gebhart/patrepeval huggingface dataset:
Genome and proteome of Listeria monocytogenes phage PSA: an unusual case for programmed + 1 translational frameshifting in structural protein synthesis (2003)

PSA is a temperate phage isolated from Listeria monocytogenes strain Scott A. We report its complete nucleotide sequence, which consists of a linear 37 618 bp DNA featuring invariable, 3'-protruding single stranded (cohesive) ends of 10 nucleotides. The physical characteristics were confirmed by partial denaturation mapping and electron microscopy of DNA molecules. Fifty-seven open reading frames were identified on the PSA genome, which are apparently organized into three major transcriptional units, in a life cycle-specific order. Functional assignments could be made to 33 gene products, including structural proteins, lysis components, DNA packaging proteins, lysogeny control functions and replication proteins. Bioinformatics demonstrated relatedness of PSA to phages infecting lactic acid bacteria and other low G + C Gram-positives, but revealed only few similarities to Listeria phage A118. Virion proteins were analysed by amino acid sequencing and mass spectrometry, which enabled identification of major capsid and tail proteins, a tape measure and a putative portal. These analyses also revealed an unusual form of translational frameshifting, which occurs during decoding of the mRNAs specifying the two major structural proteins. Frameshifting yields different length forms of Cps (gp5) and Tsh (gp10), featuring identical N-termini but different C-termini. Matrix-assisted laser-desorption ionization mass spectrometry (MALDI-MS) and electrospray ionization mass spectrometry (ESI-MS) of tryptic peptide fragments was used to identify the modified C-termini of the longer protein species, by demonstration of specific sequences resulting from + 1 programmed translational frameshifting. A slippery sequence with overlapping proline codons near the 3' ends of both genes apparently redirects the ribosomes and initiates the recoding event. Two different cis-acting factors, a shifty stop and a pseudoknot, presumably stimulate frameshifting efficiency. PSA represents the first case of + 1 frameshifting among dsDNA phages, and appears to be the first example of a virus utilizing a 3' pseudoknot to stimulate such an event.
Gas Vesicle Genes Identified in Bacillus megaterium and Functional Expression in Escherichia coli (1998)

Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in liquid to access oxygen and/or light. In halobacteria, gas vesicle production is encoded in a 9-kb cluster of 14 genes (4 of known function). In cyanobacteria, the number of genes involved has not been determined. We now report the cloning and sequence analysis of an 8,142-bp cluster of 15 putative gas vesicle genes (gvp) from Bacillus megaterium VT1660 and their functional expression in Escherichia coli. Evidence includes homologies by sequence analysis to known gas vesicle genes, the buoyancy phenotype of E. coli strains that carry this gvp gene cluster, the presence of pressure-sensitive, refractile bodies in phase-contrast microscopy, structural details in phase-contrast microscopy, structural details in direct interference-contrast microscopy, and shape and size revealed by transmission electron microscopy. In B. megaterium, the gvp region carries a cluster of 15 putative genes arranged in one orientation; they are open reading frame 1 and gvpA, -P, -Q, -B, -R, -N, -F, -G, -L, -S, -K, -J, -T, and -U, of which the last 11 genes, in a 5.7-kb gene cluster, are the maximum required for gas vesicle synthesis and function in E. coli. To our knowledge, this is the first example of a functional gas vesicle gene cluster in nonaquatic bacteria and the first example of the interspecies transfer of genes resulting in the synthesis of a functional organelle.
The lgk 3'-enhancer triggers gene expression in early B lymphocytes but its activity in enhanced on B cell activation (1996)

Ig kappa gene expression is controlled by two enhancers, one located within the major intron (Ei) and the other located downstream of C kappa (E3'). Whereas loss of E3' has previously been shown to diminish kappa expression, we show here that a rearranged kappa transgene lacking Ei is well expressed, even at the pre-B cell stage. This suggests that E3' alone might be sufficient to give properly regulated transcription throughout B cell development. Indeed, we show that a transgene composed of a beta-globin reporter linked to E3' is expressed in a B cell-specific manner, becoming activated at the late pro-B to pre-B cell stage but with dramatically enhanced activity on B cell activation. Thus, E3' becomes active as a transcription enhancer at the stage when V kappa-J kappa rearrangement is being initiated and is sufficient to yield an expression pattern in a linked reporter gene similar to that of fully rearranged kappa genes.
Evaluation of SiC VJFET Devices for Scalable Solid-State Circuit Breakers (2008)

