gebhart/patrepeval huggingface dataset:
Purification and biochemical characterization of recombinant .alpha.1-antitrypsin variants expressed in Escherichia coli (1991)

Site-directed variants of alpha 1-antitrypsin (alpha 1AT) expressed in a recombinant strain of Escherichia coli have been isolated with an overall process yield of 50% following tangential flow ultrafiltration, anion-exchange, immobilized metal affinity, and hydrophobic interaction chromatography. The primary structure of the purified variants including the integrity of the N- and C-termini has been verified by electrospray mass spectrometry of the intact molecules (44 kDa) for two of the variants (alpha 1AT Leu-358 and alpha 1AT Ala-357, Arg-358). Complementary classical peptide mapping and automated amino acid sequencing have verified 75% of the primary sequence of alpha 1AT Ala-357, Arg-358. Isoelectric focusing in an immobilized pH gradient revealed some microheterogeneity which proved to be reproducible from one purification batch to another. The isolated variants of alpha 1AT did not show any signs of proteolytic degradation during the purification process and proved to be fully active against their target proteases. The described process also allowed the complete removal of endotoxins from the preparations, opening the possibility to evaluate these novel protease inhibitors for their in vivo efficacy in different animal models of human disease.
Regeneration of Lesioned Septohippocampal Acetylcholinesterase‐positive Axons is Improved by Antibodies Against the Myelin‐associated Neurite Growth Inhibitors NI‐35/250 (1991)

Two oligodendrocyte membrane proteins, NI-35 and NI-250, have been shown to be highly inhibitory for neurite growth. Upon neutralization of these components with the specific monoclonal antibody IN-1, lesioned corticospinal tract fibres were able to regenerate over long distances. In the present study, we have investigated the behaviour of regenerating cholinergic septohippocampal tract fibres. Large fimbria/fornix aspiration lesions were bridged by human amnion extracellular matrix material containing nerve growth factor, and the inhibitor-neutralizing antibody IN-1 or a control antibody were applied. After 3 - 5 weeks survival time, acetylcholinesterase (AchE)-positive fibres had crossed the bridge and, upon entering the hippocampus, had developed a profuse fibre plexus. In the controls (antibody against peroxidase) the fibre growth within the hippocampal tissue remained limited to maximally 1 mm in the caudal and lateral directions. In the presence of the antibody IN-1, however, AchE-positive fibres were seen to grow for 2 - 4 mm both in the caudal and lateral directions. Interestingly, the regenerated fibres preferably grew to their original terminal areas in the infra- and suprapyramidal layers of the hippocampus proper and the hilus, and in the supragranular layer of the dentate gyrus. These data show that the neurite growth inhibitors severely impede regenerative axon growth also for the cholinergic fibres in the hippocampus, and that their neutralization increases axon growth and leads to partial reconstitution of the original anatomical fibre distribution.
Malignant Gliomas in Adults (2008)

Malignant gliomas, the most common type of primary brain tumor in adults, are associated with disproportionate cancer-related morbidity and mortality. Recently, there have been important advances in our understanding of the molecular pathogenesis of malignant gliomas and progress in treating them. This review summarizes the diagnosis and management of these tumors in adults, highlighting new advances.
Identification of two Mycobacterium avium subspecies paratuberculosis gene products differentially recognised by sera from rabbits immunised with live mycobacteria but not heat-killed mycobacteria (2001)

The investigation of environmentally regulated proteins has led to a better understanding of host-pathogen interactions and identified novel vaccine candidate antigens for several bacterial pathogens. In an effort to identify such proteins in Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis), a genomic expression library was differentially screened with sera from rabbits that had been immunised with live M. paratuberculosis (alpha-live) as well as sera from rabbits immunised with heat-killed M. paratuberculosis (alpha-killed). These experiments identified seven recombinant plaques that were uniquely recognised by the alpha-live sera. Sequence data showed that five of these clones overlapped with each other and contained a common open-reading frame encoding a 25-kDa protein, termed Csp1. The 25-kDa antigen shows weak similarity to a secreted Corynebacterium glutamicum protein. The remaining two clones overlapped with each other and contained two partial open-reading frames, both encoding proteins with strong homology to polyketide synthase from various species of mycobacteria. Antisera were produced against a peptide of the polyketide synthase gene product designated Pks7. Csp1-specific antibodies were affinity purified from the alpha-live sera. These purified antibodies demonstrated that Csp1 was present within infected macrophages. Collectively, these data identify novel M. paratuberculosis antigens that may be important in pathogenesis.
Characterization of Ia8 Antigen, Thy-1.2 Antigen, Complement Receptors, and Virus Production in a Group of Murine Virus-Induced Leukemia Cell Lines (1976)

