gebhart/patrepeval huggingface dataset:
Can Antiretroviral Drugs Be Used to Treat Porcine Endogenous Retrovirus (PERV) Infection after Xenotransplantation? (2017)

Porcine endogenous retroviruses (PERVs) are integrated in the genome of all pigs; they are released as infectious particles, and under certain conditions they can infect human cells. Therefore, they represent a risk when pigs are used as sources of cells, tissues, or organs for xenotransplantation. Xenotransplantation is under development due to the increasing shortage of human transplants. Whereas most porcine microorganisms which may be able to induce a disease (zoonosis) in the transplant recipient can be eliminated, this is not possible in the case of PERVs. Antiretroviral drugs which had been developed for the treatment of human immunodeficiency virus-1 (HIV-1) infections have been tested in vitro for their efficacy in inhibiting PERV replication. Inhibitors of the viral reverse transcriptase and of the integrase have been found effective. The most effective inhibitor of the reverse transcriptase was azidothymidine (AZT); the integrase inhibitors were the most potent inhibitors of PERV. Although in the past PERV transmission has not been observed after experimental or clinical xenotransplantation of pig cells or organs, and although PERVs may one day be inactivated in pigs by genome editing using CRISPR/Cas, knowing which antiretroviral drugs can effectively restrict PERV infection will still be important.
PUF60: A novel U2AF65-related splicing activity (1999)

We have identified a new pyrimidine-tract binding factor, PUF, that is required, together with U2AF, for efficient reconstitution of RNA splicing in vitro. The activity has been purified and consists of two proteins, PUF60 and the previously described splicing factor p54. p54 and PUF60 form a stable complex in vitro when cotranslated in a reaction mixture. PUF activity, in conjunction with U2AF, facilitates the association of U2 snRNP with the pre-mRNA. This reaction is dependent upon the presence of the large subunit of U2AF, U2AF65, but not the small subunit U2AF35. PUF60 is homologous to both U2AF65 and the yeast splicing factor Mud2p. The C-terminal domain of PUF60, the PUMP domain, is distantly related to the RNA-recognition motif domain, and is probably important in protein-protein interactions.
The Definitive Guide to Grails (2009)

The rise of Ruby on Rails has signified a huge shift in how we build web applications today; it is a fantastic framework with a growing community. There is, however, space for another such framework t
Miniature acoustic guidance system for endotracheal tubes (2002)

Ensuring that the distal end of an endotracheal tube (ETT) is properly located within the trachea, and that the tube is not obstructed by mucus deposition, is a major clinical concern in patients that require mechanical ventilation. A novel acoustic system was developed to allow for the continuous monitoring of ETT position and patency. A miniature sound source and two sensing microphones are placed in-line between the ventilator hose and the proximal end of the ETT. Reflections of an acoustic pulse emitted into the ETT lumen and the airways are digitally analyzed to estimate the location and degree of lumen obstruction, as well as the position of the distal end of the tube in the airway. The system was evaluated through in vitro studies and in a rabbit model. The system noninvasively estimated tube position in vivo to within roughly 4.5 mm, and differentiated between proper tracheal, and erroneous bronchial or esophageal intubation in all cases. In addition, the system estimated the area and location of lumen obstructions in vitro to within 14% and 3.5 mm, respectively. These findings indicate that this miniature technology could improve the quality of care provided to the ventilated adult and infant.
Reactivation of Latent HIV-1 by Inhibition of BRD4 (2012)

HIV-1 depends on many host factors for propagation. Other host factors, however, antagonize HIV-1 and may have profound effects on viral activation. Curing HIV-1 requires the reduction of latent viral reservoirs that remain in the face of antiretroviral therapy. Using orthologous genetic screens, we identified bromodomain containing 4 (BRD4) as a negative regulator of HIV-1 replication. Antagonism of BRD4, via RNA interference or with a small molecule inhibitor, JQ1, both increased proviral transcriptional elongation and alleviated HIV-1 latency in cell-line models. In multiple instances, JQ1, when used in combination with the NF-κB activators Prostratin or PHA, enhanced the in vitro reactivation of latent HIV-1 in primary T cells. These data are consistent with a model wherein BRD4 competes with the virus for HIV-1 dependency factors (HDFs) and suggests that combinatorial therapies that activate HDFs and antagonize HIV-1 competitive factors may be useful for curing HIV-1 infection.
Potent histone deacetylase inhibitors built from trichostatin A and cyclic tetrapeptide antibiotics including trapoxin (2000)

