gebhart/patrepeval huggingface dataset:
Survival estimates for patients with Machado–Joseph disease (SCA3) (2007)

Machado-Joseph disease (MJD), one of the most prevalent autosomal dominant cerebellar ataxias, is a neurodegenerative disease that starts during adulthood, with patients showing difficulties in gait, later becoming bedridden, and ultimately presenting premature death. There is, however, scarce data quantifying disease impact on patient survival. We investigated the overall survival of a large series of MJD patients and compared it with the survival of their asymptomatic relatives. A total of 412 affected and 413 unaffected individuals were ascertained from a consecutive sample of 82 families with a molecular diagnosis of MJD. Estimated mean survival time was 63.96 years [95% confidence interval (CI), 62.09-65.83] for the affected group and 78.61 years (95% CI, 74.75-82.47) for the unaffected group (p < 0.001). For a subset of 366 patients, mean age at onset was 36.37 years (95% CI, 35.21-37.53) and survival after disease onset was estimated as 21.18 years. Early onset and large CAG length predicted shorter overall survival times. This study presents quantitative data on the impact of MJD on overall survival, a phenomenon that is related to CAG length, age at onset, and year of birth.
Inhibition of the translocated c-myc in Burkitt's lymphoma by a PNA complementary to the E mu enhancer. (2003)

In Burkitt's Lymphoma there is an up-regulation of the c-myc oncogene caused by its translocation from chromosome 8 to chromosome 14, often close to the E mu enhancer of the immunoglobulin heavy chain locus (IgH). In Burkitt's Lymphoma cells, a peptide nucleic acid complementary for a specific unique E mu intronic sequence selectively blocked the expression of the c-myc oncogene under E mu control but not of other c-myc alleles. This Peptide Nucleic Acid also inhibited IgM expression in B cells. The finding that PNAs specific for a regulatory noncoding sequence can block gene expression has important conceptual and practical implications.
Characterization of Naturally Occurring Minor Histocompatibility Peptides Including H-4 and H-Y (1990)

Minor histocompatibility (H) antigens can be peptides derived from cellular proteins that are presented on the cell surface by major histocompatibility complex (MHC) class I molecules. This is similar to viral antigens, because in both cases cytotoxic T lymphocytes (CTLs) recognize artificially produced peptides loaded on target cells. Naturally processed minor H peptides were found to be similar to those artificial CTL-epitopes, as far as size and hydrophobicity is concerned. The peptides studied were isolated from a transfectant that expressed a model CTL-defined antigen, beta-galactosidase, from male cells that express H-Y, which has been known operationally since 1955, and from cells that express H-4, known since 1961.
EMPLOYABILITY COMPETENCIES OF THE BACHELOR OF SCIENCE IN INDUSTRIAL TECHNOLOGY: INPUTS TO A CURRICULUM REVIEW AND ENHANCEMENT (2020)

The goal of the study was to determine the extent of employability skills of the Bachelor of Science in Industrial Technology (BSIT) curriculum of three selected State Universities in Region II and the employability skills the industry required. This thesis employed the analysis method descriptive. The data sources were the twenty faculty members, twenty TESDA trainers and the 46 service managers , supervisors, consultants, chief mechanics and business partners engaged in automotive engineering. The data were handled using weighted mean and one-factor ANOVA. The findings show that the three groups of respondents have been satisfied with the BSIT program, which is of significant importance in the field of automotive technology in terms of information, skills and attitudes, the SUC instructors, the TESDA trainers and industry partners have a common understanding of the level of employability skills that the industry needs and the program in terms of awareness, skills and attitudes The findings of this study will therefore be used as a guideline for the conduct of curriculum review and enhancement for the BSIT curriculum for future acts, a curriculum review of the current BSIT curriculum should be undertaken to identify particular areas that match and do not fit the employability skills needed by the industry, and an improvement of the existing BSIT curriculum.
Activation of Matrix Metalloproteinases Precedes Left Ventricular Remodeling in Hypertensive Heart Failure Rats (2004)

