gebhart/patrepeval huggingface dataset:
Identification, using synthetic peptides, of the minimum amino acid sequence from the retroviral transmembrane protein p15E required for inhibition of lymphoproliferation and its similarity to gp21 of human T-lymphotropic virus types I and II (1989)

Synthetic peptides containing portions of a highly conserved region of retroviral transmembrane proteins of human and animal retroviruses were tested for their ability to inhibit lymphoproliferation to determine the minimum amino acid sequence required. The previously reported immunosuppression mediated by the peptide CKS-17 was confirmed and further localized to a sequence of eight residues essentially identical to the sequence present in the transmembrane protein gp21 of human T-lymphotropic virus types I and II (HTLV-I and -II). To substantiate the physiological relevance of the inhibition of lymphoproliferation observed with the synthetic peptides and to relate this activity to the intact protein, we purified the Rauscher murine leukemia virus transmembrane protein p15E by immunoaffinity chromatography and report that this purified component presented in the form of protein micelles inhibited the interleukin-2-dependent proliferation of the murine T-cell line CTLL-2 in a dose-dependent manner, with a half-maximal inhibitory dose (ID50) of approximately 16 nM. In comparison, the ID50 concentration of a recombinant form of p15E required to inhibit lymphoproliferation was approximately 2.2 microM. The results reported here support the hypothesis that the transmembrane protein gp21 of HTLV-I and -II participates in the mechanism of immunosuppression previously reported for the transmembrane proteins of feline leukemia virus and other animal retroviruses. Thus, the transmembrane protein of HTLV-I, the etiological agent of adult T-cell leukemia-lymphoma, may be partially responsible for the immunocompromised clinical course of this disease that results in fatal opportunistic infections in a majority of cases.
X-Window interface to SMART, an advanced text retrieval system (1992)

In a research environment for text and document retreival, the experimental functionality is and must be paramount. However, for long-term durability of a software product, the user-interface is seen as a critical component to successful development. In order to explore the effort involved in developing a modern user interface to a text retrieval system, the authors chose to implement a limited X-Window interface to the Cornell University SMART system. The first section of this paper will briefly introduce the history of the SMART system, its command line interface, and the goal of this project; the second will discuss the scope of the project; the development and integration strategies will be covered in sections three and four; then some ideas on the desired enchancements in section five.
Sub-pixel resolving optofluidic microscope for on-chip cell imaging (2010)

We report the implementation of a fully on-chip, lensless, sub-pixel resolving optofluidic microscope (SROFM). The device utilizes microfluidic flow to deliver specimens directly across a complementary metal oxide semiconductor (CMOS) sensor to generate a sequence of low-resolution (LR) projection images, where resolution is limited by the sensor's pixel size. This image sequence is then processed with a pixel super-resolution algorithm to reconstruct a single high resolution (HR) image, where features beyond the Nyquist rate of the LR images are resolved. We demonstrate the device's capabilities by imaging microspheres, protist Euglena gracilis, and Entamoeba invadens cysts with sub-cellular resolution and establish that our prototype has a resolution limit of 0.75 microns. Furthermore, we also apply the same pixel super-resolution algorithm to reconstruct HR videos in which the dynamic interaction between the fluid and the sample, including the in-plane and out-of-plane rotation of the sample within the flow, can be monitored in high resolution. We believe that the powerful combination of both the pixel super-resolution and optofluidic microscopy techniques within our SROFM is a significant step forwards toward a simple, cost-effective, high throughput and highly compact imaging solution for biomedical and bioscience needs.
Real-time 3D vision solution for on-orbit autonomous rendezvous and docking (2006)

Neptec has developed a vision system for the capture of non-cooperative objects on orbit. This system uses an active TriDAR sensor and a model based tracking algorithm to provide 6 degree of freedom pose information in real-time from mid range to docking. This system was selected for the Hubble Robotic Vehicle De-orbit Module (HRVDM) mission and for a Detailed Test Objective (DTO) mission to fly on the Space Shuttle. TriDAR (triangulation + LIDAR) technology makes use of a novel approach to 3D sensing by combining triangulation and Time-of-Flight (ToF) active ranging techniques in the same optical path. This approach exploits the complementary nature of these sensing technologies. Real-time tracking of target objects is accomplished using 3D model based tracking algorithms developed at Neptec in partnership with the Canadian Space Agency (CSA). The system provides 6 degrees of freedom pose estimation and incorporates search capabilities to initiate and recover tracking. Pose estimation is performed using an innovative approach that is faster than traditional techniques. This performance allows the algorithms to operate in real-time on the TriDAR's flight certified embedded processor. This paper presents results from simulation and lab testing demonstrating that the system's performance meets the requirements of a complete tracking system for on-orbit autonomous rendezvous and docking.
Multiple endocrine neoplasia induced by the promiscuous expression of a viral oncogene. (1988)

