gebhart/patrepeval huggingface dataset:
Identification of the thymidine kinase gene of infectious laryngotracheitis virus. (1992)

An an initial step in the development of a recombinant poultry infectious laryngotracheitis virus (ILTV) vaccine, we report on the identification, cloning, and sequencing of a thymidine kinase (tk) gene from a virulent U.S. field isolate of ILTV. Degenerate oligonucleotide primers for the consensus nucleotide (ATP) binding site and the nucleoside (thymidine) binding site of other herpesvirus tk genes were used in the polymerase chain reaction (PCR) to amplify a fragment of ILTV DNA. The 344-base-pair (bp) amplified fragment was cloned into plasmid pKSII and used in Southern hybridizations to locate the ILTV tk gene on a 2.4-kb HindIII fragment. Upon cloning and sequencing this fragment, a 1089-bp open reading frame was identified, which is predicted to encode a protein demonstrating 27.9% amino acid homology to the herpes simplex virus type 1 (HSV-1) thymidine kinase protein. Analysis of the sequence revealed one region of difference from that reported for the Thorne strain of ILTV. In addition, the portion of the TK protein corresponding to the nucleotide binding domain is highly conserved among the avian herpesviruses.
E-bra with nanosensors, smart electronics and smart phone communication network for heart rate monitoring (2011)

Heart related ailments have been a major cause for deaths in both men and women in United States. Since 1985, more women than men have died due to cardiac or cardiovascular ailments for reasons that are not well understood as yet. Lack of a deterministic understanding of this phenomenon makes continuous real time monitoring of cardiovascular health the best approach for both early detection of pathophysiological changes and events indicative of chronic cardiovascular diseases in women. This approach requires sensor systems to be seamlessly mounted on day to day clothing for women. With this application in focus, this paper describes a e-bra platform for sensors towards heart rate monitoring. The sensors, nanomaterial or textile based dry electrodes, capture the heart activity signals in form Electrocardiograph (ECG) and relay it to a compact textile mountable amplifier-wireless transmitter module for relay to a smart phone. The ECG signal, acquired on the smart phone, can be transmitted to the cyber space for post processing. As an example, the paper discusses the heart rate estimation and heart rate variability. The data flow from sensor to smart phone to server (cyber infrastructure) has been discussed. The cyber infrastructure based signal post processing offers an opportunity for automated emergency response that can be initiated from the server or the smartphone itself. Detailed protocols for both the scenarios have been presented and their relevance to the present emergency healthcare response system has been discussed.
Castrated Men Exhibit Bone Loss: Effect of Calcitonin Treatment on Biochemical Indices of Bone Remodeling* (1989)

To test the hypothesis that the reduction in gonadal function can lead to bone mass loss, a group of 12 men who had undergone bilateral orchidectomy at the age of 28.2 +/- 6.8 yr was evaluated. A progressive loss of the lumbar bone density was observed as a function of time after orchidectomy. Both the biochemical indices of bone resorption (urinary hydroxyproline/creatinine ratio and plasma tartrate-resistant acid phosphatase) and bone formation (serum osteocalcin and bone isoenzyme of alkaline phosphatase) were significantly increased in the patients compared with healthy controls. A positive correlation was found between urinary hydroxyproline excretion and percent change in spinal bone mineral density per yr. Because of this increase in the biochemically indicated bone resorption, nine of the patients were studied again after 1-3 yr and were thereafter treated with intranasal calcitonin. Urinary hydroxyproline excretion normalized after 3 months of treatment, and a significant decrease, but not to normal levels, was also observed in the mean values for the other biochemical indices of bone remodeling. Thus, testosterone deficiency, like estrogen deficiency, is associated with accelerated bone loss. The increase in osteoresorption was partially corrected by calcitonin treatment.
Biopharmaceuticals from Plants: A Multitude of Options for Posttranslational Modifications (2008)

