions to cold tolerance. Both basic beta-1,3-glucanases and an acidic beta-1,3;1,4-glucanase were expressed in Escherichia coli, purified, and assayed for their hydrolytic and antifreeze activities in vitro. All were found to be cold active and to retain partial hydrolytic activity at subzero temperatures (e.g. 14%-35% at -4 degrees C). The two types of glucanases had antifreeze activity as measured by their ability to modify the growth of ice crystals. Structural models for the winter rye beta-1,3-glucanases were developed on which putative ice-binding surfaces (IBSs) were identified. Residues on the putative IBSs were charge conserved for each of the expressed glucanases, with the exception of one beta-1,3-glucanase recovered from nonacclimated winter rye in which a charged amino acid was present on the putative IBS. This protein also had a reduced antifreeze activity relative to the other expressed glucanases. These results support the hypothesis that winter rye glucanases have evolved to inhibit the formation of large, potentially fatal ice crystals, in addition to having enzymatic activity with a potential role in resisting infection by psychrophilic pathogens. Glucanases of winter rye provide an interesting example of protein evolution and adaptation aimed to combat cold and freezing conditions.
The economic background [June 1997] (1997)

Concerns over the 1995 slowdown in the world economy are subsiding as recovery continues through 1996. The US and Japan are leading the recovery with European growth expected to strengthen later this year. Recent loose monetary policy, recovery from shocks and a relaxation of fiscal policy have all contributed to renewed growth. G7 growth is forecast to be 2.3% in 1996 and 2.5% in 1997 whilst OECD growth is forecast at 2.3 % and 2.6% in 1996 and 1997 respectively.