gebhart/patrepeval huggingface dataset:
Glanders in Animals: A Review on Epidemiology, Clinical Presentation, Diagnosis and Countermeasures (2012)

Glanders or farcy, caused by Burkholderia mallei, is an infectious and zoonotic disease of solipeds. Horses, donkeys and mules are the only known natural reservoir of B. mallei. Although glanders has been eradicated from most countries, it has regained the status of a re-emerging disease because of the numerous recent outbreaks. Pre-symptomatic or carrier animals are the potential source of infection for the healthy equine population and play a crucial role in the spreading of the infectious agent. Glanders is characterized by ulcerating nodular lesions of the skin and mucous membrane. Generalized symptoms include fever, malaise, depression, cough, anorexia and weight loss. Burkholderia mallei can invade its host through mucous membranes, gastrointestinal tract and the integument. Its virulence mechanisms and pathogenesis are not yet completely understood. A major problem when using serological tests for diagnosing glanders is the occurrence of false-positive and false-negative results leading to difficulties in international trade with equids and to the spread of glanders to disease-free regions. Moreover, poor tests critically result in poor control of disease. These tests are not only incapable of discriminating between B. mallei and B. pseudomallei antibodies, they are also unable to differentiate between malleinized and naturally infected animals. Combined use of both serological and molecular detection methods increases the detection rate of glanders. Countermeasures against glanders include early detection of disease in susceptible animals, stringent quarantine measures, testing and safe destruction of infected carcasses, adequate compensation to the animal owners, disinfection of infected premises and awareness about glanders and the zoonotic implications through veterinary extension services. An account of the clinical picture and successful experimental therapy of spontaneous equine glanders is also given.
Catecholborane (1,3,2-benzodioxaorole) as a new, general monohydroboration reagent for alkynes. Convenient synthesis of alkeneboronic esters and acids from alkynes via hydroboration (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCatecholborane (1,3,2-benzodioxaorole) as a new, general monohydroboration reagent for alkynes. Convenient synthesis of alkeneboronic esters and acids from alkynes via hydroborationHerbert C. Brown and S. K. GuptaCite this: J. Am. Chem. Soc. 1972, 94, 12, 4370–4371Publication Date (Print):June 1, 1972Publication History Published online1 May 2002Published inissue 1 June 1972https://pubs.acs.org/doi/10.1021/ja00767a072https://doi.org/10.1021/ja00767a072research-articleACS PublicationsRequest reuse permissionsArticle Views2936Altmetric-Citations204LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Transannular [4C+3C]-Cycloaddition Reactions of Oxyallyl Cation to Furan (2010)

For the first time, successful transannular [4+3]-cyclo­addition reactions based on an oxyallyl cation intermediate are reported. The key steps involve the synthesis of the macrocyclic precursor and the transanuular [4C+3C]-cycloaddition step.
A Single Domain–Based Anti-Her2 Antibody Has Potent Antitumor Activities (2018)

Human epidermal growth factor receptor 2 (HER2) is overexpressed in approximately 20% to 30% of breast cancers and various other types of cancers, which plays a vital role in the cancer progression. Monoclonal antibodies targeting Her2 are now used in the clinic to treat Her2 overexpression cancer patients. However, relapse or resistance is frequent with the current therapies. To generate a new treatment avenue against Her2, we immunized and selected a specific anti-Her2 single domain antibody C3 for further studies. The C3-Fc antibody drove antibody-dependent cell-mediated cytotoxicity against Her2-positive tumor cells in vitro and resulted in potent antitumor growth in vivo. These data suggest that the C3-Fc antibody may provide an alternative avenue for Her2-positive cancer therapy.
Evaluation of the ARMD1 locus on 1q25–31 in patients with age-related maculopathy: genetic variation in laminin genes and in exon 104 of HEMICENTIN-1 (2004)