Ia8, a cell membrane antigen controlled by gene(s) located in the I region of the H-2 complex, was found on 9 of 26 murine leukemia cell lines. Iaddition, 3 of the 9 Ia8-bearing lines had a membrane receptor for antigen-antibody-complement complexes. Six of 26 lines bore the Thy-1.2 antigen. Ia8 and Thy-1.2 antigens were mutually exclusive on the cell lines studied. The strain of virus used to induce the leukemia, the H-2 type of the cells, and the techniques of leukemia cell propagation all appeared to influence the antigenic characteristics of the cell lines obtained. Production of infectious murine leukemia virus in vitro and expression of leukemia virus-induced membrane antigens did not appear to correlate with the presence of I8 or Thy-1.2 antigens or with the H-2 type of the cells.
Pharmacokinetics of Single-Dose and Multi-Dose of Lovastatin/Niacin ER Tablet in Healthy Volunteers (2012)

An extended-release (ER) niacin and lovastatin fixed-dose combination has been developed for the treatment of primary hypercholesterolemia and mixed dyslipidemia. The purpose of the present study was to examine the drug interaction between niacin and lovastatin after multi-dose oral administration of lovastatin/niacin ER combination in healthy Chinese volunteers. A single-center, randomized, open-label, 5-period crossover study was conducted in thirty healthy volunteers aged 18 to 45 years with a washout period of 8 days. Subjects were randomized to receive multiple doses of treatment A (1 500 mg niacin ER tablet), B (1 20 mg lovastatin tablet), C (1 20 mg lovastatin and 500 mg niacin-ER tablet), D (2 10 mg lovastatin and 350 mg niacin-ER tablets) or E (2 10 mg lovastatin and 500 mg niacin-ER tablets) in 1 of 5 sequences (ABCDE, BCDEA, CDEAB, DEABC, EABCD) per period. Lovastatin, niacin and its metabolites (nicotinuric acid and nicotinamide) were determined in plasma by LC/MS method. Pharmacokinetic parameters were calculated, and least square mean ratios and 90% confidence intervals for <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mrow><mml:mi>C</mml:mi></mml:mrow><mml:mrow><mml:mi>max</mml:mi><mml:mo>⁡</mml:mo></mml:mrow></mml:msub></mml:math> and AUC (0–24) were determined for lovastatin/niacin ER versus niacin ER or lovastatin. It revealed that the formulation had no potential drug interaction in healthy Chinese volunteers when the dosage was increased from 500 mg to 1000 mg.
Phytophthora sojaeRaces in Ohio Over a 10-Year Interval (1994)

During 1978 and 1980, 199 isolates of Phytophthora sojae were obtained from soil samples from 16 fields in northwest Ohio using a soybean leaf disk bait procedure, and 53 isolates were obtained from diseased soybean plants. During 1990 and 1991, 282 isolates of P. sojae were obtained from diseased soybean cv. Sloan or Amcor 89 seedlings planted in soil from 88 fields in northwest Ohio, and 27 isolates were obtained from field-grown plants with the Rps1-k resistance gene. All isolates were identified as to their race phenotypes by inoculation of differential soybean cultivars having Rps1-a, Rps1-b, Rps1-c, Rps1-d, Rps1-k, Rps3-a, or Rps6 resistance genes
Interferon Regulatory Factor-2 Directs Transcription from the gp91 Promoter (1996)

