gebhart/patrepeval huggingface dataset:
Search Space Reduction via Multi-Sensory Directional Cueing (2004)

Spatial tactile displays allow for the cueing of directional information without drawing upon the visual and auditory channels. This work highlights the effectiveness of a tactual display versus a spatial auditory display baseline for augmenting a visual search task. Touch provides highly salient and covert signals that narrow the visual search space, potentially shortening response times, improving accuracy, and imposing minimal additional demand upon visual and auditory channels. Applications of this display technology for spatial location of targets include acquisition of potential threats in simulated and real combat environments, as well as improved localization of objects for first responders or for those with sensory impairments.
Predicting antibody hypervariable loop conformations II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations (1986)

We describe a method for predicting the conformations of loops in proteins and its application to four of the complementarity determining regions [CDRs] in the crystallographically determined structure of MCPC603. The method is based on the generation of a large number of randomly generated conformations for the backbone of the loop being studied, followed by either minimization or molecular dynamics followed by minimization starting from these random structures. The details of the algorithm for the generation of the loops are presented in the first paper in this series (Shenkin et al. [submitted]). The results of minimization and molecular dynamics applied to these loops is presented here. For the two shortest CDRs studied (H1 and L2, which are five and seven amino acids long), minimizations and dynamics simulations which ignore interactions of the loop amino acids beyond the carbon beta replicate the conformation of the crystal structure closely. This suggests that these loops fold independently of sequence variation. For the third CDR (L3, which is nine amino acids), those portions of the CDR near its base which are hydrogen bonded to framework are well replicated by our procedures, but the top of the loop shows significant conformational variability. This variability persists when side chain interactions for the MCPC603 sequence are included. For a fourth CDR (H3, which is 11 amino acids long), new low-energy backbone conformations are found; however, only those which are close to the crystal are compatible with the sequence when side chain interactions are taken into account. Results from minimization and dynamics on single CDRs with all other CDRs removed are presented. These allow us to explore the extent to which individual CDR conformations are determined by interactions with framework only.
Passivation of the InP surface using polysulfide and silicon nitride overlayer (1993)

For the first time, excellent passivation of the defect states at the SiNx/InP interface has been achieved using ammonium sulfide solution containing excess sulfur and phosphorous pentasulfide. Silicon nitride overlayers have been deposited at ∼200 °C using electron cyclotron resonance plasma-enhanced chemical vapor deposition technique. The room-temperature integrated photoluminescence (PL) intensity of the passivated InP approximately doubled following the nitride deposition. Under similar conditions, the PL intensity of the untreated sample decreased by a factor of five. The interface trap density, estimated using the high-low capacitance technique, is ∼1012 cm−2 eV−1. The devices are stable, with no noticeable change observed over a 30-day period.
Implications of ribozyme kinetics for targeting the cleavage of specific RNA molecules in vivo: more isn't always better. (1991)

Kinetic and thermodynamic factors that determine specificity of RNA cleavage by ribozymes are illustrated with examples from recent work with a ribozyme derived from the group I intron of Tetrahymena thermophila pre-rRNA. The conclusions also apply to other ribozymes, to antisense oligonucleotide experiments, and to RNA and DNA cleavage agents that can recognize a single-stranded or double-stranded region of variable length. At first, adding bases to a ribozyme's recognition sequence is expected to increase cleavage of the target RNA relative to cleavage of other RNAs. However, adding more bases ultimately reduces this discrimination, as cleavage occurs essentially every time the target RNA or a mismatched RNA binds the ribozyme. This occurs despite the weaker binding of the mismatched RNA because dissociation becomes too slow (binding is too strong) to allow the ribozyme to "choose" between cleavage of the target RNA and a mismatched RNA. In summary, more (base pairing) isn't always better, because maximal discrimination requires equilibrium binding prior to cleavage. The maximum discrimination that can be obtained is expected to be greater with an A + U-rich recognition sequence than with a G + C-rich recognition sequence. This is because the weaker A.U base pairs (relative to G-C base pairs) allow recognition to be spread over a larger number of bases while preventing binding that is too strong. Finally, creating an A-rich ribozyme rather than a U-rich ribozyme avoids the loss in discrimination expected with U-rich ribozymes from the formation of U.G wobble pairs in addition to the "targeted" Watson-Crick U.A pair.
Ammonia impairs neutrophil phagocytic function in liver disease† (2008)