The age-related maculopathy (ARM) genetics program at Columbia University utilizes comprehensive genetic analysis of candidate genes in large case-control studies to determine genotypes associated with the ARM complex trait. Genes encoding laminins, a class of extracellular matrix proteins, represent attractive candidates for two reasons. First, the presence of laminins in the basal lamina of the retinal pigment epithelium (RPE), Bruch's membrane, and choriocapillaris suggests a possible role in the pathophysiology of ARM. Second, three laminin genes, LAMC1, LAMC2, and LAMB3, are located in the 1q25-31 region, within the previously mapped ARMD1 locus. The entire open reading frame of the three laminin genes was screened for variants by denaturing high-performance liquid chromatography (DHPLC) and direct sequencing in at least 92, and up to 368 ARM patients and matched unaffected controls. Sixty-nine sequence variants were detected in the 69 exons of the LAMC1, LAMC2, and LAMB3 genes. Screening of exon 104 of the recently proposed ARMD1 gene, HEMICENTIN-1, residing in the 1q25-31 locus, did not detect the suggested causal variant, Q5345R, in 632 study subjects. Overall, we did not find statistically significant differences in the frequency of variants between ARM-affected individuals and age-matched controls. Four rare, non-synonymous, variants were detected in single cases of ARM patients. Our data on relatively limited numbers of study subjects do not suggest a significant role for genetic variation in the three laminin genes and in exon 104 of HEMICENTIN-1 in predisposing individuals to ARM. However, as in many instances in similar studies, involvement of rare amino acid-changing variants in a fraction of ARM cannot be ruled out.
Thyroid Hormone Action IN VITRO CHARACTERIZATION OF SOLUBILIZED NUCLEAR RECEPTORS FROM RAT LIVER AND CULTURED GH1 CELLS (1974)

We previously reported that putative nuclear receptors for thyroid hormone can be demonstrated by incubation of hormone either with intact GH(1) cells, a rat pituitary tumor cell line, or with isolated GH(1) cell nuclei and rat liver nuclei in vitro. We characterized further the kinetics of triiodothyronine (T3) and thyroxine (T4) binding and the biochemical properties of the nuclear receptor after extraction to a soluble form with 0.4 M KCl. In vitro binding of [(125)I]T3 and [(125)I]T4 with GH(1) cell and rat liver nuclear extract was examined at 0 degrees C and 37 degrees C. Equilibrium was attained within 5 min at 37 degrees C and 2 h at 0 degrees C. The binding activity from GH(1) cells was stable for at least 1 h at 37 degrees C and 10 days at - 20 degrees C. Chromatography on a weak carboxylic acid column and inactivation by trypsin and Pronase, but not by DNase or RNase, suggested that the putative receptor was a nonhistone protein. The estimated equilibrium dissociation constants (K(d)) for hormone binding to the solubilized nuclear binding activity was 1.80 x 10(-10) M (T3) and 1.20 x 10(-9) M (T4) for GH(1) cells and 1.57 x 10(-10) M (T3) and 2.0 x 10(-9) M (T4) for rat liver. These K(d) values for T3 are virtually identical to those which we previously reported with isolated rat liver nuclei and GH(1) cell nuclei in vitro. The 10-fold greater affinity for T3 compared to T4 in the nuclear extract is also identical to that observed with intact GH(1) cells. In addition, the [(125)I]T3 and [(125)I]T4 high-affinity binding in the nuclear extract were inhibited by either nonradioactive T3 or T4, which suggests that the binding activity in nuclear extract was identical for T3 and T4. In contrast, the binding activity for T4 and T3 in GH(1) cell cytosol was markedly different from that observed with nuclear extract (K(d) values were 2.87 x 10(-10) M for T4 and 1.13 x 10(-9) M for T3). Our results indicate that nuclear receptors for T3 and T4 can be isolated in a soluble and stable form with no apparent change in hormonal affinity. This should allow elucidation of the mechanisms of thyroid hormone action at the molecular level.
Disease-modifying anti-rheumatic drug therapy and structural damage in early rheumatoid arthritis. (2004)

