gebhart/patrepeval huggingface dataset:
Sequence of the pckA gene of Escherichia coli K-12: relevance to genetic and allosteric regulation and homology of E. coli phosphoenolpyruvate carboxykinase with the enzymes from Trypanosoma brucei and Saccharomyces cerevisiae (1990)

The sequence of the pckA gene coding for phosphoenolpyruvate carboxykinase in Escherichia coli K-12 and previous molecular weight determinations indicate that this allosteric enzyme is a monomer of Mr 51,316. The protein is homologous to ATP-dependent phosphoenolpyruvate carboxykinases from Trypanosoma brucei and Saccharomyces cerevisiae. A potential ATP binding site was conserved in all three sequences. A potential binding site for the allosteric activator, calcium, identified in the E. coli enzyme, was only partially conserved in T. brucei and S. cerevisiae, consistent with the observation that the enzymes from the latter organisms were not activated by calcium. The published sequence of the ompR and envZ genes from Salmonella typhimurium is followed by a partial sequence that is highly homologous to pckA from E. coli. The order of these genes and the direction of transcription of the presumptive S. typhimurium pckA gene are the same as those in E. coli. The potential calcium binding site of the E. coli enzyme is conserved in the partial predicted sequence of the S. typhimurium phosphoenolpyruvate carboxykinase, consistent with the observation that calcium activation of the S. typhimurium phosphoenolpyruvate carboxykinase is very similar to that observed for the E. coli enzyme. A pckA mRNA transcript was observed in stationary-phase cells but not in logarithmically growing cells. The mRNA start site was mapped relative to the sequence of the pckA structural gene.
Joint spatial division and multiplexing: Realizing massive MIMO gains with limited channel state information (2012)

We propose Joint Spatial Division and Multiplexing (JSDM), an approach to multiuser MIMO downlink that exploits the structure of the channel vectors correlation in order to allow for a large number of base station antennas while requiring a considerably reduced channel state information (CSI) feedback from the users. Thanks to the reduced CSI requirement, JSDM allows the use of a large number of base station antennas also in FDD systems. This work presents the correlated channel model, the main idea of JSDM precoding, and the design of JSDM precoding, formed by the concatenation of a pre-beamforming matrix based only on the structure of the channel covariance, with suitable multiuser precoding based on the CSI of the reduced dimensional transformed channels. We show that in some cases JSDM incurs no loss of optimality with respect to the MIMO broadcast channel with full CSI.
The dermatofibrosarcoma protuberans-associated collagen type Ialpha1/platelet-derived growth factor (PDGF) B-chain fusion gene generates a transforming protein that is processed to functional PDGF-BB. (1999)

Dermatofibrosarcoma protuberans (DFSP) displays chromosomal rearrangements involving chromosome 17 and 22, which fuse the collagen type Ialpha1 (COLIA1) gene to the platelet-derived growth factor (PDGF) B-chain (PDGFB) gene. To characterize the functional and structural properties of the COLIA1/PDGFB fusion protein, we generated a stable NIH3T3 cell line that contained a tumor-derived chimeric gene resulting from a COIA1 intron 7-PDGFB intron 1 fusion. Expression of the fusion protein led to morphological transformation and increased growth rate of these cells. The PDGF receptor kinase inhibitor CGP57148B reversed the transformed phenotype and reduced the growth rate of COLIA1/PDGFB-expressing cells but had no effects on control cells. The presence of dimeric COLIA1/PDGFB precursors was demonstrated through PDGFB immunoprecipitations of metabolically labeled cells and also by PDGFB immunoprecipitations followed by immunoblotting with COLIA1 antibodies. Pulse-chase studies demonstrated that the COLIA1/PDGFB precursor was processed to an end product that was indistinguishable from wild-type PDGF-BB. Finally, COLIA1/PDGFB-expressing cells generated tumors after s.c. injection into nude mice, and tumor growth was reduced by treatment with CGP57148B. We conclude that the COLIA1/PDGFB fusion associated with DFSP contributes to tumor development through ectopic production of PDGF-BB and the formation of an autocrine loop. Our findings, thus, suggest that PDGF receptors could be a target for pharmacological treatment of DFSP and giant cell fibroblastoma, e.g., through the use of PDGF receptor kinase inhibitors such as CGP57148B.
Predicting Optimal Time of Insemination in Cows that Show Visual Signs of Estrus by Estimating Onset of Estrus with Pedometers (1997)

