gebhart/patrepeval huggingface dataset:
Efficient and Practical Oxidative Bromination and Iodination of Arenes and Heteroarenes with DMSO and Hydrogen Halide: A Mild Protocol for Late-Stage Functionalization (2015)

An efficient and practical system for inexpensive bromination and iodination of arenes as well as heteroarenes by using readily available dimethyl sulfoxide (DMSO) and HX (X = Br, I) reagents is reported. This mild oxidative system demonstrates a versatile protocol for the synthesis of aryl halides. HX (X = Br, I) are employed as halogenating reagents when combined with DMSO which participates in the present chemistry as a mild and inexpensive oxidant. This oxidative system is amenable to late-stage bromination of natural products. The kilogram-scale experiment (>95% yield) shows great potential for industrial application.
Scoring Cyber Vulnerabilities based on Their Impact on Organizational Goals (2021)

Vulnerability Management, which is a vital part of risk and resiliency management efforts, is a continuous process of identifying, classifying, prioritizing, and removing vulnerabilities on devices that are likely to be used by attackers to compromise a network component. For effective and efficient vulnerability management, which requires extensive resources– such as time and personnel, vulnerabilities should be prioritized based on their criticality. One of the most common methods to prioritize vulnerabilities is the Common Vulnerability Scoring System (CVSS). However, in its severity score, the National Institute of Standards and Technology (NIST) only provides the base metric values that include exploitability and impact information for the known vulnerabilities and acknowledges the importance of temporal and environmental characteristics to have a more accurate vulnerability assessment. There is no established method to conduct the integration of these metrics. In this study, we created a testbed to assess the vulnerabilities by considering the functional dependencies between vulnerable assets, other assets, and business processes. The experiment results revealed that a vulnerability’s severity significantly changes from its CVSS base score when the vulnerable asset’s characteristics and role inside the organization are considered.
Ultra-sensitive Magnetic Microscopy with an Optically Pumped Magnetometer (2016)

Optically pumped magnetometers (OPMs) based on lasers and alkali-metal vapor cells are currently the most sensitive non-cryogenic magnetic field sensors. Many applications in neuroscience and other fields require high-resolution, high-sensitivity magnetic microscopic measurements. In order to meet this demand we combined a cm-size spin-exchange relaxation-free (SERF) OPM and flux guides (FGs) to realize an ultra-sensitive FG-OPM magnetic microscope. The FGs serve to transmit the target magnetic flux to the OPM thus improving both the resolution and sensitivity to small magnetic objects. We investigated the performance of the FG-OPM device using experimental and numerical methods, and demonstrated that an optimized device can achieve a unique combination of high resolution (80 μm) and high sensitivity (8.1 pT/). In addition, we also performed numerical calculations of the magnetic field distribution in the FGs to estimate the magnetic noise originating from the domain fluctuations in the material of the FGs. We anticipate many applications of the FG-OPM device such as the detection of micro-biological magnetic fields; the detection of magnetic nano-particles; and non-destructive testing. From our theoretical estimate, an FG-OPM could detect the magnetic field of a single neuron, which would be an important milestone in neuroscience.
Exchange enhancement of the g factor in InAs/AlSb heterostructures (2008)

The evolution of the Shubnikov-de Haas oscillations in InAs/AlSb heterostructures with twodimensional electron gas in InAs quantum wells 12–18 nm wide with considerable variation in the electron concentration (3–8) × 1011 cm−2 due to the effect of negative persistent photoconductivity is studied. The values of the effective Landé factor for electrons g* = −(15–35) are determined. It is shown that the value of the g* factor increases as the quantum well width increases.
Thiazolides, a New Class of Anti-influenza Molecules Targeting Viral Hemagglutinin at the Post-translational Level (2009)

