gebhart/patrepeval huggingface dataset:
Charge density and charge per phase as cofactors in neural injury induced by electrical stimulation (1990)

The possibility of neural injury during prolonged electrical stimulation of the brain imposes some constraints on the use of this technique for therapeutic and experimental applications. Stimulating electrodes of various sizes were used to investigate the interactions of two stimulus parameters, charge density and charge per phase, in determining the threshold of neural injury induced by electrical stimulation. Platinum electrodes ranging in size from 0.002 to 0.5 cm2 were implanted over the parietal cortex of adult cats. Penetrating microelectrodes fabricated from iridium, with surface areas of 65 +/- 3 x 10(-6) cm2 were inserted into the parietal cortex. Ten days after implantation, the electrodes were pulsed continuously for 7h using charge balanced, current regulated, symmetric pulse pairs, 400 microseconds per phase in duration, at a repetition rate of 50 Hz. The animals were perfused immediately after the stimulation for histologic evaluation of the brain tissue subjacent to the electrode sites. The results show that charge density (as measured at the surface of the stimulating electrode), and charge per phase, interact in a synergistic manner to determine the threshold of stimulation-induced neural injury. This interaction occurs over a wide range of both parameters; for charge density from at least 10 to 800 microC/cm2 and, for charge per phase, from at least 0.05 to 5.0 microC per phase. The significance of these findings in elucidating the mechanisms underlying stimulation-induced injury is discussed.
KDA: a knowledge-based database assistant (2003)

A knowledge-based database assistant, KDA, is described that has a query-guide function, an SQL-like database query generator, and an interface for subset-English. KDA can be used to design the front end of an SQL database system or a computer-based SQL tutorial system. A method is discussed for transforming a semantic network representing a user's conceptual query into one providing the information required by the system to respond to a query. The query pattern is an expression in natural language representing the semantic structure of concepts. The user expresses queries by filling parentheses in the query patterns with appropriate words. The query-pattern instances thus obtained are then translated into SQL-like relational database queries. The translation is carried out by evaluating operations defined on a semantic network named G-Net which conveys knowledge about application fields, the database schema, and the syntax of SQL.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fluoroalkyl‐s‐triazines (1973)

Abstract A series of symmetrically and asymmetrically substituted s ‐triazines was synthesized by condensation of fluorocarbon nitriles (Scheme II, compounds 1a‐c ) and by cyclodehydration of a fluorocarbon imidoylamidine utilizing a fluorocarbon anhydride (Scheme III, compounds 2a‐e ). Among the new nitriles prepared for incorporation in these reaction paths were 11‐ H ‐4,9‐dioxahexadecylfluoroundecanenitrile ( 3 ) and 6‐chloro‐6‐ H ‐4‐oxaheptafluorohexanenitrile ( 4 ), prepared by Scheme 1.
Antisense-Oligonucleotide Therapy (1996)

Many pharmacologic advances involve creating compounds that bind and disable proteins. Such compounds include propranolol, which blocks the β-adrenergic receptor; cimetidine, which blocks the H2 receptor; calcium-channel blockers; angiotensin-converting–enzyme inhibitors; and inhibitors of the H+/K+–ATPase pump. A new way to block protein function is to prevent the translation of messenger RNA (mRNA) into protein.If the nucleic acid sequence encoding a protein is known, molecules can be designed to bind the corresponding mRNA, thereby inhibiting the production of the protein (Figure 1). The nucleotide sequence of DNA or RNA that contains the information for the amino acid sequence of . . .
Control of a Mucosal Challenge and Prevention of AIDS by a Multiprotein DNA/MVA Vaccine (2001)

