gebhart/patrepeval huggingface dataset:
Click chemistry by microcontact printing on self-assembled monolayers: A structure–reactivity study by fluorescence microscopy (2011)

Microcontact printing (μCP) has developed into a powerful tool to functionalize surfaces with patterned molecular monolayers. μCP can also be used to induce a chemical reaction between a molecular ink and a self-assembled monolayer (SAM) in the nanoscale confinement between stamp and substrate. In this paper, we investigate the Huisgen 1,3-dipolar cycloaddition, the Diels-Alder cycloaddition and the thiol-ene/yne reaction induced by μCP. A range of fluorescent alkyne inks were printed on azide SAMs and fluorescence microscopy was used to monitor the extent of the 1,3-dipolar cycloaddition on a glass substrate. The rate of cycloaddition depends on the reactivity of the alkyne and on the presence of Cu(I). The cycloaddition is accelerated by Cu(I) but it also proceeds readily in the absence of Cu(I). In addition, a range of fluorescent diene inks were printed on alkene SAMs on glass. In this case, fluorescence microscopy was used to monitor the rate of the Diels-Alder cycloaddition as well as its retro-reaction. Finally, fluorescent thiol inks were printed on alkene SAMs on glass, and fluorescent alkenes and alkynes were printed on thiol SAMs. It is shown that reactions by μCP follow structure-reactivity relationships similar to solution reactions. Under optimized conditions all reactions lead to dense microarrays of addition products within minutes of printing time.
The geometry of weighted low-rank approximations (2003)

The low-rank approximation problem is to approximate optimally, with respect to some norm, a matrix by one of the same dimension but smaller rank. It is known that under the Frobenius norm, the best low-rank approximation can be found by using the singular value decomposition (SVD). Although this is no longer true under weighted norms in general, it is demonstrated here that the weighted low-rank approximation problem can be solved by finding the subspace that minimizes a particular cost function. A number of advantages of this parameterization over the traditional parameterization are elucidated. Finding the minimizing subspace is equivalent to minimizing a cost function on the Grassmann manifold. A general framework for constructing optimization algorithms on manifolds is presented and it is shown that existing algorithms in the literature are special cases of this framework. Within this framework, two novel algorithms (a steepest descent algorithm and a Newton-like algorithm) are derived for solving the weighted low-rank approximation problem. They are compared with other algorithms for low-rank approximation as well as with other algorithms for minimizing a cost function on a Grassmann manifold.
A Performance and Failure Analysis of SAPHIRE with a MEDLINE Test Collection (1994)

The current version of the Metathesaurus, as utilized by SAPHIRE, was unable to represent the conceptual content of one-fourth of physician-generated MEDLINE queries. The most likely cause for retrieval of nonrelevant articles was the presence of some or all of the search terms in the article, with frequencies high enough to lead to retrieval. The most likely cause for nonretrieval of relevant articles was the absence of the actual terms from the query, with synonyms or hierarchically related terms present instead. There were significant variations in performance when SAPHIRE's concept-weighing formulas were modified.
Withanolide A Prevents Neurodegeneration by Modulating Hippocampal Glutathione Biosynthesis during Hypoxia (2014)