MMPs are likely to trigger and promote LV remodeling, and ACE inhibition directly exerts inhibitory effect on MMPs, leading to the prevention of LV remodeling and dysfunction.
Association of bcl-1 rearrangements with lymphocytic lymphoma of intermediate differentiation (1990)

Previous studies using classical cytogenetics have demonstrated the presence of the t(11;14) (q13;q32) chromosomal translocation in some cases of lymphocytic lymphoma of intermediate differentiation (IDL), a distinct type of low grade B-cell lymphoma. This finding suggested that the bcl-1 region (located at band q13 of chromosome 11) might be involved in this neoplasm. Using a genomic probe from the major breakpoint area of the bcl-1 locus, we identified rearrangements of the bcl-1 region in 10 of 19 cases, 2 of which comigrated with a rearranged allele of the immunoglobulin heavy chain gene joining region. In contrast, bcl-1 rearrangements were not found in other types of low grade B-cell lymphoma, specifically in 36 cases of chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) and 27 cases of follicular lymphoma (FL). To further assess the molecular pathology of IDL, we analyzed these cases for rearrangements of the bcl-2 proto-oncogene, which is associated primarily with follicular lymphomas. None of the 19 cases of IDL had rearrangements. Furthermore, none of the 36 cases of CLL/SLL showed bcl-2 rearrangements, whereas, as expected, 21 of 27 cases of FL had rearrangements of the bcl-2 locus. Our findings demonstrate an association between a rearranged bcl-1 region with approximately 50% of IDLs and suggest that abnormalities of this locus may be important in the pathogenesis of IDL.
Enhanced Plasmin Inhibition by a Reactive Center Lysine Mutant of the Kunitz-type Protease Inhibitor Domain of the Amyloid β-Protein Precursor (1995)

The Alzheimer's disease related protein, amyloid beta-protein precursor (A beta PP), contains a domain homologous to Kunitz-type serine protease inhibitors (KPI). The recombinant KPI domain of A beta PP is a potent inhibitor of coagulation factors XIa and IXa and functions as an anticoagulant in vitro. Here we report the expression, purification, and characterization of a reactive center lysine mutant of the KPI domain of A beta PP (KPI-Lys17). An expression plasmid for the KPI-Lys17 domain of A beta PP encoded amino acids 285-345 of the A beta PP cDNA containing a lysine substitution at arginine 17 in the KPI domain. The secreted 61-amino acid product was purified to homogeneity and functionally characterized. The protease inhibitory properties of the KPI-Lys17 domain were compared to those of the native KPI domain of A beta PP. Both KPI domains equally inhibited trypsin, chymotrypsin, and coagulation factors IXa and Xa. However, the KPI-Lys17 domain was an approximately 25-fold less effective inhibitor of coagulation factor XIa resulting in markedly less prolongation of the activated partial thromboplastin time compared to the native KPI domain of A beta PP. On the other hand, the KPI-Lys17 domain was an approximately 10- and 5-fold better inhibitor of plasmin in a chromogenic substrate assay and in a fibrinolytic assay, respectively, than the native KPI domain of A beta PP. Together, these studies suggest that the KPI-Lys17 domain has enhanced anti-fibrinolytic and diminished factor XIa inhibitory properties compared to the native KPI domain of A beta PP.
Oral vaccination with a viral vector containing Aβ cDNA attenuates age‐related Aβ accumulation and memory deficits without causing inflammation in a mouse Alzheimer model (2007)

Immunotherapy with Abeta is expected to bring great improvement for Alzheimer disease (AD). However, clinical trials have been suspended because of meningoencephalitics, which accompanied lymphocytic infiltration. We have developed an oral vaccine for AD with a recombinant adeno-associated viral vector carrying Abeta cDNA (AAV/Abeta). The vaccine reduces the amount of Abeta deposited without lymphocytic infiltration in APP transgenic (Tg2576) mice. In the present study, Tg2576 mice showed progressive cognitive impairments in the novel object recognition test, Y-maze test, water maze test, and contextual conditioned fear learning test. A single oral administration of AAV/Abeta to Tg2576 mice at the age of 10 months alleviated progressive cognitive impairment with decreased Abeta deposition, insoluble Abeta, soluble Abeta oligomer (Abeta*56), microglial attraction, and synaptic degeneration induced in the brain regions at the age of 13 months. A histological analysis with hematoxylin and eosin and an immunohistochemical analysis with antibodies against CD3, CD4, CD8, and CD19 suggested there was no lymphocytic infiltration or microhemorrhage in the brain of AAV/Abeta-vaccinated Tg2576 mice at 13 months of age. Taken together, these results suggest that immunotherapy with AAV/Abeta is a safe and effective treatment for AD.
Human lysosomal protective protein has cathepsin A-like activity distinct from its protective function (1991)

