gebhart/patrepeval huggingface dataset:
OmpA fusion proteins for presentation of foreign antigens on the bacterial outer membrane. (1995)

The ompA genes of Escherichia coli and Shigella dysenteriae have been used to construct a group of enterobacterial surface expression vectors for foreign genes. Linker oligonucleotides were inserted into the sequence corresponding to the third or fourth outer domain to allow in-frame sandwich fusion of foreign genes or epitopes into ompA. Influenza haemagglutinin was inserted without its leader peptide and anchor sequences and shown to be transferred as an ompA fusion protein to the bacterial surface in large amounts. The stability of this system depends on the stem structure (i.e. the bottom part) of the haemagglutinin unit which apparently initiates the folding process that extends into the ompA segment. This fusion construct can be used as a vector system and has been used to transfer to the bacterial surface several other proteins inserted into it, including beta-galactosidase, foot-and-mouth disease virus (FMDV) and malaria antigens. All are exported from the cytoplasm across both the inner and outer membranes to become exposed on the bacterial surface. Very hydrophobic segments or inserts with distinct secondary structures, such as the capsid protein, VP1 of FMDV, will, however, block this process.
Behavioral-based cheating detection in online first person shooters using machine learning techniques (2013)

Cheating in online games comes with many consequences for both players and companies. Therefore, cheating detection and prevention is an important part of developing a commercial online game. Several anti-cheating solutions have been developed by gaming companies. However, most of these companies use cheating detection measures that may involve breaches to users' privacy. In our paper, we provide a server-side anti-cheating solution that uses only game logs. Our method is based on defining an honest player's behavior and cheaters' behavior first. After that, using machine learning classifiers to train cheating models, then detect cheaters. We presented our results in different organizations to show different options for developers, and our methods' results gave a very high accuracy in most of the cases. Finally, we provided a detailed analysis of our results with some useful suggestions for online games developers.
Methods for identifying proteins by using partial sequences (1979)

Methods for the identification of a protein segment by using the information from partial sequence analyses are described. If the protein sequence is known, a segment can usually be identified with confidence through comparison with the data file of all known sequences when the identity and position of only seven amino acid residues (not necessarily contiguous) are known. Partial sequences are obtained from extremely sensitive microsequencing procedures. Tissue is incubated with amino acids, one or more of which are distinctively radiolabeled. Proteins of interest are isolated and a sequenator experiment performed to locate the positions of radioactivity in an NH(2)-terminal segment of approximately 30 residues. We derive and investigate an equation for the probability of finding a unique match to any pattern of radioactivity. From this we suggest a new strategy. In one incubation, several amino acids are labeled with each kind of isotope. The most information is contained in patterns in which approximately equal numbers of positions are occupied by residues distinguished by different labels (including no label). The amino acid composition of the segment will typically not be known in advance. Labeling residues expected to occupy 36% of the positions suffices for a 98% chance of success in uniquely characterizing any human segment. Such a strategy will permit the identification of most proteins from a single tissue incubation. The mathematical discussion is general and applies to any segment from a sequence and to sequences obtained by any method. Improved identification procedures should expedite the accumulation of information on the expression and function of proteins.
Sparse matrices in CS education (2009)

Most college undergraduate computer science and mathematics textbooks on algorithms, matrix algebra, linear algebra, discrete math, or data structures do not provide even introductory material on the subject of sparse matrices. However in real world practice, most large and important applications of matrix algebra involve sparse matrices. Thus the computer science or CIS/IT student is ill prepared for real world applications in this field. This paper defines and illustrates sparse matrices, discusses the types of sparse matrices, and provides examples of general data structures and algorithms for efficient solution of sparse matrix problems.
Production of human hematopoietic survival and growth factor by a myeloid leukemia cell line (KPB-M15) and placenta as detected by a monoclonal antibody. (1987)

