gebhart/patrepeval huggingface dataset:
A tale of two clades: monkeypox viruses (2005)

Human monkeypox was first recognized outside Africa in 2003 during an outbreak in the USA that was traced to imported monkeypox virus (MPXV)-infected West African rodents. Unlike the smallpox-like disease described in the Democratic Republic of the Congo (DRC; a Congo Basin country), disease in the USA appeared milder. Here, analyses compared clinical, laboratory and epidemiological features of confirmed human monkeypox case-patients, using data from outbreaks in the USA and the Congo Basin, and the results suggested that human disease pathogenicity was associated with the viral strain. Genomic sequencing of USA, Western and Central African MPXV isolates confirmed the existence of two MPXV clades. A comparison of open reading frames between MPXV clades permitted prediction of viral proteins that could cause the observed differences in human pathogenicity between these two clades. Understanding the molecular pathogenesis and clinical and epidemiological properties of MPXV can improve monkeypox prevention and control.
Experimental studies on the origin and accumulation of coalbed gas (1978)

We investigated the plasticity effects of diabetes mellitus and diuresis on the non-adrenergic non-cholinergic (NANC) and purinergic (P2X-type) contractile responses in longitudinal rat bladder strips. Female Sprague-Dawley rats received streptozotocin to induce diabetes, or sucrose in water to induce diuresis as a control condition for polyuria. Experiments were carried out at four weeks after treatments, using bladders from non-treated rats as control. Urinary bladder strips were electrically stimulated throughout the experiments to generate neurally evoked contractions (NEC). In all cases, P2X-mediated purinergic contractions were evaluated at the beginning and end of the stimulations with α,β-methylene-adenosine triphosphate (α,βMeATP). The NANC responses were assessed by using two independent protocols. First, cholinergic receptors were activated with carbachol (CCh), followed by inhibition of the muscarinic component with atropine. In the second protocol, the application order for CCh and atropine was reversed. The NANC response, unmasked with the application of atropine, and the P2X purinergic contractions were analyzed. NANC contractions in diabetic bladder strips are more resistant to the desensitizing effects caused by activation of cholinergic receptors. In early stages of experimental diabetes, NANC responses in diabetic strips are less sensitive to functional inhibition mediated by the cholinergic activation. However, P2X-mediated purinergic contractions are more sensitive to desensitization in diabetic or diuretic bladders. For instance preventing muscarinic receptor activation with atropine does not counteract the desensitization of purinergic contractions in either diabetic or diuretic strips. We suggest that diabetes may induce a plasticity of the NANC and P2X-mediated bladder contractile responses. The first one may be associated with diabetic neuropathic damage to bladder nerves, while impaired P2X purinergic contractions might be associated with detrusor hypertrophy observed in diabetic and diuretic strips.
Two-Wavelength Speckle Interferometric Technique For Rough Surface Contour Measurement (1986)

If a rough surface is illuminated by a coherent light wave of wavelength Al, it is not possible to determine the surface profile from the phases of the speckle field formed by the scattered light. However, if the rough surface is illuminated by an additional coherent wave of wavelength A2, the phase differences between the two speckle fields do contain information about the macro-scopic surface profile even though subject to a statistical error. We present the pertinent statistical properties of dichromatic speckle fields and show that (1) the macroscopic surface profile may be determined from the phase differences if the effective wavelength A = Al X2/I Al - A21 is sufficiently larger than the standard deviation of the microscopic profile of the illuminated surface and (2) the statistical error is reasonably small if the phase measurements are obtained from speckles with sufficient intensity.
Identification of HIV-1 vpr product and function. (1990)

To investigate the role of vpr (viral protein R) in the replication and cytopathicity of human immunodeficiency virus type 1 (HIV-1), infectious proviruses were constructed that were isogenic except for the ability to produce the protein product of vpr. The experiments described here demonstrate that vpr encodes a 96 amino acid 15 kDa protein. The vpr product increases the rate of replication and accelerates the cytopathic effect of the virus in T cells. Vpr acts in trans to increase levels of viral protein expression. The stimulatory effect of vpr is observed to act on the HIV-1 LTR as well as on several heterologous promoters.
Dye‐enhanced laser welding for skin closure (1992)