The protective protein was first discovered because of its deficiency in the metabolic storage disorder galactosialidosis. It associates with lysosomal beta-galactosidase and neuraminidase, toward which it exerts a protective function necessary for their stability and activity. Human and mouse protective proteins are homologous to yeast and plant serine carboxypeptidases. Here, we provide evidence that this protein has enzymatic activity similar to that of lysosomal cathepsin A: 1) overexpression of human and mouse protective proteins in COS-1 cells induces a 3-4-fold increase of cathepsin A-like activity; 2) this activity is reduced to approximately 1% in three galactosialidosis patients with different clinical phenotypes; 3) monospecific antibodies raised against human protective protein precipitate virtually all cathepsin A-like activity in normal human fibroblast extracts. Mutagenesis of the serine and histidine active site residues abolishes the enzymatic activity of the respective mutant protective proteins. These mutants, however, behave as the wild-type protein with regard to intracellular routing, processing, and secretion. In contrast, modification of the very conserved Cys60 residue interferes with the correct folding of the precursor polypeptide and, hence, its intracellular transport and processing. The secreted active site mutant precursors, endocytosed by galactosialidosis fibroblasts, restore beta-galactosidase and neuraminidase activities as effectively as wild-type protective protein. These findings indicate that the catalytic activity and protective function of the protective protein are distinct.
Primary Antibody–Fab Fragment Complexes: A Flexible Alternative to Traditional Direct and Indirect Immunolabeling Techniques (2004)

Immunolabeling with immune complexes of primary and secondary antibodies offers an attractive method for detecting and quantifying specific antigen. Primary antibodies maintain their affinity for specific antigen after labeling with Fab fragments in vitro. Incubation of these immune complexes with excess normal serum from the same species as the primary antibody prevents free Fab fragments from recognizing immunoglobulin. Effectively a hybrid between traditional direct and indirect immunolabeling techniques, this simple technique allows primary antibodies to be non-covalently labeled with a variety of reporter molecules as and when required. Using complexes containing Fab fragments that recognize both the Fc and F(ab')2 regions of IgG, we show that this approach prevents nonspecific labeling of endogenous immunoglobulin, can be used to simultaneously detect multiple antigens with primary antibodies derived from the same species, and allows the same polyclonal antibody to be used for both antigen capture and detection in ELISA.
Tools and strategies for visualization of large image data sets in high-resolution imaging mass spectrometry (2007)

Mass spectrometry based proteomics is one of the scientific domains in which experiments produce a large amount of data that need special environments to interpret the results. Without the use of suitable tools and strategies, the transformation of the large data sets into information is not easily achievable. Therefore, in the context of the virtual laboratory of enhanced science, software tools are developed to handle mass spectrometry data sets. Using different data processing strategies for visualization, it enables fast mass spectrometric imaging of large surfaces at high-spatial resolution and thus aids in the understanding of various diseases and disorders. This article describes how to optimize the handling and processing of the data sets, including the selection of the most optimal data formats and the use of parallel processing. It also describes the tools and solutions and their application in mass spectrometric imaging strategies, including new measurement principles, image enhancement, and image artifact suppression.
SEGAN: Speech Enhancement Generative Adversarial Network (2017)