Trichostatin A (TSA) and trapoxin (TPX) are potent inhibitors of histone deacetylases (HDACs). TSA is proposed to block the catalytic reaction by chelating a zinc ion in the active-site pocket through its hydroxamic acid group. On the other hand, the epoxyketone is suggested to be the functional group of TPX capable of alkylating the enzyme. We synthesized a novel TPX analogue containing a hydroxamic acid instead of the epoxyketone. The hybrid compound cyclic hydroxamic acid-containing peptide (CHAP) 1 inhibited HDAC1 at low nanomolar concentrations. The HDAC1 inhibition by CHAP1 was reversible as it was by TSA, in contrast to the irreversible inhibition by TPX. CHAP with an aliphatic chain length of five, which corresponded to that of acetylated lysine, was stronger than those with other lengths. These results suggest that TPX is a substrate mimic and that the replacement of the epoxyketone with the hydroxamic acid converted TPX to an inhibitor chelating the zinc like TSA. Interestingly, HDAC6, but not HDAC1 or HDAC4, was resistant to TPX and CHAP1, whereas TSA inhibited these HDACs to a similar extent. HDAC6 inhibition by TPX at a high concentration was reversible, probably because HDAC6 is not alkylated by TPX. We further synthesized the counterparts of all known naturally occurring cyclic tetrapeptides containing the epoxyketone. HDAC1 was highly sensitive to all these CHAPs much more than HDAC6, indicating that the structure of the cyclic tetrapeptide framework affects the target enzyme specificity. These results suggest that CHAP is a unique lead to develop isoform-specific HDAC inhibitors.
Describable Visual Attributes for Face Verification and Image Search (2011)

We introduce the use of describable visual attributes for face verification and image search. Describable visual attributes are labels that can be given to an image to describe its appearance. This paper focuses on images of faces and the attributes used to describe them, although the concepts also apply to other domains. Examples of face attributes include gender, age, jaw shape, nose size, etc. The advantages of an attribute-based representation for vision tasks are manifold: They can be composed to create descriptions at various levels of specificity; they are generalizable, as they can be learned once and then applied to recognize new objects or categories without any further training; and they are efficient, possibly requiring exponentially fewer attributes (and training data) than explicitly naming each category. We show how one can create and label large data sets of real-world images to train classifiers which measure the presence, absence, or degree to which an attribute is expressed in images. These classifiers can then automatically label new images. We demonstrate the current effectiveness--and explore the future potential--of using attributes for face verification and image search via human and computational experiments. Finally, we introduce two new face data sets, named FaceTracer and PubFig, with labeled attributes and identities, respectively.
Gibberellin Biosynthesis from Gibberellin A12-Aldehyde in Endosperm and Embryos of Marah macrocarpus (1997)

Soluble enzyme preparations from embryos and endosperm of Marah macrocarpus (previously Echinocystis macrocarpa) were incubated with [14C4]gibberellin(GA)12-aldehyde, [14C4]GA12, [14C1] GA9, 2,3-didehydro[14C1]GA9, [14C1]GA20, and [17-13C, 3H]GA5. Embryo preparations converted GA12-aldehyde, GA12, and GA9 to GA4 and GA7; 2,3-didehydroGA9 to GA7; GA5 to GA3; and GA20 (incompletely) to GA1 and GA60, but not to GA3. Endosperm preparations converted GA12-aldehyde and GA12 to GA15, GA24, and GA9, but, unlike embryo preparations, not to GA4 or GA7. However, GA4 and GA7 were formed from GA9 and GA7 was formed from 2,3-didehydroGA9. Metabolism of GA5 to GA3 and GA20 to GA1 was low. 2,3-DidehydroGA9 accumulated when GA9 was incubated with a desalted endosperm preparation. A cDNA clone (M3-8), selected from an embryo-derived cDNA library using a DNA fragment generated by reverse transcriptase polymerase chain reaction, was expressed in Escherichia coli. The fusion protein converted GA12 to GA9 (major) and GA25 (minor); GA53 was metabolized less effectively and only to GA44. Thus, the M3-8 protein is functionally similar to GA 20-oxidases from Arabidopsis thaliana, Spinacia oleracea, and Pisum sativum, but different from that from Cucurbita maxima seeds, to which its amino acid sequence is most closely related. mRNA hybridizing to M3-8 accumulated in embryos and endosperm of M. macrocarpus, but was absent in vegetative tissues.
Effect of Oral Acyclovir Treatment on Symptomatic and Asymptomatic Virus Shedding in Recurrent Genital Herpes (1989)