There is increasing evidence for the importance of events that govern and influence the interaction between the transformed cell and its host being ultimately responsible for the establishment of the cancer phenotype. To derive an animal model that will allow us to define some of these phenomena at the molecular level, we have chosen to induce the expression of a viral oncogene in all tissue types, with the hope of identifying sites that are more susceptible to malignant transformation. When the gene for simian virus 40 large tumor antigen (T antigen) was placed under the control of a major histocompatibility complex class I gene enhancer, the resulting transgenic mice not only developed choroid plexus papillomas, as seen with wild-type simian virus 40, but also lymphoid hyperplasia and multiple endocrine neoplasias. The development of lymphoid hyperplasia was preceded by an elevated level of expression of T antigen in these tissues at an early age. Surprisingly, the striking thymic hyperplasia has not been observed to progress toward malignancy. The multiple endocrine neoplasias developed later in life and involved the pancreas, pituitary, thyroid, adrenals, and testes. While not preceded by an elevated level of expression of T antigen, once endocrine tumors appeared they quickly progressed toward malignant growth. Although other tissues also exhibited a basal level of expression of the viral oncogene similar to that detected in endocrine tissues, they rarely developed tumors. This transgenic mouse model seems particularly suitable for a molecular understanding of events responsible for certain tissue types being so much more susceptible to neoplastic conversion, with others being so refractory.
ChemInform Abstract: SYNTHESIS OF (.+‐.)‐3,3‐ETHYLENEDIOXY‐14α‐HYDROXY‐5‐PICRASENE‐11,16‐DIONE, A 14αH‐PICRASANE DERIVATIVE (1981)

Abstract Ausgehend vom bicyclischen Hydroxyketon (I) wird in einer vielstufigen Synthese das tetracyclische Tetrahydropyron (II) dargestellt.
DOES EARLY CYSTECTOMY IMPROVE THE SURVIVAL OF PATIENTS WITH HIGH RISK SUPERFICIAL BLADDER TUMORS? (2001)

Earlier cystectomy improves the long-term survival of patients with high risk superficial bladder tumors in whom BCG therapy fails.
Thermal Decomposition of Metal Nitrates in Air and Hydrogen Environments (2003)

The decomposition of metal nitrates in air has been systematically studied by thermogravimetry. Observed temperatures of decomposition (Td) have been inversely correlated to the charge densities (CD) of the metal cations. Due to a back-donation of electronic cloud from the nitrate to an unfilled d-orbital of transition and noble metals, their nitrates generally exhibited lower Tds (<700 K) than those of the base metals (>850 K). The thermal stability/reducibility of metal nitrates in an hydrogen atmosphere has also been studied by temperature-programmed reduction (TPR). Observed reduction temperatures (Tr) for nitrates of the base metals and the noble metals are lower than their Td, i.e., Tr < Td. The lowering of Tr might be attributed to a spillover of hydrogen to a nitrate moiety through heterolytic (ionic) and homolytic (atomic) dissociation of hydrogen on the respective base and noble metals. The stoichiometry of hydrogen consumption, quantitatively measured from TPR, varied with the group of metal cations. According to the stoichiometry, the end product in the TPR reduction was NH3 (NH2/NNO3− ∼4.4) and N2 (NH2/NNO3− ∼2.4) for nitrates of the noble and base metals, respectively. The Trs for nitrates of the transition metals are often ∼20 K higher than their Tds, and the ratio NH2/NNO3− varies widely between 0.7 and 3.2. Their reduction may be triggered by thermal decomposition.
Synthesis and isolation of bromo‐β‐carbolines obtained by bromination of β‐carboline alkaloids (2001)