The use of a laser to weld tissue in combination with a topical photosensitizing dye permits selective delivery of energy to the target tissue. A combination of indocyanine green (IG), absorption peak 780 nm, and the near-infrared (IR) alexandrite laser was studied with albino guinea pig skin. IG was shown to bind to the outer 25 microns of guinea pig dermis and appeared to be bound to collagen. The optical transmittance of full-thickness guinea pig skin in the near IR was 40% indicating that the alexandrite laser should provide adequate tissue penetration. Laser "welding" of skin in vivo was achieved at various concentrations of IG from 0.03 to 3 mg/cc using the alexandrite at 780 nm, 250-microseconds pulse duration, 8 Hz, and a 4-mm spot size. A spectrum of welds was obtained from 1- to 20-W/cm2 average irradiance. Weak welds occurred with no thermal damage obtained at lower irradiances: stronger welds with thermal damage confined to the weld site occurred at higher irradiances. At still higher irradiances, local vaporization occurred with failure to "weld." Thus, there was an optimal range of irradiances for "welding," which varied inversely with dye concentration. Histology confirmed the thermal damage results that were evident clinically. IG dye-enhanced laser welding is possible in skin and with further optimization may have practical application.
Collision Detection and Response for Computer Animation (1988)

When several objects are moved about by computer animation, there is the chance that they will interpenetrate. This is often an undesired state, particularly if the animation is seeking to model a realistic world. Two issues are involved: detecting that a collision has occurred, and responding to it. The former is fundamentally a kinematic problem, involving the positional relationship of objects in the world. The latter is a dynamic problem, in that it involves predicting behavior according to physical laws. This paper discusses collision detection and response in general, presents two collision detection algorithms, describes modeling collisions of arbitrary bodies using springs, and presents an analytical collision response algorithm for articulated rigid bodies that conserves linear and angular momentum.
Studies of Phospholipid Reagents Used in Coagulation I: Some General Properties and Their Sensitivity to Factor VIII (1981)

Some general properties of phospholipid reagents have been studied, particularly in relation to their use in detection and measurement of Factor VIII deficiency. There was wide variation among reagents in their total phospholipid concentration, and in the degree of contamination with tissue factor and oxidation products. Although clotting times of normal and haemophilic plasma were affected by change of phospholipid concentration, presence of oxidation products, and order of addition of reagents, these factors did not appear to influence the efficiency of detection of the Factor VIII defect. The method of activation had a definite influence on sensitivity to Factor VIII deficiency, both the type of activator and the time of activation being important. In Factor VIII one-stage assays, use of different phospholipids with the same substrate plasma gave significant differences in precision, but the estimates of potency of a Factor VIII concentrate against a plasma standard were not significantly different.
Neutralization of human immunodeficiency virus type 1 by complement occurs by viral lysis (1990)

The ability of complement to inactivate human immunodeficiency virus (HIV) in the presence of specific antibody was evaluated. HIV was treated with complement and/or antibody, and then its titer was determined on the CD4+ H9 cell line. While complement alone had no effect on the HIV titer, complement plus subneutralizing levels of antibody resulted in titer reductions. Complement sources deficient in membrane attack component C5 or C8 did not inactivate antibody-treated HIV, suggesting that neutralization occurred via lysis. This possibility was investigated by assessing release of reverse transcriptase (RT) from the virion. Antibody plus complement, but neither reagent alone, released RT from HIV in a dose-dependent manner. Release of RT did not occur with C5- or C8-deficient sera, also indicating a requirement for membrane attack components. These studies show that complement can neutralize HIV via the classical complement pathway and that this neutralization occurs via C5b-9-mediated viral lysis. Thus, complement may play a major role in resistance to disease by lysing HIV and preventing infection of Fc- and complement receptor-positive cells, as well as CD4+ cells.
An Empirical Evaluation of Deep Learning on Highway Driving (2015)

