gebhart/patrepeval huggingface dataset:
Genetics of ferulic acid bioconversion to protocatechuic acid in plant-growth-promoting Pseudomonas putida WCS358 (1998)

Transposon Tn5 genomic mutants of plant-growth-promoting Pseudomonas putida strain WCS358 have been isolated which no longer utilize ferulic and coumaric acids as sole sources of carbon and energy. Genetic studies confirmed previous biochemical data showing that ferulic acid is degraded via vanillic acid, and coumaric acid via hydroxybenzoic acid. The genes involved in these enzymic steps were cloned and characterized. Two proteins designated Fca (26.5 kDa) and Vdh (50.3 kDa) were identified as responsible for the conversion of ferulic acid to vanillic acid; the proteins are encoded by the fca and vdh genes which are organized in an operon structure in the chromosome. The Vdh protein is 69% identical at the amino acid level to the Vdh protein recently identified in Pseudomonas sp. strain HR199 and converts vanillin to vanillic acid. Homology studies revealed that the Vdh proteins exhibited significant identity to aldehyde dehydrogenases from different organisms whereas Fca belonged to the enoyl-CoA hydratase family of proteins. Two proteins, designated VanA (39.9 kDa) and VanB (34.3 kDa), encoded by two genes, vanA and vanB, are organized in an operon in the chromosome. They were found to be responsible for the demethylation of vanillic acid to protocatechuic acid. The VanA proteins showed no homology to any other known protein, while VanB belonged to the ferredoxin family of proteins. This two-component enzyme system demethylated another phenolic monomer, veratric acid, thus indicating broad specificity. Studies of the regulation of the vanAB operon demonstrated that the genes were induced by the substrate, vanillic acid; however, the strongest induction was observed when cells were grown in the presence of the product of the reaction, protocatechuic acid.
국가 및 지방정부간 위기관리 협력체계에 관한 연구 (2013)

최근 재난은 불확실성을 특징으로 하는 신종재난과 자연재난 및 인위재난이 동시 발생하여 부처간 지방정부간 책임영역이 불명확한 ``복합화`` 현상이 일어나고 있다. 따라서 이에 대응하는 위기관리 정책의 필요성이 증대되고 있다. 본 연구에서는 이러한 미래위기의 개념적 특성과 2011년 일본의 동일본 대지진의 사례를 비교 분석하여 국가 및 지방정부간 위기관리 협력체계에 대해 연구하였다. 분석의 틀로서는 우리나라 위기관리시스템의 ``유기적 통합성``, ``선제적 학습성``, ``연계적 협력성``의 문제로 구분하여 살펴보았으며 분석 결과 정책대안으로서 ``자치단체 간 재난관리 거버넌스 체제 구축`` 및 ``자치단체의 CDO 지정`` 제도 도입 등을 제언하였다. 또한, 자치단체간 협력 체제를 제도화하기 위한 ``자치단체 간 상호긴급지원조례제정`` 방안도 제시하였다.
Naturopathic Care for Anxiety: A Randomized Controlled Trial ISRCTN78958974 (2009)

Controlled-Trials.com ISRCTN78958974.
Forces applied by nasal speculums during transsphenoidal operations. (1978)

The forces exerted by nasal speculums were measured during the transsphenoidal approach to the pituitary. The highest forces were found to occur at the beginning of surgery when the speculum had been spread to the desired opening (reaching 42 kg). This force decreases during surgery due to the time dependent motion of the biological structure distant from the applied pressure (relaxation). The amount of relaxation that occurred was measured but was found not to be high enough to indicate damage to the tissues adjacent to the speculum. It is also concluded that this type of instrument was underdesigned for its intended function.
The accuracy, fairness, and limits of predicting recidivism (2018)

Algorithms for predicting recidivism are commonly used to assess a criminal defendant's likelihood of committing a crime. These predictions are used in pretrial, parole, and sentencing decisions. Proponents of these systems argue that big data and advanced machine learning make these analyses more accurate and less biased than humans. We show, however, that the widely used commercial risk assessment software COMPAS is no more accurate or fair than predictions made by people with little or no criminal justice expertise. We further show that a simple linear predictor provided with only two features is nearly equivalent to COMPAS with its 137 features.
Domain swapping of a llama VHH domain builds a crystal‐wide β‐sheet structure (2004)