Abstract β‐Carbolines ( 1–5 ) undergo electrophilic aromatic substitution with N ‐bromosuccinimide under different experimental conditions. Although 6‐bromo‐nor‐harmane ( la ) obtained by bromination of nor‐harmane ( 1 ) was isolated and fully characterized sometime ago, the other bromoderivatives of nor‐harmane ( 1b‐1e ) and harmane ( 2a‐2e ) were partially described as part of the reaction mixtures. The preparation and subsequent isolation, purification and full characterization of 1b, 1c, 1d, 1e, 2a, 2b, 2c, 2d, 2e are reported (mp, R f , 1 H‐nmr, 13 C‐nmr and ms) together with the preparation, isolation and charaterization, for the first time, of the bromoderivatives obtained from harmine ( 3a‐3e ), harmol ( 4a, 4b ) and 7‐acetylharmol ( 5a‐5c ). As brominating reagent N ‐bromosuccinimide and N ‐bromosuccinimide‐silica gel in dichloromethane and in chloroform as well as the β‐carboline ‐ N ‐bomosuccinimide solid mixture have been used and their uses have been compared. Semiempirical AMI and PM3 calculations have been performed in order to predict reactivity in terms of the energies of HOMO, HOMO‐LUMO difference and in terms of the charge density of β‐carbolines ( 1–5 ) and bromo‐β‐carbolines ( 1a‐1e, 2a‐2e, 3a‐3e, 4a, 4b, 5a, 5b and 5c ) (Scheme 1). Theoretical and experimental results are discussed briefly.
Chemical incorporation of 1-methyladenosine into oligonucleotides (2002)

The base moiety of 1-N-methyladenosine can be protected with a chloroacetyl group for incorporation of this modified nucleoside into DNA and RNA. Carefully controlled anhydrous conditions are needed for deprotection of the oligonucleotides.
Influence of hepatitis B virus genotypes on the intra‐ and extracellular expression of viral DNA and antigens†‡ (2006)

Various genotypes of the hepatitis B virus (HBV) induce liver disease of distinct severity, but the underlying virological differences are not well defined. Huh7 cells were transfected with plasmids carrying 1.24-fold the HBV genome of different genotypes/subgenotypes (2 strains each for Aa/A1, Ae/A2, Ba/B2 and D; 3 each for Bj/B1 and C). HBV DNA levels in cell lysates, determined by Southern hybridization, were the highest for C followed by Bj/Ba and D/Ae (P < .01), and the lowest for Aa (P < .01), whereas in culture media, they were the highest for Bj, distantly followed by Ba/C/D and further by Ae/Aa (P < .01). The intracellular expression of core protein was more than 3-fold lower for Ae/Aa than the others. Hepatitis B e antigen (HBeAg) was excreted in a trend similar to that of HBV DNA with smaller differences. Secretion of hepatitis B surface antigen (HBsAg) was most abundant for Ae followed by Aa, Ba, Bj/C and remotely by D, which was consistent with mRNA levels. Cellular stress determined by the reporter assay for Grp78 promoter was higher for C and Ba than the other genotypes/subgenotypes (P < .01). Severe combined immunodeficiency mice transgenic for urokinase-type plasminogen activator (uPA/SCID), with the liver replaced for human hepatocytes, were inoculated with virions passed in mouse and recovered from culture supernatants. HBV DNA levels in their sera were higher for C than Ae by 2 logs during 4-7 weeks after inoculation. In conclusion, virological differences among HBV genotypes were demonstrated both in vitro and in vivo. These differences may influence HBV infections with distinct genotypes in clinical and epidemiological settings.
Yeast SNF2/SWI2, SNF5, and SNF6 proteins function coordinately with the gene-specific transcriptional activators GAL4 and Bicoid. (1992)

