gebhart/patrepeval huggingface dataset:
Bicistronic retroviral vector reveals capacity of v-erbA to induce erythroleukemia and to co-operate with v-myb. (1995)

Previous studies have shown that v-erbA and v-myb can induce the proliferation of avian erythroid cells in culture. To study the combined effects of v-erbA and v-myb, the two oncogenes were engineered into a retrovirus bicistronic vector with an internal ribosomal entry site (IRES) or into a vector with a splice acceptor (SPL). This allowed coexpression of the two proteins and a comparison with the same vector containing either v-erbA or v-myb only. Both the erbA IRES and the erbA/myb IRES virus constructs transformed erythroid cells after infection of bone marrow or blastoderm cultures. The erbA/myb IRES virus exhibited a 5-10-fold higher transformed colony forming efficiency than the erbA IRES virus in the blastoderm assay. Surprisingly, when injected into chicken embryos in the presence of helper virus, both viruses induced an erythroleukemia in about half of the animals. In contrast, no leukemia was observed with a myb IRES virus, with spliced vectors containing v-erbA alone or v-erbA in combination with v-myb, nor with erbA IRES and erbA/myb IRES viruses produced in the absence of helper virus. The average latency of leukemia induction was shorter for the erbA/myb IRES virus (3.5 weeks) than for the erbA IRES virus (5 weeks). Nevertheless, for both viruses the leukemic blasts retained full factor dependence for growth. These results show that v-erbA is capable of inducing an erythroleukemia when expressed by a high titer bicistronic retrovirus under conditions of virus spreading and that its in vitro and in vivo transforming potential can be enhanced by v-myb.
Lentiviral vectors for efficient delivery of CD80 and granulocyte-macrophage– colony-stimulating factor in human acute lymphoblastic leukemia and acute myeloid leukemia cells to induce antileukemic immune responses (2000)

Cell vaccines engineered to express immunomodulators have shown feasibility in eliminating leukemia in murine models. Vectors for efficient gene delivery to primary human leukemia cells are required to translate this approach to clinical trials. In this study, second-generation lentiviral vectors derived from human immunodeficiency virus 1 were evaluated, with the cytomegalovirus (CMV) promoter driving expression of granulocyte-macrophage–colony-stimulating factor (GM-CSF) and CD80 in separate vectors or in a bicistronic vector. The vectors were pseudotyped with vesicular stomatitis virus G glycoprotein and concentrated to high titers (108-109 infective particles/mL). Human acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), and chronic myeloid leukemia cell lines transduced with the monocistronic pHR-CD80 vector or the bicistronic pHR-GM/CD vector became 75% to 95% CD80 positive (CD80+). More important, transduction of primary human ALL and AML blasts with high-titer lentiviral vectors was consistently successful (40%-95% CD80+). The average amount of GM-CSF secretion by the leukemia cell lines transduced with the pHR-GM-CSF monocistronic vector was 2182.9 pg/106 cells per 24 hours. Secretion was markedly lower with the bicistronic pHR-GM/CD vector (average, 225.7 pg/106 cells per 24 hours). Lower amounts of CMV-driven messenger RNA were detected with the bicistronic vector, which may account for its poor expression of GM-CSF. Primary ALL cells transduced to express CD80 stimulated T-cell proliferation in an autologous mixed lymphocyte reaction. This stimulation was specifically blocked with monoclonal antibodies reactive against CD80 or by recombinant cytotoxic T-lymphocyte antigen 4–immunoglobulin fusion protein. These results show the feasibility of efficiently transducing primary leukemia cells with lentiviral vectors to express immunomodulators to elicit antileukemic immune responses.
Skeletal troponin C reduces contractile sensitivity to acidosis in cardiac myocytes from transgenic mice. (1993)

