gebhart/patrepeval huggingface dataset:
Tissue Spectrum Analyzer for Medical Use (1985)

There are many pigments within living tissue. The color varies according to the function of the tissue andthe condition of the disease. One method of quantitatively measuring this change and obtaining useful informationfor medical diagnosis is to project light onto the tissue and then conduct spectral analysis of the reflected light. Through the use of tissue spectrum analysis, we have been able to measure the ratio (called saturation O2) of hemoglobin combined with oxygen to the total hemoglobin content in the blood. Its usefulness has been provenin the diagnosis of the existence and stage of such diseases as chronic interstitial hepatitis and gastrohelcoma, and for the monitoring of the fetus' respiratory condition during delivery. The use of this method is in theprocess of being confirmed for experimentation in other fields.
Why Can't a Computer be more Like a Brain? (2007)

This paper discusses a theory of the neocortical algorithm called the hierarchical temporal memory (HTM). Hierarchical temporal memories are built around a hierarchy of nodes. The hierarchy and how it works are the most important features of HTM theory. In an HTM, knowledge is distributed across many nodes up and down the hierarchy. As an HTM is trained, the low-level nodes learn first. Representations in high-level nodes then share what was previously learned in low-level nodes
Privacy Preserving Back-Propagation Neural Network Learning Made Practical with Cloud Computing (2013)

To improve the accuracy of learning result, in practice multiple parties may collaborate through conducting joint Back-Propagation neural network learning on the union of their respective data sets. During this process no party wants to disclose her/his private data to others. Existing schemes supporting this kind of collaborative learning are either limited in the way of data partition or just consider two parties. There lacks a solution that allows two or more parties, each with an arbitrarily partitioned data set, to collaboratively conduct the learning. This paper solves this open problem by utilizing the power of cloud computing. In our proposed scheme, each party encrypts his/her private data locally and uploads the ciphertexts into the cloud. The cloud then executes most of the operations pertaining to the learning algorithms over ciphertexts without knowing the original private data. By securely offloading the expensive operations to the cloud, we keep the computation and communication costs on each party minimal and independent to the number of participants. To support flexible operations over ciphertexts, we adopt and tailor the BGN "doubly homomorphic" encryption algorithm for the multiparty setting. Numerical analysis and experiments on commodity cloud show that our scheme is secure, efficient, and accurate.
Synthesis of TGF-&beta;<sub>1</sub> by Vascular Endothelial Cells is Correlated with Cell Spreading (1992)

Cultured vascular endothelial cells (ECs) secrete transforming growth factor beta (TGF-beta) which stimulates intimal smooth muscle cells to synthesize increased amounts of lipoprotein-binding proteoglycans. We report here that the amount of TGF-beta 1 synthesized by ECs is correlated with EC density and cell spreading. ECs cultured at low density synthesized and secreted 2- to 3-fold more TGF-beta, measured by the Mink lung cell assay, than intermediate and high density cultures, and this increase in secreted protein was matched by a corresponding increase in mRNA for TGF-beta 1 measured by Northern hybridization using a [32P]-labeled cDNA probe for TGF-beta 1. TGF-beta 1 mRNA was detected in individual cells by in situ hybridization with the cDNA probe labeled with [35S] and with a [35S]-labeled 30-mer antisense oligonucleotide. In situ mRNA levels did not relate to cell density per se but to cell area. The larger the area of substratum covered, the more mRNA per cell, irrespective of cell density. For cell areas in the range 500-1,200 microns 2, a doubling of cell area resulted in an approximately 3-fold increase in mRNA. Cells cultured at low density had a larger mean cell area than cells cultured at higher densities, and this increased area was sufficient to account for the increased TGF-beta 1 mRNA levels found for the low density cultures by Northern hybridization. Despite variations in cell area, cell volumes did not change significantly with cell density.(ABSTRACT TRUNCATED AT 250 WORDS)
Two-Layer Sample Preparation:  A Method for MALDI-MS Analysis of Complex Peptide and Protein Mixtures (1999)