Ammonia produces neutrophil swelling and impairs neutrophil phagocytosis. The p38(MAPK) intracellular signaling pathway has been shown to be important in mediating the ammonia-induced neutrophil dysfunction.
Anti-inflammatory and neuroprotective effects of an orally active apocynin derivative in pre-clinical models of Parkinson’s disease (2012)

Collectively, these results demonstrate that diapocynin exhibits profound neuroprotective effects in a pre-clinical animal model of PD by attenuating oxidative damage and neuroinflammatory responses. These findings may have important translational implications for treating PD patients.
Molecular cloning of a cell wall exo-beta-1,3-glucanase from Saccharomyces cerevisiae (1989)

A major protein of Saccharomyces cerevisiae cell walls is a 29-kilodalton glycoprotein which shows lectinlike binding to beta-1,3-glucan and chitin. It was solubilized by heating isolated cell walls at 90 degrees C and purified to homogeneity by running two high-pressure liquid chromatography columns. With the sequence information of the N terminus and seven peptides, two oligonucleotides were synthesized and the gene was cloned. Its sequence is similar to those of two plant beta-glucanases, and the protein was shown to possess beta-1,3-exoglucanase activity with laminarin as substrate. Haploid yeast cells contained one copy of the gene (BGL2). Gene disruption did not result in a phenotype.
Follicle-Stimulating Hormone Receptor and Its Messenger Ribonucleic Acid Are Present in the Bovine Cervix and Can Regulate Cervical Prostanoid Synthesis1 (1999)

The hypothesis that FSH regulates the bovine cervical prostaglandin E(2) (PGE(2)) synthesis that is known to be associated with cervical relaxation and opening at the time of estrus was investigated. Cervical tissue from pre-estrous/estrous, luteal, and postovulatory cows were examined for 1) the presence of bovine (b) FSH receptor (R) and its corresponding mRNA and 2) the effect of FSH on the PGE(2) regulatory pathway in vitro. The presence of bFSHR mRNA in the cervix (maximal during pre-estrus/estrus) was demonstrated by the expression of a reverse transcription (RT) polymerase chain reaction (PCR) product (384 base pairs) specific for bFSHR mRNA and sequencing. Northern blotting revealed three transcripts (2.5, 3.3, and 3.8 kilobases [kb]) in cervix from pre-estrous/estrous cows. The level of FSHR (75 kDa) was significantly higher (p < 0.01) in Western blots of pre-estrous/estrous cervix than in other cervical tissues. There was a good correlation between the 75-kDa protein expression and its corresponding transcript of 2.55 kb throughout the estrous cycle as described by Northern blot analysis as well as RT-PCR. Incubation of FSH (10 ng/ml) with pre-estrous/estrous cervix resulted in a 3-fold increase in the expression of FSHR and a 2-fold increase in both G protein (alpha(s)) and cyclooxygenase II. FSH (5-20 ng/ml) significantly increased (p < 0.01) cAMP, inositol phosphate (p < 0.01), and PGE(2) (p < 0.01) production by pre-estrous/estrous cervix but not by cervix at the other stages. We conclude that bovine cervix at the time of the peripheral plasma FSH peak (pre-estrus/estrus) contains high levels of FSHR and responds to FSH by increasing the PGE(2) production responsible for cervical relaxation at estrus.
[Lipoprotein (a) and plasminogen in atherosclerosis]. (1996)

The aim of this study was to evaluate plasma levels of lipoprotein (a) [LP(a)] and plasminogen in patients affected with atherosclerotic disease and to understand the mutual relationships. Eighty-four patients affected with atherosclerosis were examined and divided as follows: group I, 24 patients with peripheral arteriopathy; group II, 40 patients with ischemic heart disease (myocardial infarction and/or angina pectoris); group III, 20 patients with multi-infarct dementia; group IV (control group) with 20 healthy young subjects. The results show that Lp(a) plasma levels, in atherosclerotic patients, are higher than 30 mg/dl, while the plasminogen levels are lower than 80 mg/dl. There is an inverse correlation between these two data. Moreover, a different behaviour of Lp(a) and plasminogen rate related to age of patients, to number of atherosclerotic lesions or to acuteness of ischemic heart disease, was observed.
Vaccination againstChlamydiaGenital Infection Utilizing the MurineC. muridarumModel (2010)