Repressor elements in the gp91(phox) promoter are necessary to restrict tissue-specific transcription to mature phagocytes. Deletion of these elements leads to significant promoter activity in cell lines such as HEL and K562 that do not normally express gp91(phox). The -100 to +12 base pair gp91(phox) promoter region is sufficient to direct maximal de-repressed transcription in these cells. However, promoter activity is dramatically decreased following a 16-base pair truncation that deletes an interferon-stimulated response element. This element interacts with IRF-1 and IRF-2, members of the interferon regulatory factor family of transcription factors. In addition, this promoter region is bound by a factor with properties similar to BID, a DNA-binding protein that also interacts with three upstream sites within the gp91(phox) promoter. Transient transfection studies using mutated promoters indicate that both the IRF and BID binding sites are required for maximal gp91(phox) promoter activity. Overexpression of IRF-1 or IRF-2 in K562 cells leads to transactivation of gp91(phox) promoter constructs, which is dependent on the presence of an intact IRF binding site. IRF-2 predominates in macrophages that express the gp91(phox) gene as well as in HEL and K562 cells. We conclude that IRF-2 and BID activate gp91(phox) promoter activity in the absence of transcriptional repression.
Exact Decoding Probability Under Random Linear Network Coding (2010)

In this letter, we compute the exact probability that a receiver obtains N linearly independent packets among K ≥ N received packets, when the sender/s use/s random linear network coding over a Galois Field of size q. Such condition maps to the receiver's capability to decode the original information, and its mathematical characterization helps to design the coding so to guarantee the correctness of the transmission. Our formulation represents an improvement over the current upper bound for the decoding probability, and provides theoretical grounding to simulative results in the literature.
The Small Heat-shock Protein IbpB from Escherichia coli Stabilizes Stress-denatured Proteins for Subsequent Refolding by a Multichaperone Network (1998)

The role of small heat-shock proteins in Escherichia coli is still enigmatic. We show here that the small heat-shock protein IbpB is a molecular chaperone that assists the refolding of denatured proteins in the presence of other chaperones. IbpB oligomers bind and stabilize heat-denatured malate dehydrogenase (MDH) and urea-denatured lactate dehydrogenase and thus prevent the irreversible aggregation of these proteins during stress. While IbpB-stabilized proteins alone do not refold spontaneously, they are specifically delivered to the DnaK/DnaJ/GrpE (KJE) chaperone system where they refold in a strict ATPase-dependent manner. Although GroEL/GroES (LS) chaperonins do not interact directly with IbpB-released proteins, LS accelerate the rate of KJE-mediated refolding of IbpB-released MDH, and to a lesser extent lactate dehydrogenase, by rapidly processing KJE-released early intermediates. Kinetic and gel-filtration analysis showed that denatured MDH preferentially transfers from IbpB to KJE, then from KJE to LS, and then forms a active enzyme. IbpB thus stabilizes aggregation-prone folding intermediates during stress and, as an integral part of a cooperative multichaperone network, is involved in the active refolding of stress-denatured proteins.
Danazol in treatment of lupus thrombocytopenia. (1991)

Seven patients with systemic lupus erythematosus (SLE), persistent thrombocytopenia (TP), in whom it was considered undesirable to institute an increase in steroid or immunosuppressive agents, were treated with danazol. Five patients completed the minimum period of 8 weeks. Two patients showed early response to danazol but were switched over to cyclophosphamide or azathioprine after 4 weeks because of systemic disease. Of the remaining five patients, four had complete responses. In one patient who failed treatment the TP was considered to be related to another drug (ranitidine). Other manifestations of SLE also improved with treatment. Side effects included amenorrhea in one patient, and hypoglycemia and hyponatremia in another. Infections were absent. Danazol can be a useful alternative treatment of lupus TP.
Prospective comparison of open vs. laparoscopic colon surgery for carcinoma (1996)

After five years, this study shows that laparoscopy does no harm to the patient, offers comparable oncologic resections, and seems to be patient-friendly, with less pain, quicker return of bowel functions, shortened hospitalization, and quicker return to full activity.
The Angelman Syndrome protein Ube3A regulates synapse development by ubiquitinating arc (2018)