Heterologous prime/boost regimens have the potential for raising high levels of immune responses. Here we report that DNA priming followed by a recombinant modified vaccinia Ankara (rMVA) booster controlled a highly pathogenic immunodeficiency virus challenge in a rhesus macaque model. Both the DNA and rMVA components of the vaccine expressed multiple immunodeficiency virus proteins. Two DNA inoculations at 0 and 8 weeks and a single rMVA booster at 24 weeks effectively controlled an intrarectal challenge administered 7 months after the booster. These findings provide hope that a relatively simple multiprotein DNA/MVA vaccine can help to control the acquired immune deficiency syndrome epidemic.
Growth Mechanism of Highly Ordered Oriented Films of Copper (II)Phthalocyanine on Solid Substrates (1999)

Abstract Thin films of functional organic compound, copper phthalocyanine (Cu-Pc), are fabricated on the (001) surfaces of alkali halides (NaCl, KCl and KBr) and tin-doped indium oxide (ITO) by physical vapor deposition (PVD) technique. Dependence of sizes and distances between adjacent crystallites on substrate temperatures is evaluated from morphological observation by scanning electron microscope to determine the activation energies for crystal growth and surface migration of molecules. Increasing substrate temperature, the size and distance corresponding to the growth and diffusion rates, respectively, tend to increase. Particularly in the case of Cu-Pc on alkali halides, plate and tetrahedral crystals having different molecular orientations with respect to the surface appear depending on the kind of substrates and deposition conditions.
PHASE I STUDY OF AN ENGINEERED AGLYCOSYLATED HUMANIZED CD3 ANTIBODY IN RENAL TRANSPLANT REJECTION1 (1999)

These findings suggest that CD3 antibodies can be engineered to lose their toxicity while retaining their potency as immunosuppressants. Nonactivating humanized CD3 monoclonal antibodies now merit further investigation in the management of transplant patients and in therapy of autoimmune diseases.
Rescue of Cystathionine β-Synthase (CBS) Mutants with Chemical Chaperones (2010)

Missense mutations represent the most common cause of many genetic diseases including cystathionine beta-synthase (CBS) deficiency. Many of these mutations result in misfolded proteins, which lack biological function. The presence of chemical chaperones can sometimes alleviate or even restore protein folding and activity of mutant proteins. We present the purification and characterization of eight CBS mutants expressed in the presence of chemical chaperones such as ethanol, dimethyl sulfoxide, or trimethylamine-N-oxide. Preliminary screening in Escherichia coli crude extracts showed that their presence during protein expression had a significant impact on the amount of recovered CBS protein, formation of tetramers, and catalytic activity. Subsequently, we purified eight CBS mutants to homogeneity (P49L, P78R, A114V, R125Q, E176K, P422L, I435T, and S466L). The tetrameric mutant enzymes fully saturated with heme had the same or higher specific activities than wild type CBS. Thermal stability measurements demonstrated that the purified mutants are equally or more thermostable than wild type CBS. The response to S-adenosyl-L-methionine stimulation or thermal activation varied. The lack of response of R125Q and E176K to both stimuli indicated that their specific conformations were unable to reach the activated state. Increased levels of molecular chaperones in crude extracts, particularly DnaJ, indicated a rather indirect effect of the chemical chaperones on folding of CBS mutants. In conclusion, the chemical chaperones present in the expression medium were able to fully restore the activity of eight CBS mutants by improving their protein folding. This finding could have direct implications for the development of a therapeutical approach to pyridoxine unresponsive homocystinuria.
Interaction with p53 Enhances Binding of Cisplatin-modified DNA by High Mobility Group 1 Protein (2001)

