gebhart/patrepeval huggingface dataset:
Nucleotide sequence of the hexA gene for DNA mismatch repair in Streptococcus pneumoniae and homology of hexA to mutS of Escherichia coli and Salmonella typhimurium (1988)

The Hex system of heteroduplex DNA base mismatch repair operates in Streptococcus pneumoniae after transformation and replication to correct donor and nascent DNA strands, respectively. A functionally similar system, called Mut, operates in Escherichia coli and Salmonella typhimurium. The nucleotide sequence of a 3.8-kilobase segment from the S. pneumoniae chromosome that includes the 2.7-kilobase hexA gene was determined. An open reading frame that could encode a 17-kilodalton polypeptide (OrfC) was located just upstream of the gene encoding a polypeptide of 95 kilodaltons corresponding to HexA. Shine-Dalgarno sequences and putative promoters were identified upstream of each protein start site. Insertion mutations showed that only HexA functioned in mismatch repair and that the promoter for hexA transcription was located within the OrfC-coding region. The HexA polypeptide contains a consensus sequence for ATP- or GTP-binding sites in proteins. Comparison of the entire HexA protein sequence to that of MutS of S. typhimurium, which was determined by Haber et al. in the accompanying paper (L. T. Haber, P. P. Pang, D. I. Sobell, J. A. Mankovitch, and G. C. Walker, J. Bacteriol. 170:197-202, 1988), showed the proteins to be homologous, inasmuch as 36% of their amino acid residues were identical. This homology indicates that the Hex and Mut systems of mismatch repair evolved from an ancestor common to the gram-positive streptococci and the gram-negative enterobacteria. It is the first direct evidence linking the two systems.
Evolution of Nanoporous Pt–Fe Alloy Nanowires by Dealloying and their Catalytic Property for Oxygen Reduction Reaction (2011)

Abstract The short life and high cost of carbon‐supported Pt nanoparticle catalysts (Pt/C) are two main problems with proton exchange membrane fuel cells. Porous Pt alloy nanowires have more durability and catalytic activity than Pt/C. Dealloying is a facile way to make nanoporous Pt. However, the process of porosity formation is difficult to control. In this paper, electrospinning and chemical dealloying techniques are used to make long, thin and yet nanoporous Pt–Fe alloy nanowires. The evolution of nanoporosity is observed and studied. It is found that non‐uniform composition in the precursor PtFe 5 alloy nanowires helps the formation of nanoporous structure. The overall wire diameter is about 10–20 nm and the ligament diameter only 2–3 nm. These porous long nanowires interweave to form a self‐supporting network with a high specific activity, 2.3 times that of conventional Pt/C catalysts, and also have better durability.
Subband speech coding and matched convolutional channel coding for mobile radio channels (1991)

The effects of digital transmission errors on a family of variable-rate embedded subband speech coders (SBC) are analyzed in detail. It is shown that there is a difference in error sensitivity of four orders of magnitude between the most and the least sensitive bits of the speech coder. As a result, a family of rate-compatible punctured convolutional codes with flexible unequal error protection capabilities have been matched to the speech coder. These codes are optimally decoded with the Viterbi algorithm. Among the results, analysis and informal listening tests show that with a 4-level unequal error protection scheme transmission of 12 kb/s speech is possible with very little degradation in quality over a 16 kb/s channel with an average bit error rate (BER) of 2*10/sup -2/ at a vehicle speed of 60 m.p.h. and with interleaving over two 16 ms speech frames.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Toxin Detection by a Miniaturized in Vitro Protein Expression Array (2005)

