gebhart/patrepeval huggingface dataset:
Conserved Fungal Genes as Potential Targets for Broad-Spectrum Antifungal Drug Discovery (2006)

The discovery of novel classes of antifungal drugs depends to a certain extent on the identification of new, unexplored targets that are essential for growth of fungal pathogens. Likewise, the broad-spectrum capacity of future antifungals requires the target gene(s) to be conserved among key fungal pathogens. Using a genome comparison (or concordance) tool, we identified 240 conserved genes as candidates for potential antifungal targets in 10 fungal genomes. To facilitate the identification of essential genes in Candida albicans, we developed a repressible C. albicans MET3 (CaMET3) promoter system capable of evaluating gene essentiality on a genome-wide scale. The CaMET3 promoter was found to be highly amenable to controlled gene expression, a prerequisite for use in target-based whole-cell screening. When the expression of the known antifungal target C. albicans ERG1 was reduced via down-regulation of the CaMET3 promoter, the CaERG1 conditional mutant strain became hypersensitive, specifically to its inhibitor, terbinafine. Furthermore, parallel screening against a small compound library using the CaERG1 conditional mutant under normal and repressed conditions uncovered several hypersensitive compound hits. This work therefore demonstrates a streamlined process for proceeding from selection and validation of candidate antifungal targets to screening for specific inhibitors.
Guanidine hydrochloride denaturation studies of mutant forms of staphylococcal nuclease (1986)

Several mutant forms of staphylococcal nuclease with one or two defined amino acid substitutions have been purified, and the effects of the altered amino acid sequence on the stability of the folded conformation have been analyzed by guanidine hydrochloride denaturation. Two nuc- mutations, which greatly reduced the level of enzyme activity accumulated in E coli colonies carrying a recombinant plasmid with the mutant nuc gene (ie, a NUC- phenotype), both result in protein unfolding at significantly lower guanidine hydrochloride concentrations than the wild-type protein, whereas three sup mutations isolated on the basis of their ability to suppress partially the NUC- phenotype of the above two mutations result in unfolding at significantly higher guanidine hydrochloride concentrations. Characterization of nuclease molecules with two different amino acid substitutions, either nuc- + sup pairs or sup + sup pairs, suggests that the effect of an amino acid substitution on the stability of the native conformation, as measured by the value of delta delta GD, may not be a constant, but rather a variable that is sensitive to the presence of other substitutions at distant sites in the same molecule. Surprisingly, the slopes of the log Kapp vs guanidine hydrochloride concentration plots vary by as much as 35% among the different proteins.
Methylated DNA Immunoprecipitation (2009)

The identification of DNA methylation patterns is a common procedure in the study of epigenetics, as methylation is known to have significant effects on gene expression, and is involved with normal development as well as disease. Thus, the ability to discriminate between methylated DNA and non-methylated DNA is essential for generating methylation profiles for such studies. Methylated DNA immunoprecipitation (MeDIP) is an efficient technique for the extraction of methylated DNA from a sample of interest. A sample of as little as 200 ng of DNA is sufficient for the antibody, or immunoprecipitation (IP), reaction. DNA is sonicated into fragments ranging in size from 300-1000 bp, and is divided into immunoprecipitated (IP) and input (IN) portions. IP DNA is subsequently heat denatured and then incubated with anti-5'mC, allowing the monoclonal antibody to bind methylated DNA. After this, magnetic beads containing a secondary antibody with affinity for the primary antibody are added, and incubated. These bead-linked antibodies will bind the monoclonal antibody used in the first step. DNA bound to the antibody complex (methylated DNA) is separated from the rest of the DNA by using a magnet to pull the complexes out of solution. Several washes using IP buffer are then performed to remove the unbound, non-methylated DNA. The methylated DNA/antibody complexes are then digested with Proteinase K to digest the antibodies leaving only the methylated DNA intact. The enriched DNA is purified by phenol:chloroform extraction to remove the protein matter and then precipitated and resuspended in water for later use. PCR techniques can be used to validate the efficiency of the MeDIP procedure by analyzing the amplification products of IP and IN DNA for regions known to lack and known to contain methylated sequences. The purified methylated DNA can then be used for locus-specific (PCR) or genome-wide (microarray and sequencing) methylation studies, and is particularly useful when applied in conjunction with other research tools such as gene expression profiling and array comparative genome hybridization (CGH). Further investigation into DNA methylation will lead to the discovery of new epigenetic targets, which in turn, may be useful in developing new therapeutic or prognostic research tools for diseases such as cancer that are characterized by aberrantly methylated DNA.
Contribution of opioid and metabotropic glutamate receptor mechanisms to inhibition of bladder overactivity by tibial nerve stimulation (2013)