Among mammals, camelids have a unique immunological system since they produce functional antibodies devoid of light chains and CH1 domains. To bind antigens, whether they are proteins or haptens, camelids use the single domain VH from their heavy chain (VHH). We report here on such a llama VHH domain (VHH-R9) which was raised against a hapten, the RR6 red dye. This VHH possesses the shortest complementarity determining region 3 (CDR3) among all the known VHH sequences and nevertheless binds RR6 efficiently with a K(d) value of 83 nM. However, the crystal structure of VHH-R9 exhibits a striking feature: its CDR3 and its last beta-strand (beta9) do not follow the immunoglobulin VH domain fold, but instead extend out of the VHH molecular boundary and associate with a symmetry-related molecule. The two monomers thus form a domain-swapped dimer which establishes further contacts with symmetry-related molecules and build a crystal-wide beta-sheet structure. The driving force of the dimer formation is probably the strain induced by the short CDR3 together with the cleavage of the first seven residues.
Motion planning in the presence of movable obstacles (1988)

Motion planning algorithms have generally dealt with motion in a static environment, or more recently, with motion in an environment that changes in a known manner. We consider the problem of finding collision-free motions in a changeable environment. That is, we wish to find a motion for an object where the object is permitted to move some of the obstacles. In such an environment the final positions of the movable obstacles may or may not be part of the goal. In the case where the final positions of the obstacles are unspecified, the motion planning problem is shown to be NP-hard. An algorithm that runs in Ο(n2logn) time after Ο(n3log2n) preprocessing time is presented when the object to be moved is polygonal and there is only one movable polygonal obstacle in a polygonal environment of complexity Ο(n). In the case where the final positions of the obstacles are specified the general problem is shown to be PSPACE-hard and an algorithm is given when there is one movable obstacle with the same preprocessing time as the previous algorithm but with Ο(n2) query time.
Polymeric ionic liquid–ionic plastic crystal all-solid-state electrolytes for wide operating temperature range lithium metal batteries (2017)

Solid polymer electrolytes show flexible mechanical characters, excellent electrochemical properties, and impressive battery performance over a wide temperature range.
Information-Based Objective Functions for Active Data Selection (1992)

Learning can be made more efficient if we can actively select particularly salient data points. Within a Bayesian learning framework, objective functions are discussed that measure the expected informativeness of candidate measurements. Three alternative specifications of what we want to gain information about lead to three different criteria for data selection. All these criteria depend on the assumption that the hypothesis space is correct, which may prove to be their main weakness.
Measurements of Radio Frequency Noise from Severe and Nonsevere Thunderstorms (1977)

Abstract Thunderstorm radio noise measurements at several frequencies in the range 0.01–74 MHz have been made with specially designed remote recording stations in Iowa. The data were recorded during the spring and summer of 1974 when a series of severe storm systems produced a great number of large hail and tornado reports in Iowa. Computer analyses were made of nearly a billion bits of data, corresponding to 170 h of real-time recordings. Careful compilations of surface severe weather reports, hail damage information from insurance companies, and studies on the Des Moines WSR-57 radar echoes were compared with the analyzed radio noise data. The results include the following: 1) In agreement with earlier work, large‐amplitude radio noise impulse rates were found to he generally good indicators of thunderstorm severity. Although the majority of the radio energy radiated from major lightning strokes occurs in the 0.01 MHz range, this frequency was found to be a poor indicator of storm severity; the higher f...
Hyperbolic heat conduction due to axisymmetric continuous or pulsed surface heat sources (1990)

Irradiation of metals with laser pulses in the nanosecond to picosecond range may give rise to temperature fields which are significantly different from those predicted by the classical Fourier heat conduction model. In this work we examine the very short-time temperature response of a semi-infinite region to an axisymmetric laser surface source, which is either continuous or activated for a period Δt and has a spatial profile which is Gaussian, doughnut, or a combination of the Gaussian and doughnut modes. The material properties are assumed constant, and radiation and convection from the irradiated surface are neglected. The non-Fourier temperature responses are compared with their diffusive counterparts and shown to give rise to steep local temperature concentrations.
New Synthesis of Alkyl Polysulfides by Treatment of Thiols, Disulfides and Thionitrites with Anhydrous Copper(II) Chloride (1979)