Numerous groups have applied a variety of deep learning techniques to computer vision problems in highway perception scenarios. In this paper, we presented a number of empirical evaluations of recent deep learning advances. Computer vision, combined with deep learning, has the potential to bring about a relatively inexpensive, robust solution to autonomous driving. To prepare deep learning for industry uptake and practical applications, neural networks will require large data sets that represent all possible driving environments and scenarios. We collect a large data set of highway data and apply deep learning and computer vision algorithms to problems such as car and lane detection. We show how existing convolutional neural networks (CNNs) can be used to perform lane and vehicle detection while running at frame rates required for a real-time system. Our results lend credence to the hypothesis that deep learning holds promise for autonomous driving.
The uptake of family screening in hypertrophic cardiomyopathy and an online video intervention to facilitate family communication (2019)

Despite care in a specialized cardiovascular genetics clinic, approximately one half of FDRs of patients with HCM remained unscreened. Online interventions and videos may serve as supplemental tools for patients communicating genetic risk information to relatives.
Rapid motif compliance scoring with match weight sets (1993)

Most current implementations of motif matching in biological sequences have sacrificed the generality of weight matrix scoring for shorter runtimes. The program MOTIF incorporates a weight matrix and a rapid, backtracking tree-search algorithm to score motif compliance with greatly enhanced performance while placing no constraints on the motif. In addition, any positions within a motif can be marked as 'inviolate', thereby requiring an exact match. MOTIF allows a choice of regular expression formats and can use both motif and sequence libraries as either targets or queries. Nucleic acid sequences can optionally be translated by MOTIF in any frame(s) and used against peptide motifs.
Single-Component Biohybrid Light-Emitting Diodes Using a White-Emitting Fused Protein (2018)

This work presents a pioneering multidisciplinary approach toward enhancing biohybrid light-emitting diodes (BioHLEDs), merging synthetic biology tools, polymer chemistry, and device engineering to design a thin color down-converting coating with a single white-emitting fluorescent protein (WFP). In particular, the WFP consists of fused red-, green-, and blue-emitting FPs following the so-called protein superglue approach. This WFP shows an efficient and stable white emission originated from a Förster resonance energy transfer between FP moieties. The emission chromaticity is, in addition, easily controlled by the rigidity of the polymer matrix of the coating, reaching photoluminescence quantum yields of 26% that stand out among intrinsic white-emitting materials. The WFP single-component color down-converting packaging was applied to fabricate BioHLEDs featuring efficient neutral white emission that is stable over 400 h. This represents the most stable BioHLED reported to date. Thus, this work is a landmark for the use of synthetic biology tools to design tailored luminescent biomaterials for lighting applications.
Computing arbitrary functions of encrypted data (2010)

Suppose that you want to delegate the ability to process your data, without giving away access to it. We show that this separation is possible: we describe a "fully homomorphic" encryption scheme that keeps data private, but that allows a worker that does not have the secret decryption key to compute any (still encrypted) result of the data, even when the function of the data is very complex. In short, a third party can perform complicated processing of data without being able to see it. Among other things, this helps make cloud computing compatible with privacy.
The Repertoire of Fos and Jun Proteins Expressed during the G1 Phase of the Cell Cycle Is Determined by the Duration of Mitogen-Activated Protein Kinase Activation (1999)