Fifty-five hematopoietic cell lines, including 19 T-, 16 B-, 5 pre-B-, 5 non-T non-B-, 1 erythroid, and 9 myeloid-monocytoid cells, were screened for production of human hematopoietic survival and stem cell growth factor (SCGF) by enzyme immunoassay using anti-SCGF monoclonal antibody. The KPB-M15 myeloid cell line constitutionally secreted a considerable quantity of SCGF, while other T- or myeloid-monocytoid cell lines did not secrete SCGF. Other biomaterials investigated were fetal calf, horse, and human serum; granulocyte-macrophage colony-stimulating factor and erythropoietin preparations; human placental conditioned medium; lectin (phytohemagglutinin, concanavalin A, and pokeweed mitogen); and mixed leukocyte reaction-stimulated leukocyte-conditioned medium. SCGF was detected only in human placental conditioned medium. SCGF produced by the KPB-M15 cells was a protein with a molecular weight of 20,000. The molecule, highly purified by immunoadsorbent affinity chromatography, retained SCGF activity in vitro, e.g., erythroid burst-promoting activity and granulocyte-macrophage-colony potentiation. With the availability of purified SCGF, it is now possible to study in detail the mechanisms regulating hematopoietic stem cells.
Metal–Organic Frameworks Based on Previously Unknown Zr8/Hf8 Cubic Clusters (2013)

The ongoing study of zirconium- and hafnium-porphyrinic metal-organic frameworks (MOFs) led to the discovery of isostructural MOFs based on Zr8 and Hf8 clusters, which are unknown in both cluster and MOF chemistry. The Zr8O6 cluster features an idealized Zr8 cube, in which each Zr atom resides on one vertex and each face of the cube is capped by one μ4-oxygen atom. On each edge of the cube, a carboxylate from a porphyrinic ligand bridges two Zr atoms to afford a 3D MOF with a very rare (4,12)-connected ftw topology, in which two types of polyhedral cages with diameters of ∼1.1 and ∼2.0 nm and a cage opening of ∼0.8 nm are found. The isostructural Zr- and Hf-MOFs exhibit high surface areas, gas uptakes, and catalytic selectivity for cyclohexane oxidation.
A>400 GHz f/sub max/ transferred-substrate heterojunction bipolar transistor IC technology (1998)

We report transferred-substrate AlInAs/GaInAs bipolar transistors. A device having a 0.6 μm×25 μm emitter and a 0.8 μm×29 μm collector exhibited f/sub /spl tau//=134 GHz and f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> >400 GHz. A device with a 0.6 μm×25 μm emitter and a 1.8 μm×29 μm collector exhibited 400 GHz f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> 164 GHz f/sub /spl tau//. The improvement in f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> over previous transferred-substrate HBT's is due to improved base Ohmic contacts, narrower emitter-base and collector-base junction areas, and slightly reduced transit times. The transferred-substrate fabrication process provides electroplated gold thermal vias for transistor heat-sinking and a microstrip wiring environment on a low dielectric constant polymer substrate.
Intrahepatic Transplanted Islets in Humans Secrete Insulin in a Coordinate Pulsatile Manner Directly Into the Liver (2006)

Intrahepatic islet transplantation is an experimental therapy for type 1 diabetes. In the present studies, we sought to address the following questions: 1) In humans, do intrahepatic transplanted islets reestablish coordinated puslatile insulin secretion? and 2) To what extent is insulin secreted by intrahepatic transplanted islets delivered to the hepatic sinusoids (therefore effectively restoring a portal mode of insulin delivery) versus delivered to the hepatic central vein (therefore effectively providing a systemic form of insulin delivery)? To address the first question, we examined insulin concentration profiles in the overnight fasting state and during a hyperglycemic clamp ( approximately 150 mg/dl) in 10 recipients of islet transplants and 10 control subjects. To address the second question, we measured first-pass hepatic insulin clearance in two recipients of islet autografts after pancreatectomy for pancreatitis versus five control subjects by direct catheterization of the hepatic vein. We report that coordinate pulsatile insulin secretion is reestablished in islet transplant recipients and that glucose-mediated stimulation of insulin secretion is accomplished by amplification of insulin pulse mass. Direct hepatic catheterization studies revealed that intrahepatic islets in humans do deliver insulin directly to the hepatic sinusoid because approximately 80% of the insulin is extracted during first pass. In conclusion, intrahepatic islet transplantation effectively restores the liver to pulsatile insulin delivery.
Selective deamidation by tissue transglutaminase strongly enhances gliadin-specific T cell reactivity. (1998)