Abstract Reaction of several divalent organic sulfur compounds with copper(II) chloride in acetonitrile gave the corresponding disulfides or other polysulfides in good yields under mild conditions.
Embryonic stem cells and prospects for their use in regenerative medicine approaches to motor neurone disease (2007)

Human embryonic stem cells are pluripotent cells with the potential to differentiate into any cell type in the presence of appropriate stimulatory factors and environmental cues. Their broad developmental potential has led to valuable insights into the principles of developmental and cell biology and to the proposed use of human embryonic stem cells or their differentiated progeny in regenerative medicine. This review focuses on the prospects for the use of embryonic stem cells in cell-based therapy for motor neurone disease or amyotrophic lateral sclerosis, a progressive neurodegenerative disease that specifically affects upper and lower motor neurones and leads ultimately to death from respiratory failure. Stem cell-derived motor neurones could conceivably be used to replace the degenerated cells, to provide authentic substrates for drug development and screening and for furthering our understanding of disease mechanisms. However, to reliably and accurately culture motor neurones, the complex pathways by which differentiation occurs in vivo must be understood and reiterated in vitro by embryonic stem cells. Here we discuss the need for new therapeutic strategies in the treatment of motor neurone disease, the developmental processes that result in motor neurone formation in vivo, a number of experimental approaches to motor neurone production in vitro and recent progress in the application of stem cells to the treatment and understanding of motor neurone disease.
A selective human beta3 adrenergic receptor agonist increases metabolic rate in rhesus monkeys. (1998)

Activation of beta3 adrenergic receptors on the surface of adipocytes leads to increases in intracellular cAMP and stimulation of lipolysis. In brown adipose tissue, this serves to up-regulate and activate the mitochondrial uncoupling protein 1, which mediates a proton conductance pathway that uncouples oxidative phosphorylation, leading to a net increase in energy expenditure. While chronic treatment with beta3 agonists in nonprimate species leads to uncoupling protein 1 up-regulation and weight loss, the relevance of this mechanism to energy metabolism in primates, which have much lower levels of brown adipose tissue, has been questioned. With the discovery of L-755,507, a potent and selective partial agonist for both human and rhesus beta3 receptors, we now demonstrate that acute exposure of rhesus monkeys to a beta3 agonist elicits lipolysis and metabolic rate elevation, and that chronic exposure increases uncoupling protein 1 expression in rhesus brown adipose tissue. These data suggest a role for beta3 agonists in the treatment of human obesity.
Crystallization of the Zα domain of the human editing enzyme ADAR1 complexed with a DNA–RNA chimeric oligonucleotide in the left-handed Z-conformation (2001)

The Zalpha domain of human double-stranded RNA adenosine deaminase (ADAR1) has been crystallized with a hexanucleotide containing alternating deoxyribose and ribose furanose sugars. Solution circular dichroism experiments show that this double-stranded chimera (dCrG)(3) initially adopts the right-handed A-conformation. However, addition of stoichiometric amounts of Zalpha causes a rapid transition to the Z-conformation. Raman spectroscopy of crystals of the Zalpha-(dCrG)(3) complex confirm that the chimeric oligonucleotide is stabilized in the Z-conformation. A complete data set has been obtained at 2.5 A resolution. The Zalpha-(dCrG)(3) crystals belong to the tetragonal I422 space group, with unit-cell parameters a = b = 104.2, c = 117.6 A. Work is under way to solve the structure by molecular replacement.
Ginsenosides Rb1 and Rg1 Suppress Triglyceride Accumulation in 3T3-L1 Adipocytes and Enhance β-Cell Insulin Secretion and Viability in Min6 Cells<i>via</i>PKA-Dependent Pathways (2008)