Chlamydia trachomatis genital infection is a worldwide public health problem, and considerable effort has been expended on developing an efficacious vaccine. The murine model of C. muridarum genital infection has been extremely useful for identification of protective immune responses and in vaccine development. Although a number of immunogenic antigens have been assessed for their ability to induce protection, the majority of studies have utilized the whole organism, the major outer membrane protein (MOMP), or the chlamydial protease-like activity factor (CPAF). These antigens, alone and in combination with a variety of immunostimulatory adjuvants, have induced various levels of protection against infectious challenge, ranging from minimal to nearly sterilizing immunity. Understanding of the mechanisms of natural infection-based immunity and advances in adjuvant biology have resulted in studies that are increasingly successful, but a vaccine licensed for use in humans has not yet been brought to fruition. Here we review immunity to chlamydial genital infection and vaccine development using the C. muridarum model.
GAD65-reactive T cells are activated in patients with autoimmune type 1a diabetes (2002)

Insulin-dependent type 1 diabetes is an autoimmune disease mediated by T lymphocytes recognizing pancreatic islet cell antigens. Glutamic acid decarboxylase 65 (GAD65) appears to be an important autoantigen in the disease. However, T cells from both patients with type 1 diabetes and healthy subjects vigorously proliferate in response to GAD65 stimulation ex vivo, leading us to postulate that the critical event in the onset of human diabetes is the activation of autoreactive T cells. Thus, we investigated whether GAD65-reactive T cells in patients with diabetes functioned as previously activated memory T cells, no longer requiring a second, costimulatory signal for clonal expansion. We found that in patients with new-onset type 1 diabetes, GAD65-reactive T cells were strikingly less dependent on CD28 and B7-1 costimulation to enter into cell cycle and proliferate than were equivalent cells derived from healthy controls. We hypothesize that these autoreactive T cells have been activated in vivo and have differentiated into memory cells, suggesting a pathogenic role in type 1 diabetes. In addition, we observed different effects with selective blockade of either B7-1 or B7-2 molecules; B7-1 appears to deliver a negative signal by engaging CTLA-4, while B7-2 engagement of CD28 upregulates T cell proliferation and cytokine secretion.
Asymmetric Non-local Neural Networks for Semantic Segmentation (2019)

The non-local module works as a particularly useful technique for semantic segmentation while criticized for its prohibitive computation and GPU memory occupation. In this paper, we present Asymmetric Non-local Neural Network to semantic segmentation, which has two prominent components: Asymmetric Pyramid Non-local Block (APNB) and Asymmetric Fusion Non-local Block (AFNB). APNB leverages a pyramid sampling module into the non-local block to largely reduce the computation and memory consumption without sacrificing the performance. AFNB is adapted from APNB to fuse the features of different levels under a sufficient consideration of long range dependencies and thus considerably improves the performance. Extensive experiments on semantic segmentation benchmarks demonstrate the effectiveness and efficiency of our work. In particular, we report the state-of-the-art performance of 81.3 mIoU on the Cityscapes test set. For a 256x128 input, APNB is around 6 times faster than a non-local block on GPU while 28 times smaller in GPU running memory occupation. Code is available at: https://github.com/MendelXu/ANN.git.
Controlling Drug Release from Imprinted Hydrogels by Modifying the Characteristics of the Imprinted Cavities (2005)