The analytical performance of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for direct analysis of peptide and protein mixtures is strongly dependent on the sample and matrix preparation. A two-layer sample preparation method is demonstrated to be very effective for analyzing complex mixtures. In this method, the first layer on the MALDI probe is the densely packed matrix microcrystals formed by fast solvent evaporation of a matrix solution. A mixture solution containing both matrix and sample is then deposited onto the first layer to form uniform analyte/matrix micrococrystals. It is found that the addition of matrix to the second-layer sample solution proves to be critical in analyzing mixtures of peptides and proteins covering a broad mass range. The effect of solvent conditions for preparing the second-layer solution is discussed. The application of this method is demonstrated for the analysis of cow's milk where milk proteins as well as peptide fragments produced from proteins by indigenous proteinases are detected. Direct analyses of peptides and proteins from a bacteria extract and crude egg white are also illustrated.
Phylogenetic and Evolutionary Relationships among Torovirus Field Variants: Evidence for Multiple Intertypic Recombination Events (2003)

Toroviruses (family Coronaviridae, order Nidovirales) are enveloped, positive-stranded RNA viruses that have been implicated in enteric disease in cattle and possibly in humans. Despite their potential veterinary and clinical relevance, little is known about torovirus epidemiology and molecular genetics. Here, we present the first study into the diversity among toroviruses currently present in European swine and cattle herds. Comparative sequence analysis was performed focusing on the genes for the structural proteins S, M, HE, and N, with fecal specimens serving as sources of viral RNA. Sequence data published for animal and human torovirus variants were included. Four genotypes, displaying 30 to 40% divergence, were readily distinguished, exemplified by bovine torovirus (BToV) Breda, porcine torovirus (PToV) Markelo, equine torovirus Berne, and the putative human torovirus. The ungulate toroviruses apparently display host species preference. In phylogenetic analyses, all PToV variants clustered, while the recent European BToVs mostly resembled the New World BToV variant Breda, identified 19 years ago. However, we found ample evidence for recurring intertypic recombination. All newly characterized BToV variants seem to have arisen from a genetic exchange, during which the 3' end of the HE gene, the N gene, and the 3' nontranslated region of a Breda virus-like parent had been swapped for those of PToV. Moreover, some PToV and BToV variants carried chimeric HE genes, which apparently resulted from recombination events involving hitherto unknown toroviruses. From these observations, the existence of two additional torovirus genotypes can be inferred. Toroviruses may be even more promiscuous than their closest relatives, the coronaviruses and arteriviruses.
Fluorescence resonance energy transfer studies on the proximity relationship between the intrinsic metal ion and substrate binding sites of Escherichia coli RNA polymerase. (1987)

DNA-dependent RNA polymerase from Escherichia coli contains 2 mol of zinc/mol of holoenzyme (alpha 2 beta beta' sigma) with one zinc each in the beta and beta' subunits. A new method to substitute selectively the zinc in the beta subunit was developed by the inactivation of RNA polymerase with 0.25 M NaNO3, 1 M NaCl, 1 mM diaminocyclohexane tetraacetic acid, and 0.1 mM dithiothreitol followed by reconstitution with Co(II), Cd(II), or Cu(II). The hybrid Co-Zn, Cd-Zn, or Cu-Zn RNA polymerase thus obtained retains, respectively, 91, 88, and 50% enzyme activity of the reconstituted Zn-Zn RNA polymerase. Co-Zn RNA polymerase exhibits absorption maxima at 395 and 465 nm, and Cu-Zn RNA polymerase at 637 nm (epsilon = 815 M-1 cm-1). 1-Aminonaphthalene-5-sulfonic acid (AmNS) derivatives of ATP, UTP, and dinucleoside monophosphates (diNMPs), UpA or ApU, were synthesized with AmNS attached to NTP via a gamma-phosphoamidate bond or to diNMPs via a 5'-secondary amine linkage. Since the fluorescence emission maxima of (5'-AmNS)UpA, (gamma-AmNS)ATP, and (gamma-AmNS)UTP at 445, 464, and 464 nm, respectively, when excited at 340 nm, overlap the 465-nm absorption band of Co-Zn RNA polymerase, the spatial relationship between fluorescence substrate analogs and the intrinsic Co(II) in Co-Zn RNA polymerase was studied by fluorescence resonance energy transfer technique. The fluorescence of the initiator, (5'-AmNS)UpA, and elongator, (gamma-AmNS)UTP, of the RNA chain, was quenched 20.3 and 7.1%, by the addition of saturation concentration of Zn-Zn RNA polymerase, and 21.3 and 14.7%, respectively, by the addition of template, poly(dA-dT). The fluorescence of (5'-AmNS)UpA and (gamma-AmNS)UTP was quenched 81.8 and 80.6%, respectively, by the addition of the saturation concentration of Co-Zn RNA polymerase in the absence of template, and 82.7 and 82.9% in the presence of template. On the basis of respective Ro values of 21.3 and 21.9 A for the (5'-AmNS)UpA-Co and (gamma-AmNS)UTP-Co pairs, the distances from Co(II) to the initiation site and to the elongation site were calculated to be 17.4 and 17.5 A, respectively, in the absence and 17.2 and 17.4 A in the presence of template.
A 71-Gene Signature of TRAIL Sensitivity in Cancer Cells (2011)