Twenty-six men and women with recurrent genital herpes maintained diaries of their symptoms and signs of infection and submitted 6,515 self-collected cultures during a one-year study of acyclovir therapy. As compared with periods before or after treatment, the mean rates of experiencing symptoms or lesions, and of shedding virus were significantly lower during treatment. Acyclovir treatment reduced the rate of symptomatic shedding from 95 positive cultures to six per 1,000 cultures, but the rate of asymptomatic shedding remained relatively constant, averaging eight per 1,000 cultures. Among the isolates of herpes simplex virus studied, there was no differences in sensitivity to acyclovir between strains recovered on or off therapy or during symptomatic or asymptomatic recurrences. The endonuclease cleavage profiles of asymptomatically shed viruses were essentially the same as those of the symptomatically shed viruses from the same individual. Chronic acyclovir therapy significantly reduced the symptoms and signs of recurrent genital herpes but did not eliminate virus shedding, nor, therefore, the possibility of disease transmission.
Video enhancement using per-pixel virtual exposures (2005)

We enhance underexposed, low dynamic range videos by adaptively and independently varying the exposure at each photoreceptor in a post-process. This virtual exposure is a dynamic function of both the spatial neighborhood and temporal history at each pixel. Temporal integration enables us to expand the image's dynamic range while simultaneously reducing noise. Our non-linear exposure variation and denoising filters smoothly transition from temporal to spatial for moving scene elements. Our virtual exposure framework also supports temporally coherent per frame tone mapping. Our system outputs restored video sequences with significantly reduced noise, increased exposure time of dark pixels, intact motion, and improved details.
The rate of surplus value in the postwar US economy: a critique of Weisskopf's estimates (1985)

Journal Article The rate of surplus value in the postwar US economy: a critique of Weisskopf's estimates Get access Fred Moseley Fred Moseley *Colby CollegeWaterville, Maine Search for other works by this author on: Oxford Academic Google Scholar Cambridge Journal of Economics, Volume 9, Issue 1, March 1985, Pages 57–79, https://doi.org/10.1093/oxfordjournals.cje.a035564 Published: 01 March 1985
A Novel Mutation Glyl672→Arg in Type 2A and a Homozygous Mutation in Type 2B von Willebrand Disease (1996)

Genetic materials from 16 unrelated Japanese patients with von Willebrand disease (vWD) were analyzed for mutations. Exon 28 of the von Willebrand factor (vWF) gene, where point mutations have been found most frequent, was screened by various restriction-enzyme analyses. Six patients were observed to have abnormal restriction patterns. By sequence analyses of the polymerase chain-reaction products, we identified a homozygous R1308C missense mutation in a patient with type 2B vWD; R1597W, R1597Q, G1609R and G1672R missense mutations in five patients with type 2A; and a G1659ter nonsense mutation in a patient with type 3 vWD. The G1672R was a novel missense mutation of the carboxyl-terminal end of the A2 domain. In addition, we detected an A/C polymorphism at nucleotide 4915 with HaeIII. There was no particular linkage disequilibrium of the A/C polymorphism, either with the G/A polymorphism at nucleotide 4391 detected with Hphl or with the C/T at 4891 detected with BstEII.
Reasons for Admisson among Six Profile Subgroups of Recidivists of Inpatient Services (1993)

The incidence pattern of medication and program non compliance, violent acts, suicide attempts and chemical abuse defined as reasons for hospital admission was evaluated in a total sample (n = 416) of recidivists and their six constituent profile subgroups (n = 272). The total sample was drawn from two different state-operated hospitals and two different time periods. The incidence pattern observed for the total sample in order of descending priority was medication non compliance, program non compliance, chemical abuse, violent acts and suicide attempts. The incidence pattern ordering and the relevant percentages of occurrence were observed for both hospitals. There were time period differences in the ordering and percentages of the reasons for admission which revealed an increase in both medication and program non compliance as well as chemical abuse in the more recent sample. There were also specific subgroup differences in the incidence pattern concerning some reasons for admission. These subgroup differences are discussed in detail.
50-GHz self-aligned silicon bipolar transistors with ion-implanted base profiles (1990)