The SNF2 (SWI2), SNF5, and SNF6 genes are required for transcription of many diversely regulated genes in Saccharomyces cerevisiae. Previously, we showed that SNF2, SNF5, and SNF6 function interdependently in transcriptional activation, possibly forming a heteromeric complex. Here, we present evidence that SNF6 has a more direct role in stimulating transcription than SNF2 and SNF5. The global effects of mutations in SNF2, SNF5, and SNF6 suggested that these SNF proteins may function coordinately with many gene-specific activators. We show that LexA-GAL4 and LexA-Bicoid fusion proteins are both dependent on SNF2, SNF5, and SNF6 for activation of target genes containing one or multiple lexA operators. The stringency of the requirement for the SNF proteins varies with the activator, the number of binding sites for the activator, and the target promoter. Thus, these SNF proteins appear to represent a class of intermediary proteins that facilitate transcriptional activation by gene-specific regulatory proteins.
A new kinesin tree (2004)

Dagenbach, E. M. and Endow, S. A. (2004). A new kinesin tree. J. Cell Sci.117, 3-7.The neck analysis entries in Table 1 were not aligned correctly in both the print and online versions of this paper. The corrected Table 1 is shown below. We apologise for any inconvenience caused.
Lymphoid Cell Surface Interaction Structures Detected Using Cytolysis‐Inhibiting Monoclonal Antibodies (1982)

We screened monoclonal antibodies obtained by xenogeneic immunization for their capacity to inhibit T cell-mediated cytolysis. These antibodies fell into two classes according to the cell structures they recognized, of 30-35 K and 94-180 K apparent molecular weight, respectively. The main features of these structures and of their interaction with the corresponding antibodies were reviewed. The inhibition of cytolysis by these antibodies was shown to occur mainly at the effector cell level, at the recognition stage of cytolysis, and to depend on the nature of target cells, effector cells, and link between these cells. T cell functions other than cytolysis were also inhibited by some of these antibodies. We considered various possible mechanisms to account for the inhibition of cytolysis by these mAb. We favor an hypothesis based on inhibition by these mAb of lymphoid cell surface interaction structures. This hypothesis was discussed within the general framework of cell interaction structures in immunological and non-immunological experimental systems.
Pathophysiology of insulin resistance in human disease (1995)

The ability of insulin to stimulate glucose uptake varies widely from person to person, and these differences, as well as how the individual attempts to compensate for them, are of fundamental importance in the development and clinical course of what are often designated as diseases of Western civilization. Evidence is presented that non-insulin-dependent diabetes mellitus (NIDDM) results from a failure on the part of pancreatic beta-cells to compensate adequately for the defect in insulin action in insulin-resistant individuals. In addition, a coherent formulation of the physiological changes that lead from the defect in cellular insulin action to the loss in glucose homeostasis is presented. However, the ability to maintain the degree of compensatory hyperinsulinemia necessary to prevent loss of glucose tolerance in insulin-resistant individuals does not represent an unqualified homeostatic victory. In contrast, evidence is presented supporting the view that the combination of insulin resistance and compensatory hyperinsulinemia predisposes to the development of a cluster of abnormalities, including some degree of glucose intolerance, an increase in plasma triglyceride and a decrease in high-density lipoprotein cholesterol concentrations, high blood pressure, hyperuricemia, smaller denser low-density lipoprotein particles, and higher circulating levels of plaminogen activator inhibitor 1. The cluster of changes associated with insulin resistance has been said to comprise syndrome X, and all of the manifestations of syndrome X have been shown to increase risk of coronary heart disease. Thus it is concluded that insulin resistance and its associated abnormalities are of utmost importance in the pathogenesis of NIDDM, hypertension, and coronary heart disease.
Controlling wound bioburden with a novel silver‐containing Hydrofiber® dressing (2004)

Clinicians now recognize that both aerobic and anaerobic microorganisms have the ability to degrade or damage host tissue at a wound site through the production of a variety of enzymes and toxins. Silver-containing dressings offer one method for controlling this polymicrobial wound bioburden, and research efforts are currently ongoing to determine their efficacy against aerobic, anaerobic, and antibiotic-resistant microorganisms. The current study aimed to determine the antimicrobial activity of a new silver-containing Hydrofiber dressing (AQUACEL Ag) on both aerobic and anaerobic microorganisms, using the zone-of-inhibition method. This method provides a measure of the ability of the dressing to make available a sufficient concentration of silver to have an antimicrobial effect. To some extent this test mimics the clinical use of the dressing and predicts its microbicidal activity at the wound-dressing interface. The results show that the silver-containing dressing makes silver available at a dressing-agar interface at a concentration that is effective against a broad range of aerobic, anaerobic, and antibiotic-resistant microorganisms. In the context of wound healing, the results showing antimicrobial activity against antibiotic-resistant microorganisms are particularly important, as the control and eradication of these organisms is a major concern within the health care profession.
Sequence Analysis ofp44Homologs Expressed byAnaplasma phagocytophilumin Infected Ticks Feeding on Naive Hosts and in Mice Infected by Tick Attachment (2004)