TNF-related apoptosis inducing ligand (TRAIL) is a promising anticancer agent because of its ability to selectively induce apoptosis in cancer cells but not in most normal cells. However, some cancer cells are resistant to TRAIL cytotoxicity thereby limiting its therapeutic efficacy. Using genome-wide mRNA expression profiles from the NCI60 panel and their differential sensitivities to TRAIL-induced apoptosis, we have identified 71 genes whose expression levels are systemically higher in TRAIL-sensitive cell lines than resistant lines. The elevated expression of the 71 genes was able to accurately predict TRAIL sensitivity in the NCI60 training set and two test sets consisting of a total of 95 human cancer cell lines. Interestingly, the 71-gene signature is dominated by two functionally related gene families-interferon (IFN)-induced genes and the MHC genes. Consistent with this result, treatment with IFN-γ augmented TRAIL-induced apoptosis. The 71-gene signature could be evaluated clinically for predicting tumor response to TRAIL-related therapies.
Nitrovasodilators Have Proliferative as Well as Antiproliferative Effects (1991)

Summary: The nitrovasodilator sodium nitroprusside (SNP) is mitogenic in rabbit dermal fibroblasts within the concentration range of 0.1-100 μM. In contrast, SNP at >100 μM is antiproliferative and at concentrations >250 μM is cytotoxic in fibroblasts. SNP (5-1,000 μM) is mitogenic in porcine and rabbit aortic smooth muscle cells but is antiproliferative at concentrations >1,000 μM. A prolonged incubation period (24 h) with SNP is necessary to observe mitogenic effects and the effects of SNP on smooth muscle cells occur at near-maximal stimulation of the soluble guanylate cyclase. These data demonstrate that SNP has both mitogenic and antiproliferative effects in fibroblasts and smooth muscle cells and that the mitogenic effect may be related to stimulation by nitric oxide of the soluble guanylate cyclase.
Nomenclaturas Estratigráficas Naconales E Internacionales: Descripción Y Evaluación (1989)

espanolSe sintetizan y comparan las unidades establecidas en el American Stratigraphic con las aceptadas y recomendadas por la International Subcommission on Stratigraphic Classification ademas de hacer referencia critica a otros codigos y normas de Europa Occidental y de la URSS. EnglishA description of defined units in stratigraphy is given according to the North American Stratigraphic Code and official publications of the Intetnational Subcommission on Stratigraphic Classification. In addition, a comparison is made between the different perspectives and kinds of units accepted, by the North American Commission on Stratigraphic Nomenclature and the ISSC, and also by other codes and norms issued in occidental European countries and in the USSR
MicroRNA-21 Is an Antiapoptotic Factor in Human Glioblastoma Cells (2005)

MicroRNAs (miRNAs) are small noncoding RNA molecules that regulate protein expression by targeting the mRNA of protein-coding genes for either cleavage or repression of translation. The roles of miRNAs in lineage determination and proliferation as well as the location of several miRNA genes at sites of translocation breakpoints or deletions has led to the speculation that miRNAs could be important factors in the development or maintenance of the neoplastic state. Here we show that the highly malignant human brain tumor, glioblastoma, strongly over-expresses a specific miRNA, miR-21. Our studies show markedly elevated miR-21 levels in human glioblastoma tumor tissues, early-passage glioblastoma cultures, and in six established glioblastoma cell lines (A172, U87, U373, LN229, LN428, and LN308) compared with nonneoplastic fetal and adult brain tissues and compared with cultured nonneoplastic glial cells. Knockdown of miR-21 in cultured glioblastoma cells triggers activation of caspases and leads to increased apoptotic cell death. Our data suggest that aberrantly expressed miR-21 may contribute to the malignant phenotype by blocking expression of critical apoptosis-related genes.
Contrasting cognitive deficits in attention deficit hyperactivity disorder versus reading disability. (1993)