The emergence of highly contagious influenza A virus strains, such as the new H1N1 swine influenza, represents a serious threat to global human health. Efforts to control emerging influenza strains focus on surveillance and early diagnosis, as well as development of effective vaccines and novel antiviral drugs. Herein we document the anti-influenza activity of the anti-infective drug nitazoxanide and its active circulating-metabolite tizoxanide and describe a class of second generation thiazolides effective against influenza A virus. Thiazolides inhibit the replication of H1N1 and different other strains of influenza A virus by a novel mechanism: they act at post-translational level by selectively blocking the maturation of the viral hemagglutinin at a stage preceding resistance to endoglycosidase H digestion, thus impairing hemagglutinin intracellular trafficking and insertion into the host plasma membrane, a key step for correct assembly and exit of the virus from the host cell. Targeting the maturation of the viral glycoprotein offers the opportunity to disrupt the production of infectious viral particles attacking the pathogen at a level different from the currently available anti-influenza drugs. The results indicate that thiazolides may represent a new class of antiviral drugs effective against influenza A infection.
Beam switching with binary single-order diffractive gratings (1998)

A new type of a micro-optomechanical dielectric switch in free-space configuration for visible light is proposed and experimentally demonstrated. The combination of scalar and rigorous diffraction analysis of Gaussian beams predicts high high switching efficiency with a single/noise ratio of better than 40 dB.
Evidence for radical anion formation during liquid secondary ion mass spectrometry analysis of oligonucleotides and synthetic oligomeric analogs: a deconvolution algorithm for molecular ion region clusters (1989)

It is shown that one-electron reduction is a common process that occurs in negative ion liquid secondary ion mass spectrometry (LSIMS) of oligonucleotides and synthetic oligonucleosides and that this process is in competition with proton loss. Deconvolution of the molecular anion cluster reveals contributions from (M-2H).-, (M-H)-, M.-, and (M + H)-. A model based on these ionic species gives excellent agreement with the experimental data. A correlation between the concentration of species arising via one-electron reduction [M.- and (M + H)-] and the electron affinity of the matrix has been demonstrated. The relative intensity of M.- is mass-dependent; this is rationalized on the basis of base-stacking. Base sequence ion formation is theorized to arise from M.- radical anion among other possible pathways.
Integrin Interactions with Immobilized Peptides in Polyethylene Glycol Diacrylate Hydrogels (2004)

This study employs tissue-engineering technologies to evaluate neutrophil interactions with extracellular matrix (ECM)-mimetic peptides. We have used a polyethylene glycol (PEG) diacrylate derivative to form a hydrogel as a biologically inert surface. Covalent attachment of bioactive moieties to the hydrogel makes it bioactive. The goal is to define the mechanisms by which these moieties influence the interactions of neutrophils with this bioactive hydrogel, and thus understand the likely effects of similar ligands in the ECM. The current experiments analyze the interactions of isolated human neutrophils with PEG hydrogels modified with Arg-Gly-Asp-Ser (RGDS), a known ligand for some beta(1) and beta(3) integrins, and Thr-Met-Lys-Ile-Ile-Pro-Phe-Asn-Arg-Leu-Thr-Ile-Gly-Gly (TMKIIPFNRLTIGG), a ligand for Mac-1, a beta(2) integrin. Our results demonstrate that neutrophils, independent of chemotactic stimulation, show little ability to adhere to unmodified PEG hydrogels. However, cell adhesion and spreading are robust on peptide-modified hydrogels. Incorporating distinct bioactive peptides, either alone or in combination, has enabled recognition of differential functions of alpha(v)beta(3), beta(1), and beta(2) integrins on neutrophil adhesion and spreading. Combined interactions result in activity that differs markedly from that seen with either integrin independently engaged. This model allows investigation of specific ligand-induced leukocyte functions and the development of engineered matrices with defined bioactive properties.
Ubiquinone (Coenzyme Q<sub>10</sub>) and Mitochondria in Oxidative Stress of Parkinson’s Disease (2001)