Angelman Syndrome is a debilitating neurological disorder caused by mutation of the E3 ubiquitin ligase Ube3A, a gene whose mutation has also recently been associated with autism spectrum disorders (ASDs). The function of Ube3A during nervous system development and how Ube3A mutations give rise to cognitive impairment in individuals with Angleman Syndrome and ASDs are not clear. We report here that experience-driven neuronal activity induces Ube3A transcription and that Ube3A then regulates excitatory synapse development by controlling the degradation of Arc, a synaptic protein that promotes the internalization of the AMPA subtype of glutamate receptors. We find that disruption of Ube3A function in neurons leads to an increase in Arc expression and a concomitant decrease in the number of AMPA receptors at excitatory synapses. We propose that this deregulation of AMPA receptor expression at synapses may contribute to the cognitive dysfunction that occurs in Angelman Syndrome and possibly other ASDs.
Novel boundary determination algorithm for lane detection (2013)

A novel boundary determination algorithm (BDA) for robust lane detection is presented. The algorithm can track a complete lane boundary based on partial lane edge points provided there exist sufficient orientation similarity there between. BDA mainly comprises two parts: (a) utilizing an edge detection method to extract orientations and coordinates of edge points; (b) repeatedly applying two circular masks, i.e., a probing circular mask followed by a tracing circular mask, to collect two separate sets of orientations of edge points and from which to sift out a primary orientation for tracking a curve as perceived by human eyes. The algorithm is characterized in that the probing circular mask acts to probe ahead for the tracing circular mask in order to avoid deviation from the right track.
Therapeutic Antibodies (2004)

Monoclonal antibodies had the lure of drugs very much since their first description. The ability to bind to a predetermined chemical structure stimulated the imagination of drug discoverers and developers. Nevertheless it took many years before a drug was registered which started to make good on the promise. The complexity of the molecule, made up of four polypeptide chains, its large molecular weight, its multiple and versatile functional domains and its mouse origin initially were obstacles for the production and the utilisation. Also the selection of appropriate target structures on the surface of cells turned out be difficult. Many of these difficulties have been overcome. The replacement of most of the murine sequences with equivalent human sequences and the concomittant decrease in immunogenicity, and the identification of cell surface components which are causative and limiting in cellular transformation have made monoclonal antibodies valuable weapons in the fight against cancer. Multiple mechanisms of monoclonal antibody action are being exploited for this purpose. Antibodies can sequester growth factors and prevent the activation of crucial growth factor receptors. A monoclonal antibody directed against the vascular endothelial growth factor (VEGF) has been shown to be a potent neo-vascularisation inhibitor (bevacizumab). An antibody against the extracellular domain of the EGF receptor prevents the binding of the ligand to the receptor and thereby its activation (cetuximab). EGFR activity, however, is absolutely required for the survival and proliferation of certain human tumour cells. An antibody which interferes with the dimerisation of the ErbB2 and the ErbB3 members of the EGF receptor family prevents the association of a most potent signaling module (pertuxumab). The signals emenating from this dimer determine many phenotypic properties of e.g. human breast cancer cells. A monoclonal antibody also directed against ErbB2 has been most successful, clinically and commercially (trastuzumab). This antibody interferes with signals generated by the receptor and causes the arrest of the cell cycle in tumour cells. In addition, it recruits immune effector cells as cytotoxic agents. Finally, monoclonal antibody derivatives, single chain Fv fragments, have been used as a basis for the construction of recombinant tumour toxins. These molecules harness the exquisite binding specificity of the antibodies and combine them with the toxic principles of bacteria.
Highly active zinc-finger nucleases by extended modular assembly (2012)

Zinc-finger nucleases (ZFNs) are important tools for genome engineering. Despite intense interest by many academic groups, the lack of robust noncommercial methods has hindered their widespread use. The modular assembly (MA) of ZFNs from publicly available one-finger archives provides a rapid method to create proteins that can recognize a very broad spectrum of DNA sequences. However, three- and four-finger arrays often fail to produce active nucleases. Efforts to improve the specificity of the one-finger archives have not increased the success rate above 25%, suggesting that the MA method might be inherently inefficient due to its insensitivity to context-dependent effects. Here we present the first systematic study on the effect of array length on ZFN activity. ZFNs composed of six-finger MA arrays produced mutations at 15 of 21 (71%) targeted loci in human and mouse cells. A novel drop-out linker scheme was used to rapidly assess three- to six-finger combinations, demonstrating that shorter arrays could improve activity in some cases. Analysis of 268 array variants revealed that half of MA ZFNs of any array composition that exceed an ab initio B-score cutoff of 15 were active. These results suggest that, when used appropriately, MA ZFNs are able to target more DNA sequences with higher success rates than other current methods.
Autoantibody-associated kappa light chain variable region gene expressed in chronic lymphocytic leukemia with little or no somatic mutation. Implications for etiology and immunotherapy. (1988)