Withania somnifera root extract has been used traditionally in ayurvedic system of medicine as a memory enhancer. Present study explores the ameliorative effect of withanolide A, a major component of withania root extract and its molecular mechanism against hypoxia induced memory impairment. Withanolide A was administered to male Sprague Dawley rats before a period of 21 days pre-exposure and during 07 days of exposure to a simulated altitude of 25,000 ft. Glutathione level and glutathione dependent free radicals scavenging enzyme system, ATP, NADPH level, γ-glutamylcysteinyl ligase (GCLC) activity and oxidative stress markers were assessed in the hippocampus. Expression of apoptotic marker caspase 3 in hippocampus was investigated by immunohistochemistry. Transcriptional alteration and expression of GCLC and Nuclear factor (erythroid-derived 2)-related factor 2 (Nrf2) were investigated by real time PCR and immunoblotting respectively. Exposure to hypobaric hypoxia decreased reduced glutathione (GSH) level and impaired reduced gluatathione dependent free radical scavenging system in hippocampus resulting in elevated oxidative stress. Supplementation of withanolide A during hypoxic exposure increased GSH level, augmented GSH dependent free radicals scavenging system and decreased the number of caspase and hoescht positive cells in hippocampus. While withanolide A reversed hypoxia mediated neurodegeneration, administration of buthionine sulfoximine along with withanolide A blunted its neuroprotective effects. Exogenous administration of corticosterone suppressed Nrf2 and GCLC expression whereas inhibition of corticosterone synthesis upregulated Nrf2 as well as GCLC. Thus present study infers that withanolide A reduces neurodegeneration by restoring hypoxia induced glutathione depletion in hippocampus. Further, Withanolide A increases glutathione biosynthesis in neuronal cells by upregulating GCLC level through Nrf2 pathway in a corticosterone dependenet manner.
Ketamine aggravates symptoms of acute stress disorder in a naturalistic sample of accident victims (2008)

The glutamatergic N-methyl-D-aspartate receptor antagonist ketamine produces transient dissociative states and alters cognitive functioning in healthy humans, thus resembling the core symptoms of acute and chronic post-traumatic stress disorder (PTSD). First evidence exists that the common use of the analgesic and sedative properties of ketamine during emergency care correlates with sustained symptoms of PTSD in accident victims. The aim of the present study was to examine whether ketamine administration after moderate accidental trauma modulates dissociation and other symptoms of acute stress disorder (ASD) in the direct aftermath of the event. Accident victims were screened within the third day after admission to hospital for symptoms of ASD (Peritraumatic Dissociative Experiences Questionnaire, ASD Scale) and prior stressful life events (Traumatic Life Events Questionnaire). Subjects had received a single or fractionated dose of either racemic ketamine (n=13), opioids (n=24) or non-opioid analgesics (n=13) during initial emergency treatment. There were no significant differences between medication groups in demographic and clinical characteristics such as injury severity or prior traumatization. With respect to ASD symptomatology three days post-event there were significant associations between ketamine analgosedation and increased symptoms of dissociation, reexperiencing, hyperarousal and avoidance relative to the comparison groups.Growing evidence exists that ketamine might modulate or aggravate early post-traumatic stress reactions when given in the acute trauma phase, which in turn might contribute to long-lasting symptomatology.
Ultra-Early Hemostatic Therapy for Intracerebral Hemorrhage (2003)

Ultra-early hemostatic therapy, given within 3 to 4 hours of onset, may potentially arrest ongoing bleeding and minimize hematoma growth after ICH. Given the current lack of effective therapy for ICH, clinical trials testing this treatment approach are justified.
Direct-acting antivirals and host-targeting strategies to combat enterovirus infections (2017)

Enteroviruses (e.g., poliovirus, enterovirus-A71, coxsackievirus, enterovirus-D68, rhinovirus) include many human pathogens causative of various mild and more severe diseases, especially in young children. Unfortunately, antiviral drugs to treat enterovirus infections have not been approved yet. Over the past decades, several direct-acting inhibitors have been developed, including capsid binders, which block virus entry, and inhibitors of viral enzymes required for genome replication. Capsid binders and protease inhibitors have been clinically evaluated, but failed due to limited efficacy or toxicity issues. As an alternative approach, host-targeting inhibitors with potential broad-spectrum activity have been identified. Furthermore, drug repurposing screens have recently uncovered promising new inhibitors with disparate viral and host targets. Together, these findings raise hope for the development of (broad-range) anti-enteroviral drugs.
Deposition of Suspended Magnetite in High Temperature High Pressure Boiler Environments (2015)