In Rat-1 fibroblasts nonmitogenic doses of lysophosphatidic acid (LPA) stimulate a transient activation of mitogen-activated protein kinase (MAPK), whereas mitogenic doses elicit a sustained response. This sustained phase of MAPK activation regulates cell fate decisions such as proliferation or differentiation, presumably by inducing a program of gene expression which is not observed in response to transient MAPK activation. We have examined the expression of members of the AP-1 transcription factor complex in response to stimulation with different doses of LPA. c-Fos, c-Jun, and JunB are induced rapidly in response to LPA stimulation, whereas Fra-1 and Fra-2 are induced after a significant lag. The expression of c-Fos is transient, whereas the expression of c-Jun, JunB, Fra-1, and Fra-2 is sustained. The early expression of c-Fos can be reconstituted with nonmitogenic doses of LPA, but the response is transient compared to that observed with mitogenic doses. In contrast, expression of Fra-1, Fra-2, and JunB and optimal expression of c-Jun are observed only with doses of LPA which induce sustained MAPK activation and DNA synthesis. LPA-stimulated expression of c-Fos, Fra-1, Fra-2, c-Jun, and JunB is inhibited by the MEK1 inhibitor PD098059, indicating that the Raf-MEK-MAPK cascade is required for their expression. In cells expressing a conditionally active form of Raf-1 (DeltaRaf-1:ER), we observed that selective, sustained activation of Raf-MEK-MAPK was sufficient to induce expression of Fra-1, Fra-2, and JunB but, interestingly, induced little or no c-Fos or c-Jun. The induction of c-Fos observed in response to LPA was strongly inhibited by buffering the intracellular [Ca2+]. Moreover, although Raf activation or calcium ionophores induced little c-Fos expression, we observed a synergistic induction in response to the combination of DeltaRaf-1:ER and ionomycin. These results suggest that kinetically distinct phases of MAPK activation serve to regulate the expression of distinct AP-1 components such that sustained MAPK activation is required for the induced expression of Fra-1, Fra-2, c-Jun, and JunB. However, in contrast to the case for Fra-1, Fra-2, and JunB, activation of the MAPK cascade alone is not sufficient to induce c-Fos expression, which rather requires cooperation with other signals such as Ca2+ mobilization. Finally, the identification of the Fra-1, Fra-2, c-Jun, and JunB genes as genes which are selectively regulated by sustained MAPK activation or in response to activated Raf suggests that they are candidates to mediate certain of the effects of Ras proteins in oncogenic transformation.
Distinct Expression ofCDX2 andGATA4/5, Development-Related Genes, in Human Gastric Cancer Cell Lines (2000)

CDX2 is a tumor-suppressor homeobox gene involved in colon carcinogenesis, but its role in gastric cancer is unknown. Although GATA4, -5 and, -6 transcription factors have distinct functions in the regulation of gastrointestinal epithelial cell differentiation, there have been no reports regarding GATA4/5/6 alterations in gastrointestinal carcinomas. By using a semiquantitative reverse transcription-polymerase chain reaction assay, we studied the expression of gut development-related genes CDX2/1 and GATA4/5/6 in 11 human gastric cancer cell lines. The expression of CDX2 appeared to progressively decrease with the transition from well differentiated to poorly differentiated cancer cell lines. CDX1 was below detectable levels in all cell lines. The expression of GATA4 and GATA5 was undetectable in four and six cell lines, respectively, whereas the majority of the cell lines expressed GATA6 abundantly. These results suggest that CDX2 and GATA4/5 may be associated with the carcinogenesis of the stomach. Mol. Carcinog. 28:184-188, 2000.
Mechanisms of cell entry by influenza virus (2001)

A wide range of viruses, including many human and animal pathogens representing various taxonomic groups, contain genomes that are enclosed in lipid envelopes. These envelopes are generally acquired in the final stages of assembly, as viruses bud from regions of the membrane of the infected cell at which virally encoded membrane proteins have accumulated. The viruses procure their membranes during this process and mature particles ‘pinch off’ from the cellular membranes. Under most circumstances, initiation of another round of infection is dependent on two critical functions supplied by the envelope proteins. The virus must bind to cell-surface receptors of a new host cell, and fusion of the viral and cellular membranes must occur to transfer the viral genome into the cell. Enveloped viruses have evolved a variety of mechanisms to execute these two basic functions. Owing to their relative simplicity, studies of binding and fusion using enveloped viruses and their components have contributed significantly to the overall understanding of receptor–ligand interactions and membrane fusion processes – fundamental activities involved in a plethora of biological functions.
Angiogenic network formation in the developing vertebrate trunk (2003)