Celiac disease (CD) is caused by gluten ingestion in susceptible individuals. Tissue transglutaminase (tTG)-specific Abs are characteristic of CD, and increased tTG activity has been observed in the jejunal biopsies of patients. Here we demonstrate that tTG selectively deamidates gluten peptides, which results in strongly enhanced T cell-stimulatory activity. To our knowledge, this is the first example of an enzymatic modification of a food protein that affects T cell recognition. Moreover, these modifications may lead to the amplification of gluten-specific T cell responses in the gut and consequently may be important for the development of CD.
Monocyte chemotactic proteins MCP‐1, MCP‐2, and MCP‐3 are major attractants for human CD4 + and CD8 + T lymphocytes (1994)

The responses of lymphocytes to six CC chemokines--MCP-1, MCP-2, MCP-3, MIP-1 alpha, MIP-1 beta, and RANTES--were studied using cloned human CD4+ and CD8+ T cells. All CC chemokines tested induced migration of both types of lymphocytes, whereas two CXC chemokines used as controls, IL-8 and IP-10, were inactive. The monocyte chemotactic proteins (MCP-1, MCP-2, and MCP-3) showed a typically bimodal concentration dependence, and were considerably more effective than MIP-1 alpha, MIP-1 beta, or RANTES. All CC chemokines also induced a rapid and transient rise in cytosolic free Ca2+ in either type of T cell. The rise was prevented by Bordetella pertussis toxin treatment, indicating that G-protein-coupled receptors are involved in signaling. It was most pronounced with MCP-1 and MCP-3, which is in agreement with the efficacy of these chemokines as chemoattractants. The responses to MCP-2, MIP-1 alpha, MIP-1 beta, and RANTES were weaker, and no changes were obtained on stimulation with IL-8 or IP-10. Freshly isolated human blood lymphocytes were also tested, but neither migration nor Ca2+ changes were observed. Low numbers of high-affinity receptors for MCP-1 were found on CD4+ and CD8+ cells ( < 900 per cell, Kd < 1 nM), and desensitization experiments showed that MCP-1, MCP-2, and MCP-3 share receptors. Owing to their superior effectiveness on CD4+ and CD8+ T cells, the monocyte chemotactic proteins could play a major role in the recruitment of activated T lymphocytes.
Structural Analysis of the Mitotic Regulator hPin1 in Solution (2003)

The peptidyl-prolyl cis/trans isomerase hPin1 is a phosphorylation-dependent regulatory enzyme whose substrates are proteins involved in regulation of cell cycle, transcription, Alzheimer's disease, and cancer pathogenesis. We have determined the solution structure of the two domain protein hPin1-(1-163) and its separately expressed PPIase domain (50-163) (hPin1PPIase) with an root mean square deviation of <0.5 A over backbone atoms using NMR. Domain organization of hPin1 differs from that observed in structures solved by x-ray crystallography. Whereas PPIase and WW domain are tightly packed onto each other and share a common binding interface in crystals, our NMR-based data revealed only weak interaction of both domains at their interface in solution. Interaction between the two domains of full-length hPin1 is absent when the protein is dissected into the catalytic and the WW domain. It indicates that the flexible linker, connecting both domains, promotes binding. By evaluation of NOESY spectra we can show that the alpha1/beta1 loop, which was proposed to undergo a large conformational rearrangement in the absence of sulfate and an Ala-Pro peptide, remained in the closed conformation under these conditions. Dissociation constants of 0.4 and 2.0 mm for sulfate and phosphate ions were measured at 12 degrees C by fluorescence spectroscopy. Binding of sulfate prevents hPin1 aggregation and changes surface charges across the active center and around the reactive and catalytically essential Cys113. In the absence of sulfate and/or reducing agent this residue seems to promote aggregation, as observed in hPin1 solutions in vitro.
Structural features of Salmonella typhimurium lipopolysaccharide required for activation of tissue factor in human mononuclear cells. (1977)