Depressed contractile function plays a primary role in the pathophysiology of acute myocardial ischemia. Intracellular acidification is an important factor underlying the inhibition of force production in the ischemic myocardium. The effect of acidosis to depress contractility is markedly greater in cardiac as compared to skeletal muscle; however, the molecular basis of this difference in sensitivity to acidosis is not clearly understood. In this report, we describe transgenic mice that express the fast skeletal isoform of troponin C (sTnC) in cardiac muscle. In permeabilized single cardiac myocytes the shift in the midpoint of the tension-pCa relationship (i.e., pCa50, where pCa is -log[Ca2+]) due to lowering pH from 7.00 to 6.20 was 1.27 +/- 0.03 (n = 7) pCa units in control cardiac TnC (cTnC) expressing myocytes and 0.96 +/- 0.04 (n = 11) pCa unit in transgenic cardiac myocytes (P < 0.001). The effect of pH to alter maximum Ca(2+)-activated tension was unchanged by TnC isoforms in these cardiac myocytes. In a reciprocal experiment, contractile sensitivity to acidosis was increased in fast skeletal muscle fibers following extraction of endogenous sTnC and reconstitution with purified cTnC in vitro. Our findings demonstrate that TnC plays an important role in determining the profound sensitivity of cardiac muscle to acidosis and identify cTnC as a target for therapeutic interventions designed to modify ischemia-induced myocardial contractile dysfunction.
Binding of surfactant protein A to the lipid A moiety of bacterial lipopolysaccharides (1994)

Surfactant protein A (SP-A) enhances the phagocytosis of opsonized and non-opsonized bacteria by alveolar macrophages, but it is not known with which component of the bacterial surface it associates. We investigated the interaction of SP-A with lipopolysaccharides (LPS), which are important biologically active constituents of the outer membranes of Gram-negative bacteria. Flow cytometry was used to study the binding of fluorescein isothiocyanate-labelled SP-A either to LPS of various chain lengths coupled to magnetic beads or to Gram-negative bacteria. The binding of SP-A to LPS-coated beads was saturable, both time- and concentration-dependent, and required both Ca2+ and Na+. SP-A bound to the lipid A moiety of LPS and to LPS from either the Re-mutant of Salmonella minnesota or the J5-mutant of Escherichia coli. In contrast, it did not bind to O111 LPS of E. coli, suggesting that SP-A binds only to rough LPS. The binding of SP-A to LPS was not affected by mannan and heparin or by deglycosylation of the SP-A, indicating that the carbohydrate-binding domain and the carbohydrate moiety of SP-A are not involved in its interaction with LPS. We also observed saturable and concentration-dependent binding of SP-A to the live J5 mutant of whole E. coli, but not to its O111 mutant. In addition, Re LPS aggregated in the presence of SP-A, Ca2+ and Na+. We conclude that SP-A associates with LPS via the lipid A moiety of rough LPS and may be involved in the anti-bacterial defences of the lung.
Computer‐aided mechanogenesis of skeletal muscle organs from single cells in vitro (1991)

Complex mechanical forces generated in the growing embryo play an important role in organogenesis. Computerized mechanical application of similar forces to differentiating skeletal muscle myoblasts in vitro generate three-dimensional artificial muscle organs. These organs contain parallel networks of long unbranched myofibers organized into fascicle-like structures. Tendon development is initiated and the muscles are capable of performing directed, functional work. Kinetically engineered organs provide a new method for studying the growth and development of normal and diseased tissue.
Re-Engineering Adenovirus Vector Systems to Enable High-Throughput Analyses of Gene Function (2008)

With the enhanced capacity of bioinformatics to interrogate extensive banks of sequence data, more efficient technologies are needed to test gene function predictions. Replication-deficient recombinant adenovirus (Ad) vectors are widely used in expression analysis since they provide for extremely efficient expression of transgenes in a wide range of cell types. To facilitate rapid, high-throughput generation of recombinant viruses, we have re-engineered an adenovirus vector (designated AdZ) to allow single-step, directional gene insertion using recombineering technology. Recombineering allows for direct insertion into the Ad vector of PCR products, synthesized sequences, or oligonucleotides encoding shRNAs without requirement for a transfer vector Vectors were optimized for high-throughput applications by making them "self-excising" through incorporating the I-SceI homing endonuclease into the vector removing the need to linearize vectors prior to transfection into packaging cells. AdZ vectors allow genes to be expressed in their native form or with strep, V5, or GFP tags. Insertion of tetracycline operators downstream of the human cytomegalovirus major immediate early (HCMV MIE) promoter permits silencing of transgenes in helper cells expressing the tet repressor thus making the vector compatible with the cloning of toxic gene products. The AdZ vector system is robust, straightforward, and suited to both sporadic and high-throughput applications.
Transcriptional activation of the tumor necrosis factor alpha-inducible zinc finger protein, A20, is mediated by kappa B elements. (1992)