Parkinson's disease is the second most common neurodegenerative disorder after Alzheimer's disease affecting approximately1% of the population older than 50 years. There is a worldwide increase in disease prevalence due to the increasing age of human populations. A definitive neuropathological diagnosis of Parkinson's disease requires loss of dopaminergic neurons in the substantia nigra and related brain stem nuclei, and the presence of Lewy bodies in remaining nerve cells. The contribution of genetic factors to the pathogenesis of Parkinson's disease is increasingly being recognized. A point mutation which is sufficient to cause a rare autosomal dominant form of the disorder has been recently identified in the alpha-synuclein gene on chromosome 4 in the much more common sporadic, or 'idiopathic' form of Parkinson's disease, and a defect of complex I of the mitochondrial respiratory chain was confirmed at the biochemical level. Disease specificity of this defect has been demonstrated for the parkinsonian substantia nigra. These findings and the observation that the neurotoxin 1-methyl-4-phenyl-1,2,3, 6-tetrahydropyridine (MPTP), which causes a Parkinson-like syndrome in humans, acts via inhibition of complex I have triggered research interest in the mitochondrial genetics of Parkinson's disease. Oxidative phosphorylation consists of five protein-lipid enzyme complexes located in the mitochondrial inner membrane that contain flavins (FMN, FAD), quinoid compounds (coenzyme Q10, CoQ10) and transition metal compounds (iron-sulfur clusters, hemes, protein-bound copper). These enzymes are designated complex I (NADH:ubiquinone oxidoreductase, EC 1.6. 5.3), complex II (succinate:ubiquinone oxidoreductase, EC 1.3.5.1), complex III (ubiquinol:ferrocytochrome c oxidoreductase, EC 1.10.2.2), complex IV (ferrocytochrome c:oxygen oxidoreductase or cytochrome c oxidase, EC 1.9.3.1), and complex V (ATP synthase, EC 3.6.1.34). A defect in mitochondrial oxidative phosphorylation, in terms of a reduction in the activity of NADH CoQ reductase (complex I) has been reported in the striatum of patients with Parkinson's disease. The reduction in the activity of complex I is found in the substantia nigra, but not in other areas of the brain, such as globus pallidus or cerebral cortex. Therefore, the specificity of mitochondrial impairment may play a role in the degeneration of nigrostriatal dopaminergic neurons. This view is supported by the fact that MPTP generating 1-methyl-4-phenylpyridine (MPP(+)) destroys dopaminergic neurons in the substantia nigra. Although the serum levels of CoQ10 is normal in patients with Parkinson's disease, CoQ10 is able to attenuate the MPTP-induced loss of striatal dopaminergic neurons.
Specific binding of angiogenin to calf pulmonary artery endothelial cells. (1989)

Specific binding of angiogenin (ANG) to calf pulmonary artery endothelial cells was demonstrated. Cellular binding at 4 degrees C of 125I-labeled human recombinant ANG was time and concentration dependent, reversible, and saturable in the presence of increasing amounts of the unlabeled molecules. The interaction was shown to be specific since a large excess of unlabeled ANG reduced labeled ANG binding by 80%, whereas similar doses of RNase A, a structurally related protein, had no effect. Scatchard analyses of binding data revealed two apparent components. High-affinity sites with an apparent dissociation constant of 5 x 10(-9) M were shown to represent cell-specific interactions. The second component, comprising low-affinity/high-capacity sites with an apparent dissociation constant of 0.2 x 10(-6) M, was essentially associated with pericellular components. High-affinity ANG binding sites varied with cell density and were found on other endothelial cells from bovine aorta, cornea, and adrenal cortex capillary but not on Chinese hamster lung fibroblasts. Divalent copper, a modulator of angiogenesis, was found to induce a severalfold increase in specific cell-bound radioactivity. Placental ribonuclease inhibitor, a tight-binding inhibitor of both ribonucleolytic and angiogenic activities of ANG, abolished 125I-labeled human recombinant ANG binding only in the absence of copper.
Plasma PLTP (phospholipid-transfer protein): an emerging role in ‘reverse lipopolysaccharide transport’ and innate immunity (2011)

Plasma PLTP (phospholipid-transfer protein) is a member of the lipid transfer/LBP [LPS (lipopolysaccharide)-binding protein] family, which constitutes a superfamily of genes together with the short and long PLUNC (palate, lung and nasal epithelium clone) proteins. Although PLTP was studied initially for its involvement in the metabolism of HDL (high-density lipoproteins) and reverse cholesterol transport (i.e. the metabolic pathway through which cholesterol excess can be transported from peripheral tissues back to the liver for excretion in the bile), it displays a number of additional biological properties. In particular, PLTP can modulate the lipoprotein association and metabolism of LPS that are major components of Gram-negative bacteria. The delayed association of LPS with lipoproteins in PLTP-deficient mice results in a prolonged residence time, in a higher toxicity of LPS aggregates and in a significant increase in LPS-induced mortality as compared with wild-type mice. It suggests that PLTP may play a pivotal role in inflammation and innate immunity through its ability to accelerate the 'reverse LPS transport' pathway.
Differential Regulation of Murine T Lymphocyte Subsets (1993)