Abstract : Power electronic converters functioning as components in high power systems, such as those of hybrid military ground vehicles require fast fault isolation, and in most cases benefit additionally from bi-directional fault isolation. To prevent converter damage or failure, fault current interrupt speeds in the hundreds of microseconds to few millisecond range are necessary. Presently used mechanical contractors do not provide adequate actuation speeds, and suffer severe degradation during repeated fault isolation. Instead, it is desired to use a large array of semiconductor devices having a collectively low conduction loss to provide large current handling capability and fast transition speed for current interruption. This report discusses the use of SiC MOSFETs and the evaluation of SiC JFETs for a bi-directional solid-state circuit breaker application.
Marginal zone B-cell lymphomas of different sites share similar cytogenetic and morphologic features [see comments] (1996)

Clinical, histologic, cytogenetic, and molecular genetic data of 31 patients with extranodal, nodal, and splenic marginal zone B-cell lymphoma (MZBCL) are presented. Despite these variable clinical manifestations, a similar spectrum of morphologic features as well as distinctive immunophenotypic findings were noted. In all cases, a monotypic B-cell proliferation consistently negative for CD5, CD10, and CD23 was found expanding the marginal zone of the B follicle with and without colonization of the follicle centers. Clonal chromosomal abnormalities were detected in 23 of the 31 patients. Recurrent aberrations included whole or partial trisomy 3 (18 cases), trisomy 18 (9 cases), and structural rearrangements of chromosome 1 with breakpoints in 1q21 (9 cases) or 1p34 (6 cases), all of which were seen in extranodal, nodal, as well as splenic MZBCL. Abnormalities of the additional chromosome 3, such as +del(3)(p13),+i(3)(q10), or structural changes involving the distal part of the long arm, were evident in 9 of the 18 cases. All recurrent abnormalities were found in MZBCL more frequently than in other histologic entities of B-cell non-Hodgkin's lymphoma (B-NHL). None of the known lymphoma-associated chromosomal changes or rearrangements of the BCL1, BCL2, BCL3, BCL6, and CMYC genes were detected. We conclude that MZBCL represent a distinct entity of B-NHL with characteristic morphologic and immunophenotypic features and particular chromosomal abnormalities, and that a close histogenetic relationship between extranodal, nodal, and splenic MZBCL is likely, although the clinical presentation may vary.
Anti-serum albumin domain antibodies in the development of highly potent, efficacious and long-acting interferon (2010)

Serum albumin-binding domain antibodies (AlbudAbs) have previously been shown to greatly extend the serum half-life of the interleukin-1 receptor antagonist IL-1ra. We have subsequently extended this approach to look at the in vitro activity, in vivo efficacy and pharmacokinetics of an agonist molecule, interferon (IFN)-alpha2b, fused to an AlbudAb. Here we describe this molecule and show that in this format AlbudAb half-life extension technology displays significant advantages in comparison with other methods of half-life extension, in particular genetic fusion to serum albumin. When compared directly IFN-alpha2b fused to an Albudab shows higher potency, increased serum half-life and greater efficacy than human serum albumin fused to IFN-alpha2b. AlbudAbs are therefore an ideal platform technology for creation of therapeutics with agonist activity and long serum half-lives.
The Hepatoprotective Effect of Sodium Nitrite on Cold Ischemia-Reperfusion Injury (2012)

