gebhart/patrepeval huggingface dataset:
The Genome of Swinepox Virus (2002)

Swinepox virus (SWPV), the sole member of the Suipoxvirus genus of the Poxviridae, is the etiologic agent of a worldwide disease specific for swine. Here we report the genomic sequence of SWPV. The 146-kbp SWPV genome consists of a central coding region bounded by identical 3.7-kbp inverted terminal repeats and contains 150 putative genes. Comparison of SWPV with chordopoxviruses reveals 146 conserved genes encoding proteins involved in basic replicative functions, viral virulence, host range, and immune evasion. Notably, these include genes with similarity to genes for gamma interferon (IFN-gamma) receptor, IFN resistance protein, interleukin-18 binding protein, IFN-alpha/beta binding protein, extracellular enveloped virus host range protein, dUTPase, hydroxysteroid dehydrogenase, superoxide dismutase, serpin, herpesvirus major histocompatibility complex inhibitor, ectromelia virus macrophage host range protein, myxoma virus M011L, variola virus B22R, four ankyrin repeat proteins, three kelch-like proteins, five vaccinia virus (VV) A52R-like family proteins, and two G protein-coupled receptors. The most conserved genomic region is centrally located and corresponds to the VV region located between genes F9L and A38L. Within the terminal 13 kbp, colinearity is disrupted and multiple poxvirus gene homologues are absent or share a lower percentage of amino acid identity. Most of these differences involve genes and gene families with likely functions involving viral virulence and host range. Three open reading frames (SPV018, SPV019. and SPV020) are unique for SWPV. Phylogenetic analysis, genome organization, and amino acid identity indicate that SWPV is most closely related to the capripoxvirus lumpy skin disease virus, followed by the yatapoxvirus yaba-like disease virus and the leporipoxviruses. The gene complement of SWPV better defines Suipoxvirus within the Chordopoxvirinae subfamily and provides a basis for future genetic comparisons.
Potent and Selective Inhibition of Membrane-Type Serine Protease 1 by Human Single-Chain Antibodies (2003)

Specific human antibodies targeting proteases expressed on cancer cells can be valuable reagents for diagnosis, prognosis, and therapy of cancer. To this end, a phage-displayed antibody library was screened against a cancer-associated serine protease, MT-SP1. A protein inhibitor of serine proteases that binds to a defined surface of MT-SP1 was used in an affinity-based washing procedure. Six antibodies were selected on the basis of their ELISA profiles and ability to serve as useful immunological reagents. The apparent K(i), indicative of the potency of the antibodies at inhibiting human MT-SP1 activity, ranged from 50 pM to 129 nM. Two of the antibodies had approximately 800-fold and 1500-fold selectivity when tested against the most homologous serine protease family member, mouse MT-SP1, that exhibits 86.6% sequence identity. Surface plasmon resonance was used as an independent means of determining the binding constants of the six antibodies. Association rates were as high as 1.15 x 10(7) s(-)(1) M(-)(1), and dissociation rates were as low as 3.8 x 10(-)(4) s(-)(1). One antibody was shown to detect denatured MT-SP1 with no cross reactivity to other family members in HeLa or PC3 cells. Another antibody recognized the enzyme in human prostate tissue samples for immunohistochemistry analysis. The mode of binding among the six antibodies and the protease was analyzed by competition ELISA using three distinctly different inhibitors that mapped the enzyme surface. These antibodies constitute a new class of highly selective protease inhibitors that can be used to dissect the biological roles of proteolytic enzymes as well as to develop diagnostic and therapeutic reagents.
2.6 μm/h High-Speed Growth of GaN by RF-Molecular Beam Epitaxy and Improvement of Crystal Quality by Migration Enhanced Epitaxy (1999)

High-quality GaN films were grown by molecular beam epitaxy (MBE) using elemental Ga and rf-plasma nitrogen as source with 1.2 μm/h growth rate. GaN films were grown on the migration enhanced epitaxy (MEE)-GaN buffers deposited on (0001) sapphire substrates. The room temperature (RT) mobility was 372 cm2/Vs at 1.2 × 1017 cm—3. Furthermore, extreme high-speed GaN growth of 2.6 μm/h was also demonstrated by increase of radical nitrogen supply at the substrates. The electron density of Si-doped GaN films was controlled in the range of 5.3 × 1015 to 4.9 × 1020 cm—3 and the room temperature mobility was 252 cm2/Vs at 3.4 × 1017 cm—3. The narrowest full width at half maximum (FWHM) of photoluminescence at 15 K was 10.5 meV.
Fundamentals of circadian entrainment by light (2021)