A20 was first identified as a tumor necrosis factor (TNF) primary response transcript encoding a 790-amino acid protein with a unique zinc finger motif. Recently, A20 was shown to protect cells from TNF-induced cytotoxicity in a variety of cell lines. Nuclear run-on studies previously established that TNF activates A20 at the transcriptional level. To further characterize the mechanism by which TNF activates the A20 gene, we have cloned the A20 5'-flanking sequences and identified TNF-responsive elements within the promoter. The transcription initiation site was mapped by both primer extension and S1 nuclease protection experiments to a position 4.2 kilobases (kb) upstream of the initiator methionine; the first and second exon were separated by a 3.9-kb intron. Sequences upstream of the transcription start site were 76% GC-rich and contained six Sp1 binding sites and a TATA-like sequence at -29 but lacked a consensus CCAAT site. Transfection of Jurkat T-cells with an array of A20 promoter CAT constructs showed that two kappa B elements residing at -54 and -66 were required for induction by TNF. Supporting this notion, DNA electrophoretic mobility shift assays using nuclear extracts from unstimulated and TNF-stimulated Jurkat cells demonstrated kappa B-specific binding of a TNF-activated factor to an end-labeled probe containing the two A20 kappa B sequences. Finally, evidence obtained from cotransfection experiments showed that A20 negatively regulated its own expression.
WDM upgrading of an installed submarine optical amplifier system (2001)

This paper describes the WDM upgrading of a submarine optical amplifier system installed for single-channel transmission in commercial use. The key technologies used include 10-Gb/s high-speed forward error correction, preemphasis to overcome the optical passband-width constraint, optimized signal pulse format that leads to partial return-to-zero (PRZ) signaling, and dispersion compensation to suppress the degradation caused by fiber nonlinearity and dispersion. It also reports field experimental results on upgraded system performance. The results confirm that simply upgrading the terminal equipment allows the transmission capacity of a submersed line consisting of submarine repeaters and cables to be flexibly increased from 10 Gb/s to 40 Gb/s per fiber pair.
Rainfall Prediction using Artificial Neural Network on Map-Reduce Framework (2015)

Big data is a celebrated topic in Business as well as research community for several years. With the revolution of Big Data, it is becoming easy and less expensive to store tremendous amount of data for future analysis. Weather data gets accumulated very fast and on a large scale. Thorough analysis and research is required on handling this big data and utilizing it for accurate weather prediction. As deterministic weather forecasting models are usually time consuming, it becomes challenging to efficiently use this large volume of data in hand. Machine learning methods are already proved to be good replacement for traditional deterministic approaches in weather prediction. These algorithms are popular for their scalability and hence more suitable in big data solutions. This paper proposes an approach of processing such Big volume of weather Data using Hadoop. Proposal includes Artificial Neural Network implemented on Map-reduce framework for short term rainfall prediction. Rainfall is predicted one day ahead using temperature and rainfall data of immediately preceding days. Temperature and Rainfall data of India over past 63 years (1951-2013) is used for this study.
Receptor-Mediated Transport of Drugs Across the BBB (2009)

Blood–brain barrier (BBB) limits drug delivery to the brain parenchyma. The ultimate goal of brain drug targeting technology is to deliver therapeutic agents across BBB. Insulin or transferrin as well as other endogenous peptides undergo receptor-mediated transcytosis or transport (RMT) across the BBB in vivo. Certain peptidomimetic monoclonal antibodies (mAb) for insulin receptor or transferrin receptor can also cross the BBB via RMT on the endogenous receptors. These mAb can act as molecular Trojan horses to shuttle into the brain a wide range of therapeutics including recombinant proteins, antibodies, RNA interference drugs, or non-viral gene products. During the last two decades, RMT-based brain drug transport techniques have been developed. This chapter will focus on introducing three major technologies in the arena of RMT brain drug delivery: (1) Avidin–biotin technology; (2) Fusion protein technology; and (3) Trojan horse liposomes (THLs).
Isolation and Sequence of a cDNA Clone for Human Calcineurin B, the Ca 2+ -Binding Subunit of the Ca 2+ /Calmodulin-Stimulated Protein Phosphatase (1989)