A novel concept for toxin detection is presented that is based on the inhibitory effects of certain toxins on protein synthesis. Biological synthesis of proteins is called protein expression, which consists of the steps of DNA transcription and protein translation. In the toxin detection concept, a group of proteins are expressed simultaneously in a device consisting of an array of miniaturized wells. The expression yields of these proteins are inhibited by presence of a toxin. Differential inhibitory effects of each toxin on the expression of proteins in wells result in a response pattern (or signature) of the array device, which can be used as a tool for detection and identification of known and unknown agents. The concept has been demonstrated by in vitro protein expression of three proteins, including green fluorescent protein (GFP), chloramphenicol acetyltransferase (CAT), and luciferase. The production yields of these proteins in a cell-free medium were inhibited differentially by two toxin simulants, tetracycline (TC) and cycloheximide (CH). We confirmed that TC has an inhibitory effect on the production of GFP and CAT in the E. coli expression system whereas CH has a negligible effect. Moreover, the degree of TC's inhibitory effect on GFP is different from that on CAT. We also observed an opposite disparity; TC has a negligible inhibitory effect on the luciferase production in the rabbit reticulocyte expression system, whereas CH has a significant inhibitory effect. In addition, we obtained a response pattern in a 3 x 4 array device; the results suggest the feasibility of toxin detection based on the mechanisms of toxin actions. The device and method are also likely applicable to high-throughput drug screening, evident from the fact that TC is an antibiotic medicine.
Sequence analysis of cDNA's derived from the RNA of Sindbis virions and of defective interfering particles (1982)

Sindbis virus generates defective interfering (DI) particles during serial high-multiplicity passage in cultured cells. These DI particles inhibit the replication of infectious virus and can be an important factor in the establishment and maintenance of persistent infection in BHK cells. In an effort to understand how these DI particles are generated and how they interfere with the replication of standard virus, we performed a partial sequence analysis of the RNA obtained from two independently isolated populations of DI particles and from two Sindbis virus variants and compared these with the RNA of the parental wild-type virus. The 3'-terminal regions of the RNAs were sequenced by the dideoxy chain terminating method. Internal regions of the RNA were examined by restriction endonuclease digestion of cDNA's made to the various RNAs and by direct chemical sequencing of 5' end-labeled restriction fragments from cDNA made to the DI RNAs. One of the variant viruses examined was originally derived from cells persistently infected with Sindbis virus for 16 months and is resistant to interference by the DI strains used. In the 3'-terminal region of the RNA from this variant, only two base changes were found; one of these occurs in the 20-nucleotide 3'-terminal sequence which is highly conserved among alphaviruses. The DI RNA sequences were found to have been produced not by a single deletional event, but by multiple deletion steps combined with sequence rearrangements; all sequences examined are derived from the plus strand of Sindbis virion RNA. Both DI RNAs had at least 50 nucleotides of wild-type sequence conserved at the 3' terminus; in addition, they both contained conserved and perhaps amplified sequences derived from the non-26S region of the genome which may be of importance in their replication and interference ability.
High-Dose Daunorubicin in Older Patients with Acute Myeloid Leukemia (2009)

In patients with AML who are older than 60 years of age, escalation of the dose of daunorubicin to twice the conventional dose, with the entire dose administered in the first induction cycle, effects a more rapid response and a higher response rate than does the conventional dose, without additional toxic effects. (Current Controlled Trials number, ISRCTN77039377; and Netherlands National Trial Register number, NTR212.)
Characterization of human immunodeficiency virus type 1 integrase expressed in Escherichia coli and analysis of variants with amino-terminal mutations (1993)

Replication of a retroviral genome depends upon integration of the viral DNA into a chromosome of the host cell. The integration reaction is mediated by integrase, a viral enzyme. Human immunodeficiency virus type 1 integrase was expressed in Escherichia coli and purified to near homogeneity. Optimum conditions for the integration and 3'-end-processing activities of integrase were characterized by using an in vitro assay with short, double-stranded oligonucleotide substrates. Mutants containing amino acid substitutions within the HHCC region, defined by phylogenetically conserved pairs of histidine and cysteine residues near the N terminus, were constructed and characterized by using three assays: 3'-end processing, integration, and the reverse of the integration reaction (or disintegration). Mutations in the conserved histidine and cysteine residues abolished both integration and processing activities. Weak activity in both assays was retained by two other mutants containing substitutions for less highly conserved amino acids in this region. All mutants retained activity in the disintegration assay, implying that the active site for DNA cleavage-ligation is not located in this domain and that the HHCC region is not the sole DNA-binding domain in the protein. However, the preferential impairment of processing and integration rather than disintegration by mutations in the HHCC region is consistent with a role for this domain in recognizing features of the viral DNA. This hypothesis is supported by the results of disintegration assays performed with altered substrates. The results support a model involving separate viral and target DNA-binding sites on integrase.
A tipping pulse scheme for a rf-SQUID qubit (2001)