The aim of this study was to analyse the influence of the template/functional monomer proportion on the achievement of molecularly imprinted hydrogels with cavities with a high enough affinity for the drug to sustain drug release. Imprinted hydrogels were prepared from N,N-dimethylacrylamide and tris(trimethylsiloxy)sililpropyl methacrylate (DMAA and TRIS; main components), methacrylic acid (MAA; functional monomer), ethylene glycol dimethacrylate (EGDMA; cross-linker), and timolol (template drug). Photo-polymerization of the monomer solutions was carried out in poly(propylene) molds (0.3 mm thickness) to obtain contact lens-like devices. Non-imprinted control hydrogels were also prepared in the same way but without the addition of timolol. The imprinted hydrogels showed a higher affinity for timolol and a slower release rate than the non-imprinted hydrogels. The release rate decreased by increasing the MAA/timolol ratio in the gel recipe. Hydrogels prepared with 400 x 10(-3) M MAA, 600 x 10(-3) M EGDMA, and a timolol/MAA mole ratio of 1:16-1:32 had drug diffusion coefficients two orders of magnitude below those of non-imprinted hydrogels. The results obtained clearly indicate that the timolol release rate is critically affected by the conditions under which the hydrogels were synthesized. These effects are discussed on the basis of the influence of drug proportion on the conformation of the imprinted cavities.
Molecular mechanisms governing Pcdh -γ gene expression: Evidence for a multiple promoter and cis -alternative splicing model (2002)

The genomic architecture of protocadherin (Pcdh) gene clusters is remarkably similar to that of the immunoglobulin and T cell receptor gene clusters, and can potentially provide significant molecular diversity. Pcdh genes are abundantly expressed in the central nervous system. These molecules are primary candidates for establishing specific neuronal connectivity. Despite the extensive analyses of the genomic structure of both human and mouse Pcdh gene clusters, the definitive molecular mechanisms that control Pcdh gene expression are still unknown. Four theories have been proposed, including (1) DNA recombination followed by cis-splicing, (2) single promoter and cis-alternative splicing, (3) multiple promoters and cis-alternative splicing, and (4) multiple promoters and trans-splicing. Using a combination of molecular and genetic analyses, we evaluated the four models at the Pcdh-gamma locus. Our analysis provides evidence that the transcription of individual Pcdh-gamma genes is under the control of a distinct but related promoter upstream of each Pcdh-gamma variable exon, and posttranscriptional processing of each Pcdh-gamma transcript is predominantly mediated through cis-alternative splicing.
Improvement of saturation output power in a semiconductor laser amplifier through pumping light injection (1996)

Pumping light injection for semiconductor laser amplifiers is proposed as an effective way to improve their saturation output power. An experiment demonstrates 4.9 dB improvement in saturation output power for 1546 nm signal light using 1480 nm pumping light.
Effective control of crystal grain size in CH3NH3PbI3perovskite solar cells with a pseudohalide Pb(SCN)2additive (2016)

We demonstrate effective morphology control of a CH3NH3PbI3 perovskite film with a lead(II) thiocyanate additive. The perovskite crystal size is remarkably enlarged from the nanometer to the micrometer scale with only 3% Pb(SCN)2 in solid perovskite films. Large-sized perovskite crystals enable effective enhancement of the carrier lifetime, which eventually leads to the overall improvement of the device performance of perovskite solar cells.
Electric stimulation of human fibroblasts causes an increase in Ca2+ influx and the exposure of additional insulin receptors (1989)

Previously we reported that treating human fibroblasts in cell culture with high-voltage, pulsed galvanic stimulation (HVPGS) can significantly increase cellular protein and DNA synthesis (Bourguignon and Bourguignon: FASEB J., 1:398-402, 1987). In this study we have identified two of the early cellular events which occur following exposure to HVPGS: 1) an increase in Ca2+ uptake from the external medium and 2) an increase in the number of insulin receptors on the fibroblast cell surface. The increase in Ca2+ uptake begins within the first minute of electric stimulation while increased insulin binding is not detected until the second minute of stimulation. The HVPGS-induced increase in insulin binding can be inhibited by bepridil, a specific Ca2+ channel blocker, suggesting that the Ca2+ influx is required for the exposure of additional insulin receptors on the cell surface. Furthermore, we have determined that the addition of insulin to electrically stimulated cultures results in 1) an immediate, second increase in Ca2+ uptake and 2) significant increases in both protein and DNA synthesis compared to cells which were not stimulated. All three of these insulin-dependent effects are also inhibited by bepridil. Based on these results, we propose that HVPGS initially triggers the opening of voltage-sensitive calcium channels in the fibroblast plasma membrane. The increased level of intracellular Ca2+ then induces the exposure of additional insulin receptors, the fibroblasts will significantly increase both protein and DNA synthesis.
Molecular Defects in Variant Forms of Mannose-Binding Protein Associated with Immunodeficiency (1999)