A nonhistone chromosomal protein, high mobility group (HMG) 1, is ubiquitous in higher eukaryotic cells and binds preferentially to cisplatin-modified DNA. HMG1 also functions as a coactivator of p53, a tumor suppressor protein. We investigated physical interactions between HMG1 and p53 and the influence of p53 on the ability of HMG1 to recognize damaged DNA. Using immunochemical coprecipitation, we observed binding of HMG1 and p53. Interaction between HMG1 and p53 required the HMG A box of HMG1 and amino acids 363-376 of p53. Cisplatin-modified DNA binding by HMG1 was significantly enhanced by p53. An HMG1-specific antibody that recognized the A box of this protein also stimulated cisplatin-modified DNA binding. These data suggest that an interaction with either p53 or antibody may induce conformational change in the HMG1 A box that optimizes DNA binding by HMG1. Interaction of p53 with HMG1 after DNA damage may promote activation of specific HMG1 binding to damaged DNA in vivo and provide a molecular link between DNA damage and p53-mediated DNA repair.
Community Development in Bacterial Biofilms of the Oral Cavity (2008)

Extended abstract of a paper presented at Microscopy and Microanalysis 2008 in Albuquerque, New Mexico, USA, August 3 – August 7, 2008
RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription (2007)

Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the associations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nucleotides (nt) and whole-cell RNAs less than 200 nt were investigated in this genome-wide study. Subcellular addresses for nucleotides present in detected RNAs were assigned, and their potential processing into short RNAs was investigated. Taken together, these observations suggest a novel role for some unannotated RNAs as primary transcripts for the production of short RNAs. Three potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes. These data support a highly interleaved organization of the human transcriptome.
Averaging Different Alignment Axes Improves Femoral Rotational Alignment in Computer-Navigated Total Knee Arthroplasty (2008)

Background: Computer navigation systems generally establish the rotational alignment axis of the femoral component on the basis of user-defined anatomic landmarks. However, navigation systems can also record knee kinematics and average alignment axes established with multiple techniques. We hypothesized that establishing femoral rotational alignment with the use of kinematic techniques is more accurate and precise (repeatable) than the use of anatomic techniques and that establishing femoral rotational alignment by averaging the results of different alignment techniques is more accurate and precise than the use of a single technique. Methods: Twelve orthopaedic surgeons used three anatomic and two kinematic alignment techniques to establish femoral rotational alignment axes in a series of nine cadaver knees. The axes derived with the individual anatomic and kinematic techniques as well as the axes derived with six combination techniques—i.e., those involving averaging of the alignments established with two of the individual techniques—were compared against a reference axis established with computed tomography images of each femur. Results: The kinematic methods were not more accurate (did not have smaller mean errors) or more precise (repeatable) than the anatomic techniques. The combination techniques were accurate (five of the six had a mean error of <5°) and significantly more precise than all but one of the single methods. The percentage of measurements with <5° of error as compared with the reference epicondylar axis was 37% for the individual anatomic techniques, 30% for the individual kinematic techniques, and 58% for the combination techniques. Conclusions: Averaging the results of kinematic and anatomic techniques, which is possible with computer navigation systems, appears to improve the accuracy of rotational alignment of the femoral component. The number of rotational alignment outliers was reduced when combination techniques were used; however, they are still a problem and continued improvement in methods to accurately establish rotation of the femoral component in total knee arthroplasty is needed.
Abrogation of the G2 checkpoint results in differential radiosensitization of G1 checkpoint-deficient and G1 checkpoint-competent cells. (1995)

We have examined the effect of abrogation of the G2 checkpoint on the radiosensitivity of G1 checkpoint-proficient and G1 checkpoint-deficient cells. A549 human lung adenocarcinoma cells were transduced with the E6 oncogene of the human papillomavirus type 16 to eliminate their radiation-induced G1 arrest. These E6+ cells exhibited a dose-dependent increase in radiation resistance compared to control A549 cells transduced with the vector alone. Treatment (96 h) with 2 mM caffeine resulted in an abrogation of the cellular G2 checkpoint in both E6+ and control cells and a differential radiosensitizing effect on the two cell lines such that the E6+ clones and the vector controls became equally radiosensitive. These data show that human tumors which are radioresistant due to the loss of the p53-mediated G1 checkpoint can be made radiosensitive by abrogation of the G2 checkpoint. The implications of these results for cancer therapy are discussed.
An Analytical Method for Inverse Problems in Electromagnetics Using Genetic Algorithms. (1994)