An experiment was designed to estimate the optimal interval from the beginning of estrus to artificial insemination (AI). The data were analyzed by means of a mathematical model. The analysis was based on pedometer readings and results of rectal palpation at 42 to 49 d post-AI of 171 breedings in 121 cows. The chance of conception was highest between 6 and 17 h after increased pedometer activity; the estimated optimum was at 11.8 h. In this data file, the effects of disease, inseminator, time of AI (a.m. or p.m.), and bull did not contribute to the improvement of the model. The effects of disease were not significant because of the low incidence of any specific disease. Activity measurements can be used as a tool for AI strategy to improve conception in groups of healthy cows and heifers already showing visual signs of estrus.
B Cell Responses to a Peptide Epitope. V. Kinetic Regulation of Repertoire Discrimination and Antibody Optimization for Epitope (1998)

The influence of imposing various conformational constraints on immune responses to a model epitope within a synthetic peptide immunogen was examined in mice. Although overall immunogenicity was affected, the model epitope (sequence DPAF) remained the predominant recognition site regardless of the conformation in which it was presented. A comparison of anti-DPAF mAbs obtained in response to two analogue peptides, PS1CT3 and CysCT3, in which the DPAF segment was either unconstrained or held within a cyclic loop, respectively, revealed a significant homology in the paratope composition. At one level a subset of anti-PS1CT3 and anti-CysCT3 mAbs was found to share a common heavy chain variable region. In addition, nucleotide sequence homology comparisons of both heavy and light chain variable regions identified the presence of anti-PS1CT3 and anti-CysCT3 mAbs that collectively appeared to derive from a common progenitor, but with nonidentical somatic mutations. Interestingly, however, no bias toward homologous Ag could be discerned on measurement of relative affinities of the mAbs for the two peptides. In contrast, mAb binding on-rates clearly discriminated between peptides representing the homologous vs the heterologous confomer of the DPAF epitope. Thus, it would appear that the kinetics of Ag recognition dominate over equilibrium binding criteria both in epitope-driven repertoire selection and Ab maturation in a humoral response.
CHEMISTRY OF PUFFER FISH TOXIN (2001)

Tetrodotoxin (TTX) is well known as the puffer fish toxin. Naturally occurring analogs of TTX have been isolated from puffer fish, newts and frogs, and their structures have been determined by spectroscopic methods. Additionally, TTX analogs have been prepared by chemical modification to investigate its binding site on sodium channels and the structure-activity relationship of TTX. In this article, the NMR data of TTX analogs are listed, and the chemical modification methods for preparation of TTX probes are summarized.
Non-invasive monitoring of oxygen in the lungs of newborn infants using diode laser spectroscopy (2016)

The main purpose of this study was to investigate a novel non-invasive optical technique for rapid bedside detection of oxygen gas in the lungs of full-term newborn infants. The results suggest that the technique will be clinically useful as a diagnostic and monitoring tool for infants with lung disorders.
Hand Pointing Estimation for Human Computer Interaction Based on Two Orthogonal-Views (2010)

Hand pointing has been an intuitive gesture for human interaction with computers. Big challenges are still posted for accurate estimation of finger pointing direction in a 3D space. In this paper, we present a novel hand pointing estimation system based on two regular cameras, which includes hand region detection, hand finger estimation, two views' feature detection, and 3D pointing direction estimation. Based on the idea of binary pattern face detector, we extend the work to hand detection, in which a polar coordinate system is proposed to represent the hand region, and achieved a good result in terms of the robustness to hand orientation variation. To estimate the pointing direction, we applied an AAM based approach to detect and track 14 feature points along the hand contour from a top view and a side view. Combining two views of the hand features, the 3D pointing direction is estimated. The experiments have demonstrated the feasibility of the system.
Development of a Broad-Spectrum Oxime for the Treatment of Nerve Agent Toxicity (2006)