Activation of mononuclear cell tissue factor was examined utilizing lipopolysaccharides obtained from wild-type and both Rc and Re mutants of Salmonella typhimurium. Wild-type (smooth) lipopolysaccharide, galactose-deficient (Rc) lipopolysaccharide, heptose-deficient (Re) lipopolysaccharide, and lipid A preparations were all active in their ability to generate tissue factor activity in human mononuclear cells grown in tissue culture. Polymyxin B has been reported to prevent some of the lethal effects of endotoxin in vivo, and the drug reportedly binds to the 2-keto-3-deoxyoctulosonate-lipid A region of the lipopolysaccharide molecule. Polymyxin B was effective in inhibiting the tissue factor generating activity of wild-type lipopolysaccharide, Re lipopolysaccharide, and lipid A in a dose-dependent fashion. Treatment of lipid A preparations with mild alkali abolished the ability of these preparations to activate tissue factor in cells. Analogous to many of the other biologic properties of lipopolysaccharide, tissue factor activation in human mononuclear cells appears to depend upon the integrity of the lipid A portion of the molecule.
Optical network unit based on a bidirectional reflective semiconductor optical amplifier for fiber-to-the-home networks (2004)

An optical access network transceiver based on a reflective semiconductor optical amplifier operating as modulator and photodetector is demonstrated. Device characterization and modulation/detection tests show the system proper operation at 1.25 Gb/s to 30-km reach. This optical network unit design is a simple and capable solution for future fiber-to-the-home networks.
Synthesis of nuclelc acid methylphosphonothloates (1988)

The reagent obtained in situ by treating methylphosphonothioic dichloride with 1-hydroxy-6-trifluoromethylbenzotriazole could be used for the introduction of methylphosphonothioate linkages. The individual diastereomers of the protected dimer d-Tp(S,Me)A were applied in the synthesis of the chiral pure (R or S) hexamers d-[CpCpTp(S,Me)ApGpG]. The reagent showed also to be very effective for the preparation of the 3',5'-cyclic methylphosphonothioate of uridine.
Kinetics of Hyaluronan Hydrolysis in Acidic Solution at Various pH Values (2008)

Hyaluronic acid (HA) was hydrolyzed using varying temperatures (40, 60, and 80 degrees C) and acid concentrations (0.0010, 0.010, 0.10, 0.50, 1.0, and 2.0 M HCl). The degradation process was monitored by determination of weight average molecular weight ( M w) by size-exclusion chromatography with online multiangle laser light scattering, refractive index, and intrinsic viscosity detectors (SEC-MALLS-RI-visc) on samples taken out continuously during the hydrolysis. SEC-MALLS-RI-visc showed that the degradation gave narrow molecular weight distributions with polydispersity indexes ( M w/ M n) of 1.3-1.7. Kinetic plots of 1/ M w versus time gave linear plots showing that acid hydrolysis of HA is a random process and that it follows a first order kinetics. For hydrolysis in HCl at 60 and 80 degrees C, it was shown that the kinetic rate constant ( k h) for the degradation depended linearly on the acid concentration. Further, the dependence of temperature on the hydrolysis in 0.1 M HCl was found to give a linear Arrhenius plot (ln k h vs 1/ T), with an activation energy ( E a) of 137 kJ/mol and Arrhenius constant ( A) of 7.86 x 10 (15) h (-1). (1)H NMR spectroscopy was used to characterize the product of extensive hydrolysis (48 h at 60 degrees C in 0.1 M HCl). No indication of de- N-acetylation of the N-acetyl glucosamine (GlcNAc) units or other byproducts were seen. Additionally, a low molecular weight HA was hydrolyzed in 0.1 M DCl for 4 h at 80 degrees C. It was shown that it was primarily the beta-(1-->4)-linkage between GlcNAc and glucuronic acid (GlcA) that was cleaved during hydrolysis at pH < p K a,GlcA. The dependence of the hydrolysis rate constant was further studied as a function of pH between -0.3 and 5. The degradation was found to be random (linear kinetic plots) over the entire pH range studied. Further, the kinetic rate constant was found to depend linearly on pH in the region -0.3 to 3. Above this pH (around the p K a of HA), the kinetic constant decreased more slowly, probably due to either a change in polymer conformation or due to an increased affinity for protons due to the polymer becoming charged as the GlcA units dissociated.
The past, present, and future of soils and human health studies (2015)