The 44-kDa immunodominant outer membrane proteins (P44 proteins) of Anaplasma phagocytophilum are encoded by the p44 polymorphic multigene family. The present study examined p44 expression and analyzed the cDNA sequences of various p44 transcripts from the spleens and blood of mice infected by the bites of ticks infected with the A. phagocytophilum NTN-1 strain or of naturally infected nymphal ticks and in the salivary glands and midgut tissues of these ticks. A total of 300 p44 cDNAs were subjected to sequence analysis. Of these, 40 distinct p44 species were found, and all of these had orthologs in the A. phagocytophilum HZ strain genome that shared 95 to 100% base sequence identity. The number of unique p44 species expressed in mouse blood was greater than that for mouse spleens. Higher numbers of different p44 transcripts were also expressed in the salivary glands of ticks than in the midgut tissues. Variations in the sequences of the same p44 cDNA species within a single A. phagocytophilum strain and among different strains were concentrated in the conserved regions flanking the central hypervariable region of p44 genes. No mosaic sequences derived from two or more p44 species were found within the p44 hypervariable region. The conservation of the hypervariable region of each p44 cDNA species of A. phagocytophilum in naturally infected ticks and in different geographic isolates suggests that each A. phagocytophilum genome carries a set of p44 paralogs to be expressed. Thus, a large but restricted repertoire of p44 hypervariable sequences exists in A. phagocytophilum strains in the Northeastern United States.
Design and fabrication of 50-nm thin-body p-MOSFETs with a SiGe heterostructure channel (2002)

Thin-body p-channel MOS transistors with a SiGe/Si heterostructure channel were fabricated on silicon-on-insulator (SOI) substrates. A novel lateral solid-phase epitaxy process was employed to form the thin-body for the suppression of short-channel effects. A selective silicon implant that breaks up the interfacial oxide was shown to facilitate unilateral crystallization to form a single crystalline channel. Negligible threshold voltage roll-off was observed down to a gate length of 50 nm. The incorporation of Si/sub 0.7/Ge/sub 0.3/ in the channel resulted in a 70% enhancement in the drive current. This is the smallest SiGe heterostructure-channel MOS transistor reported to date. This is also the first demonstration of a thin-body MOS transistor incorporating a SiGe heterostructure channel.
Switchgrass (Panicum virgatum) possesses a divergent family of cinnamoyl CoA reductases with distinct biochemical properties (2009)

The down-regulation of enzymes of the monolignol pathway results in reduced recalcitrance of biomass for lignocellulosic ethanol production. Cinnamoyl CoA reductase (CCR) catalyzes the first step of the phenylpropanoid pathway specifically dedicated to monolignol biosynthesis. However, plants contain multiple CCR-like genes, complicating the selection of lignin-specific targets. This study was undertaken to understand the complexity of the CCR gene family in tetraploid switchgrass (Panicum virgatum) and to determine the biochemical properties of the encoded proteins. Four switchgrass cDNAs (most with multiple variants) encoding putative CCRs were identified by phylogenetic analysis, heterologously expressed in Escherichia coli, and the corresponding enzymes were characterized biochemically. Two cDNAs, PvCCR1 and PvCCR2, encoded enzymes with CCR activity. They are phylogenetically distinct, differentially expressed, and the corresponding enzymes exhibited different biochemical properties with regard to substrate preference. PvCCR1 has higher specific activity and prefers feruloyl CoA as substrate, whereas PvCCR2 prefers caffeoyl and 4-coumaroyl CoAs. Allelic variants of each cDNA were detected, but the two most diverse variants of PvCCR1 encoded enzymes with similar catalytic activity. Based on its properties and expression pattern, PvCCR1 is probably associated with lignin biosynthesis during plant development (and is therefore a target for the engineering of improved biomass), whereas PvCCR2 may function in defense.