Recently, the necessity of analytical method for inverse problems has become much higher because of their usefulness in various application fields, such as non-destructive inspection and so on. Most inverse problems are, however, suffering from ill-posed problems. As a result, they are difficult to solve analytically and uniquely. We have been investigating an estimation of static two-dimensional current distribution in materials, using the observed external magnetic fields as a practical example. By discretizing the above problem, it can be regarded as a combinatorial optimization problem. And we proposed the estimation method by incorporating Genetic Algorithms. Genetic Algorithms are heuristic search algorithms that find solutions to problems based on the mechanism of natural selection. In this paper, we discuss the estimation method for uneven current distribution by devising a coding method. Finally, the feasibility of the proposed method is quantitatively confirmed by simulations.
The persistent release of HMGB1 contributes to tactile hyperalgesia in a rodent model of neuropathic pain (2012)

We have identified that a persistent endogenous release of HMGB1 by sensory neurons may be a potent, physiologically relevant modulator of neuronal excitability. More importantly, the use of the anti-inflammatory compound and known inhibitor of HMGB1, glycyrrhizin, has the ability to diminish persistent pain behavior in a model of peripheral neuropathy, presumably through its ability to neutralize the cyotkine. The identification of HMGB1 as a potential therapeutic target may contribute to a better understanding of mechanisms associated with chronic pain syndromes.
Lyn tyrosine kinase regulates androgen receptor expression and activity in castrate-resistant prostate cancer (2014)

Castrate-resistant prostate cancer (CRPC) progression is a complex process by which prostate cells acquire the ability to survive and proliferate in the absence or under very low levels of androgens. Most CRPC tumors continue to express the androgen receptor (AR) as well as androgen-responsive genes owing to reactivation of AR. Protein tyrosine kinases have been implicated in supporting AR activation under castrate conditions. Here we report that Lyn tyrosine kinase expression is upregulated in CRPC human specimens compared with hormone naive or normal tissue. Lyn overexpression enhanced AR transcriptional activity both in vitro and in vivo and accelerated CRPC. Reciprocally, specific targeting of Lyn resulted in a decrease of AR transcriptional activity in vitro and in vivo and prolonged time to castration. Mechanistically, we found that targeting Lyn kinase induces AR dissociation from the molecular chaperone Hsp90, leading to its ubiquitination and proteasomal degradation. This work indicates a novel mechanism of regulation of AR stability and transcriptional activity by Lyn and justifies further investigation of the Lyn tyrosine kinase as a therapeutic target for the treatment of CRPC.Oncogenesis (2014) 3, e115; doi:10.1038/oncsis.2014.30; published online 18 August 2014.
Acellular bladder matrix allografts in the regeneration of functional bladders: evaluation of large‐segment (> 24 cm 2 ) substitution in a porcine model (2000)

The implantation of large patches of BAMA is technically feasible and may prove to be a viable surgical alternative to bladder augmentation with intestinal segments. The advantages of BAMA include the potential for complete and functional regeneration of a bladder substitute. This model provides a tool with which to obtain a better understanding of the cellular and molecular aspects of matrix re-population.
Inhibition of the integrated stress response reverses cognitive deficits after traumatic brain injury (2017)