The contribution of metabotropic glutamate receptors (mGluR) and opioid receptors to inhibition of bladder overactivity by tibial nerve stimulation (TNS) was investigated in cats under α-chloralose anesthesia using LY341495 (a group II mGluR antagonist) and naloxone (an opioid receptor antagonist). Slow infusion cystometry was used to measure the volume threshold (i.e., bladder capacity) for inducing a large bladder contraction. After measuring the bladder capacity during saline infusion, 0.25% acetic acid (AA) was infused to irritate the bladder, activate the nociceptive C-fiber bladder afferents, and induce bladder overactivity. AA significantly (P < 0.0001) reduced bladder capacity to 26.6 ± 4.7% of saline control capacity. TNS (5 Hz, 0.2 ms) at 2 and 4 times the threshold (T) intensity for inducing an observable toe movement significantly increased bladder capacity to 62.2 ± 8.3% at 2T (P < 0.01) and 80.8 ± 9.2% at 4T (P = 0.0001) of saline control capacity. LY341495 (0.1-5 mg/kg iv) did not change bladder overactivity, but completely suppressed the inhibition induced by TNS at a low stimulus intensity (2T) and partially suppressed the inhibition at high intensity (4T). Following administration of LY341495, naloxone (0.01 mg/kg iv) completely eliminated the high-intensity TNS-induced inhibition. However, without LY341495 treatment a 10 times higher dose (0.1 mg/kg) of naloxone was required to completely block TNS inhibition. These results indicate that interactions between group II mGluR and opioid receptor mechanisms contribute to TNS inhibition of AA-induced bladder overactivity. Understanding neurotransmitter mechanisms underlying TNS inhibition of bladder overactivity is important for the development of new treatments for bladder disorders.
Synthesis of Thieno [2, 3-d] pyrimidine Derivatives and Their Antifungal Activities (1989)

4-Chlorothieno[2,3-d]pyrimidines were prepared by the chlorination of 4-oxo-3,4-dihydrothieno[2,3-d]pyrimidines with phosphoryl chloride. 4-Oxo-3,4,5,6,7,8-hexahydro[1]-benzo- and 4-oxo-6-phenylthieno[2,3-d]pyrimidine were synthesized by the cyclization of 2-acylaminothiophene-3-carboxamide derivatives with base. 2-Methyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine was prepared by the treatment of 2-methyl-4-trichloromethylthieno-[2,3-d]pyrimidine with sodium hydroxide in aqueous methanol. A series of 4-alkylamino- and 4-arylaminothieno[2,3-d]pyrimidines were synthesized by the nucleophilic substitution of 4-chlorothieno[2,3-d]pyrimidines with various amines. These compounds were evaluated for antifungal activity against Piricularia oryzae. The preventive effects on Rice blast, Sheath blight, and Cucumber powdery mildew were also determined by pot tests.
The Transmeta Code Morphing/spl trade/ Software: using speculation, recovery, and adaptive retranslation to address real-life challenges (2003)

Transmeta's Crusoe microprocessor is a full, system-level implementation of the x86 architecture, comprising a native VLIW microprocessor with a software layer, the Code Morphing Software (CMS), that combines an interpreter, dynamic binary translator, optimizer, and run-time system. In its general structure, CMS resembles other binary translation systems described in the literature, but it is unique in several respects. The wide range of PC workloads that CMS must handle gracefully in real-life operation, plus the need for full system-level x86 compatibility, expose several issues that have received little or no attention in previous literature, such as exceptions and interrupts, I/O, DMA, and self-modifying code. In this paper we discuss some of the challenges raised by these issues, and present the techniques developed in Crusoe and CMS to meet those challenges. The key to these solutions is the Crusoe paradigm of aggressive speculation, recovery to a consistent x86 state using unique hardware commit-and-rollback support, and adaptive retranslation when exceptions occur too often to be handled efficiently by interpretation.
Microflotronics: A Flexible, Transparent, Pressure‐Sensitive Microfluidic Film (2014)