Light at dawn and dusk is the key signal for the entrainment of the circadian clock. Light at dusk delays the clock. Light at dawn advances the clock. The threshold for human entrainment requires relatively bright light for a long duration, but the precise irradiance/duration relationships for photoentrainment have yet to be fully defined. Photoentrainment is achieved by a network of photosensitive retinal ganglion cells (pRGCs) which utilise the short-wavelength light-sensitive photopigment, melanopsin. Although rods and cones are not required, they do play a role in photoentrainment, by projecting to and modulating the endogenous photosensitivity of the pRGCs, but in a manner that remains poorly understood. It is also important to emphasise that the age and prior light exposure of an individual will modify the efficacy of entrainment stimuli. Because of the complexity of photoreceptor interactions, attempts to develop evidence-based human centric lighting are not straightforward. We need to study how humans respond to dynamic light exposure in the ‘real world’ where light intensity, duration, spectral quality and the time of exposure vary greatly. Defining these parameters will allow the development of electric lighting systems that will enhance human circadian entrainment.
Androgen-independent cancer progression and bone metastasis in the LNCaP model of human prostate cancer. (1994)

Our laboratory has previously reported on the derivation of LNCaP cell sublines from LNCaP tumors maintained in castrated and intact athymic male mice. These LNCaP sublines differ from the parental line in tumorigenicity and androgen dependence. This paper demonstrates that one of these sublines acquired metastatic potential. When inoculated either s.c. or orthotopically, the C4-2 subline metastasized to the lymph node and bone with an incidence of 11-50%. Interestingly, the incidence of osseous metastasis was higher in castrated than in intact male hosts. We evaluated the chromosomal, immunohistochemical, and biochemical characteristics of the LNCaP sublines derived from C4-2 tumors that metastasized to the lymph node and bone. Cytogenetic analysis showed that all sublines were human and shared common marker chromosomes with the parental LNCaP cells. This experimental human prostate cancer model may permit, for the first time, the study of the molecular mechanisms underlying human prostate cancer metastasis.
Periodic Component Analysis: An Eigenvalue Method for Representing Periodic Structure in Speech (2000)

An eigenvalue method is developed for analyzing periodic structure in speech. Signals are analyzed by a matrix diagonalization reminiscent of methods for principal component analysis (PCA) and independent component analysis (ICA). Our method—called periodic component analysis (πCA)—uses constructive interference to enhance periodic components of the frequency spectrum and destructive interference to cancel noise. The front end emulates important aspects of auditory processing, such as cochlear filtering, nonlinear compression, and insensitivity to phase, with the aim of approaching the robustness of human listeners. The method avoids the inefficiencies of autocorrelation at the pitch period: it does not require long delay lines, and it correlates signals at a clock rate on the order of the actual pitch, as opposed to the original sampling rate. We derive its cost function and present some experimental results. 1
Viral activation and recruitment of metacaspases in the unicellular coccolithophore, Emiliania huxleyi (2007)

Lytic viral infection and programmed cell death (PCD) are thought to represent two distinct death mechanisms in phytoplankton, unicellular photoautotrophs that drift with ocean currents. Here, we demonstrate an interaction between autocatalytic PCD and lytic viral infection in the cosmopolitan coccolithophorid, Emiliania huxleyi. Successful infection of E. huxleyi strain 374 with a lytic virus, EhV1, resulted in rapid internal degradation of cellular components, a dramatic reduction in the photosynthetic efficiency (F(v)/F(m)), and an up-regulation of metacaspase protein expression, concomitant with induction of caspase-like activity. Caspase activation was confirmed through in vitro cleavage in cell extracts of the fluorogenic peptide substrate, IETD-AFC, and direct, in vivo staining of cells with the fluorescently labeled irreversible caspase inhibitor, FITC-VAD-FMK. Direct addition of z-VAD-FMK to infected cultures abolished cellular caspase activity and protein expression and severely impaired viral production. The absence of metacaspase protein expression in resistant E. huxleyi strain 373 during EhV1 infection further demonstrated the critical role of these proteases in facilitating viral lysis. Together with the presence of caspase cleavage recognition sequences within virally encoded proteins, we provide experimental evidence that coccolithoviruses induce and actively recruit host metacaspases as part of their replication strategy. These findings reveal a critical role for metacaspases in the turnover of phytoplankton biomass upon infection with viruses and point to coevolution of host-virus interactions in the activation and maintenance of these enzymes in planktonic, unicellular protists.
Histochemical studies of keratoconus (1988)