Silicon bipolar transistors having cutoff frequencies from 40 to 50 GHz have been fabricated in a double -polysilicon self-aligned structure using a process which relies on ion implantation for the intrinsic base formation. The devices have nearly ideal DC characteristics, with breakdown voltages adequate for most digital applications. The results demonstrate that the performance limits of conventional implanted technologies are significantly higher than previously thought.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Slide‐based cytometry for predicting malignancy in solid salivary gland tumors by fine needle aspirate biopsies (2003)

This pilot study demonstrates the validity of slide-based cytometry for the preoperative prediction of malignancy in solid tumors being inaccessible for incision biopsy but suitable for FNABs such as those of the parotid gland.
Sutureless Cholecystojejunostomy in Pigs Using an Absorbable Intraluminal Stent and Fibrin Glue (1996)

The absence of foreign bodies in sutureless anastomoses provides faster healing. The first sutureless cholecystojejunostomies were reported by Murphy in 1892. The common bile duct was tied and 11 cholecystojejunostomies plus 12 jejunojejunostomies were performed in 12 Landrace pigs employing sliding absorbable intraluminal nontoxic stents (SAINTs) and fibrin glue. One cholecystojejunostomy was not performed owing to a gallbladder morphologic anomaly. Three animals died of problems unrelated to the SAINT-glue anastomoses. Of the 18 anastomoses in the 9 remaining animals, all were patent at the verification times of 14, 30, 120, and 480 days. Morphologically,there was greater edema and reduced height of the glandular epithelium in the 30-day CJs when compared to the jejunojejunal anastomoses. Results indicate that the sutureless SAINT-fibrin glue procedure is quite versatile and may be utilized for cholecystoenteric anastomoses.
Determination of the blood lactate:pyruvate ratio as a noninvasive test for the diagnosis of zidovudine myopathy (1994)

The lactate:pyruvate ratio, when determined repeatedly, is a sensitive test for detecting mitochondrial muscular toxicity of zidovudine.
Amino acid substitutions can influence the natural killer (NK)-mediated recognition of HLA-C molecules. Role of serine-77 and lysine-80 in the target cell protection from lysis mediated by "group 2" or "group 1" NK clones. (1995)

Natural killer (NK) cells have been shown to express a clonally distributed ability to recognize HLA class I alleles. The previously defined NK clones belonging to "group 1" recognize HLA-C*0401 (Cw4) and other HLA-C alleles sharing Asn at position 77 and Lys at position 80. Conversely, the "group 2" NK clones recognize HLA-Cw*0302 (Cw3) and other HLA-C alleles characterized by Ser at position 77 and Asn at position 80. We assessed directly the involvement of these two residues in the capacity of NK cell clones to discriminate between the two groups of HLA-C alleles. To this end, Cw3 and Cw4 alleles were subjected to site-directed mutagenesis. Substitution of the amino acids typical of the Cw3 allele (Ser-77 and Asn-80) with those present in Cw4 (Asn-77 and Lys-80) resulted in a Cw3 mutant that was no longer recognized by group 2 NK cell clones, but that was recognized by group 1 clones. Analysis of Cw3 or Cw4 molecules containing single amino acid substitutions indicates roles for Lys-80 in recognition mediated by group 1 clones and for Ser-77 in recognition mediated by group 2 clones. These results demonstrate that NK-mediated specific recognition of HLA-C allotypes is affected by single natural amino acid substitutions at positions 77 and 80 of the heavy chain.
PATHWAYS OF GLUCOSE CATABOLISM IN BACILLUS SUBTILIS (1963)