Suspended magnetite particles in boiler waters were found to deposit in orifice headers, impeding flow and causing inefficiencies and boiler tube failures from overheating. Particle interactions due to the zeta potential developed on the colloidal magnetite particles could also be a factor in deposition. To study the mechanism behind the deposition of suspended magnetite on stainless steel, a high temperature high pressure electrophoretic deposition cell with provisions to test 304 stainless steel substrates has been developed. The tests, conducted at pH 25 °C of 9.3 in simulated boiler conditions in terms of temperature, pressure and water chemistry. The deposition was monitored using in-situ Electrochemical Impedance Spectroscopy (EIS) and post-test surface analyses were carried out on the substrate. The results of the tests concurred with the theory on oxide particle behavior in aqueous systems and colloidal stability. The specific conditions in the boiler that favor deposition have been successfully replicated.
Structurally Designed Attenuated Subunit Vaccines for S. aureus LukS-PV and LukF-PV Confer Protection in a Mouse Bacteremia Model (2013)

Previous efforts towards S. aureus vaccine development have largely focused on cell surface antigens to induce opsonophagocytic killing aimed at providing sterile immunity, a concept successfully applied to other Gram-positive pathogens such as Streptococcus pneumoniae. However, these approaches have largely failed, possibly in part due to the remarkable diversity of the staphylococcal virulence factors such as secreted immunosuppressive and tissue destructive toxins. S. aureus produces several pore-forming toxins including the single subunit alpha hemolysin as well as bicomponent leukotoxins such as Panton-Valentine leukocidin (PVL), gamma hemolysins (Hlg), and LukED. Here we report the generation of highly attenuated mutants of PVL subunits LukS-PV and LukF-PV that were rationally designed, based on an octameric structural model of the toxin, to be deficient in oligomerization. The attenuated subunit vaccines were highly immunogenic and showed significant protection in a mouse model of S. aureus USA300 sepsis. Protection against sepsis was also demonstrated by passive transfer of rabbit immunoglobulin raised against LukS-PV. Antibodies to LukS-PV inhibited the homologous oligomerization of LukS-PV with LukF-PV as well heterologous oligomerization with HlgB. Importantly, immune sera from mice vaccinated with the LukS mutant not only inhibited the PMN lytic activity produced by the PVL-positive USA300 but also blocked PMN lysis induced by supernatants of PVL-negative strains suggesting a broad protective activity towards other bicomponent toxins. These findings strongly support the novel concept of an anti-virulence, toxin-based vaccine intended for prevention of clinical S. aureus invasive disease, rather than achieving sterile immunity. Such a multivalent vaccine may include attenuated leukotoxins, alpha hemolysin, and superantigens.
Heterozygotes for HFE mutations have no increased risk of advanced alcoholic liver disease (1998)

Possession of a single copy of either of the two HFE mutations influences neither liver iron content nor the risk of fibrotic disease in alcoholics.
Hierarchical object-based visual attention for machine vision (2003)

Human vision uses mechanisms of covert attention to selectively process interesting information and overt eye movements to extend this selectivity ability. Thus, visual tasks can be effectively dealt with by limited processing resources. Modelling visual attention for machine vision systems is not only critical but also challenging. In the machine vision literature there have been many conventional attention models developed but they are all space-based only and cannot perform object-based selection. In consequence, they fail to work in real-world visual environments due to the intrinsic limitations of the space-based attention theory upon which these models are built. The aim of the work presented in this thesis is to provide a novel human-like visual selection framework based on the object-based attention theory recently being developed in psychophysics. The proposed solution -- a Hierarchical Object-based Attention Framework (HOAF) based on grouping competition, consists of two closely-coupled visual selection models of (1) hierarchical object-based visual (covert) attention and (2) object-based attention-driven (overt) saccadic eye movements. The Hierarchical Object-based Attention Model (HOAM) is the primary selection mechanism and the Object-based Attention-Driven Saccading model (OADS) has a supporting role, both of which are combined in the integrated visual selection framework HOAF.
Antidepressant Drug Therapy and Suicide in Severely Depressed Children and Adults (2006)

In these high-risk patients, antidepressant drug treatment does not seem to be related to suicide attempts and death in adults but might be related in children and adolescents. These findings support careful clinical monitoring during antidepressant drug treatment of severely depressed young people.
Respiratory Syncytial Virus That Lacks Open Reading Frame 2 of the M2 Gene (M2-2) Has Altered Growth Characteristics and Is Attenuated in Rodents (2000)