We quantitated the amount of collagen in corneas obtained from patients with keratoconus. Following a previously described procedure, we deparaffinized tissue sections and stained them with the collagen-specific dye Sirius red. Twenty-two (group I) of 31 keratoconus corneas examined were normal, whereas the remaining 9 (group II) showed reduced collagen staining per mm2 of surface area compared with the controls. These results agreed with our previous data demonstrating heterogeneity in keratoconus in terms of collagen content analyzed biochemically. In addition, we adapted another histochemical method, using safranin O, to measure the polyanion (mainly glycosaminoglycan) content in paraffin sections of the same specimens. All except two keratoconus corneas showed markedly higher polyanion staining per mm2 of surface area than the controls. This suggests that keratoconus corneas may contain an increased amount of glycosaminoglycans and other polyanions. Such an abnormality may be related to some of the pathologic changes seen in these corneas.
Periodontal Disease and Mortality From All Causes in the VA Dental Longitudinal Study (1998)

(The role that oral conditions may play as risk factors or indicators for various medical outcomes, including mortality, is not well understood. We have examined the relationship of periodontal disease to mortality from all causes in the VA Dental Longitudinal Study and Normative Aging Study, a prospective cohort study of the determinants of disease in aging men. Subjects were screened for entry into the closed-panel cohort in the mid-1960s, based on good medical health. They are not VA patients. We have used proportional hazards regression models to assess the relationship of periodontal health status at baseline to all-cause mortality over a 25+-year follow-up period. A total of 804 dentate subjects who were alive and medically healthy through their first follow-up exam were used in the analysis; of these, 166 died during subsequent follow-up through December 1996. Survival was calculated in years from baseline exam to death or censoring (most recent study examination date). To define periodontal health status at baseline, we separately used radiographic alveolar bone loss (ABL) (person-level scores of mean whole-mouth % ABL, measured with a Schei ruler using full-mouth series of periapical films) and periodontal clinical probing depths. Covariates included age at baseline, and assessments at baseline of smoking and alcohol use, education, body mass index, serum cholesterol, white blood cell count, blood pressure, family history of heart disease, and number of teeth present. We found that periodontal status at baseline was a significant and independent predictor of mortality in this cohort, while controlling for other recognized predictors in multivariate models. For each 20% increment in mean whole-mouth ABL, the subject's risk of death increased by 51% (RR = 1.51; 95% CI = 1.11-2.04). The increase in risk attributable to periodontal status was found to be similar in magnitude to, and independent of that attributable to cigarette smoking in this cohort. While the increased risk due to smoking was 1.52-fold (95% CI = 1.06-2.19), being in the population quintile with highest ABL scores (i.e., worst periodontal status) was associated with a 1.85 fold increase in risk (95% CI = 1.25-2.74) using multivariate analyses. The hypothesis that chronic oral infections, as in periodontitis, may have important systemic sequelae merits further investigation in prospective controlled studies.
Human T Cell Receptor γδ Cells Recognize Endogenous Mevalonate Metabolites in Tumor Cells (2003)