Inhibition of synaptic acetylcholinesterase (AChE) by organophosphate (OP) nerve agents is the main reason for their toxicity. Oximes are used as antidotes to reactivate nerve agent-inhibited AChE. To understand the mechanism of oxime-induced reactivation, we generated several mutant AChEs. Reactivation studies conducted with wild-type and mutant AChEs revealed that the peripheral anionic site of AChE plays a critical role in the reactivation of nerve agent-inhibited AChE by bis-pyridinium oximes, and not by mono-pyridinium oximes. Results showed that Y124 is an important determinant for the enhanced reactivation potency of HI-6 and HLo-7. Results also suggest that both the second pyridinium structure and the ether oxygen of HI-6 and HLo-7 are involved in interactions with the peripheral anionic site of AChE. These interactions are important considerations for the development of a next generation broad-spectrum oxime.
Nematode pathogenesis and resistance in plants. (1996)

Nematodes comprise a large phylum of animals that includes plant and animal parasites as well as many free-living species (Maggenti, 1981). Plant parasitic nematodes are obligate parasites, obtaining nutrition only from the cytoplasm of living plant cells. These tiny roundworms (generally 4 mm long and barely visible to the human eye) damage food and fiber crops throughout the world and cause billions of dollars in losses annually (Sasser and Freckman, 1987). Some plant parasitic nematodes are ectoparasites, living outside their host. These species cause severe root damage and can be important virus vectors (Brown et al., 1995). Other species spend much of their lives inside roots as migratory or sedentary endoparasites. Migratory parasites move through the root, causing massive cellular necrosis. However, it is the sedentary endoparasites of the family Heteroderidae that cause the most economic damage worldwide. This group is the focus of the review. The Heteroderidae can be divided into two groups: the cyst nematodes, which include the genera Heterodera and Globodera; and the root-knot nematodes (genus Meloidogyne). The soybean cyst nematode (Heterodera glycines) is the most economically important pathogen of soybean in the United States. Potato cyst nematodes (Globodera pallida and G. rosfochiensis) cause losses in potato-growing areas worldwide (Ross, 1986). Root-knot nematodes, so-called for the characteristic root galls or root knots that they form on many hosts (Figure lA), infect thousands of plant species and cause sevele losses in yield of many crops throughout the world (Mai, 1985). Symptoms of diseased plants infected by these groups of nematodes include stunted growth, wilting, and susceptibility to other pathogens. Nematodes in these three genera have complex interactions with their host plants that generally last more than a month and result in major morphological and developmental changes in both organisms. During the infection, elaborate developmental and morphological changes occur in host root cells, especially in those that become the feeding cells that provide the sole source of nutrients for the nematode. There has been a recent burst of activity in the investigation of the molecular changes that mediate the host-parasite interaction. This ac-
Improvement of LEV/ULEV Potential of Fuel Efficient High Performance Engines (1992)

&lt;div class="htmlview paragraph"&gt;The combined requirement of achieving CAFE values between 32 to 38 mpg plus LEV/ULEV emission standards to comply with US legal requirements between 1995 and 2000 represents the most demanding challenge for engine engineering.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Thus all possible methods of engine improvement towards fuel economy and emissions have to be considered. Besides using new ideas also the methods of engine development have to be modernized to cope with the challenge.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The paper presents advanced combustion and exhaust gas aftertreatment systems which combine high power output, favourable torque characteristics and high fuel economy with the potential for obtaining LEV/ULEV emission values, as well as improved development techniques.&lt;/div&gt;
Fatal and Near-Fatal Anaphylactic Reactions to Food in Children and Adolescents (1992)

Dangerous anaphylactic reactions to food occur in children and adolescents. The failure to recognize the severity of these reactions and to administer epinephrine promptly increases the risk of a fatal outcome.
Screening the Brain: Molecular Fingerprints of Neural Stem Cells (2006)