The appearance of measurable structural damage in rheumatoid arthritis (RA) is an indicator of disease severity and future disability. Disease-modifying anti-rheumatic drugs (DMARDs) used in combination appear to be more effective than monotherapies at reducing the rate of progressive joint damage during randomized controlled trials. In clinical practice, however, combination DMARD therapy is still largely reserved for patients who have failed to respond to monotherapy. High dose corticosteroid, when given in early disease with combination DMARD therapy, may continue to ameliorate disease severity and progression for years after discontinuation of the high dose. To date, no DMARD combination has totally arrested joint damage in all patients with early RA. Future randomised controlled trials should always include prospective radiographic data as a primary outcome measure.
Digital light field photography (2006)

Focusing images well has been difficult since the beginnings of photography in 1839. Three manifestations of the problem are: the chore of having to choose what to focus on before clicking the shutter, the awkward coupling between aperture size and depth of field, and the high optical complexity of lenses required to produce aberration-free images. 
These problems arise because conventional cameras record only the sum of all light rays striking each pixel on the image plane. This dissertation presents a unified solution to these focus problems by instead recording the light field inside the camera: not just the position but also the direction of light rays striking the image plane. I describe the design, prototyping and performance of a digital camera that records this light field in a single photographic exposure. The basic idea is to use an array of microlenses in front of the photosensor in a regular digital camera. 
The main price behind this new kind of photography is the sacrifice of some image resolution to collect directional ray information. However, it is possible to smoothly vary the optical configuration from the light field camera back to a conventional camera by reducing the separation between the microlenses and photosensor. This allows a selectable trade-off between image resolution and refocusing power. More importantly, current semiconductor technology is already capable of producing sensors with an order of magnitude more resolution than we need in final images. 
The extra ray directional information enables unprecedented capabilities after exposure. For example, it is possible to compute final photographs that are refocused at different depths, or that have extended depth of field, by re-sorting the recorded light rays appropriately. Theory predicts, and experiments corroborate, that blur due to incorrect focus can be reduced by a factor approximately equal to the directional resolution of the recorded light rays. Similarly, digital correction of lens aberrations re-sorts aberrant light rays to where they should ideally have converged, improving image contrast and resolution. Future cameras based on these principles will be physically simpler, capture light more quickly, and provide greater flexibility in finishing photographs.
Lysyl oxidase-like-1 enhances lung metastasis when lactate accumulation and monocarboxylate transporter expression are involved (2011)

The role that lysyl oxidase-like‑1 (LOXL-1) may play in cancer metastasis due to its specific collagen accumulation characteristics has not been investigated extensively. This study was performed to examine the role of LOXL-1 in cancer metastasis. In vitro and in vivo cancer metastasis experiments were performed with B16F10 cells. Using the immunoblotting technique, the expression of LOXL-1, monocarboxylate transporter (MCT)1/2 and matrix metalloproteinase (MMP)2/9 was examined in a cell culture model and in primary and metastatic site samples from non‑small cell lung carcinoma patients. Immunohistochemistry was also performed. According to immunohistochemical analysis of the non-small cell lung carcinoma patient samples, LOXL-1, MCT1/2 and MMP2/9 were expressed more highly in metastatic sites compared to primary sites. In in vivo studies, LOXL-1-overexpressing B16F10 cells yielded higher numbers of cancer nodules following their injection into mouse tail veins. Transfection of LOXL-1 siRNA into the cells prior to injection blocked lung metastasis. In vitro, the overexpression of LOXL-1 increased cell mobility and invasiveness, with increased extracellular accumulation of lactate at a low pH. The lactate transporter, MCT1/2, was highly expressed in LOXL‑1-overexpressing cells. LOXL-1 knockdown through siRNA inhibited cell motility and invasiveness, showing relatively lower lactate accumulation and expression of MCT1/2 than under control conditions. This study elucidates extracellular pH-associated matrix degradation as a potential mechanism for LOXL-1-induced cancer metastasis.
The pair of bacteriophytochromes from Agrobacterium tumefaciens are histidine kinases with opposing photobiological properties (2003)