We present a technique to control the quantum state of a rf-SQUID qubit. We propose to employ a stream of single flux quantum (SFQ) pulses magnetically coupled to the qubit junction to momentarily suppress its critical current. This effectively lowers the barrier in the double-well rf SQUID potential thereby increasing the tunneling oscillation frequency between the wells. By carefully choosing the time interval between SFQ pulses one may accelerate the interwell tunneling rate. Thus it is possible to place the qubit into a chosen superposition of flux states and then effectively to freeze the qubit state. We present both numerical simulations and analytical time-dependent perturbation theory calculations that demonstrate the technique. Using this strategy one may control the quantum state of the rf SQUID in a way analogous to the /spl pi/ pulses in other qubit schemes.
proTeOn and proTeOff, New Protein Devices That Inducibly Activate Bacterial Gene Expression (2011)

Using an original workflow, we have modeled, constructed, and characterized two new molecular devices that inducibly activate gene expression in Escherichia coli. The devices, prokaryotic-TetOn and prokaryotic-TetOff, were built by fusing an inducible DNA-binding protein domain to a transcription activation domain and constructing a complementary synthetic promoter sequence through which they could control downstream gene expression. In particular, the transactivators were built using variants of the tetracycline repressor, TetR, and the transactivating domain of the LuxR activator. The complementary promoter sequence included TetR's operator, tetO, and elements of the lux promoter. These specific protein domains and their operator sites were chosen as they have been thoroughly studied and well characterized. First, our methodology began with optimizing the geometry of the molecular components using molecular modeling. We did so to achieve an unprecedented combination of controllable and transactivating function in bacterial organisms. The devices were then built to activate the expression of green fluorescent protein. Their unique function was found to be robustly tight and activating many-fold increases of expressed gene levels, as measured by flow cytometry experiments. The devices were further characterized with stochastic kinetic models. The new devices presented herein may become useful additions to the molecular toolboxes used by biologists to control bacterial gene expression. The methodology used may also be a foundation for the design, development, and characterization of a library of such devices and more complex gene regulatory networks.
IB4, a monoclonal antibody against the CD18 leukocyte adhesion protein, reduces intracranial pressure following thromboembolic stroke in the rabbit (1996)

Neutrophil activation and accumulation as a consequence of cerebral ischemia-reperfusion has been suggested to exacerbate tissue injury. The current study is designed to examine the effect of IB4, a monoclonal antibody directed against the neutrophil adhesion protein, CD18, in a rabbit model of thromboembolic stroke. New Zealand rabbits (3-3.5 kg n=8 each group), were given an autologous clot embolus, delivered to the anterior circulation of the brain via the internal carotid artery. Immediately following thromboembolism, the mean arterial pressure in all animals was reduced to 30 mmHg by controlled exsanguination for a period of 45 min. All animals were mechanically ventilated and following parameters were monitored hourly: arterial blood gases, intracranial pressure, regional cerebral blood flow, hematocrit, and core temperature. Rabbits were given either IB4 (1 mg kg(-1)), or vehicle (1 percent albumin, IV) 30 min following the thromboembolic event. The mean arterial pressure of all animals was restored to the baseline value of 50-60 mmHg for the remainder of the 4-h experiment. Following the thromboembolic event, the intracranial pressure rose in both groups, although this was significantly less in the IB4-treated group, with the final values being 195.9 +/- 38.3 vs. 135.5 +/- 26.0 percent of baseline (mean +/- SEM, p < 0.05). However, regional cerebral blood flow and infarct size (TTC staining) were virtually identical in both groups. It is concluded that blockade of the neutrophil adhesion protein, CD18, may contribute to a reduction in the intracranial pressure following cerebral ischemia and reperfusion, providing further evidence that activated neutrophils may contribute to cerebral edema.
Efficacy and Safety of a Specific Inhibitor of the BCR-ABL Tyrosine Kinase in Chronic Myeloid Leukemia (2001)