T lymphocytes expressing the T cell receptor (TCR)-gammadelta recognize unknown antigens on tumor cells. Here we identify metabolites of the mevalonate pathway as the tumor ligands that activate TCR-gammadelta cells. In tumor cells, blockade of hydroxy-methylglutaryl-CoA reductase (HMGR), the rate limiting enzyme of the mevalonate pathway, prevents both accumulation of mevalonate metabolites and recognition by TCR-gammadelta cells. When metabolite accumulation is induced by overexpressing HMGR or by treatment with nitrogen-containing bisphosphonate drugs, tumor cells derived from many tissues acquire the capacity to stimulate the same TCR-gammadelta population. Accumulation of mevalonate metabolites in tumor cells is a powerful danger signal that activates the immune response and may represent a novel target of tumor immunotherapy.
Discovery of human antibodies against the C5aR target using phage display technology (2005)

Phage display technologies have been increasingly utilized for the generation of therapeutic, imaging and purification reagents for a number of biological targets. Using a variety of different approaches, we have developed antibodies with high specificity and affinity for various targets ranging from small peptides to large proteins, soluble or membrane-associated as well as to activated forms of enzymes. We have applied this approach to G-protein coupled receptors (GPCRs), often considered difficult targets for antibody therapeutics and targeting. Here we demonstrate the use of this technology for the identification of human antibodies targeting C5aR, the chemoattractant GPCR receptor for anaphylatoxin C5a. The N-terminal region (residues 1-31) of C5aR, one of the ligand binding sites, was synthesized, biotinylated and used as the target for selection. Three rounds of selection with our proprietary human Fab phage display library were performed. Screening of 768 isolates by phage ELISA identified 374 positive clones. Based on sequence alignment analysis, the positive clones were divided into 22 groups. Representative Fab clones from each group were reformatted into IgGs and tested for binding to C5aR-expressing cells, the differentiated U-937 cells. Flow cytometric analysis demonstrated that nine out of 16 reformatted IgGs bound to cells. Competition with a C5aR monoclonal antibody S5/1 which recognizes the same N-terminal region showed that S5/1 blocked the binding of positive cell binders to the peptide used for selections, indicating that the identified cell binding IgGs were specific to C5aR. These antibody binders represent viable candidates as therapeutic or imaging agents, illustrating that phage display technology provides a rapid means for developing antibodies to a difficult class of targets such as GPCRs.
FQbin a compatible and optimized format for storing and managing sequence data. (2013)

Existing hardware environments may be stressed when storing and processing the enormous amount of data generated by nextgeneration sequencing technology. Here, we propose FQbin, a novel and versatile tool in C for compressing, storing and reading such sequencing data in a new and Fasta/FastQ-compatible format that outperforms the existing proposals. It is based on the general-purpose zLib library and offers up to 10X compression. The compressed file is read and decompressed up to 3X faster than a FastQ file is read, and a nearly ‘instant’ random access to every entry in the FQbin container is allowed. Fast file reading is maintained even in shared storage environments, where different processes are simultaneously accessing the same FQbin file. Slow networks can take even more advantage from FQbin.
Statistical expression deconvolution from mixed tissue samples (2010)

R code (http://www.r-project.org/) for estimating sample proportions is freely available to non-commercial users and available at http://www.med.miami.edu/medicine/x2691.xml.
CGRPin the trigeminovascular system: a role forCGRP, adrenomedullin and amylin receptors? (2013)

This article is part of a themed section on Neuropeptides. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2013.170.issue-7.
Designing microorganisms for heterologous biosynthesis of cannabinoids (2017)

During the last decade, the use of medical Cannabis has expanded globally and legislation is getting more liberal in many countries, facilitating the research on cannabinoids. The unique interaction of cannabinoids with the human endocannabinoid system makes these compounds an interesting target to be studied as therapeutic agents for the treatment of several medical conditions. However, currently there are important limitations in the study, production and use of cannabinoids as pharmaceutical drugs. Besides the main constituent tetrahydrocannabinolic acid, the structurally related compound cannabidiol is of high interest as drug candidate. From the more than 100 known cannabinoids reported, most can only be extracted in very low amounts and their pharmacological profile has not been determined. Today, cannabinoids are isolated from the strictly regulated Cannabis plant, and the supply of compounds with sufficient quality is a major problem. Biotechnological production could be an attractive alternative mode of production. Herein, we explore the potential use of synthetic biology as an alternative strategy for synthesis of cannabinoids in heterologous hosts. We summarize the current knowledge surrounding cannabinoids biosynthesis and present a comprehensive description of the key steps of the genuine and artificial pathway, systems biotechnology needs and platform optimization.
PERCUTANEOUS NUCLEOTOMY: TECHNIQUE WITH DISCOSCOPY (1991)