Ginseng root is known to induce anti-diabetic activity, but the key components involved are unknown. We investigated which major ginsenosides in ginseng enhanced glucose homeostasis by in vitro studies. Rb1 and Rg1 reduced the triglyceride accumulation in 3T3-L1 adipocytes by activating PKA with increased intracellular cAMP. However, the insulin-stimulated glucose uptake was enhanced by Rb1 and Rg1 via activation of phosphatidylinositol-3 kinase. Rb1 and Rg1 promoted glucose-stimulated insulin secretion and cell viability in Min6 cells through PKA which augmented IRS2 expression to enhance insulin/IGF-1 signaling. These results suggest that Rb1 and Rg1 improved glucose homeostasis through the activation of a PKA like glucagon-like peptide-1 receptor agonist.
Allelic polymorphism and site‐specific recombination in the <i>opc</i> locus of <i>Neisseria meningitidis</i> (1996)

The opc gene is widespread in epidemic and endemic Neisseria meningitidis, but most strains of certain epidemic clones (ET-37 complex, Cluster A4) and a few random endemic isolates lack an opc gene. Four percent of the 1148 bp that contain opc plus the surrounding intergenic region was polymorphic (18 alleles), and many of the alleles contained a 230 bp insertion at a fixed location in the intergenic region. The presence or absence of the insertion reflects site-specific recombination. The alleles are stably inherited within clonal groupings for up to at least 50 years, with rare cases of horizontal genetic exchange. Most statistical methods indicated significant intragenic recombination events within this dataset.
Orbiviruses and<i>Bluetongue Virus</i> (2009)

Abstract Bluetongue virus (BTV) is the type species of the genus Orbivirus within the family Reoviridae (the largest double‐stranded ribonucleic acid (dsRNA) virus family). BTV is an arthropod‐borne pathogen that is transmitted by the bites of its vector, the Culicoides midges, which transmit the virus between its ruminant hosts. The virus can infect most species of domestic and wild ruminants. BT clinical signs are most common in sheep and some species of deer. In recent years, the distribution of BTV has changed considerably, particularly in Europe. New outbreaks have occurred each year from 1998 to 2006 in southern and central Europe, involving several strains from five different serotypes. In 2006, BTV serotype 8 caused an outbreak approximately 5° further north in Europe than ever before, infecting ruminants in a wide area across northern Europe and bringing the number of European serotypes to six. A new virus ( Toggenburg virus ) has been identified in goats from Switzerland in 2008 and designated as the twenty‐fifth serotype of BTV. Key concepts: Genus Orbivirus is the most diverse genus of family Reoviridae containing 22 virus species. Bluetongue disease affects mainly sheep causing severe clinical signs and high mortality. Bluetongue virus is transmitted by competent species of Culicoides midges. Phylogenetic analysis identifies two major groups of orbiviruses, those with their subcore shell protein (T2 protein) being the VP2 and those with the T2 being VP3. Orbiviruses are nonturreted members of family Reoviridae , and the atomic structure of BTV core has been determined.
Extended field-of-view and increased-signal 3D holographic illumination with time-division multiplexing (2015)

Phase spatial light modulators (SLMs) are widely used for generating multifocal three-dimensional (3D) illumination patterns, but these are limited to a field of view constrained by the pixel count or size of the SLM. Further, with two-photon SLM-based excitation, increasing the number of focal spots penalizes the total signal linearly--requiring more laser power than is available or can be tolerated by the sample. Here we analyze and demonstrate a method of using galvanometer mirrors to time-sequentially reposition multiple 3D holograms, both extending the field of view and increasing the total time-averaged two-photon signal. We apply our approach to 3D two-photon in vivo neuronal calcium imaging.
The effect of red phosphorus on the flammability of poly(ethylene terephthalate) (1976)

Abstract Addition of red phosphorus in concentrations of about 4% to poly(ethylene terephthalate) (PET) reduces the flammability of that polymer. The rates of flame propagation and the ignitability are reduced, while the oxygen index (O.I.) is increased. The surface temperature of burning PET amounts to T S ≈ 380°C; addition of 4% red phosphorus raises this value to T S ≈ 450°C. An increase of the environmental temperature T E enhances the flammability of PET and PET + phosphorus samples; the O.I. decreases and the rate of flame propagation increases with temperature. The flame‐retardant effectiveness of red phosphorus is reduced if the sample is burned in a N 2 O atmosphere. This indicates that part of the flame retardancy imparted by phosphorus involves gas‐phase inhibition. The major flame‐retardant action does, however, occur in the condensed phase, since the rate of pyrolysis of PET is affected by the presence of red phosphorus.
<i>N</i>-Cyanomethyl-2-chloroisonicotinamide Induces Systemic Acquired Resistance in<i>Arabidopsis</i>without Salicylic Acid Accumulation (2003)