The M2 gene of respiratory syncytial virus (RSV) encodes two putative proteins: M2-1 and M2-2; both are believed to be involved in the RNA transcription or replication process. To understand the function of the M2-2 protein in virus replication, we deleted the majority of the M2-2 open reading frame from an infectious cDNA clone derived from the human RSV A2 strain. Transfection of HEp-2 cells with the cDNA clone containing the M2-2 deletion, together with plasmids that encoded the RSV N, P, and L proteins, produced a recombinant RSV that lacked the M2-2 protein (rA2DeltaM2-2). Recombinant virus rA2DeltaM2-2 was recovered and characterized. The levels of viral mRNA expression for 10 RSV genes examined were unchanged in cells infected with rA2DeltaM2-2, except that a shorter M2 mRNA was detected. However, the ratio of viral genomic or antigenomic RNA to mRNA was reduced in rA2DeltaM2-2-infected cells. By use of an antibody directed against the bacterially expressed M2-2 protein, the putative M2-2 protein was detected in cells infected with wild-type RSV but not in cells infected with rA2DeltaM2-2. rA2DeltaM2-2 displayed a small-plaque morphology and grew much more slowly than wild-type RSV in HEp-2 cells. In infected Vero cells, rA2DeltaM2-2 exhibited very large syncytium formation compared to that of wild-type recombinant RSV. rA2DeltaM2-2 appeared to be a host range mutant, since it replicated poorly in HEp-2, HeLa, and MRC5 cells but replicated efficiently in Vero and LLC-MK2 cells. Replication of rA2DeltaM2-2 in the upper and lower respiratory tracts of mice and cotton rats was highly restricted. Despite its attenuated replication in rodents, rA2DeltaM2-2 was able to provide protection against challenge with wild-type RSV A2. The genotype and phenotype of the M2-2 deletion mutant were stably maintained after extensive in vitro passages. The attenuated phenotype of rA2DeltaM2-2 suggested that rA2DeltaM2-2 may be a potential candidate for use as a live attenuated vaccine.
A Randomized, Controlled Trial of Promogran (a Collagen/Oxidized Regenerated Cellulose Dressing) vs Standard Treatment in the Management of Diabetic Foot Ulcers (2002)

Promogran was comparable to moistened gauze in promoting wound healing in diabetic foot ulcers. It showed an additional efficacy for ulcers of less than 6 months' duration that was of marginal statistical significance. Furthermore, Promogran had a safety profile that was similar to that of moistened gauze, with greater user satisfaction. Therefore, Promogran may be a useful adjunct in the management of diabetic foot ulceration, especially in ulcers of less than 6 months' duration.
Influence of cathode geometry on electron dynamics in an ultrafast electron microscope (2017)

Efforts to understand matter at ever-increasing spatial and temporal resolutions have led to the development of instruments such as the ultrafast transmission electron microscope (UEM) that can capture transient processes with combined nanometer and picosecond resolutions. However, analysis by UEM is often associated with extended acquisition times, mainly due to the limitations of the electron gun. Improvements are hampered by tradeoffs in realizing combinations of the conflicting objectives for source size, emittance, and energy and temporal dispersion. Fundamentally, the performance of the gun is a function of the cathode material, the gun and cathode geometry, and the local fields. Especially shank emission from a truncated tip cathode results in severe broadening effects and therefore such electrons must be filtered by applying a Wehnelt bias. Here we study the influence of the cathode geometry and the Wehnelt bias on the performance of a photoelectron gun in a thermionic configuration. We combine experimental analysis with finite element simulations tracing the paths of individual photoelectrons in the relevant 3D geometry. Specifically, we compare the performance of guard ring cathodes with no shank emission to conventional truncated tip geometries. We find that a guard ring cathode allows operation at minimum Wehnelt bias and improve the temporal resolution under realistic operation conditions in an UEM. At low bias, the Wehnelt exhibits stronger focus for guard ring than truncated tip cathodes. The increase in temporal spread with bias is mainly a result from a decrease in the accelerating field near the cathode surface. Furthermore, simulations reveal that the temporal dispersion is also influenced by the intrinsic angular distribution in the photoemission process and the initial energy spread. However, a smaller emission spot on the cathode is not a dominant driver for enhancing time resolution. Space charge induced temporal broadening shows a close to linear relation with the number of electrons up to at least 10 000 electrons per pulse. The Wehnelt bias will affect the energy distribution by changing the Rayleigh length, and thus the interaction time, at the crossover.
Cloning of the cellular receptor for amphotropic murine retroviruses reveals homology to that for gibbon ape leukemia virus. (1994)