In its first decade of use, percutaneous nucleotomy has proven its value in decompressive indications for lumbar disc disease. Indications include contained disc herniations as isolated pathology, or in combination with other lumbar pathology at risk for decompensation after open hemilaminotomy, eg, spondylolysis/olisthesis or former open operative procedures. The precise indications underline the need for conclusive preoperative screening, such as disco-scan and contrast-discomanometry. Overall results are 85% favorable. Percutaneous intervertebral fusion is also presented.
Enabling nanotechnology with self assembled block copolymer patterns (2003)

Block copolymers (BCPs) have received great attention for the past 40 years but only within the past decade have they been seriously considered for nanotechnological applications. Their applicability to nanotechnology stems from the scale of the microdomains and the convenient tunability of size, shape, and periodicity afforded by changing their molecular parameters. The use of the tensorial physical properties of BCPs in such areas as transport, mechanical, electrical, and optical properties will provide substantial benefits in the future. In this review article, we first focus on the current efforts to utilize BCPs in nanotechnologies including nanostructured membranes, BCP templates for nanoparticle synthesis, photonic crystals, and high-density information storage media. In order to realize these applications, control over microdomain spatial and orientational order is paramount. This article reviews various methods to control BCP microdomain structures in the bulk state as well as in thin films. A variety of biases such as mechanical flow fields, electric fields, temperature gradients, and surface interactions can manipulate the microstructures of BCPs. A particular emphasis is made on two approaches, epitaxy and graphoepitaxy, and their combinations. Manipulation of BCP microdomain structures employing multiple external fields promises realization of many potential nanotechnological applications.
L-ornithine and phenylacetate synergistically produce sustained reduction in ammonia and brain water in cirrhotic rats # (2009)

The results of this study provide proof of the concept that L-ornithine and phenylbutyrate/phenylacetate act synergistically to produce sustained improvement in arterial ammonia, its brain metabolism, and brain water in cirrhotic rats.
Polyelectrolyte Surface Interface for Single-Molecule Fluorescence Studies of DNA Polymerase (2003)

We report the use of polyelectrolyte multilayers in a stable robust surface chemistry for specific anchoring of DNA to glass. The nonspecific binding of fluorescently tagged nucleotides is suppressed down to the single-molecule level, and DNA polymerase is active on the anchored DNA template. This surface-chemistry platform can be used for single-molecule studies of DNA and DNA polymerase and may be more broadly applicable for other situations in which it is important to have specific biomolecular surface chemistry with extremely low nonspecific binding.
Loading acetoxymethyl ester fluorescent dyes into the cytoplasm of Arabidopsis and Commelina guard cells (2002)

• Cytosolic calcium and pH changes are integral components of guard cell signal transduction. Acetoxymethyl (AM) ester-linked Ca<sup>2+</sup> sensitive dyes are usually degraded before loading by extracellular esterases or partitioned into plant vacuoles using standard techniques, thereby preventing cytoplasmic Ca<sup>2+</sup> imaging. • Here a method is described for improved loading of the calcium sensitive fluorescent dyes Calcium Green-1 and Fura-2 AM ester into the cytoplasm of Commelina and Arabidopsis guard cells in epidermal strips, allowing fluorescence from several guard cells in an epidermal strip to be imaged and measured simultaneously. • Calcium Green-1 based imaging, external Ca<sup>2+</sup> buffering and Mn<sup>2+</sup> quenching in Commelina guard cells suggest that abscisic acid stimulates plasma membrane Ca<sup>2+</sup> influx. The Ca<sup>2+</sup> sensitive dye Fura-2 was loaded into the cytoplasm of Arabidopsis guard cells, allowing ratiometric analyses of these cells. Data indicated that intact Ca<sup>2+</sup> homeostasis mechanisms were present in Fura-2 AM loaded cells. • Loading of acetoxymethyl ester dyes provides a viable alternative method to cameleon imaging, which will be useful in loading Arabidposis mutants that are difficult to transform. This method may also be applicable to loading other ester linked dyes into the cytoplasm of plant cells.