Systemic acquired resistance (SAR) is a potent innate immunity system in plants that is induced through the salicylic acid-mediated pathway. N-cyanomethyl-2-chloroisonicotinamide (NCI) is able to induce a broad range of disease resistance in tobacco and rice and induces SAR marker gene expression without SA accumulation in tobacco. To clarify the detailed mode of action of NCI, we analyzed its ability to induce defense gene expression and resistance in Arabidopsis mutants that are defective in various defense signaling pathways. Wild-type Arabidopsis treated with NCI exhibited increased expression of several pathogenesis-related genes and enhanced resistance to the bacterial pathogen, Pseudomonas syringae pv. tomato DC3000. NCI induced disease resistance and PR gene expression in NahG transgenic plants, but not in the npr1 mutant. NCI could induce PR gene expression in the etr1-1, ein2-1 and jar1-1 mutants. Thus, NCI activates SAR, independently from ethylene and jasmonic acid, by stimulating the site between SA and NPR1.
Incidence and Risk Factors for Acute Hepatitis B in the United States, 1982–1998: Implications for Vaccination Programs (2002)

From 1982-1998, enhanced sentinel surveillance for acute hepatitis B was conducted in 4 counties in the United States to determine trends in disease incidence and risk factors for infection. During this period, the reported incidence of acute hepatitis B declined by 76.1% from 13.8 cases per 100,000 in 1987 to 3.3 cases per 100,000 in 1998. Cases associated with injection drug use (IDU) decreased by 90.6%, men who have sex with men (MSM) by 63.5%, and heterosexual activity by 50.7%. During 1994-1998, the most commonly reported risk factor for infection was high-risk heterosexual activity (39.8%) followed by MSM activity (14.6%) and IDU (13.8%). Over half of all patients (55.5%) reported treatment for a sexually transmitted disease (STD) or incarceration in a prison or jail prior to their illness, suggesting that more than half of the acute hepatitis B cases might have been prevented through routine hepatitis B immunization in STD clinics and correctional health care programs.
Evolution of Hematophagy in Ticks: Common Origins for Blood Coagulation and Platelet Aggregation Inhibitors from Soft Ticks of the Genus Ornithodoros (2002)

Identification and characterization of antihemostatic components from hematophagous organisms are useful for the elucidation of the evolutionary mechanisms involved in adaptation to a highly complex host hemostatic system. Although many bioactive components involved in the regulation of the host's hemostatic system have been described, the evolutionary mechanisms of how arthropods adapted to a blood-feeding environment have not been elucidated. This study describes common origins of both blood coagulation inhibitors and platelet aggregation inhibitors (PAIs) from soft ticks of the genus Ornithodoros. Neighbor-joining analysis indicates that fXa, thrombin, and PAIs share a common ancestor. Maximum parsimony analysis and a phylogeny based on root mean square deviation values of alpha-carbon backbone structures suggest a novel evolutionary pathway by which different antihemostatic functions have evolved through a series of paralogous gene duplication events. In this scenario, the thrombin inhibitors preceded the fXa and PAIs. This evolutionary model explains why the tick serine protease inhibitors have inhibition mechanisms that differ from that of the canonical bovine pancreatic trypsin inhibitor (BPTI)-like inhibitors. Higher nonsynonymous-to-synonymous substitution rates indicate positive Darwinian selection for the fXa and PAIs. Comparison with hemostatic inhibitors of hard ticks suggests that the two main tick families have independently evolved novel antihemostatic mechanisms. Independent evolution of these mechanisms in ticks points to a rapid divergence between tick families that could be dated between 120 and 92 MYA. This coincides with current molecular phylogeny views on the early divergence of modern birds and placental mammals in the Late Cretaceous, which suggests that this event might have been a driving force in the evolution of hematophagy in ticks.