STI571 is well tolerated and has significant antileukemic activity in patients with CML in whom treatment with interferon alfa had failed. Our results provide evidence of the essential role of BCR-ABL tyrosine kinase activity in CML and demonstrate the potential for the development of anticancer drugs based on the specific molecular abnormality present in a human cancer.
Function and Dynamics of Auxin and Carbohydrates during Earlywood/Latewood Transition in Scots Pine (2001)

In temperate regions the annual pattern of wood development is characterized by the formation of radially narrow and thick walled latewood cells. This takes place at the later part of the growing season when cambial cell division declines. To gain new insight into the regulation of this process, micro-analytical techniques were used to visualize the distribution of indole-3-acetic acid (IAA), soluble carbohydrates, and activities of sucrose (Suc)-metabolizing enzymes across the cambial region tissues in Scots pine (Pinus sylvestris). The total amount of IAA in the cambial region did not change with latewood initiation. But its radial distribution pattern was altered, resulting in an increased concentration in the cambial meristem and its recent derivatives. Thus, initiation of latewood formation and cessation of cambial cell division is not a consequence of decreased IAA concentrations in dividing and expanding cells. Rather, IAA most likely has a role in defining the altered developmental pattern associated with latewood formation. Carbohydrates and enzyme activities showed distinctive radial distribution patterns. Suc peaked in the phloem and decreased sharply to low levels across the cambial zone, whereas fructose and glucose reached their highest levels in the maturing tracheids. Suc synthase was the dominating Suc cleaving enzyme with a peak in the secondary wall-forming tracheids and in the phloem. Soluble acid invertase peaked in dividing and expanding cells. Suc-phosphate synthase had its highest activities in the phloem. Activities of cell wall bound invertase were low. The absence of major seasonal variations indicates that carbohydrate availability is not a trigger for latewood initiation. However, steep concentration gradients of the sugars suggest a role for sugar signaling in vascular development.
Anodic Insulated Tantalum Oxide Electrocardiograph Electrodes (1971)

The use of anodic tantalum oxide films as insulators for insulated electrocardiograph electrodes is described. These films have better chemical and electrical properties than the previously reported aluminum oxide films. The electrodes performed satisfactorily.
Contribution of Residues A54 and L55 of the Human Insulin-like Growth Factor-II (IGF-II) A Domain to Type 2 IGF Receptor Binding Specificity (2001)

The underlying specificity of the interaction between insulin-like growth factor-II (IGF-II) and mammalian Type 2 insulin-like growth factor/cation-independent mannose 6 phosphate receptor (IGF2R) is not understood. We have mutated residues A54 and L55 of IGF-II in the second A domain helix to arginine (found in the corresponding positions of IGF-I) and measured IGF2R binding. There is a 4- and 3.3-fold difference in dissociation constants for A54R IGF-II and L55R IGF-II, respectively, and a 6.6-fold difference for A54R L55R IGF-II compared with IGF-II as measured by BlAcore analysis using purified rat IGF2R. This is also confirmed using cross-linking and soluble rat placental membrane receptor binding assays. Binding to the type I IGF receptor (IGF1R) and IGF binding protein-2 (IGFBP-2) is not altered. We can, therefore, conclude that residues at positions 54 and 55 in IGF-II are important for and equally contribute to IGF2R binding.
Ganancia de peso de terneros al pie de la madre y su posterior evolución en rodeos de cría de la zona semiárida (1989)

Entre noviembre de 1981 y Julio de 1982 se realizó el seguimiento de la evolución del peso de los terneros de cuatro rodeos de cría durante la lactancia y los primeros meses postdestete para obtener información básica de pesadas de terneros al pie de la madre en rodeos de cría de la Zona semiárida, analizar su evolución y algunos de los factores que influyen sobre el peso del ternero en el otoño. El trabajo se efectuó en establecimientos pertenecientes al grupo CREA Santa Rosa y a la Facultad de Agronomía de la Universidad Nacional de La Pampa (Unidad experimental de producción bovina). Se trabajó sobre un total de 1034 terneros machos y hembras de razas Aberdeen Angus y sus cruzas con Hereford y Santa Gertrudis. Durante el período analizado los terneros siempre ganaron peso, con una ganancia diaria promedio acumulada de 600 gr/día hasta los 10 meses de edad, en todos los campos las ganancias diarias de peso en primavera fueron mayores que las de verano y otoño, coincidiendo las primeras con un buen estado de la vaca lactante y una buena producción forrajera. Se analizan los resultados obtenidos en cada estación y las diferencias entre sexo, cruzas y sistemas de manejo. Futuros trabajos deberían estar orientados a mejorar la ganancia de peso de los terneros en la etapa de recría (desde los 4 a los 12 meses de edad), que coinciden con los meses que van desde enero hasta agosto y donde es máximo el potencial de crecimiento. Dirección: J. P. Torroba, Prof. Cátedra de Zootecnia I
Overexpression of RhoA enhances peritoneal dissemination: RhoA suppression with Lovastatin may be useful for ovarian cancer (2008)