We compared 2 common and sometimes comorbid developmental disorders, reading disability (RD) and attention deficit hyperactivity disorder (ADHD), in 2 cognitive domains, phonological processes (PP) and executive functions (EF). Subjects were 70 boys of early school age, studied by means of a 2 (RD vs. no RD) × 2 (ADHD vs. no ADHD) × 2 (domain type) mixed-model design. The 2 RD groups (RD-only and RD plus ADHD) were significantly impaired compared with both the control and ADHD-only groups on a PP composite score but performed normally on the EF composite score. The ADHD-only group had an opposite profile and was significantly different from both RD groups and from controls on the EF composite score. Thus, there was a double-dissociation between the RD-only and ADHD-only groups. The comorbid group resembled the RDonly group, consisttent with the hypothesis that their ADHD symptoms are secondary to RD
Mechanism by Which the Prone Position Improves Oxygenation in Acute Lung Injury (1994)

The mechanism by which oxygenation improves when patients with ARDS are turned from supine to prone position is not known. From results of our previous studies we reasoned that (1) when supine, in the setting of lung injury, transpulmonary pressure will be less than airway opening pressure and (2) atelectasis will develop preferentially in dorsal lung areas, and (3) both ventilation and ventilation/perfusion ratios would improve in these regions on turning prone. To study this directly, we measured regional ventilation and perfusion using 81mKr and 99mTc-MAA, respectively, and single photon emission computed tomography, both prone and supine, in four control animals and four given oleic acid. After oleic acid, the prone position improved (1) oxygenation (mean +/- SD PaO2 = 140 +/- 112 versus 453 +/- 54 mm Hg), (2) median ventilation/perfusion ratios (0.77 versus 0.95), (3) ventilation/perfusion heterogeneity (coefficient of variation 86 +/- 15 versus 61 +/- 6), and (4) the gravitational ventilation/perfusion gradient (dependent to non-dependent slopes of 0.22 versus -0.02, all p < 0.05). The prone position generates a transpulmonary pressure sufficient to exceed airway opening pressure in dorsal lung regions, i.e., in regions where atelectasis, shunt, and ventilation/perfusion heterogeneity are most severe, without adversely affecting ventral lung regions.
A peptide recognized by human cytolytic T lymphocytes on HLA-A2 melanomas is encoded by an intron sequence of the N-acetylglucosaminyltransferase V gene. (1996)

A cytolytic T lymphocyte (CTL) clone that lyses many HLA-A2 melanomas was derived from a population of tumor-infiltrating lymphocytes of an HLA-A2 melanoma patient. The gene coding for the antigen recognized by this CTL was identified by transfection of a cDNA library. It is the gene which has been reported to code for N-acetylglucosaminyltransferase V (GnT-V). Remarkably, the antigenic peptide recognized by the CTL is encoded by a sequence located in an intron. In contrast to the fully spliced GnT-V mRNA, which was found in a wide range of normal and tumoral tissues, the mRNA containing the intron region coding for the antigen was not found at a significant level in normal tissues. This mRNA was observed to be present in about 50% of melanomas. Our results suggest that a promoter located near the end of the relevant intron is activated in melanoma cells, resulting in the production of an mRNA coding for the antigen.
Transcriptional Activation Modulated by Homopolymeric Glutamine and Proline Stretches (1994)

Many transcription factors contain proline- or glutamine-rich activation domains. Here it is shown that simple homopolymeric stretches of these amino acids can activate transcription when fused to the DNA binding domain of GAL4 factor. In vitro, activity increased with polymer length, whereas in cell transfection assays maximal activity was achieved by 10 to 30 glutamines or about 10 prolines. Similar results were obtained when glutamine stretches were placed within a [GAL4]-VP16 chimeric protein. Because these stretches are encoded by rapidly evolving triplet repeats (microsatellites), they may be the main cause for modulation of transcription factor activity and thus result in subtle or overt genomic effects.
Construction and validation of an activating and inhibitory Chimeric Antigen Receptor (CAR) system (2016)

Os autores externos submeteram sua publicação para apresentação de trabalho no evento 'International Symposium on Immunobiologicals', que foi coordenado e organizado pelo Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), da Fundação Oswaldo Cruz.
Comprehensive assessment of DNA copy number alterations in human prostate cancers using Affymetrix 100K SNP mapping array (2006)