Liver ischemia-reperfusion injury is a major cause of primary graft non-function or initial function failure post-transplantation. In this study, we examined the effects of sodium nitrite supplementation on liver IRI in either Lactated Ringer's (LR) solution or University of Wisconsin (UW) solution. The syngeneic recipients of liver grafts were also treated with or without nitrite by intra-peritoneal injection. Liver AST and LDH release were significantly reduced in both nitrite-supplemented LR and UW preservation solutions compared to their controls. The protective effect of nitrite was more efficacious with longer cold preservation times. Liver histological examination demonstrated better preserved morphology and architecture with nitrite treatment. Hepatocellular apoptosis was significantly reduced in the nitrite-treated livers compared their controls. Moreover, liver grafts with extended cold preservation time of 12 to 24 hours demonstrated improved liver tissue histology and function post-reperfusion with either the nitrite-supplemented preservation solution or in nitrite-treated recipients. Interestingly, combined treatment of both the liver graft and recipient did not confer protection. Thus, nitrite treatment affords significant protection from cold ischemic and reperfusion injury to donor livers and improves liver graft acute function post-transplantation. The results from this study further support the potential for nitrite therapy to mitigate ischemia-reperfusion injury in solid organ transplantation.
Computationally efficient electronic-circuit noise calculations (1971)

The interreciprocal adjoint network concept is applied to the computer simulation of electronic-circuit noise performance. The method described is extremely efficient, allowing consideration of an arbitrarily large number of uncorrelated noise sources with less effort than for the original small signal a.c. analysis. Because all noise sources may be considered, no a priori assumption need be made as to which noise sources are dominant in a complicated circuit. The method is illustrated with an operational- amplifier example.
Ultrafast Rotational Anisotropy Measurements:  Strong-Field Nonlinear Saturation Effects (2001)

Nonlinear saturation effects in ultrafast time-resolved rotational anisotropy measurements are explored as a function of increased pump laser intensity. Femtosecond pump−probe experimental data were obtained over 3 orders of magnitude in pump laser intensity ranging from no saturation to highly nonlinear saturation. Data were obtained for molecular iodine vapor at room temperature following resonant excitation of the B←X transition. For low pump laser intensities, the data are shown to fit the conventional anisotropy formalism for unidirectional detection well. For higher pump laser intensities, the overall anisotropy diminishes because of saturation and the conventional fits diverge from the experimental data. In this regime, a saturation parameter can be introduced in the formulation to improve the fit between the model and the experimental data, thereby improving the accuracy of the resulting rotational temperatures. At the highest laser intensities, an additional photochemical pathway arising from the A←X transition is observed. Incorporation of this pathway into the nonlinear rotational anisotropy model yields accurate rotational populations even for the highest laser intensities. Applications of this nonlinear anisotropy model to reactive and nonreactive ultrafast studies in order to extract quantitative information are discussed.
Role of aralar, the mitochondrial transporter of aspartate‐glutamate, in brain N‐acetylaspartate formation and Ca2+ signaling in neuronal mitochondria (2007)

Aralar, the Ca(2+)-dependent mitochondrial aspartate-glutamate carrier expressed in brain and skeletal muscle, is a member of the malate-aspartate NADH shuttle. Disrupting the gene for aralar, SLC25a12, in mice has enabled the discovery of two new roles of this carrier. On the one hand, it is required for synthesis of brain aspartate and N-acetylaspartate, a neuron-born metabolite that supplies acetate for myelin lipid synthesis; and on the other, it is essential for the transmission of small Ca(2+) signals to mitochondria via an increase in mitochondrial NADH.
Setting Standards for Human Embryonic Stem Cells (2003)

Human embryonic stem cells (HESCs) have great potential in regenerative medicine and provide a window on early human embryonic development. In their Perspective,
 Brivanlou and colleagues
 review our current understanding of the cellular, molecular, and embryological properties of HESCs and suggest how standardized measures could be used to facilitate comparison across different human embryonic cell lines.
Synthesis and characterization of photodefinable polycarbonates for use as sacrificial materials in the fabrication of microfluidic devices (2002)