With the development of high-throughput technologies like microarrays for genomic and transcriptomic analysis, and two-dimensional gel electrophoresis, mass spectrometry, and protein arrays for proteomic analysis, it is possible to monitor the changes in gene or protein expression of several hundreds, or even thousands of molecules simultaneously. Within the last years, these technologies have been applied successfully to stem cell research. One of the aims of stem cell expression profiling is to find specific marker genes or proteins which may determine the "stemness" of these cells. In the current review, we will evaluate the results of genomic, transcriptomic and proteomic approaches to find stem cell markers. We compare the criteria of "stemness" to recent results in adult neural stem cell research. Neural stem cells have been isolated from various regions of the adult brain. They self-renew and give rise to progeny capable to generate neurons, astrocytes, and oligodendrocytes. Besides morphological differentiation, these cells can integrate into functional neuronal circuits, making them suitable targets for cell replacement strategies. General properties seem to be the responsiveness to growth factors, and the activation of developmental signaling pathways. In conclusion, we suggest that stem cell properties can be specified by global gene or proteomic expression patterns rather than by the analysis of individual genes or proteins.
Trends in fiber for cable (TV) (2003)

The cable industry has been relatively slow to adopt optical fiber as a major element of its networks. This arises in part because coaxial cable has suited cable's needs relatively well. Also, cable's basic task of delivering scores of video signals has posed some difficult economic and technical challenges for fiber technology. Fiber optic transmission offers the promise of significant benefit to the cable industry and it is important that one explores this potential and its relationship to consumer electronics issues.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Interleukin-8 induces fever by a prostaglandin-independent mechanism (1994)

We have studied the mechanism by which interleukin-8 (IL-8) induces fever in rats. Intracerebroventricular injections of IL-8 (5.5-50 ng) evoked dose-dependent increases in body temperature, which reached a plateau 5 h after injection, i.e., later than intracerebroventricular interleukin-1 beta (IL-1 beta; 2 h). The pyrogenic activity of IL-8 was not due to contamination with lipopolysaccharide (LPS) because preincubation of IL-8 with a specific antibody or boiling the IL-8 for 30 min abolished its activity but not that of LPS; also, IL-8 but not LPS induced fever in LPS-tolerant rats. Indomethacin significantly reduced the pyrogenic effects of intracerebroventricular injections of LPS and IL-1 beta but not responses to IL-8, suggesting that pyrogenic responses to IL-8 were mediated independently of prostaglandins. In contrast, dexamethasone markedly attenuated pyrogenic responses to IL-8 and IL-1 beta. These data suggest that inhibition of IL-8 by glucocorticoids contributes to the antipyretic effects of these drugs in fevers resistant to cyclooxygenase inhibitors.
Recurrent Variable Region Gene Usage and Somatic Mutation in the Human Antibody Response to the Capsular Polysaccharide ofStreptococcus pneumoniaeType 23F (2002)

Combinatorial cloning and expression library analysis were used to isolate human antibody Fab fragments specific for the capsular polysaccharide of Streptococcus pneumoniae serotype 23F. Thirty 23F-specific Fabs were isolated from seven vaccinated donors, and the sequences of the heavy (H)- and light (L)-chain variable regions were determined. All individuals utilized either the Vkappa A23 L chain, the Vkappa L6 L chain, or both chains in forming the 23F-specific combining site. Vkappa A23 L chains paired primarily with VH3-23 H chains. Vkappa L6 L chains were more promiscuous in heavy-chain usage between individuals. Both H and L chains were mutated, primarily in the complementarity-determining regions, compared to their closest germ line counterpart, suggesting a recall response that has undergone affinity maturation. H-chain isotypes were reflective of those found in the serum. Shared somatic modifications demonstrated that immunoglobulin G2 (IgG2) and IgA antibodies arose from the same somatically matured B cell. Our results indicate that the response to the serotype 23F pneumococcal capsular polysaccharide is oligoclonal within the individual, with one or two paratope families accounting for the majority of expressed antibody. We also determined that, in spite of the combinatorial diversity available to the immune system, the 23F-specific response is highly restricted at the population level, with the same two L-chain-determined paratope families recurring in all individuals. Lastly, analysis of the isolated Fabs indicate all have undergone extensive somatic mutation, as well as class switch, maturational events that presumably require the participation of T cells.
Small‐for‐Size Syndrome After Partial Liver Transplantation: Definition, Mechanisms of Disease and Clinical Implications (2005)