Bacteriophytochrome photoreceptors (BphPs) are a family of phytochrome-like sensor kinases that help a wide variety of bacteria respond to their light environment. In Agrobacterium tumefaciens, a unique pair of BphPs with potentially opposing roles in light sensing are present. Both AtBphPs contain an N-terminal chromophore-binding domain that covalently attaches a biliverdin chromophore. Whereas AtBphP1 assumes a Pr ground state, AtBphP2 is unusual in that it assumes a Pfr ground state that is produced nonphotochemically after biliverdin binding through a transient Pr-like intermediate. Photoconversion of AtBphP2 with far-red light then generates Pr but this Pr is also unstable and rapidly reverts nonphotochemically to Pfr. AtBphP1 contains a typical two-component histidine kinase domain at its C terminus whose activity is repressed after photoconversion to Pfr. AtBphP2 also functions as a histidine kinase but instead uses a distinct two-component kinase motif that is repressed after photoconversion to Pr. We identified sequences related to this domain in numerous predicted sensing proteins in A. tumefaciens and other bacteria, indicating that AtBphP2 might represent the founding member of a family of histidine phosphorelay proteins that is widely used in environmental signaling. By using these mutually opposing BphPs, A. tumefaciens presumably has the capacity to simultaneously sense red light-rich and far-red light-rich environments through deactivation of their associated kinase cascades.
Neuroprotective effects of M826, a reversible caspase‐3 inhibitor, in the rat malonate model of Huntington's disease (2004)

1. Caspases, key enzymes in the apoptosis pathway, have been detected in the brain of HD patients and in animal models of the disease. In the present study, we investigated the neuroprotective properties of a new, reversible, caspase-3-specific inhibitor, M826 (3-([(2S)-2-[5-tert-butyl-3-[[(4-methyl-1,2,5-oxadiazol-3-yl)methyl]amino]-2-oxopyrazin-1(2H)-yl]butanoyl]amino)-5-[hexyl(methyl)amino]-4-oxopentanoic acid), in a rat malonate model of HD. 2. Pharmacokinetic and autoradiography studies after intrastriatal (i.str.) injection of 1.5 nmol of M826 or its tritiated analogue [(3)H]M826 indicated that the compound diffused within the entire striatum. The elimination half-life (T(1/2)) of M826 in the rat striatum was 3 h. 3. I.str. injection of 1.5 nmol of M826 10 min after malonate infusion induced a significant reduction (66%) in the number of neurones expressing active caspase-3 in the ipsilateral striatum. 4. Inhibition of active caspase-3 translated into a significant but moderate reduction (39%) of the lesion volume, and of cell death (24%), 24 h after injury. The efficacy of M826 at inhibiting cell death was comparable to that of the noncompetitive NMDA receptor antagonist MK801. 5. These data provide in vivo proof-of-concept of the neuroprotective effects of reversible caspase-3 inhibitors in a model of malonate-induced striatal injury in the adult rat.
Interconnect characterization and design optimization for high speed digital applications (2002)

Interconnect plays a key role in determining the performance of high speed digital systems such as the direct Rambus/sup (R)/ DRAM (RDRAM/sup (R)/) channel, which supports an 800 Mbit/s transfer rate with a 200 ps signal edge transition time. Design challenges are to achieve reliable high speed operations using low cost interconnect and conventional printed circuit board technologies. Impedance discontinuities and crosstalk due to interconnects must be minimized. Design optimization techniques must be employed to achieve desired system performance and robustness. This paper describes a set of experiments used to quantify the effects of various interconnect structures commonly found in printed circuit board design. Techniques for optimizing the performance of these interconnects are investigated.
A directional acoustic array using silicon micromachined piezoresistive microphones (2003)