In 1982 the first recombinant therapeutic, human insulin, was introduced into the market and started a new branch of pharmaceutical development, manufacture, and therapy options. To date, more than 130 recombinant protein therapeutics have been approved by the US Food and Drug Administration (FDA) and many more are being developed world wide. With the increasing number of protein therapeutics the number of potential production organisms is also expanding, and posttranslational modification of proteins has become a topic of special focus. One major difference between small-molecule drugs and protein therapeutics is that the latter are reliant on a host organism for their production and this can have a large influence on the final structure and can ultimately affect the pharmacokinetics, immunogenicity, and the function of the protein depending on the production process. Plants can be efficiently used as production systems for recombinant proteins thereby offering a variety of options for transgene targeting and modification. This review is intended to give an overview about the potential of plants to serve as a production system for therapeutic and prophylactic biopharmaceuticals with respect to posttranslational modifications.
Comprehensive organic functional group transformations II (2005)

Volume 1 - synthesis - carbon with no attached heteroatoms volume 2 - synthesis - carbon with one heteroatom attached by a single bond volume 3 - synthesis - carbon with one heteroatom attached by a multiple bond volume 4 - synthesis - carbon with two heteroatoms, each attached by a single bond volume 5 - synthesis - carbon with two attached heteroam with at least one carbon-to-heteroatom multiple link volume 6 - synthesis - carbon with three or four attached heteroatoms volume 7 - indices.
A non-volatile run-time FPGA using thermally assisted switching MRAMS (2008)

This paper describes the integration of a thermally assisted switching magnetic random access memory (TAS-MRAM) in FPGA design. The non-volatility of the latter is achieved through the use of magnetic tunneling junctions (MTJ) in the MRAM cell. A thermally assisted switching scheme is used to write data in the MTJ device, which helps to reduce power consumption during write operation in comparison to the writing scheme in classical MTJ device. Plus, the non-volatility of such a design should reduce both power consumption and configuration time required at each power up of the circuit in comparison to classical SRAM based FPGAs. A real time reconfigurable (RTR) micro-FPGA using TAS-MRAM allows dynamic reconfiguration mechanisms, while featuring simple design architecture.
Magnitude and variation of ratio of total body potassium to fat-free mass: a cellular level modeling study (2001)

Potassium is an essential element of living organisms that is found almost exclusively in the intracellular fluid compartment. The assumed constant ratio of total body potassium (TBK) to fat-free mass (FFM) is a cornerstone of the TBK method of estimating total body fat. Although the TBK-to-FFM (TBK/FFM) ratio has been assumed constant, a large range of individual and group values is recognized. The purpose of the present study was to undertake a comprehensive analysis of biological factors that cause variation in the TBK/FFM ratio. A theoretical TBK/FFM model was developed on the cellular body composition level. This physiological model includes six factors that combine to produce the observed TBK/FFM ratio. The ratio magnitude and range, as well as the differences in the TBK/FFM ratio between men and women and variation with growth, were examined with the proposed model. The ratio of extracellular water to intracellular water (E/I) is the major factor leading to between-individual variation in the TBK/FFM ratio. The present study provides a conceptual framework for examining the separate TBK/FFM determinants and suggests important limitations of the TBK/FFM method used in estimating total body fat in humans and other mammals.
Enhanced Cellulose Degradation Using Cellulase-Nanosphere Complexes (2012)

Enzyme catalyzed conversion of plant biomass to sugars is an inherently inefficient process, and one of the major factors limiting economical biofuel production. This is due to the physical barrier presented by polymers in plant cell walls, including semi-crystalline cellulose, to soluble enzyme accessibility. In contrast to the enzymes currently used in industry, bacterial cellulosomes organize cellulases and other proteins in a scaffold structure, and are highly efficient in degrading cellulose. To mimic this clustered assembly of enzymes, we conjugated cellulase obtained from Trichoderma viride to polystyrene nanospheres (cellulase:NS) and tested the hydrolytic activity of this complex on cellulose substrates from purified and natural sources. Cellulase:NS and free cellulase were equally active on soluble carboxymethyl cellulose (CMC); however, the complexed enzyme displayed a higher affinity in its action on microcrystalline cellulose. Similarly, we found that the cellulase:NS complex was more efficient in degrading natural cellulose structures in the thickened walls of cultured wood cells. These results suggest that nanoparticle-bound enzymes can improve catalytic efficiency on physically intractable substrates. We discuss the potential for further enhancement of cellulose degradation by physically clustering combinations of different glycosyl hydrolase enzymes, and applications for using cellulase:NS complexes in biofuel production.
Model Based Test Generation for Processor Verification (1994)