Widespread application of cadaveric split or living donor liver transplantation bears considerable potential to increase the pool of available organs and thus alleviate the problem of organ shortage. Although splitting of a cadaveric liver into two grafts for adult recipients can be performed successfully, sufficient function of undersized grafts is a major concern. To minimize the risk for living donors, transplant surgeons aim at procuring the least necessary liver volume, also leading to potentially small grafts. When small partial grafts are unable to meet the functional demands, the recipients can develop a so-called small-for-size syndrome (SFSS). There is currently limited data on the pathogenesis of SFSS, with clinical studies mainly focusing on portal hyperperfusion. Additional aspects include graft-related factors such as functional and regenerative capacity, as well as recipient-related factors, such as overall health status and severity of cirrhosis. However, there is currently no consensus on the definition of SFSS. We propose a novel definition, based on simple clinical criteria, which divides the syndrome into either nonfunction or dysfunction of a small graft after the exclusion of other causes. This definition should ease comparability of future clinical trials, and thus improve understanding of the pathogenesis of SFSS.
Optimal Eavesdropping in Quantum Cryptography. I (1997)

We consider the Bennett-Brassard cryptographic scheme, which uses two conjugate quantum bases. An eavesdropper who attempts to obtain information on qubits sent in one of the bases causes a disturbance to qubits sent in the other basis. We derive an upper bound to the accessible information in one basis, for a given error rate in the conjugate basis. Independently fixing the error rate in the conjugate bases, we show that both bounds can be attained simultaneously by an optimal eavesdropping probe, consisting of two qubits. The qubits' interaction and their subsequent measurement are described explicitly. These results are combined to give an expression for the optimal information an eavesdropper can obtain for a given average disturbance when her interaction and measurements are performed signal by signal. Finally, the relation between quantum cryptography and violations of Bell's inequalities is discussed.
Adenosine, AMP, and protein phosphatase activity in sandfly saliva. (2000)

As they probe the skin for blood, sand flies inject saliva that prevents hemostasis. Sand fly saliva also promotes leishmaniasis by suppressing immunologic functions of macrophages. Saliva of Phlebotomus papatasi, the vector of Old World cutaneous leishmaniasis, contains adenosine and AMP. We show that Ph. papatasi saliva as well as pure adenosine down-regulate the expression of the inducible nitric oxide (NO) synthase gene in activated macrophages. In addition Ph. papatasi, but not Lutzomyia longipalpis, saliva inhibits the production of NO. Taken together, these data suggest that salivary adenosine is responsible for the down-regulation of NO synthesis. Saliva of both genera Phlebotomus and Lutzomyia contains significant levels of endogenous protein phosphatase-1/2A-like activity that is heat labile, inhibitable by okadaic acid and calyculine a, and does not require divalent cations.
Interleukin (IL) 1β Induction of IL-6 Is Mediated by a Novel Phosphatidylinositol 3-Kinase-dependent AKT/IκB Kinase α Pathway Targeting Activator Protein-1 (2008)

Here we describe a novel role for the phosphatidylinositol 3-kinase/AKT pathway in mediating induction of interleukin-6 (IL-6) in response to IL-1. Pharmacological inhibition of phosphatidylinositol 3-kinase (PI3K) inhibited IL-6 mRNA and protein production. Overexpression of either dominant-negative AKT or IB kinase mutant, IKKT23A, containing a mutation in a functional AKT phosphorylation site, shown previously to be important for NFB activation, completely abrogated IL-6 promoter activation in response to IL-1. However, mutation of the consensus NFB site on the IL-6 promoter did not abrogate promoter activation by IL-1 in contrast to the AP-1 site mutation. IL-1 induces phosphorylation of IKK on the NFB inducing kinase (NIK) phosphorylation sites Ser 176 /Ser 180 and on the Thr 23 site, and although phosphorylation of IKKT23 is inhibited both by LY294002 and wortmannin, phosphorylation of Ser 176 /Ser 180 is not. Neither inhibition of PI 3-kinase/AKT nor IKKT23A overexpression affected IB degradation in response to IL-1. Only partial inhibition by dominant-negative AKT and no inhibitory effect of IKKT23A was observed on an IL-6 promoter-specific NFB site in contrast to significant inhibitory effects on the AP-1 site. Taken together, we have discovered a novel PI 3-kinase/AKT-dependent pathway in response to IL-1, encompassing PI 3-kinase/AKT/IKKT23 upstream of AP-1. This novel pathway is a parallel pathway to the PI 3-kinase/AKT upstream of NFB and both are involved in IL-6 gene transcription in response to IL-1.