The need for noise source localization and characterization has driven the development of advanced sound field measurement techniques using microphone arrays. Unfortunately, the cost and complexity of these systems currently limit their widespread use. Directional acoustic arrays are commonly used in wind tunnel studies of aeroacoustic sources and may consist of hundreds of condenser microphones. A microelectromechanical system (MEMS)-based directional acoustic array system is presented to demonstrate key technologies to reduce the cost, increase the mobility, and improve the data processing efficiency versus conventional systems. The system uses 16 hybrid-packaged MEMS silicon piezoresistive microphones that are mounted to a printed circuit board. In addition, a high-speed signal processing system was employed to generate the array response in near real time. Dynamic calibrations of the microphone sensor modules indicate an average sensitivity of 831 microV/Pa with matched magnitude (+/-0.6 dB) and phase (+/-1 degree) responses between devices. The array system was characterized in an anechoic chamber using a monopole source as a function of frequency, sound pressure level, and source location. The performance of the MEMS-based array is comparable to conventional array systems and also benefits from significant cost savings.
Interpreting Neuronal Population Activity by Reconstruction: Unified Framework With Application to Hippocampal Place Cells (1998)

Physical variables such as the orientation of a line in the visual field or the location of the body in space are coded as activity levels in populations of neurons. Reconstruction or decoding is an inverse problem in which the physical variables are estimated from observed neural activity. Reconstruction is useful first in quantifying how much information about the physical variables is present in the population and, second, in providing insight into how the brain might use distributed representations in solving related computational problems such as visual object recognition and spatial navigation. Two classes of reconstruction methods, namely, probabilistic or Bayesian methods and basis function methods, are discussed. They include important existing methods as special cases, such as population vector coding, optimal linear estimation, and template matching. As a representative example for the reconstruction problem, different methods were applied to multi-electrode spike train data from hippocampal place cells in freely moving rats. The reconstruction accuracy of the trajectories of the rats was compared for the different methods. Bayesian methods were especially accurate when a continuity constraint was enforced, and the best errors were within a factor of two of the information-theoretic limit on how accurate any reconstruction can be and were comparable with the intrinsic experimental errors in position tracking. In addition, the reconstruction analysis uncovered some interesting aspects of place cell activity, such as the tendency for erratic jumps of the reconstructed trajectory when the animal stopped running. In general, the theoretical values of the minimal achievable reconstruction errors quantify how accurately a physical variable is encoded in the neuronal population in the sense of mean square error, regardless of the method used for reading out the information. One related result is that the theoretical accuracy is independent of the width of the Gaussian tuning function only in two dimensions. Finally, all the reconstruction methods considered in this paper can be implemented by a unified neural network architecture, which the brain feasibly could use to solve related problems.
Lactobacillus casei Abundance Is Associated with Profound Shifts in the Infant Gut Microbiome (2010)

Colonization of the infant gut by microorganisms over the first year of life is crucial for development of a balanced immune response. Early alterations in the gastrointestinal microbiota of neonates has been linked with subsequent development of asthma and atopy in older children. Here we describe high-resolution culture-independent analysis of stool samples from 6-month old infants fed daily supplements of Lactobacillus casei subsp. Rhamnosus (LGG) or placebo in a double-blind, randomized Trial of Infant Probiotic Supplementation (TIPS). Bacterial community composition was examined using a high-density microarray, the 16S rRNA PhyloChip, and the microbial assemblages of infants with either high or low LGG abundance were compared. Communities with high abundance of LGG exhibited promotion of phylogenetically clustered taxa including a number of other known probiotic species, and were significantly more even in their distribution of community members. Ecologically, these aspects are characteristic of communities that are more resistant to perturbation and outgrowth of pathogens. PhyloChip analysis also permitted identification of taxa negatively correlated with LGG abundance that have previously been associated with atopy, as well as those positively correlated that may prove useful alternative targets for investigation as alternative probiotic species. From these findings we hypothesize that a key mechanism for the protective effect of LGG supplementation on subsequent development of allergic disease is through promotion of a stable, even, and functionally redundant infant gastrointestinal community.