We have used time-lapse multiphoton microscopy of living Tg(fli1:EGFP)y1 zebrafish embryos to examine how a patterned, functional network of angiogenic blood vessels is generated in the early vertebrate trunk. Angiogenic vascular sprouts emerge from the longitudinal trunk axial vessels (the dorsal aorta and posterior cardinal vein) in two spatially and temporally distinct steps. Dorsal aorta-derived sprouts form an initial primary network of vascular segments, followed by emergence of vein-derived secondary vascular sprouts that interact and interconnect dynamically with the primary network to initiate vascular flow. Using transgenic silent heart mutant embryos, we show that the gross anatomical patterning of this network of vessels does not require blood circulation. However, our results suggest that circulatory flow dynamics play an important role in helping to determine the pattern of interconnections between the primary network and secondary sprouts, and thus the final arterial or venous identity of the vessels in the functional network. We discuss a model to explain our results combining genetic programming of overall vascular architecture with hemodynamic determination of circulatory flow patterns.
Chemical studies on oils derived from aspen poplar wood, cellulose, and an isolated aspen poplar lignin (1983)

An initial study has been made of the chemical nature of the oil phase resulting from the the conversion of aspen poplar wood, cellulose, and an isolated lignin from the aspen poplar as a result of their interactions with water and carbon monoxide in the presence of sodium carbonate at 360 °C. Gas chromatographic analysis of the sodium hydroxide soluble fractions from each substrate revealed similar spectra of alkyl-substituted phenols. The relative abundance of identified low molecular weight phenolic compounds decreased from lignin to wood to cellulose. This was in agreement with the known phenolic nature of lignin. As well, it confirmed the synthesis during reaction of such compounds from a carbohydrate substrate. Gas chromatographic analysis of the whole oils also revealed the presence in each case of several alkyl-substituted cyclopentanones whose relative abundance decreased from cellulose to wood to lignin. Silica gel column separation of the oils, after a charcoal treatment, followed by capillary gas chromatographic – mass spectrometric analyses of the resulting fractions indicated the presence of other higher molecular weight phenols, napthols, cycloalkanols, cycloalkanones, and polycyclic and long chain alkanes and alkenes.
Sequence and Expression of a Candidate for the Human Secretor Blood Group α(1,2)Fucosyltransferase Gene (FUT2) (1995)

Synthesis of soluble A, B, H, and Lewis b blood group antigens in humans is determined by the Secretor (Se) (FUT2) blood group locus. Genetic, biochemical, and molecular analyses indicate that this locus corresponds to an alpha(1,2)fucosyltransferase gene distinct from the genetically-linked H blood group alpha(1,2)fucosyltransferase locus. The accompanying paper (Rouquier, S., Lowe, J. B., Kelly, R. J., Fertitta, A. L., Lennon, G. G., and Giorgi, D. (1995) J. Biol. Chem. 270, 4632-4639) describes the molecular cloning and mapping of two human DNA segments that are physically linked to, and cross-hybridize with, the H locus. We present here an analysis of these two new DNA segments. One of these, termed Sec1, is a pseudogene, because translational frameshifts and termination codons interrupt potential open reading frames that would otherwise share primary sequence similarity with the H alpha(1,2)fucosyltransferase. The other DNA segment, termed Sec2, predicts a 332-amino acid-long polypeptide, and a longer isoform, that share 68% sequence identity with the COOH-terminal 292 residues of the human H blood group alpha(1,2)fucosyltransferase. Sec2 encodes an alpha(1,2)fucosyltransferase with catalytic properties that mirror those ascribed to the Secretor locus-encoded alpha(1,2)fucosyltransferase. Approximately 20% of randomly-selected individuals were found to be apparently homozygous for an enzyme-inactivating nonsense allele (Trp143-->ter) at this locus, in correspondence to the frequency of the non-secretor phenotype in most human populations. Furthermore, each of six unrelated non-secretor individuals are also apparently homozygous for this null allele. These results indicate that Sec2 corresponds to the human Secretor blood group locus (FUT2) and indicate that homozygosity for a common nonsense allele is responsible for the nonsecretor phenotype in many non-secretor individuals.