Small guanosine triphosphatase RhoA has been known to re‐organize cytoskeletons and regulate cell migration. The present authors have previously reported that expression of RhoA is significantly increased in advanced ovarian carcinomas and also in the peritoneal disseminated lesions. The present study investigated whether overexpression of RhoA could alter the progressive behavior of ovarian cancer cells. The effect of various Rho inhibitors on the biological behavior of ovarian cancer cells in vitro and in vivo was also examined. A stable RhoA‐transfectant of an ovarian cancer cell line SKOV3 was generated and examined in vitro for alterations of proliferative activity and invasiveness, and also in the nude mice model for peritoneal dissemination. In addition, the effect of a specific Rho inhibitor (C3 exoenzyme), Rho kinase inhibitor (Y27632) and hydroxymethylglutaryl coenzyme A (HMG–CoA) reductase inhibitor (Lovastatin and Pravastatin) were studied in vitro and in vivo . Forced overexpression of RhoA did not alter proliferative activity but significantly increased the invasiveness in vitro , which was suppressed by addition of C3 exoenzyme, Y27834, Lovastatin and Pravastatin. In the nude mice model, the frequency of dissemination and the number of disseminated lesions were significantly increased in the RhoA transfectant than in the control. In addition, oral administration of Lovastatin significantly decreased the number of metastatic sites compared with the control. These findings suggest that upregulation and/or activation of RhoA play an important role in the peritoneal dissemination of ovarian carcinoma, and that Lovastatin might be a candidate for the possible, novel treatment for ovarian carcinoma patients with peritoneal dissemination. ( Cancer Sci 2008; 99: 2532–2539)
IL-9 as a mediator of Th17-driven inflammatory disease (2009)

We report that like other T cells cultured in the presence of transforming growth factor (TGF) beta, Th17 cells also produce interleukin (IL) 9. Th17 cells generated in vitro with IL-6 and TGF-beta as well as purified ex vivo Th17 cells both produced IL-9. To determine if IL-9 has functional consequences in Th17-mediated inflammatory disease, we evaluated the role of IL-9 in the development and progression of experimental autoimmune encephalomyelitis, a mouse model of multiple sclerosis. The data show that IL-9 neutralization and IL-9 receptor deficiency attenuates disease, and this correlates with decreases in Th17 cells and IL-6-producing macrophages in the central nervous system, as well as mast cell numbers in the regional lymph nodes. Collectively, these data implicate IL-9 as a Th17-derived cytokine that can contribute to inflammatory disease.
Expression of sulfated glycoprotein 2 is associated with carcinogenesis induced by N-nitroso-N-methylurea in rat prostate and seminal vesicle. (1993)

To understand the molecular mechanism of carcinogenesis in androgen-dependent tumors, we have searched for new markers which are associated with this process. In normal rat prostate and seminal vesicle, sulfated glycoprotein 2 (SGP-2) messenger RNA is barely detectable. However, we have found high levels of SGP-2 expression in the epithelial component of carcinomas of the prostate and seminal vesicle after initiation with N-nitroso-N-methylurea and promotion with testosterone propionate. We have also observed induction of SGP-2 expression in epithelial cells at early stages in carcinogenesis when cytologically malignant cells first begin to appear. SGP-2 has been reported previously to be associated with a variety of models of programmed cell death (apoptosis), including the prostate following castration. Our present findings provide a novel marker for carcinogenesis in the rat prostate and seminal vesicle.