Current speech enhancement techniques operate on the spectral domain and/or exploit some higher-level feature. The majority of them tackle a limited number of noise conditions and rely on first-order statistics. To circumvent these issues, deep networks are being increasingly used, thanks to their ability to learn complex functions from large example sets. In this work, we propose the use of generative adversarial networks for speech enhancement. In contrast to current techniques, we operate at the waveform level, training the model end-to-end, and incorporate 28 speakers and 40 different noise conditions into the same model, such that model parameters are shared across them. We evaluate the proposed model using an independent, unseen test set with two speakers and 20 alternative noise conditions. The enhanced samples confirm the viability of the proposed model, and both objective and subjective evaluations confirm the effectiveness of it. With that, we open the exploration of generative architectures for speech enhancement, which may progressively incorporate further speech-centric design choices to improve their performance.
Cell proliferation in human soft tissue tumors correlates with platelet-derived growth factor B chain expression: an immunohistochemical and in situ hybridization study. (1994)

The authors tested the hypothesis that the B chain of the platelet-derived growth factor (PDGF), a known connective tissue mitogen and growth factor, could be expressed by human soft tissue tumors, and that its expression could play a role in the control of cell proliferation in these tumors. Using a set of 56 soft tissue tumors, including benign tumors and all three grades of sarcomas, PDGF-B chain protein was localized using immunohistochemistry and PDGF-B mRNA was localized using in situ hybridization. The hypothesis that PDGF-B expression was related to cell proliferation was tested by simultaneously demonstrating the expression of the proliferating cell nuclear antigen in sequential tissue sections of the same tumors. Sixty and 82% of tumors had demonstrable PDGF-B mRNA and protein, respectively, with a strong correlation between their degrees of expression (P = 0.0001). Among the sarcomas, a strong correlation between PDGF-B expression and increasing malignant tumor grade (P = 0.006), and between PDGF-B expression and increasing proliferating cell nuclear antigen index (P = 0.01) was found. All tumors were also demonstrated to express the beta receptor of PDGF via immunohistochemistry. These studies suggest that PDGF-B expression may be an important mediator of cell proliferation control, via an autocrine mechanism, in human soft tissue tumors and may correlate with clinical outcome in the sarcomas.
Synergism in the activation of human CD8 T cells by cross-linking the T-cell receptor complex with the CD8 differentiation antigen. (1986)

Resting human T cells can be activated and induced to proliferate by cross-linking the T-cell receptor complex (Ti/CD3) with anti-CD3 (T3) antibodies, such as OKT3, together with interleukin 2. Here we describe functional properties of another monoclonal anti-CD3 antibody (BMA 030) that, cross-linked in various ways, only weakly stimulates accessory-cell-depleted T-cell cultures. However, when cross-linked to anti-CD4 or anti-CD8 antibodies a markedly enhanced proliferation of the corresponding subpopulation is observed. We have concentrated on the analysis of CD8 cells and have found that BMA 030, when cross-linked together with anti-CD8 (T811), induced proliferation more than 100-fold greater than BMA 030 alone, whereas cross-linking with antibodies to other T-cell membrane antigens (HLA-A, B, or CD5) provided no or marginal synergistic signals. There was no synergistic effect when only one of the two antibodies, BMA 030 or T811, was cross-linked and the other was applied in soluble form. In contrast, each of the two antibodies alone, when applied in soluble form, inhibited activation induced by the cross-linked antibodies. The T-cell differentiation antigen CD8 has been implicated in the major histocompatibility complex (MHC) class I restricted specificity of CD8 T cells. In previous work from other laboratories only the negative influences of soluble anti-CD8 antibodies have been noted. In contrast, our results suggest that cross-linking between Ti/CD3 and CD8 may be a critical event in the activation of mature CD8 cells. We hypothesize that, in antigen-induced T-cell activation, CD8 and Ti/CD3 become cross-linked by their simultaneous binding to class I-associated structures. Such a mechanism, if required for proliferation in early T-cell ontogeny, could generate a selective pressure for CD8 cells to recognize class I-associated antigens.
Increased Neurofilament Light Chain Blood Levels in Neurodegenerative Neurological Diseases (2013)