A few simple Expert-System techniques have been invaluable in developing a new test program generator for design verification of hardware processors. The new generator uses a formal declarative model of the processor architecture; it allows generation of test programs for a variety of processors without duplication of effort.
The National Ignition Facility - applications for inertial fusion energy and high-energy-density science (1999)

Over the past several decades, significant and steady progress has been made in the development of fusion energy and its associated technology and in the understanding of the physics of high-temperature plasmas. While the demonstration of net fusion energy (fusion energy production exceeding that required to heat and confine the plasma) remains a task for the next millennia and while challenges remain, this progress has significantly increased confidence that the ultimate goal of societally acceptable (e.g. cost, safety, environmental considerations including waste disposal) central power production can be achieved. This progress has been shared by the two principal approaches to controlled thermonuclear fusion--magnetic confinement (MFE) and inertial confinement (ICF). ICF, the focus of this article, is complementary and symbiotic to MFE. As shown, ICF invokes spherical implosion of the fuel to achieve high density, pressures, and temperatures, inertially confining the plasma for times sufficient long (t {approx} 10{sup -10} sec) that {approx} 30% of the fuel undergoes thermonuclear fusion.
The Promoter of the Prostate-Specific Antigen Gene Contains a Functional Androgen Responsive Element (1991)

Expression of prostate-specific antigen (PA) mRNA was tested at various time periods after incubation of the human prostate tumor cell line LNCaP with the synthetic androgen R1881. Androgen-stimulated expression was observed within 6 h after addition of R1881 to the cells. Run-on experiments with nuclei isolated from LNCaP cells showed that expression of the PA gene could be regulated by R1881 on the level of transcription. DNase I footprints of the promoter region of the PA gene (-320 to +12) with nuclear protein extracts from LNCaP cells showed at least four protected regions. The protected areas include the TATA-box, a GC-box sequence, and a sequence AGAACAgcaAGTGCT at position -170 to -156, which closely resembles the reverse complement of the consensus sequence GGTACAnnnTGTTCT for binding of the glucocorticoid receptor and the progesterone receptor. Fragments of the PA promoter region were cloned in front of the chloramphenicol acetyltransferase (CAT) reporter gene and cotransfected with an androgen receptor expression plasmid into COS cells in a transient expression assay. CAT activity of COS cells grown in the presence of 1 nM R1881 was compared to untreated controls. A 110-fold induction of CAT activity was found if a -1600 to +12 PA promoter fragment was used in the construct. By further deletion mapping of the PA promoter a minimal region (-320 to -155) was identified as being essential for androgen-regulated gene expression. Mutation of the sequence AGAACAgcaAGTGCT (at -170 to -156) to AAAAAAgcaAGTGCT almost completely abolished androgen inducibility of the reporter gene constructs. One or more copies of the sequence AGAACAgcaAGTGCT cloned in front of a thymidine kinase promoter-CAT reporter gene confers androgen regulation to the reporter gene. These findings provide strong evidence for transcription regulation of the PA gene by androgens via the sequence AGAACAgcaAGTGCT. Interestingly, in addition to the AGAACAgcaAGTGCT element, an upstream region (-539 to -320) is needed for optimal androgen inducibility of the PA promoter.
Liposome-mediated in vivo gene transfer of antisense K-ras construct inhibits pancreatic tumor dissemination in the murine peritoneal cavity. (1995)

K-ras point mutation occurs at a characteristically high incidence in human pancreatic cancer. Plasmids expressing antisense (AS), AS-K-ras-LNSX or sense K-ras gene fragment, were first transduced into three human pancreatic cancer cell lines (AsPC-1, MIAPaCa-2, and BxPC-3) by liposome-mediated transfection. A stable expression of antisense or sense K-ras RNA was detected by Northern blot analysis, and Western blot analysis confirmed a reduction of up to 20% of K-ras-specific p21 protein in AsPC-1 cells transduced with AS-K-ras-LNSX. The growth of pancreatic cancer cells with K-ras point mutations (AsPC-1 and MIAPaCa-2) was significantly suppressed after transduction of AS-K-ras-LNSX, although the effect of antisense construct was not found in cells with a wild-type K-ras gene (BxPC-3). Next, to test the efficacy in vivo, AsPC-1 cells were inoculated into the intraperitoneal cavity of nude mice, and 3 days later, the AS-K-ras-LNSX:liposome complex was injected i.p. 3 times. Twenty-eight days after tumor cell inoculation, 9 of 10 control mice developed peritoneal dissemination and/or solid tumors on the pancreas, whereas only 2 of 12 mice treated with AS-K-ras-LNSX showed any evidence of tumors. Although PCR analysis indicated that the injected DNA was delivered to various organs except for the brain, treatment-related toxicity was not observed. This study shows that the liposome-mediated in vivo gene transfer of antisense K-ras construct may be a useful therapeutic strategy for pancreatic cancer.
A neutralizable epitope common to the envelope glycoproteins of ecotropic, polytropic, xenotropic, and amphotropic murine leukemia viruses (1990)