There is an increasing demand for sensitive, flexible, and low‐cost pressure sensing solutions for health monitoring, wearable sensing, robotic and prosthetic applications. Here, the first flexible and pressure‐sensitive microfluidic film is reported, referred to as a microflotronic, with high transparency and seamless integratability with the state‐of‐the‐art microelectronics. The microflotronic film represents the initial effort to utilize a continuous microfluidic layer as the sensing elements for large‐area dynamic pressure mapping applications, and meanwhile an ultrahigh sensitivity of 0.45 kPa −1 has been achieved in a compact, flexible, and transparent packaging. The response time of the device is in the millisecond range, which is at least an order of magnitude faster than that of its conventional flexible solid‐state counterparts. In addition, the fabrication process of the device is fully compatible with the industrial‐scale manufacturing of capacitive touchscreen devices and liquid‐crystal displays. The overall device packaging can be as thin as 200 μm with an optical transparency greater than 80%. Several practical applications were successfully demonstrated, including surface topology mapping and dynamic blood pressure monitoring. The microflotronic devices offer an alternative approach to the solid‐state pressure sensors, by offering an unprecedented sensitivity and ultrafast response time in a completely transparent, flexible and adaptive platform.
Effects of an Acute Dose of <i>L-</i>Arginine during Coronary Angiography in Patients with Chronic Renal Failure (2003)

CM injection causes an impairment of renal function. Addition of intravenous L-arginine during cardiac catheterizations in patients with chronic renal failure does not prevent CM-induced nephrotoxicity and does not affect endothelial dysfunction in the particular population studied by the authors, i.e. patients with coronary artery disease (CAD) of various degrees, or suspicion of CAD and chronic mild renal failure.
Dopaminergic Loss and Inclusion Body Formation in α-Synuclein Mice: Implications for Neurodegenerative Disorders (2000)

To elucidate the role of the synaptic protein alpha-synuclein in neurodegenerative disorders, transgenic mice expressing wild-type human alpha-synuclein were generated. Neuronal expression of human alpha-synuclein resulted in progressive accumulation of alpha-synuclein-and ubiquitin-immunoreactive inclusions in neurons in the neocortex, hippocampus, and substantia nigra. Ultrastructural analysis revealed both electron-dense intranuclear deposits and cytoplasmic inclusions. These alterations were associated with loss of dopaminergic terminals in the basal ganglia and with motor impairments. These results suggest that accumulation of wild-type alpha-synuclein may play a causal role in Parkinson's disease and related conditions.
Loss of cone photoreceptors caused by chromophore depletion is partially prevented by the artificial chromophore pro-drug, 9-cis-retinyl acetate (2009)

Inactivating mutations in the retinoid isomerase (RPE65) or lecithin:retinol acyltransferase (LRAT) genes cause Leber congenital amaurosis (LCA), a severe visual impairment in humans. Both enzymes participate in the retinoid (visual) cycle, the enzymatic pathway that continuously generates 11-cis-retinal, the chromophore of visual pigments in rod and cone photoreceptor cells needed for vision. We investigated human RPE65-LCA patients and mice with visual cycle abnormalities to determine the impact of chronic chromophore deprivation on cones. Young patients with RPE65 mutations showed foveal cone loss along with shortened inner and outer segments of remaining cones; cone cell loss also was dramatic in young mice lacking Rpe65 or Lrat gene function. To selectively evaluate cone pathophysiology, we eliminated the rod contribution to electroretinographic (ERG) responses by generating double knockout mice lacking Lrat or Rpe65 together with an inactivated rod-specific G protein transducin gene (Gnat1-/-). Cone ERG responses were absent in Gnat1-/-Lrat-/- mice which also showed progressive degeneration of cones. Cone ERG responses in Gnat1-/-Rpe65-/- mice were markedly reduced and declined over weeks. Treatment of these mice with the artificial chromophore pro-drug, 9-cis-retinyl acetate, partially protected inferior retinal cones as evidenced by improved ERGs and retinal histochemistry. Gnat1-/- mice chronically treated with retinylamine, a selective inhibitor of RPE65, also showed a decline in the number of cones that was ameliorated by 9-cis-retinyl acetate. These results suggest that chronic lack of chromophore leads to progressive loss of cones in mice and humans. Therapy for LCA patients should be geared toward early adequate delivery of chromophore to cone photoreceptors.
Ontogeny and distribution of glial cell line-derived neurotrophic factor (GDNF) mRNA in rat (1995)