Although multiple recurrent chromosomal alterations have been identified in prostate cancer cells, the specific genes driving the apparent selection of these changes remain largely unknown. In part, this uncertainty is due to the limited resolution of the techniques used to detect these alterations. In this study, we applied a high-resolution genome-wide method, Affymetrix 100K SNP mapping array, to screen for somatic DNA copy number (CN) alterations among 22 pairs of samples from primary prostate cancers and matched nonmalignant tissues. We detected 355 recurrent deletions and 223 recurrent gains, many of which were novel. As expected, the sizes of novel alterations tend to be smaller. Importantly, among tumors with increasing grade, Gleason sum 6, 7, and 8, we found a significant trend of larger number of alterations in the tumors with higher grade. Overall, gains are significantly more likely to occur within genes (74%) than are deletions (49%). However, when we looked at the most frequent CN alterations, defined as those in > or =4 subjects, we observed that both gains (85%) and deletions (57%) occur preferentially within genes. An example of a novel, recurrent alteration observed in this study was a deletion between the ERG and TMPRSS2 genes on chromosome 21, presumably related to the recently identified fusion transcripts from these two genes. Results from this study provide a basis for a systematic and comprehensive cataloging of CN alterations associated with grades of prostate cancer, and the subsequent identification of specific genes that associated with initiation and progression of the disease. This article contains supplementary material available via the Internet at http://www.interscience.wiley.com/jpages/1045-2257/suppmat
The molecular biology of mixed lineage leukemia (2009)

Mixed lineage leukemia is a very aggressive blood cancer that predominantly occurs in pediatric patients. In contrast to other types of childhood acute leukemias, mixed lineage leukemia presents with a dismal prognosis and despite the availability of advanced treatment methods cure rates have stagnated over the last years. Mixed lineage leukemia is characterized by the presence of MLL fusion proteins that are the result of chromosomal translocations affecting the MLL gene at 11q23. These events juxtapose the amino-terminus of the histone methyltransferase MLL with a variety of different fusion partners that destroy normal histone methyltransferase function of MLL and replace it by heterologous functions contributed by the fusion partner. The resulting chimeras are transcriptional regulators that take control of targets normally controlled by MLL with the clustered HOX homeobox genes as prominent examples. Recent studies suggested that MLL fusion partners activate transcription by two different mechanisms. Some of these proteins are themselves chromatin modifiers that introduce histone acetylation whereas other fusion partners can recruit histone methyltransferases. In particular, histone H3 specific methylation at lysine 79 catalyzed by DOT1L has been recognized as a hallmark of chromatin activated by MLL fusion proteins. Interestingly, several frequent MLL fusion partners seem to coordinate DOT1L activity with a protein complex that stimulates the elongation phase of transcription by phosphorylating the carboxy-terminal repeat domain of RNA polymerase II. The discovery of these novel enzymatic activities that are essentially involved in MLL fusion protein function presents potential new targets for a rational drug development.
Evidence of Rickettsia typhi and the potential for murine typhus in Jayapura, Irian Jaya, Indonesia. (2002)

Murine typhus (etiologic agent: Rickettsia typhi) is endemic to Indonesia, especially on the highly populated island of Java. A survey of rodents from Irian Jaya, the eastern-most province of Indonesia, indicated striking geographic variation in risk factors associated with murine typhus. Murid rodents (n = 112) collected from two villages in the Arso district of northeastern Irian Jaya, were found to be free of ectoparasites normally associated with transmission of R. typhi (i.e., Xenopsylla cheopis). All rodents (n = 72) tested by enzyme-linked immunosorbent assay were negative for antibodies to R. typhi, whereas 12.5% (9/72) were positive for antibodies to Orienta tsutsugamushi. In contrast, both Rattus norvegicus and R. rattles (combined n = 87) from the harbor area of the provincial capital, Jayapura, were infested with flea ectoparasites. X. cheopis was found on 31 (35.6%) of the live-captured rodents. Serum samples from nine of 82 rodents contained antibodies reactive to R. typhi (11.0%). These data show for the first time that rodents exposed to R. typhi are well established in Jayapura, and that some of these rodents harbor fleas potentially capable of transmitting murine typhus and plague.
Fumarate treatment in progressive forms of multiple sclerosis: first results of a single-center observational study (2014)

Our pilot data indicate that fumarate therapy appears to be safe and well tolerated by patients with progressive MS. In more than 75% of cases no further disease progression was evident. However, controlled studies are warranted to evaluate the detailed therapeutic potential of fumarates and their long-term effects in progressive MS.