An epitope common to all classes of murine leukemia viruses (MuLVs) was detected by reactivity of MuLVs with a rat monoclonal antibody (MAb) termed 83A25. The antibody is of the immunoglobulin G2a isotype and was derived after fusion of NS-1 myeloma cells with spleen cells from a Fischer rat immunized with a Friend polytropic MuLV. The antibody reacted with nearly all members of the ecotropic, polytropic, xenotropic, and amphotropic classes of MuLVs. Unreactive viruses were limited to the Friend ecotropic MuLV, Rauscher MuLV, and certain recombinant derivatives of Friend ecotropic MuLV. The presence of an epitope common to nearly all MuLVs facilitated a direct quantitative focal immunofluorescence assay for MuLVs, including the amphotropic MuLVs for which no direct assay has been previously available. Previously described MAbs which react with all classes of MuLVs have been limited to those which react with virion core or transmembrane proteins. In contrast, protein immunoblot and immunoprecipitation analyses established that the epitope reactive with MAb 83A25 resides in the envelope glycoproteins of the viruses. Structural comparisons of reactive and nonreactive Friend polytropic viruses localized the epitope near the carboxyl terminus of the glycoprotein. The epitope served as a target for neutralization of all classes of MuLV with MAb 83A25. The efficiency of neutralization varied with different MuLV isolates but did not correlate with MuLV interference groups.
Metal Films Prepared by Stepwise Assembly. 2. Construction and Characterization of Colloidal Au and Ag Multilayers (2000)

This manuscript describes the stepwise, ligand-directed assembly, characterization, and prospective applications of three-dimensional Au and Ag nanoparticle, multlilayered films. Films were prepared by successive treatments of a Au nanoparticle monolayer with a bifunctional cross-linker and colloidal Au or Ag solutions. Changes in film electrical and optical properties are reported for a series of bifunctional cross-linkers of varying molecular lengths. Interestingly, these films exhibit Beer's law behavior despite the presence of strong interparticle optical coupling. Multilayer films with greater than six exposures to 2-mercaptoethylamine and Au colloid were highly conductive and resembled bulk Au in appearance. In contrast, films of similar particle coverage generated using a longer cross-linker (1,6-hexanedithiol) exhibited higher transmission in the near-infrared region and exhibited a reduced conductivity. Measurement of the multilayer morphology with atomic force microscopy , electrostatic force microscopy, and field emission scanning electron microscopy revealed a porous, discontinuous morphology composed of large, continuous regions of aggregated nanoparticles. This, in turn, results in a surface roughness contribution to surface plasmon scattering and surface-enhanced Raman scattering observed for Au, Au/Ag, and Ag colloid multilayers. Particulate multilayer films made using horseradish peroxidase as a cross-linker remained enzymatically active, even beneath three layers of colloidal Au. Multilayers could also be prepared on surfaces patterned by microcontact printing. These data show how Au colloid multilayers grown in solution are a viable alternative to evaporated metal films for a number of applications.
Thrombin-activatable fibrinolysis inhibitor and the risk for recurrent venous thromboembolism (2004)