Glial cell line-derived neurotrophic factor (GDNF) is a member of the transforming growth factor-beta family isolated from the rat glial tumor cell line, B49. In embryonic dopaminergic (DA) neurons in vitro, GDNF promotes survival, high-affinity dopamine uptake, and neurite outgrowth. We have used a semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) with primers specific to GDNF to study the developmental expression of GDNF mRNA in central nervous system (CNS) and peripheral organs of embryonic rat on gestational days E11.5, E13.5 and E18, neonatal rat on postnatal days P0 and P10, and adult rat. GDNF mRNA is expressed throughout the CNS, with highest levels in P0 spinal cord and in P0 and P10 striatum. Lower levels are present in the brainstem (including the ventral mesencephalon, which contains the DA neurons of the substantia nigra), cerebellum, diencephalon, and telencephalon, as well as in primary cultures of cerebellar granule cells prepared from P7 cerebellum and astrocytes prepared from P1 cortex. The cerebellum has an unusual temporal pattern of expression, high at birth and in the adult, but undetectable at P10. GDNF mRNA is also expressed in many peripheral tissues at higher levels than in brain. These include embryonic limb bud, kidney and gut; neonatal kidney, gut, lung and testis; and adult lung, liver and ovary. In addition to the predicted RT-PCR product, we also observed a minor band which was shown to be identical to GDNF in the mature peptide sequence, but which has a 78 base pair deletion in the preproprotein sequence.(ABSTRACT TRUNCATED AT 250 WORDS)
Geometry projection method for optimizing photonic nanostructures (2006)

A geometry projection method for the design of photonic nanostructures is demonstrated and compared with a topology optimization method. By using a higher-dimensional surface to delineate the material interfaces, the projection method restricts the regions of intermediate dielectric properties to a narrow user-defined band and gives some implicit control over feature size. Topology optimization addresses these issues by using a penalization to avoid areas of intermediate dielectric and a filter to obtain implicit control over feature size. The directional emission from a photonic crystal waveguide termination is improved by both methods by generating a series of irregularly shaped dielectric posts. Results are presented, and the relative merits of each method are discussed.
Application of Deep Belief Networks for Natural Language Understanding (2014)

Applications of Deep Belief Nets (DBN) to various problems have been the subject of a number of recent studies ranging from image classification and speech recognition to audio classification. In this study we apply DBNs to a natural language understanding problem. The recent surge of activity in this area was largely spurred by the development of a greedy layer-wise pretraining method that uses an efficient learning algorithm called Contrastive Divergence (CD). CD allows DBNs to learn a multi-layer generative model from unlabeled data and the features discovered by this model are then used to initialize a feed-forward neural network which is fine-tuned with backpropagation. We compare a DBN-initialized neural network to three widely used text classification algorithms: Support Vector Machines (SVM), boosting and Maximum Entropy (MaxEnt). The plain DBN-based model gives a call-routing classification accuracy that is equal to the best of the other models. However, using additional unlabeled data for DBN pre-training and combining DBN-based learned features with the original features provides significant gains over SVMs, which, in turn, performed better than both MaxEnt and Boosting.
Retractor-induced brain shift compensation in image-guided neurosurgery (2013)