Signaling pathways in T lymphocytes have been incompletely characterized. It is evident that differences exist among the T cell subsets. We have defined several distinct mechanisms that affect differentially the activities of murine T lymphocyte clones representing various CD4+ and CD8+ subsets: Interferon-gamma (IFN-gamma) inhibits proliferation of but not lymphokine production by TH2 cells. IL-10 inhibits antigen-presenting cell (APC)-induced lymphokine production by TH1 cells but not by TH2 cells. Murine TH1 and TH2 clones proliferate optimally in response to distinct APC populations. TH1 and TH2 clones utilize different TCR-associated signaling pathways. High concentrations of antigen (or anti-TCR mAb) inhibit IL-2-induced proliferation (but not lymphokine production) by TH1 and cytolytic T lymphocyte (CTL) clones only. Exposure of TH1 clones (but not TH2 clones or CD8+ CTL clones) to IL-2 induces unresponsiveness to antigen. TH1 and TH2 clones as well as CD8+ clones can be cytolytic, but not all T cells use the same cytolytic mechanisms. CD4+ clones from some mouse strains are not cytolytic if they do not secrete IFN-gamma. Understanding the mechanisms that differentially regulate the various kinds of T cells, in addition to providing insights into the molecular events associated with activation of those subsets, should facilitate modulation of their activities in vivo, making it possible to influence favorably the outcome of disease processes.
Measurement of gluconeogenesis using glucose fragments and mass spectrometry after ingestion of deuterium oxide (2008)

We report a new method to measure the fraction of glucose derived from gluconeogenesis using gas chromatography-mass spectrometry and positive chemical ionization. After ingestion of deuterium oxide by subjects, glucose derived from gluconeogenesis is labeled with deuterium. Our calculations of gluconeogenesis are based on measurements of the average enrichment of deuterium on carbon 1, 3, 4, 5, and 6 of glucose and the deuterium enrichment in body water. In a sample from an adult volunteer after ingestion of deuterium oxide, fractional gluconeogenesis using the "average deuterium enrichment method" was 48.3 +/- 0.5% (mean +/- SD) and that with the C-5 hexamethylenetetramine (HMT) method by Landau et al. (Landau BR, Wahren J, Chandramouli V, Schumann WC, Ekberg K, Kalhan SC; J Clin Invest 98: 378-385, 1996) was 46.9 +/- 5.4%. The coefficient of variation of 10 replicate analyses using the new method was 1.0% compared with 11.5% for the C-5 HMT method. In samples derived from an infant receiving total parenteral nutrition, fractional gluconeogenesis was 13.3 +/- 0.3% using the new method and 13.7 +/- 0.8% using the C-5 HMT method. Fractional gluconeogenesis measured in six adult volunteers after 66 h of continuous fasting was 83.7 +/- 2.3% using the new method and 84.2 +/- 5.0% using the C-5 HMT method. In conclusion, the average deuterium enrichment method is simple, highly reproducible, and cost effective. Furthermore, it requires only small blood sample volumes. With the use of an additional tracer, glucose rate of appearance can also be measured during the same analysis. Thus the new method makes measurements of gluconeogenesis available and affordable to large numbers of investigators under conditions of low and high fractional gluconeogenesis ( approximately 10 to approximately 90) in all subject populations.
Cannabinomimetic Control of Mast Cell Mediator Release: New Perspective in Chronic Inflammation (2008)