Goldman, Manuel (The University of Michigan, Ann Arbor) and Harold J. Blumenthal. Pathways of glucose catabolism in Bacillus subtilis. J. Bacteriol. 86:303-311. 1963.-Under aerobic conditions, resting cells of Bacillus subtilis Marburg C4 catabolized 60 to 70% of glucose by the Embden-Meyerhof pathway and the remainder by the hexose monophosphate pathway; under anaerobic conditions, the percentages were 70 to 80 and 20 to 30, respectively. These estimates, based on two different radio-isotopic procedures, were the same whether the cells were grown in a glucose medium containing a complex, organic nitrogen source (C cells) or a simple inorganic nitrogen source (S cells). In C cells, respiration was inhibited by fluoride, whereas S cells were relatively insensitive to this influence. Factors such as the initial concentration of inorganic phosphate or glucose during growth, and the concentration of inorganic phosphate or even the presence of fluoride during glucose utilization by resting cells, had no major effects on the pathways of glucose catabolism. From an examination of the isotopic distribution in an isolated intermediate, lactic acid, it seems unlikely that the radioisotopic estimates were influenced by such other factors as participation of an Entner-Doudoroff pathway, extensive randomization of C(1) activity into other positions of the hexose molecule, or extensive CO(2) fixation.
Laser image cytometer for analysis of circulating tumor cells (2008)

Brigthfield and fluorescent image of a whole blood sample spiked with SKBR-3 breast cancer tumor cells, illustrating the presence of tumors cells in the blood.
Effects of Type I Interferons on Friend Retrovirus Infection (2006)

The type I interferon (IFN) response plays an important role in the control of many viral infections. However, since there is no rodent animal model for human immunodeficiency virus, the antiviral effect of IFN-alpha and IFN-beta in retroviral infections is not well characterized. In the current study we have used the Friend virus (FV) model to determine the activity of type I interferons against a murine retrovirus. After FV infection of mice, IFN-alpha and IFN-beta could be measured between 12 and 48 h in the serum. The important role of type I IFN in the early immune defense against FV became evident when mice deficient in IFN type I receptor (IFNAR(-/-)) or IFN-beta (IFN-beta(-/-)) were infected. The levels of FV infection in plasma and in spleen were higher in both strains of knockout mice than in C57BL/6 wild-type mice. This difference was induced by an antiviral effect of IFN-alpha and IFN-beta and was most likely mediated by antiviral enzymes as well as by an effect of these IFNs on T-cell responses. Interestingly, the lack of IFNAR and IFN-beta enhanced viral loads during acute and chronic FV infection. Exogenous IFN-alpha could be used therapeutically to reduce FV replication during acute but not chronic infection. These findings indicate that type I IFN plays an important role in the immediate antiviral defense against Friend retrovirus infection.
User Requirements for the Session Initiation Protocol (SIP) in Support of Deaf, Hard of Hearing and Speech-impaired Individuals (2002)

This document presents a set of Session Initiation Protocol (SIP) user requirements that support communications for deaf, hard of hearing and speech-impaired individuals. These user requirements address the current difficulties of deaf, hard of hearing and speech-impaired individuals in using communications facilities, while acknowledging the multi-functional potential of SIP-based communications.
Gene transfer of the ly‐3 chain gene of the mouse cd8 molecular complex: co‐transfer with the ly‐2 polypeptide gene results in detectable cell surface expression of the ly‐3 antigenic determinants (1988)

The CD8 molecule is a glycoprotein expressed on a subset of mature T lymphocytes. It has been postulated to be a receptor for class I major histocompatibility complex molecules. In the mouse, CD8 is a heterodimer composed of Ly-2 and Ly-3 chains. We have isolated and analyzed cDNA and cosmid clones corresponding to the Ly-3 subunit. One of the isolated, cosmid clones was subsequently transfected, alone or in combination with the Ly-2 gene, into mouse Ltk- cells. Analysis of the Ly-2,3 molecules expressed at the surface of the double transfectants indicated that they are serologically and biochemically indistinguishable from their normal counterparts expressed on lymphoid cells. Ltk- cells transfected with the Ly-2 gene alone were shown to react with a subset of anti-CD8 monoclonal antibodies whereas Ly-3 transfectants did not stain with any of the anti-Ly-3 antibodies employed in this study. Since at least one of these antibodies (53-5.8) has been previously shown to recognize an epitope which is retained on the Ly-3 subunit after dissociation of the heterodimeric Ly-2,3 complex, these observations suggest that the expression of the Ly-2 polypeptide is required to permit the detectable cell surface expression of the antigenic determinants carried by the Ly-3 subunit.