In image-guided neurosurgery, intraoperative brain shift significantly degrades the accuracy of neuronavigation that is solely based on preoperative magnetic resonance images (pMR). To compensate for brain deformation and to maintain the accuracy in image guidance achieved at the start of surgery, biomechanical models have been developed to simulate brain deformation and to produce model-updated MR images (uMR) to compensate for brain shift. To-date, most studies have focused on shift compensation at early stages of surgery (i.e., updated images are only produced after craniotomy and durotomy). Simulating surgical events at later stages such as retraction and tissue resection are, perhaps, clinically more relevant because of the typically much larger magnitudes of brain deformation. However, these surgical events are substantially more complex in nature, thereby posing significant challenges in model-based brain shift compensation strategies. In this study, we present results from an initial investigation to simulate retractor-induced brain deformation through a biomechanical finite element (FE) model where whole-brain deformation assimilated from intraoperative data was used produce uMR for improved accuracy in image guidance. Specifically, intensity-encoded 3D surface profiles at the exposed cortical area were reconstructed from intraoperative stereovision (iSV) images before and after tissue retraction. Retractor-induced surface displacements were then derived by coregistering the surfaces and served as sparse displacement data to drive the FE model. With one patient case, we show that our technique is able to produce uMR that agrees well with the reconstructed iSV surface after retraction. The computational cost to simulate retractor-induced brain deformation was approximately 10 min. In addition, our approach introduces minimal interruption to the surgical workflow, suggesting the potential for its clinical application.
Energetic Characterization of the Basic Fibroblast Growth Factor-Heparin Interaction: Identification of the Heparin Binding Domain (1994)

Fibroblast growth factors (FGF's) interact on cell surfaces with "low-affinity" heparan sulfate proteoglycans (HSPG) and "high-affinity" FGF receptors (FGFR) to initiate cell proliferation. Previous reports have implicated the binding of heparin, or heparan sulfate, to FGF as essential for FGF-mediated signal transduction and mitogenicity. However, the molecular recognition events which dictate the specificity of this interaction have remained elusive. Amino acid residues on the surface of basic FGF (bFGF) were targeted as potential heparin contacts on the basis of the position of sulfate anions in the X-ray crystal structure of bFGF and of a modeled pentasaccharide heparin-bFGF complex. Each identified amino acid was replaced individually with alanine by site-directed mutagenesis, and the resulting mutant proteins were characterized for differences in binding to a low molecular weight heparin (approximately 3000) by isothermal titrating calorimetry and also for differences in [NaCl] elution from a heparin-Sepharose affinity resin. The combination of site-directed mutagenesis and titrating calorimetry permitted an analysis of the energetic contributions of individual bFGF residues in the binding of heparin to bFGF. The key amino acids which comprise the heparin binding domain on bFGF constitute a discontinuous binding epitope and include K26, N27, R81, K119, R120, T121, Q123, K125, K129, Q134, and K135. Addition of the observed delta delta G degrees of binding for each single site mutant accounts for 8.56 kcal/mol (> 95%) of the free energy of binding. The delta delta G degrees values for N27A, R120A, K125A, and Q134A are all greater than 1 kcal/mol each, and these four amino acids together contribute 4.8 kcal/mol (56%) to the total binding free energy. Amino acid residues K119 through K135 reside in the C-terminal domain of bFGF and collectively contribute 6.6 kcal/mol (76%) of the binding free energy. Although 7 out of the 11 identified amino acids in the heparin binding domain are positively charged, a 7-fold increase in [NaCl] decreases the affinity of wild-type bFGF binding to heparin only 37-fold (Kd at 0.1 M NaCl = 470 nM vs Kd at 0.7 M NaCl = 17.2 microM). This indicates that pure electrostatic interactions contribute only 30% of the binding free energy as analyzed by polyelectrolyte theory and that more specific nonionic interactions, such as hydrogen bonding and van der Waals packing, contribute the majority of the free energy for this binding reaction.
Faculty Perceptions on the Goals and Achievements of Information Systems Executive Advisory Boards (2009)

Information Systems executive advisory boards have become an increasingly important way for faculty to draw upon the expertise and resources of industry members. This benefits students and faculty and ensures the relevance of information systems programs. This paper describes a study of faculty member’s perspectives regarding the goals and achievements of their advisory boards. 194 faculty members responded to a survey about the extent to which faculty agree or disagree that ten specific items serve as major goals for their advisory boards. The respondents also provided perspectives on the success of their boards along those same dimensions as well as the overall perceived success of the board. The results of the study provide empirical data to guide current and prospective IS advisory boards and as a foundation for future research on academic-industry relationships.