We have identified and cloned human cDNA for the Ca2+-binding subunit of calcineurin, the brain isozyme of the Ca2+/calmodulin-stimulated protein phosphatase. The 2.5-kb cDNA has an open reading frame of 510 bp, a leader sequence of at least 500 bp, and a 1,277-bp 3'-noncoding sequence. The deduced sequence of the human protein differs from bovine brain calcineurin B by an additional valine at the carboxyl terminus and substitution of Met-11 and Ser-153 by cysteine. A partial clone of the mouse protein corresponding to amino acids 75-150 was also isolated. This portion of the human and mouse protein sequence is identical, with the DNA sequences showing 94% identity. The respective mRNAs in human and mouse are also of similar size. As was observed with protein levels, mRNA abundance in brain is 20-60 times that found in other tissues with the exception of HeLa cells which, like brain, contain abundant calcineurin B mRNA.
Epstein-Barr virus and human diseases: recent advances in diagnosis. (1988)

Since the discovery of Epstein-Barr virus (EBV) from a cultured Burkitt's lymphoma cell line in 1964, the virus has been associated with Burkitt's lymphoma, nasopharyngeal carcinoma, and infectious mononucleosis. During the recent decade, EBV has been etiologically implicated in a broad spectrum of human diseases. The precise role of this virus in these diseases is not well understood, but clearly, defective immunosurveillance against the virus may permit an uncontrolled proliferation of EBV-infected cells. As a result, a growing number of cases of EBV-associated B-cell proliferative diseases or lymphoma have been noted in patients with primary and acquired immunodeficiencies. These lymphoproliferative diseases and others, such as chronic mononucleosis syndrome, are leading to new areas of investigation which are providing information regarding the pathogenetic mechanisms of EBV-induced diseases. The early accurate diagnosis of EBV infection can be achieved by performing EBV-specific serology, detecting for EBV-determined nuclear antigen in tissues, establishing spontaneous lymphoid cell lines, and using molecular hybridization techniques for demonstrating the presence of viral genome in affected lesions.
ABRA: improved coding indel detection via assembly-based realignment (2014)

ABRA is implemented in a combination of Java and C/C++ and is freely available for download at https://github.com/mozack/abra.
Structure-guided Engineering of Human Thymidine Kinase 2 as a Positron Emission Tomography Reporter Gene for Enhanced Phosphorylation of Non-natural Thymidine Analog Reporter Probe (2011)

Positron emission tomography (PET) reporter gene imaging can be used to non-invasively monitor cell-based therapies. Therapeutic cells engineered to express a PET reporter gene (PRG) specifically accumulate a PET reporter probe (PRP) and can be detected by PET imaging. Expanding the utility of this technology requires the development of new non-immunogenic PRGs. Here we describe a new PRG-PRP system that employs, as the PRG, a mutated form of human thymidine kinase 2 (TK2) and 2'-deoxy-2'-18F-5-methyl-1-β-L-arabinofuranosyluracil (L-18F-FMAU) as the PRP. We identified L-18F-FMAU as a candidate PRP and determined its biodistribution in mice and humans. Using structure-guided enzyme engineering, we generated a TK2 double mutant (TK2-N93D/L109F) that efficiently phosphorylates L-18F-FMAU. The N93D/L109F TK2 mutant has lower activity for the endogenous nucleosides thymidine and deoxycytidine than wild type TK2, and its ectopic expression in therapeutic cells is not expected to alter nucleotide metabolism. Imaging studies in mice indicate that the sensitivity of the new human TK2-N93D/L109F PRG is comparable with that of a widely used PRG based on the herpes simplex virus 1 thymidine kinase. These findings suggest that the TK2-N93D/L109F/L-18F-FMAU PRG-PRP system warrants further evaluation in preclinical and clinical applications of cell-based therapies.
Effects of Chemistries of Trifunctional Amines on Mechanisms of Michael Addition Polymerizations with Diacrylates (2004)