A fabrication technique recently developed at Georgia Institute of Technology involving thermally sacrificial polymeric materials allows for fabrication of microfluidic devices with greater degrees of functionality (i.e., fully integrated, complex, multi-level fluidic systems with functional valves, pumping systems, and other micro- electromechanical system [MEMS] components). In this method, thermally sacrificial polymers are coated onto a substrate and patterned into the shape of the desired channels and devices. These polymeric structures are then over-coated with a permanent structural material such as an inorganic glass or polymer. These steps can be repeated to produce complex, three-dimensional systems. Once the device build-up is complete, the structure is heated to a temperature at which the sacrificial polymer slowly decomposes, thus leaving behind the desired open-channeled structures. This process was first developed using functionalized polynorbornenes that decompose at temperatures in the range of 425 degree(s)C. In order to make this approach compatible with a wider range of substrates and structural materials, polymers with lower decomposition temperatures were desired. Polycarbonates were identified as a class of polymers with the desired lower decomposition temperatures (200- 300 degree(s)C). A disadvantage of commercially available polycarbonates, like poly (propylene carbonate), is that they have low glass transition temperatures (T<SUB>g</SUB>approximately equals 40 degree(s)C). This introduces several problems, including pattern deformation at elevated processing temperatures. Also, a significant number of process steps are required to pattern the channel structures using simple polymer materials. Therefore, this paper will describe recent results of work on photodefinable polycarbonates with improved thermal properties. Utilizing a polymer that can be patterned directly by conventional lithography greatly simplifies the fabrication process and eliminates the need for the plasma etch steps required in the original process. Results of the synthesis and characterization of polycarbonates patterned with the use of a photoacid generator, thus exploiting the acid-catalyzed thermolysis of polycarbonates, will be presented.
Molecular Characterization of Rifampin- and Isoniazid-Resistant Mycobacterium tuberculosis Strains Isolated in Poland (2004)

A total of 105 rifampin (RMP)- and/or isoniazid (INH)-resistant strains of Mycobacterium tuberculosis isolated from different parts of Poland in 2000 were screened for mutations associated with resistance to these drugs by two molecular methods, namely sequence analysis and real-time PCR technology. Three loci associated with drug resistance were selected for characterization: they were rpoB (RMP), katG, and the regulatory region of inhA (INH). Nineteen different mutations were identified in 64 RMP-resistant strains, and five new alleles were described. The most common point mutations were in codons 531 (41%), 516 (16%), and 526 (9%) of the rpoB gene. Mutations were not found in two (3%) of the isolates. In the case of resistance to INH, six different mutations in the katG gene of 83 resistant strains were detected. Fifty-seven (69%) isolates exhibited nucleotide substitutions at codon 315. One strain harbored a mutation affecting codon 279 (Gly279Thr). Twelve of 26 INH-resistant strains with the wild-type codon 315 (14.5% of all strains tested) had the mutation -15C-->T in the regulatory region of inhA. A full correlation between the DNA sequence analysis and real-time PCR data was obtained. We conclude that the real-time PCR method is fast and reliable for the detection of RMP and INH resistance-associated mutations in M. tuberculosis clinical isolates.
Cutaneous leishmaniasis (2000)

Leishmaniasis is a major World health problem, which is increasing in incidence. In Northern Europe it is seen in travellers returning from endemic areas. The protozoa is transmitted by sandflies and may produce a variety of clinical syndromes varying from a simple ulcer to fatal systemic disease. This review considers the management of simple cutaneous leishmaniasis. Patients usually have a single ulcer which may heal spontaneously, requiring only topical, or no treatment at all. Lesions caused by Leishmania braziliensis may evolve into the mucocutaneous form, 'espundia', and should be treated with systemic antimony. Sodium stiboglucoante 20 mg/kg/day i. v. for 20 days is the appropriate first line treatment in these cases. Although it may cause transient bone marrow suppression, liver damage, a chemical pancreatitis, and disturbances in the electrocardiogram, it appears to be safe. The success of treatment should be assessed 6 weeks after it has been completed and patients should be followed up for 6 months.
Septic reactions to platelet transfusions. A persistent problem. (1991)

Contamination of platelet concentrates remains a significant clinical problem. Septic episodes may be reduced by transfusion of platelets with shorter storage intervals.
Defects in Mitochondrial ATP Synthesis in Dystrophin-Deficient Mdx Skeletal Muscles May Be Caused by Complex I Insufficiency (2014)