Recently the minor B cell subpopulation that expresses the CD5 (Leu-1) antigen has been implicated as a source of IgM autoantibodies. Chronic lymphocytic leukemia (CLL), the most common leukemia in humans, represents a malignancy of small B lymphocytes that also express the CD5 antigen. However, little is known concerning the antibody variable region genes (V genes) that are used by these malignant CD5 B cells. We have found that a relatively high frequency of CLL patients have leukemic B cells with surface immunoglobulin (sIg) recognized by 17.109, a murine mAb specific for a kappa light chain associated crossreactive idiotype (CRI) associated with rheumatoid factor and other IgM autoantibodies. Flow cytometric analyses revealed that the relative expression of the 17.109-CRI by circulating leukemic B cells was directly proportional to the levels of sIg kappa light chain, indicating that there exists stable idiotype expression in the leukemic population. To examine this at the molecular level, the nucleic acid sequences encoding the Ig kappa light chains of two unrelated patients with CLL bearing sIg with the 17.109-CRI were determined. Analyses of multiple independent kappa light chain cDNA clones did not reveal any evidence for sequence heterogeneity in the CLL cell population. Furthermore, the nucleic acid sequences expressed by the leukemic cells of these two patients were identical or very homologous to a germline V kappa gene isolated from placental DNA, designated Humkv 325, or "V kappa RF" because of its association with IgM autoantibodies. This study suggests; (a) that the malignant CD5+ B lymphocytes in CLL use the same V kappa gene that has been highly associated with IgM autoantibodies and (b) that the expression of V genes is stable in CLL, in contrast to other B cell malignancies examined to date. We propose that many CLL cases represent malignancies of autoreactive CD5 B cells that use a restricted set of conserved V genes. This property may render CLL particularly amenable to immunotherapy with antiidiotypic antibodies.
Activation of Hypoxia-inducible Transcription Factor Depends Primarily upon Redox-sensitive Stabilization of Its α Subunit (1996)

Hypoxia-inducible factor 1 (HIF-1) is a heterodimeric transcription factor that is critical for hypoxic induction of a number of physiologically important genes. We present evidence that regulation of HIF-1 activity is primarily determined by the stability of the HIF-1alpha protein. Both HIF-1alpha and HIF-1beta mRNAs were constitutively expressed in HeLa and Hep3B cells with no significant induction by hypoxia. However, the HIF-1alpha protein was barely detectable in normoxic cells, even when HIF-1alpha was overexpressed, but was highly induced in hypoxic cells, whereas HIF-1beta protein levels remained constant, regardless of pO2. Hypoxia-induced HIF-1 binding as well as the HIF-1alpha protein were rapidly and drastically decreased in vivo following an abrupt increase to normal oxygen tension. Moreover, short pre-exposure of cells to hydrogen peroxide selectively prevented hypoxia-induced HIF-1 binding via blocking accumulation of HIF-1alpha protein, whereas treatment of hypoxic cell extracts with H2O2 had no effect on HIF-1 binding. These observations suggest that an intact redox-dependent signaling pathway is required for destablization of the HIF-1alpha protein. In hypoxic cell extracts, HIF-1 DNA binding was reversibly abolished by sulfhydryl oxidation. Furthermore, the addition of reduced thioredoxin to cell extracts enhanced HIF-1 DNA binding. Consistent with these results, overexpression of thioredoxin and Ref-1 significantly potentiated hypoxia-induced expression of a reporter construct containing the wild-type HIF-1 binding site. These experiments indicate that activation of HIF-1 involves redox-dependent stabilization of HIF-1alpha protein.