The mechanisms of the Michael addition polymerizations of different trifunctional amines with an equimolar 1,4-butanediol diacrylate (BDA) were investigated by using 1H and 13C NMR to in situ monitor the polymerization processes. The trifunctional amine monomers adopted were 1-(2-aminoethyl)piperazine (AEPZ) and 4-(aminomethyl)piperidine (AMPD) and linear aliphatic amines with different steric hindrance on the 2° amines (original), i.e., N-methylethylenediamine (MEDA), N-ethylethylenediamine (EEDA), and N-hexylethylenediamine (HEDA). For AEPZ, AMPD, and MEDA with low steric hindrance on the 2° amines (original), the reactivity sequence of the three types of amines was 2° amines (original) > 1° amines ≫ 2° amines (formed) and linear poly(amino ester)s were formed via AB-type intermediates due to the 2° amines (formed) being kept out of the reaction. However, AB-type intermediates were only formed from the 2° amines (original) for AEPZ and AMPD, but from both the 2° amines (original) and 1° amines due to their smaller reactivity difference for MEDA. Nevertheless for EEDA and HEDA, the increased steric hindrance on the 2° amines (original) changed the reactivity sequence of the three types of amines to 1° amines > 2° amines (original) > 2° amines (formed) and branched polymers with degrees of branching of ca. 33% and 37%, respectively, were obtained due to all the three types of amines participating in the reaction. The molecular weights, glass transition temperatures, and thermal stability of the linear or branched poly(amino ester)s obtained were characterized by GPC, DSC, and TGA, respectively.
Molecular, Biological, and In Vivo Characterization of the Guinea Pig Cytomegalovirus (CMV) Homologs of the Human CMV Matrix Proteins pp71 (UL82) and pp65 (UL83) (2004)

We recently identified the genes encoding the guinea pig cytomegalovirus (GPCMV) homologs of the upper and lower matrix proteins of human CMV, pp71 (UL82) and pp65 (UL83), which we designated GP82 and GP83, respectively. Transient-expression studies with a GP82 plasmid demonstrated that the encoded protein targets the nucleus and that the infectivity and plaquing efficiency of cotransfected GPCMV viral DNA was enhanced by GP82. The transactivation function of GP82 was not limited to GPCMV, but was also observed for a heterologous virus, herpes simplex virus type 1 (HSV-1). This was confirmed by its ability to complement the growth of an HSV-1 VP16 transactivation-defective mutant virus in an HSV viral DNA cotransfection assay. Study of a GP82 "knockout" virus (and its attendant rescuant), generated on a GPCMV bacterial artificial chromosome construct, confirmed the essential nature of the gene. Conventional homologous recombination was used to generate a GP83 mutant to examine the role of GP83 in the viral life cycle. Comparison of the one-step growth kinetics of the GP83 mutant (vAM409) and wild-type GPCMV indicated that GP83 protein is not required for viral replication in tissue culture. The role of GP83 in vivo was examined by comparing the pathogenesis of wild-type GPCMV, vAM409, and a control virus, vAM403, in guinea pigs. The vAM409 mutant was significantly attenuated for dissemination in immunocompromised strain 2 guinea pigs, suggesting that the GP83 protein is essential for full pathogenicity in vivo.
Purification and Some Properties of a Hitherto‐Unknown Enzyme Reducing the Carbon‐Carbon Double Bond of α,β‐Unsaturated Carboxylate Anions (1979)

2-Enoate-reductase, a previously unknown soluble enzyme is present in Clostridium kluyveri and another Clostridium species growing on (E)-2-butenoate. From the latter the reductase was purified 88-fold with an overall yield up to 74%. The enzyme was pure as judged by polyacrylamide gel electrophoresis with and without sodium dodecyl sulphate as well as by isoelectric focusing. The purification of the enzyme was performed in the presence of (E)-2-methyl-2-butenoate as substrate to keep the enzyme in the oxidized state and under anaerobic conditions. The purification procedure included an ammonium sulphate precipitation, chromatography on DEAE-Sepharose CL-6B, hydroxylapatite and Sepharose CL-6B. The enzyme reduces different alpha,beta-unsaturated carboxylate anions such as (E)-2-butenoate, (E)-2-methyl-2-butenoate, (E)-cinnamate and probably many others in a NADH-dependent reaction to the saturated carboxylate anions. Fumarate, 3-phenyl-2-propinate, 2-enoyl-methyl and CoA esters proved not to be substrates for the purified reductase. NADPH does not act as an electron donor. The enzyme was shown to have a molecular weight of about 450,000 by gel chromatography. It consists of subunits with a molecular weight of 78,000. Per subunit about 1 FAD, 3.5--3.8 atoms of iron and 4.0 labile sulphur atoms have been found indicating a conjugated iron-sulphur flavo-protein. Copper could not be detected. The isoelectric point was 8.4. As shown by absorption spectroscopy the enzyme can be reduced by NADH and reoxidized with dichloroindophenol, hexacyanoferrate III, oxygen and substrates. Addition of 8 mol p-hydroxymercuribenzoate to 1 mol subunit completely destroyed the activity of the reductase. So far no physiological role of the enzyme is known.