The host and tissue specificity of retrovirus infection is largely determined by specific cellular receptors that mediate virus entry. Genes encoding these receptors are widely distributed in the genome, and the receptors identified to date show no sequence similarity. We have identified the cellular receptor for amphotropic murine retroviruses, Ram-1, by screening a rat cDNA expression library introduced into amphotropic virus-resistant hamster cells. The 656-amino acid receptor is homologous to the gibbon ape leukemia virus receptor at both hydrophobic termini but is highly divergent in the central hydrophilic region. Both receptors appear to be integral membrane proteins having multiple membrane-spanning regions. Identification of this family of receptors will help define the evolutionary relationship between retroviruses and their cellular receptors.
Short-read DNA sequence alignment with custom designed FPGA-based hardware (2010)

The alignment of short DNA read sequencing data to a human reference genome sequence has become a standard step in the analysis pipeline for short DNA read sequence data. As the rate at which short read DNA sequence data is being produced doubles every 5 months, analysis of this data in a computationally efficient way is becoming increasingly important. We demonstrate how we can exploit the ``embarrassingly parallel'' property of short read sequence alignment in custom-designed hardware in FPGA’s. Hardware is chosen, a system is designed, and this system is implemented. My FPGA-based hit finder was demonstrated to produce correct hit results. The performance of this single FPGA implementation was demonstrated to be 71,000 seed hits found per hour on a human genome sized reference sequence. The implementation was demonstrated to produce identical results to the hit finder stage of the MAQ aligner. We demonstrate that the price/performance of this sliding-window FPGA aligner (approximately ~355 seeds/hr/$) compares favorably to the price/performance of sliding-window software aligners (approximately ~67.5 seeds/hr/$ for MAQ). However, software aligners which are based on the superior Burrows-Wheeler alignment algorithm still have a significant price/performance advantage over the FPGA-based approach (approximately ~7,200 seeds/hr/$). We predict that as chips continue to increase in size due to Moore’s Law and computation is performed in high-density cloud-computing datacenters the FPGA-based approach will become preferable to current software aligners.
Extraction of Constitutive Relation Tensor Parameters of SRR Structures using Transmission Line Theory (2006)

10.1163/156939306775777413
Source consistency filtering-a new tool for ECG noise reduction (2002)

A novel filter, called SCF (source consistency filtering), is introduced. In its spatial form, SCF uses the constraints provided by the redundancy of leads of multichannel recordings to distinguish noise from signal. Quantitatively, each lead is predicted using least-squares-method-derived coefficients, and a multichannel coherence of leads and their respective predictions results in an effective noise reduction in electrocardiogram recording.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nuclear matriax attachment occurs in several regions of the IgH locus (1990)

The genome is thought to be divided into domains by DNA elements which mediate anchorage of chromosomal DNA to the nuclear matrix or chromosome scaffold. The positions of nuclear matrix anchorage regions (MARs) have been mapped within the 200 kb mouse immunoglobulin heavy chain constant region locus, thereby allowing an estimate of the size of DNA domains within a segment of the genome. MARs were identified in four regions, which appear to divide the locus into looped DNA domains of 30, 20, 30 and greater than 70 kb in length. These DNA domain sizes fall within the range of DNA loop sizes observed in histone-extracted nuclei and chromosomes. In two regions, large clusters of MARs were identified, and many of these MARs lie on DNA fragments that include repetitive DNA elements, perhaps indicating that repetitive DNA integrates into the genome close to MARs, or that some classes of repeats could themselves act as MARs.