We developed and validated a novel ECL based sandwich immunoassay for the NfL protein in serum (NfL(Umea47:3)); levels in ALS were more than 20-fold higher than in controls. Our data supports further longitudinal studies of serum NfL in neurodegenerative diseases as a potential biomarker of on-going disease progression, and as a potential surrogate to quantify effects of neuroprotective drugs in clinical trials.
Expression of two human beta-adrenergic receptors in Escherichia coli: functional interaction with two forms of the stimulatory G protein. (1991)

When expressed in Escherichia coli, the human beta 1- and beta 2-adrenergic receptors retain their ligand binding specificity. Their functional integrity was investigated by analyzing receptor-guanine nucleotide-binding regulatory (G) protein coupling by using two splice variants of the alpha subunit of the stimulatory G protein Gs synthesized in E. coli (rGs alpha-S and rGs alpha-L) and the beta gamma subunits of G protein purified from bovine brain. In competition binding experiments with (-)-[125I]iodocyanopindolol and (-)-isoproterenol, rGs alpha-S.beta gamma and rGs alpha-L.beta gamma reconstituted guanine nucleotide-sensitive high-affinity agonist binding with comparable affinities, whereas rGs alpha PT, a mutant of rGs alpha-L with an altered carboxyl terminus, and a recombinant subtype of the alpha subunit of the inhibitory G protein, rGi alpha-1, were approximately 20- and approximately 200-fold less potent, respectively. A comparison of the beta 1- and beta 2-adrenergic receptor expressed in E. coli with the beta 2-receptor in S49 murine lymphoma cyc- cell membranes revealed a similar affinity of rGs alpha-S and rGs alpha-L for the recombinant and native receptors. After stable incorporation of rGs alpha-S.beta gamma into E. coli membranes, receptor-G protein coupling was also verified by determining the isoproterenol-mediated acceleration of the rate for guanine 5'-[gamma-[35S]thio]triphosphate binding. These results show that (i) receptor-G protein coupling can be reconstituted in E. coli using recombinant components and that (ii) such an approach may be more generally used to evaluate coupling preferences between defined molecular species of receptors and G-protein subunits.
Proficiencies of Three Anaerobic Culture Systems for Recovering Periodontal Pathogenic Bacteria (1999)

Anaerobic culture is employed routinely in the primary isolation of periodontal pathogenic bacteria. However, little or no data exist on the relative abilities of the Coy anaerobic chamber (Coy Laboratory Products, Grass Lake, Mich.), the GasPak (Becton Dickinson Microbiology Systems, Cockeysville, Md.), and the AnaeroPack (Mitsubishi Gas Chemical America, Inc., New York, N.Y.) systems to grow important periodontal species, including Porphyromonas gingivalis, Prevotella intermedia/nigrescens, Bacteroides forsythus, Eubacterium species, Campylobacter species, Fusobacterium species, and Peptostreptococcus micros. A total of 78 specimens from advanced periodontitis lesions were collected anaerobically, plated on enriched blood agar medium, and incubated at 35 degrees C for 5 to 7 days in each anaerobic culture system. The three culture systems were equally efficient in isolating Porphyromonas gingivalis and Prevotella intermedia/nigrescens. The Coy anaerobic chamber yielded the highest proportional recoveries of Campylobacter (P = 0.0001; nonparametric analysis of variance) and Eubacterium (P = 0.009). The Coy anaerobic chamber and the GasPak system demonstrated higher proportional recoveries of Bacteroides forsythus (P = 0.0006) and Peptostreptococcus micros (P = 0.0001) than the AnaeroPack system. The AnaeroPack system was most efficient in growing Fusobacterium species (P = 0.0001). Overall, the Coy anaerobic chamber and the GasPak system showed the highest proportional recoveries of putative periodontal pathogens, but the recoveries by the various anaerobic test systems varied considerably from sample to sample.
The 60° grid: routing channels in width d/√3. (1991)

The 60 grid consists of vertical columns and diagonal tracks running at slopes of 2 30. This model offers a potentially large reduction in channel width, without resorting to wire overlap. For a channel routing problem with density d, the availability of the diagonal tracks leads to a lower bound of $: We present two nearoptimal channel routing algorithms. The first uses 5