Abstract. The idea that human health is tied to the soil is not a new one. As far back as circa 1400 BC the Bible depicts Moses as understanding that fertile soil was essential to the well-being of his people. In 400 BC the Greek philosopher Hippocrates provided a list of things that should be considered in a proper medical evaluation, including the properties of the local ground. By the late 1700s and early 1800s, American farmers had recognized that soil properties had some connection to human health. In the modern world, we recognize that soils have a distinct influence on human health. We recognize that soils influence (1) food availability and quality (food security), (2) human contact with various chemicals, and (3) human contact with various pathogens. Soils and human health studies include investigations into nutrient supply through the food chain and routes of exposure to chemicals and pathogens. However, making strong, scientific connections between soils and human health can be difficult. There are multiple variables to consider in the soil environment, meaning traditional scientific studies that seek to isolate and manipulate a single variable often do not provide meaningful data. The complete study of soils and human health also involves many different specialties such as soil scientists, toxicologists, medical professionals, anthropologists, etc. These groups do not traditionally work together on research projects, and do not always effectively communicate with one another. Climate change and how it will affect the soil environment/ecosystem going into the future is another variable affecting the relationship between soils and health. Future successes in soils and human health research will require effectively addressing difficult issues such as these.
Polymerized pyridoxylated hemoglobin: a red cell substitute with normal oxygen capacity. (1984)

Polymerization of pyridoxylated stroma free hemoglobin (poly SFH-P) yields a solution with a normal hemoglobin concentration, normal colloid osmotic pressure (COP), and a suitable P50. In the present study we compared its in vivo O2-carrying capacity and intravascular persistence with those of pyridoxylated hemoglobin (SFH-P), following a partial exchange transfusion (900 ml) in adult baboons (n = 4 in each group). Poly SFH-P in plasma had an O2-carrying capacity that was 77% greater than that achieved with SFH-P (8.0 versus 4.5 vol%). Furthermore, poly SFH-P provided 5.0 vol% at the end of 24 hours and 2.5 vol% at the end of 48 hours; in contrast SFH-P provided only 2.2 vol% at the end of 6 hours and none within 24 hours. A normal COP was maintained throughout the postexchange period with poly SFH-P despite a 68% increase in plasma protein concentration (from 7.1 to 11.9 gm/dl). The plasma P50 of poly SFH-P decreased from 16 torr immediately after exchange to 12 torr at the end of 48 hours. The in vivo rate of conversion to methemoglobin was similar with both solutions. Polymerized pyridoxylated hemoglobin is currently the only modification of hemoglobin solution that approximates the O2-carrying capacity of whole blood and can be infused without altering the plasma COP.
Suppressive effect of Lactobacillus gasseri OLL 2716 (LG21) on Helicobacter pylori infection in humans (2001)

To examine the efficacy of Lactobacillus gasseri OLL2716 (LG21) as a probiotic for Helicobacter pylori in humans, 31 subjects infected with the bacterium ingested yogurt containing LG21 daily for an 8 week period. The [(13)C]urea breath test and assays of serum pepsinogens revealed a significant improvement following LG21 treatment. LG21 was thus determined to be effective in both suppressing H. pylori and reducing gastric mucosal inflammation.
On robustness of on-line boosting - a competitive study (2009)

On-line boosting is one of the most successful on-line algorithms and thus applied in many computer vision applications. However, even though boosting, in general, is well known to be susceptible to class-label noise, on-line boosting is mostly applied to self-learning applications such as visual object tracking, where label-noise is an inherent problem. This paper studies the robustness of on-line boosting. Since mainly the applied loss function determines the behavior of boosting, we propose an on-line version of GradientBoost, which allows us to plug in arbitrary loss-functions into the on-line learner. Hence, we can easily study the importance and the behavior of different loss-functions. We evaluate various on-line boosting algorithms in form of a competitive study on standard machine learning problems as well as on common computer vision applications such as tracking and autonomous training of object detectors. Our results show that using on-line Gradient-Boost with robust loss functions leads to superior results in all our experiments.
Darwinian invention and problem solving by means of genetic programming (2003)

Demonstrates that genetic programming is capable of automatically creating computer programs from a high-level statement of a problem's requirements and of producing human-competitive results.