The impact of fibrinolysis for predicting the risk for recurrent venous thromboembolism (VTE) is low. We prospectively followed up 600 patients with a first VTE and evaluated the thrombin-activatable fibrinolysis inhibitor (TAFI) as a risk factor for recurrence. A high TAFI level (75th or higher percentile in thrombosis patients) was associated with a 2-fold higher risk for recurrence compared with lower levels. The probability of recurrence 2 years after anticoagulation was 14.5% (95% confidence interval [CI], 8.6-20.4) among patients with high TAFI levels and 6.8% (95% CI, 4.3-9.3) among patients with lower levels (P =.006). Our data also support the concept of a linkage between fibrinolysis and the coagulation system. Patients with high TAFI levels had significantly higher levels of factors XI, VIII, and IX, and a high risk of recurrence was seen among patients with high TAFI levels and high levels of one of these factors. The relative risk (RR) for recurrence was highest among patients with high TAFI and high factor XI (RR, 2.9; 95% CI, 1.3-6.9), high factor VIII (RR, 6.5; 95% CI, 2.9-14.8), or high factor IX (RR, 2.0; 95% CI, 1.0-3.9) levels compared with patients with low levels of TAFI and one of these factors.
Gaming language Getting a handle on slots (1995)

The gaming industry has its own colorful, often wry, and elusive vocabulary. Here's a primer focusing on one segment—slot machines.
Serological response to Chlamydia pneumoniae in adults with coronary arterial fatty streaks and fibrolipid plaques (1993)

The antigen-specific serological response to Chlamydia pneumoniae was studied in 45 adults with coronary artery atherosclerosis and compared with that in 40 adults with acute respiratory infection. C. pneumoniae antigen and DNA were detected in lesions more frequently in patients with low immunoglobulin G titers against C. pneumoniae than in those with high immunoglobulin G titers. Reactivities with the 42-kDa (46%) and 52-kDa (31%) proteins were observed more frequently in sera from seropositive individuals with atherosclerosis than in sera from patients with acute respiratory infection. Antibodies against the C. pneumoniae-specific 42- and/or 52-kDa protein may be a marker for chronic C. pneumoniae infection.
Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing (2010)

With this highly sensitive UDPS protocol preexisting drug resistance was infrequently observed; only M184I, T215A and T215I were detected at very low levels. Similarly, drug resistant variants in plasma quickly decreased to undetectable levels after treatment interruption. The study gives important insights into the dynamics of the HIV-1 quasispecies and is of relevance for future research and clinical use of the UDPS technology.
Retrons and their applications in genome engineering (2019)

Precision genome editing technologies have transformed modern biology. These technologies have arisen from the redirection of natural biological machinery, such as bacteriophage lambda proteins for recombineering and CRISPR nucleases for eliciting site-specific double-strand breaks. Less well-known is a widely distributed class of bacterial retroelements, retrons, that employ specialized reverse transcriptases to produce noncoding intracellular DNAs. Retrons' natural function and mechanism of genetic transmission have remained enigmatic. However, recent studies have harnessed their ability to produce DNA in situ for genome editing and evolution. This review describes retron biology and function in both natural and synthetic contexts. We also highlight areas that require further study to advance retron-based precision genome editing platforms.
Transgenic expression of CCL2 in the central nervous system prevents experimental autoimmune encephalomyelitis (2004)

CC chemokine ligand 2 (CCL2)/monocyte chemotactic protein-1, a member of the CC chemokine family, is a chemoattractant for monocytes and T cells through interaction with its receptor CCR2. In the present study, we examined a T helper cell type 1 (Th1)-dependent disease, proteolipid protein-induced experimental autoimmune encephalomyelitis, in a transgenic mouse line that constitutively expressed low levels of CCL2 in the central nervous system (CNS) under control of the astrocyte-specific glial fibrillary acidic protein promoter. CCL2 transgenic mice developed significantly milder clinical disease than littermate controls. As determined by flow cytometry, mononuclear cell infiltrates in the CNS tissues of CCL2 transgenic and littermate-control mice contained equal numbers of CD4+ and CD8+ T cells, and the CCL2 transgenic mice showed an enhanced number of CNS-infiltrating monocytes. CNS antigen-specific T cells from CCL2 transgenic mice produced markedly less interferon-gamma. Overexpression of CCL2 in the CNS resulted in decreased interleukin-12 receptor expression by antigen-specific T cells. Collectively, these results indicate that sustained, tissue-specific expression of CCL2 in vivo down-regulates the Th1 autoimmune response, culminating in milder clinical disease.