Traumatic brain injury (TBI) is a leading cause of long-term neurological disability, yet the mechanisms underlying the chronic cognitive deficits associated with TBI remain unknown. Consequently, there are no effective treatments for patients suffering from the long-lasting symptoms of TBI. Here, we show that TBI persistently activates the integrated stress response (ISR), a universal intracellular signaling pathway that responds to a variety of cellular conditions and regulates protein translation via phosphorylation of the translation initiation factor eIF2α. Treatment with ISRIB, a potent drug-like small-molecule inhibitor of the ISR, reversed the hippocampal-dependent cognitive deficits induced by TBI in two different injury mouse models-focal contusion and diffuse concussive injury. Surprisingly, ISRIB corrected TBI-induced memory deficits when administered weeks after the initial injury and maintained cognitive improvement after treatment was terminated. At the physiological level, TBI suppressed long-term potentiation in the hippocampus, which was fully restored with ISRIB treatment. Our results indicate that ISR inhibition at time points late after injury can reverse memory deficits associated with TBI. As such, pharmacological inhibition of the ISR emerges as a promising avenue to combat head trauma-induced chronic cognitive deficits.
CD4 peptide-protein conjugates, but not recombinant human CD4, bind to recombinant gp120 from the human immunodeficiency virus in the presence of serum from AIDS patients. (1991)

Sera from human immunodeficiency virus-positive (HIV+; Walter Reed stage 6) individuals inhibit the interaction between recombinant human CD4 and recombinant gp120 from HIV (rCD4 and rgp120, respectively), thereby interfering with the ability of soluble rCD4 to block infection with HIV or rCD4-toxin conjugates to kill HIV-infected cells. In this report we demonstrate that the inhibitory activity of such sera is caused primarily by anti-gp120 antibodies that do not recognize the CD4 interaction site on gp120. To circumvent the problem of inhibition, we have generated a construct containing a peptide of CD4 (residues 41-84) conjugated to ovalbumin (three to five peptides per molecule). This multivalent conjugate binds to rgp120 and binding is not inhibited by antibodies in HIV+ sera.
Investigation of Vortex Interaction in Canard-FSW Configurations Based on the Numerical Wind Tunnel Method (2010)

The vortex interference mechanism on low Reynolds number between the canard and main wing of the canard-forward sweep wing (Canard-FSW) configurations is simulated numerically by employing the numerical wind tunnel method. The variations of aerodynamic characteristics of Canard-FSW configurations with different positions of the canard are investigated, finding that the aerodynamic interference and mutual coupling effect between the canard and main wing have made great contributions to the lift and stability characteristics of the whole aircraft. Canard can radically improve the surface flow pattern of the main wing. And its own vortex can have a favorable interference on the main wing and can effectively control the airflow boundary layer separation. At small angles of attack, the aerodynamic characteristics are sensitive to the positions of the canard and the main wing, but at high angles of attack, the aerodynamic performances of the configuration are not only related to the shape of the canard (forward or backward), but also with the size of control force as well as the features of the vortices generated above the main wing and the canard. The different configurations and vortices are illustrated using the velocity vector, streamlines and pressure contours.
Safety and efficacy of intravitreal triamcinolone for cystoid macular oedema in uveitis (2001)

One injection of intravitreal triamcinolone was an effective short-term treatment for resistant CMO in uveitis. As with steroids given by other routes, raised intraocular pressure and cataract may occur. As it was so effective in these eyes with resistant CMO, a larger study is warranted to evaluate this form of therapy.
Join cost for unit selection speech synthesis (2004)

In unit-selection speech synthesis systems, synthetic speech is produced by concatenating speech units selected from a large database, or inventory, which contains many instances of each speech unit with varied prosodic and spectral characteristics. Hence, by selecting an appropriate sequence of
The Complete 685-Kilobase DNA Sequence of the Human β T Cell Receptor Locus (1996)

The human beta T cell receptor (TCR) locus, comprising a complex family of genes, has been sequenced. The locus contains two types of coding elements--TCR elements (65 variable gene segments and two clusters of diversity, joining, and constant segments) and eight trypsinogen genes --that constitute 4.6 percent of the DNA. Genome-wide interspersed repeats and locus-specific repeats span 30 and 47 percent, respectively, of the 685-kilobase sequence. A comparison of the germline variable elements with their approximately 300 complementary DNA counterparts reveals marked differential patterns of variable gene expression, the importance of exonuclease activity in generating TCR diversity, and the predominant tendency for only functional variable elements to be present in complementary DNA libraries.