Distinct molecular mechanisms underlying immunodeficiency caused by three different naturally occurring point mutations within the collagen-like domain of human mannose-binding protein (MBP; also known as mannose-binding lectin) have been revealed by introduction of analogous mutations into rat serum MBP. The change Arg23-->Cys results in a lower proportion of the large oligomers most efficient at activating the complement cascade. The presence of cysteine at position 23, which forms aberrant interchain disulfide bonds, causes disruption of the normal oligomeric state. The deficiency in MBPs containing Gly25-->Asp and Gly28-->Glu substitutions also results in part from reduced formation of higher oligomers. However, decreased ability to interact with downstream components of the complement cascade due to changes in both the N-terminal disulfide-bonding arrangement and the local structure of the collagenous domain make more important contributions to the loss of activity in these mutants.
Design of miniaturized wireless power receivers for mm-sized implants (2017)

Advances in free-floating miniature medical implants promise to offer greater effectiveness, safety, endurance, and robustness than today's prevailing medical implants. Wireless power transfer (WPT) is key to miniaturized implants by eliminating the need for bulky batteries. This paper reviews design strategies for WPT with mm-sized implants focusing on resonant electromagnetic and ultrasonic transmission. While ultrasonic WPT offers shorter wavelengths for sub-mm implants, electromagnetic WPT above 100 MHz offers superior power transfer and conversion efficiency owing to better impedance matching through inhomogeneous tissue. Electromagnetic WPT also allows for fully integrating the entire wireless power receiver system with an on-chip coil. Attaining high power transfer efficiency requires careful design of the integrated coil geometry for high quality factor as well as loop-free power and signal distribution routing to avoid eddy currents. Regulating rectifiers have improved power and voltage conversion efficiency by combining the two RF to DC conversion steps into a single process. Example designs of regulating rectifiers for fully integrated wireless power receivers are presented.
Glucose oxidase from Aspergillus niger. Cloning, gene sequence, secretion from Saccharomyces cerevisiae and kinetic analysis of a yeast-derived enzyme. (1990)

The gene for Aspergillus niger glucose oxidase (EC 1.1.3.4) has been cloned from both cDNA and genomic libraries using oligonucleotide probes derived from the amino acid sequences of peptide fragments of the enzyme. The mature enzyme consists of 583 amino acids and is preceded by a 22-amino acid presequence. No intervening sequences are found within the coding region. The enzyme contains 3 cysteine residues and 8 potential sites for N-linked glycosylation. The protein shows 26% identity with alcohol oxidase of Hansenuela polymorpha, and the N terminus has a sequence homologous with the AMP-binding region of other flavoenzymes such as p-hydroxybenzoate hydroxylase and glutathione reductase. Recombinant yeast expression plasmids have been constructed containing a hybrid yeast alcohol dehydrogenase II-glyceraldehyde-3-phosphate dehydrogenase promoter, either the yeast alpha-factor pheromone leader or the glucose oxidase presequence, and the mature glucose oxidase coding sequence. When transformed into yeast, these plasmids direct the synthesis and secretion of between 75 and 400 micrograms/ml of active glucose oxidase. Analysis of the yeast-derived enzymes shows that they are of comparable specific activity and have more extensive N-linked glycosylation than the A. niger protein.
Understanding the dehumidification performance of air-conditioning equipment at part-load conditions. Final report. (2006)

This report summarizes the results of a comprehensive project to better understand and quantify the moisture removal (dehumidification) performance of cooling coils at part-load conditions. Extract from the table of contents: literature review; laboratory and field testing; model development and validation (better predictions of off-cycle moisture evaporation; an improved latent degradation model; recommended model parameters for various cooling systems: part-load latent performance for modulating and staged direct-expansion systems; latent degradation with modulating chilled water coils); best practices to mitigate latent capacity degradation (the importance of coil temperature control; the impact of off-cycle moisture evaporation from the cooling coil); conclusions and recommendations. The report can be downloaded from the following Web site: www.fsec.ucf.edu/bldg/pubs/dp_air/DehumidificationPerformance.pdf