Duchenne Muscular Dystrophy is a chronic, progressive and ultimately fatal skeletal muscle wasting disease characterised by sarcolemmal fragility and intracellular Ca2+ dysregulation secondary to the absence of dystrophin. Mounting literature also suggests that the dysfunction of key energy systems within the muscle may contribute to pathological muscle wasting by reducing ATP availability to Ca2+ regulation and fibre regeneration. No study to date has biochemically quantified and contrasted mitochondrial ATP production capacity by dystrophic mitochondria isolated from their pathophysiological environment such to determine whether mitochondria are indeed capable of meeting this heightened cellular ATP demand, or examined the effects of an increasing extramitochondrial Ca2+ environment. Using isolated mitochondria from the diaphragm and tibialis anterior of 12 week-old dystrophin-deficient mdx and healthy control mice (C57BL10/ScSn) we have demonstrated severely depressed Complex I-mediated mitochondrial ATP production rate in mdx mitochondria that occurs irrespective of the macronutrient-derivative substrate combination fed into the Kreb's cycle, and, which is partially, but significantly, ameliorated by inhibition of Complex I with rotenone and stimulation of Complex II-mediated ATP-production with succinate. There was no difference in the MAPR response of mdx mitochondria to increasing extramitochondrial Ca2+ load in comparison to controls, and 400 nM extramitochondrial Ca2+ was generally shown to be inhibitory to MAPR in both groups. Our data suggests that DMD pathology is exacerbated by a Complex I deficiency, which may contribute in part to the severe reductions in ATP production previously observed in dystrophic skeletal muscle.
The use of genetically altered astrocytes to provide nerve growth factor to adrenal chromaffin cells grafted into the striatum (1991)

Transplantation of adrenal chromaffin cells into the striatum of Parkinson's disease patients is unlikely to become a reliable therapy unless techniques are devised to improve cell survival. To address this issue, we investigated the use of genetically altered astrocytes that constitutively secrete beta-nerve growth factor (NGF) to provide trophic support for adrenal chromaffin cells grafted into the dopamine-denervated striatum of the rat. Primary rat astrocytes were altered genetically in vitro by infection with a retroviral vector harboring a mouse beta-NGF transgene under constitutive long terminal repeat transcriptional control. Confluent cultures of these genetically altered astrocytes secrete NGF into their culture medium at a rate of approximately 9 pg/10(5) cells/h. This rate of NGF secretion is at least 10-fold higher than that of confluent sister cultures of uninfected astrocytes. The effects of the NGF-secreting astrocytes on the survival and neuronal transformation of dissociated adrenal chromaffin cells were assessed in vitro and following transplantation into the dopamine-denervated striatum of the adult rat. In vitro experiments demonstrated that neuritic outgrowth is stimulated when postnatal day 12 chromaffin cells are grown on a monolayer of the genetically altered astrocytes. When co-grafted with genetically altered astrocytes, young postnatal chromaffin cells displayed extensive neuritic outgrowth within the host brain 2 weeks postimplantation, whereas chromaffin cells grafted alone or with normal astrocytes retain an endocrine-like morphology. Survival of the chromaffin cells is also enhanced 3-6-fold when co-grafted with the genetically altered astrocytes. In addition, the neuronally transformed chromaffin cells appear to lose adrenergic properties as assessed by diminished immunoreactivity to the adrenergic marker, phenylethanolamine-N-methyltransferase. Although their survival is also enhanced approximately 4-fold relative to controls, adult chromaffin cells do not convert to a neuronal morphology when co-grafted with the genetically altered astrocytes. These studies demonstrate that rat astrocytes carrying a mouse NGF transgene provide trophic support for intrastriatal chromaffin cell grafts.
Genetics of inclusion body myopathies (1998)

We review the current knowledge about the genetic susceptibility to develop inflammatory inclusion body myositis, especially in relation to the increased presence of the HLA DR3 allele in patients with familial and sporadic forms, indicating an autoimmune predisposition. The main focus of the review is the clinical and genetic presentations of the various hereditary inclusion body myopathies. Criteria for diagnosis and classification of these myopathies are presented. The spectrum of the recessive forms of hereditary inclusion body myopathies currently linked to chromosome 9p1-q1 is described, with emphasis on the up-to-date status of the gene search for these forms.