The present review aims to elucidate the emerging role played by cannabinomimetic compounds in the control of mast cell activation. Mast cells are immune competent cells strategically localised at the sites directly interfacing with the external environment, which, in case of injury, regulate the immune response by the release of a plethora of both pre-formed and newly-synthesised mediators. However, although the main goal of mast cell activation is to initiate the inflammatory reaction, and thus maintain internal homeostasis, the consequences of dysregulated mast cell activation could be to chronically activate the inflammatory response as occurs in arthritis, inflammatory bowel diseases, atherosclerosis and asthma. Therefore, much effort has been made to develop compounds that act to prevent mast cell degranulation. Cannabinomimetic compounds (i.e. agents able to modulate endocannabinoid function) are considered as an emerging class of regulators of mast cell behaviour. We focus on the evidence for a cannabinomimetic control of both acute and chronic inflammatory disease, recognising a common mast cell origin for problems such as dermatitis, inflammatory gastrointestinal syndrome and granuloma formation. Special emphasis is provided for the recent promising results obtained with palmitoylethanolamide in human studies. In the light of evidence suggesting that the control of mast cell activation at an early time during an inflammatory process may account for its resolution, it is reasonable to propose that cannabinomimetic compounds, including palmitoylethanolamide and its congeners, could represent possible candidates for treating several chronic inflammatory diseases.
Antibacterial activities and modes of action of vancomycin and related glycopeptides (1991)

Vancomycin (21) is produced by Amycolatopsis orientalis (18) (previously designated Nocardia orientalis and Streptomyces orientalis). The antibiotic has been marketed for the past 30 years and continues to be marketed, as the hydrochloride salt, to treat deep-seated gram-positive bacterial infections. It is the drug of choice for infections caused by Staphylococcus aureus, especially those caused by strains resistant to methicillin. Vancomycin is bactericidal to most gram-positive organisms, but gram-negative organisms are resistant. Vancomycin is not absorbed from the gastrointestinal tract, and the antibiotic is used to treat enterocolitis, especially that caused by Clostridium difficile
Social Hash: an assignment framework for optimizing distributed systems operations on social networks (2016)

How objects are assigned to components in a distributed system can have a significant impact on performance and resource usage. Social Hash is a framework for producing, serving, and maintaining assignments of objects to components so as to optimize the operations of large social networks, such as Facebook's Social Graph. The framework uses a two-level scheme to decouple compute-intensive optimization from relatively low-overhead dynamic adaptation. The optimization at the first level occurs on a slow timescale, and in our applications is based on graph partitioning in order to leverage the structure of the social network. The dynamic adaptation at the second level takes place frequently to adapt to changes in access patterns and infrastructure, with the goal of balancing component loads.

We demonstrate the effectiveness of Social Hash with two real applications. The first assigns HTTP requests to individual compute clusters with the goal of minimizing the (memory-based) cache miss rate; Social Hash decreased the cache miss rate of production workloads by 25%. The second application assigns data records to storage subsystems with the goal of minimizing the number of storage subsystems that need to be accessed on multiget fetch requests; Social Hash cut the average response time in half on production workloads for one of the storage systems at Facebook.
Compiler-controlled caching in superword register files for multimedia extension architectures (2003)

In this paper, we describe an algorithm and implementation of locality optimizations for architectures with instruction sets such as Intel's SSE and Motorola's AltiVec that support operations on superwords, i.e., aggregate objects consisting of several machine words. We treat the large superword register file as a compiler-controlled cache, thus avoiding unnecessary memory accesses by exploiting reuse in superword registers. This research is distinguished from previous work on exploiting reuse in scalar registers because it considers not only temporal but also spatial reuse. As compared to optimizations to exploit reuse in cache, the compiler must also manage replacement, and thus, explicitly name registers in the generated code. We describe an implementation of our approach integrated with a compiler that exploits superword-level parallelism (SLP). We present a set of results derived automatically on 4 multimedia kernels and 2 scientific benchmarks. Our results show speedups ranging from 1.3 to 2.8X on the 6 programs as compared to using SLP alone, and we eliminate the majority of memory accesses.
Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates (2007)

We speculate that if specific miRNA molecules are involved in evolutionarily conserved regulatory systems in vertebrates, this would entail a high level of conservation of the promoter of miRNA gene as well as the miRNA molecule. By our current screening of putative promoter regions of miRNA genes (miPPRs) on this base, we identified 59 miPPRs that would direct production of 79 miRNAs. We present both biochemical and bioinformatical verifications of these putative promoters.