gebhart/patrepeval huggingface dataset:
T-Cell Responses to Autoantigens in IDDM: The Search for the Holy Grail (1996)

IDDM (type I diabetes) is generally believed to result from T-cell-mediated autoimmune destruction of the insulin-producing beta-cells in the pancreatic islets of Langerhans. In the last few years, considerable progress has been made with regard to the identification and characterization of candidate autoantigens recognized by autoantibodies; several of these candidate autoantigens are recognized by T-cells, including insulin, GAD65 and GAD67, heat-shock protein 65 (hsp65), and islet-cell antigen 69 (ICA69). In addition to these, a number of unidentified beta-cell antigens, including insulin-secretory granule membrane proteins and a 38-kDa protein, have been shown to stimulate T-cells of IDDM patients. However, T-cell autoreactivity to islet antigens is not specific for IDDM, and the T-cell target antigens are not specific for beta-cells. Moreover, the autoantigens involved in the initiation of the insulitis must be defined, and the mechanism of the T-cell-dependent beta-cell destruction remains to be unraveled. This review focuses on T-cell autoreactivity in IDDM in humans and the implications of the present knowledge for immunointervention and monitoring of immunotherapeutic trials.
Detection of Prostatic Specific Membrane Antigen Messenger RNA Using Immunobead Reverse Transcriptase Polymerase Chain Reaction (1999)

The present study was performed to detect circulating prostatic carcinoma (PC) cells using a novel three-step immunobead reverse transcriptase (RT) polymerase chain reaction (PCR) assay for prostatic specific membrane antigen (PSMA) messenger RNA (mRNA). The sensitivity and specificity of this technique was assessed and the incidence of immunobead RT-PCR positivity correlated with progressive metastatic disease and serum prostatic specific antigen (PSA) levels. Fifty peripheral blood (PB) samples from 46 patients with PC were incubated with magnetic beads coated with Ber-EP4 antibody directed against the human epithelial antigen a membrane antigen widely expressed by epithelial cells. The epithelial cell-enriched magnetic fraction was then subjected to mRNA isolation using oligo-deoxythymidine (dT) magnetic beads. Nested RT-PCR for PSMA was performed on the mRNA oligo-dT complex and the identity of the RT-PCR products was confirmed by Southern blotting. Twenty-one PB samples from 8 control subjects without PC were also evaluated. Three-step immunobead PSMA RT-PCR was able to detect one PC cell per 1 mL of PB. The positivity rate of the RT-PCR assay was significantly higher (11 of 25; 44%) in patients with metastatic tumor than in patients with non-metastatic disease (1 of 21; 5%) (P = 0.003). In patients with metastatic PC, RT-PCR positivity was much higher in patients with progressive disease (10 of 13; 77%) than in patients with responding or stable disease (1 of 12; 8%) (P = 0.001). There was a statistically significant correlation between immunobead PSMA PCR positivity and high levels of serum PSA (P = 0.005). All control subjects without PC tested negative for PSMA PCR. The three-step immunobead RT-PCR for PSMA can detect circulating PC cells with high specificity and sensitivity. Preliminary data show a strong correlation between immunobead PCR positivity, the presence of progressive metastatic disease, and high levels of serum PSA.
Immunoneutralization of Growth Differentiation Factor 9 Reveals It Partially Accounts for Mouse Oocyte Mitogenic Activity1 (2004)

Paracrine factors secreted by oocytes play a pivotal role in promoting early ovarian follicle growth and in defining a morphogenic gradient in antral follicles, yet the exact identities of these oocyte factors remain unknown. This study was conducted to determine the extent to which the mitogenic activity of mouse oocytes can be attributed to growth differentiation factor 9 (GDF9). To do this, specific anti-human GDF9 monoclonal antibodies were generated. Based on epitope mapping and bioassays, a GDF9 neutralizing antibody, mAb-GDF9-53, was characterized with very low cross-reactivity with related transforming growth factor (TGF)beta superfamily members, including BMP15 (also called GDF9B). Pep-SPOT epitope mapping showed that mAb-GDF9-53 recognizes a short 4-aa sequence, and three-dimensional peptide modeling suggested that this binding motif lies at the C-terminal fingertip of mGDF9. As predicted by sequence alignments and modeling, the antibody detected recombinant GDF9, but not BMP15 in a Western blot and GDF9 protein in oocyte extract and oocyte-conditioned medium. In a mouse mural granulosa cell (MGC) bioassay, mAb-GDF9-53 completely abolished the mitogenic effects of GDF9, but had no effect on TGFbeta1 or activin A-stimulated MGC proliferation. An unrelated IgG at the same dose had no effect on GDF9 activity. This GDF9 neutralizing antibody was then tested in an established oocyte-secreted mitogen bioassay, where denuded oocytes cocultured with granulosa cells promote cell proliferation in a dose-dependent manner. The mAb-GDF9-53 dose dependently (0-160 microg/ml) decreased the mitogenic activity of oocytes but only by approximately 45% at the maximum dose of mAb. Just 5 microg/ml of mAb-GDF9-53 neutralized 90% of recombinant mGDF9 mitogenic activity, but only 15% of oocyte activity. Unlike mAb-GDF9-53, a TGFbeta pan-specific neutralizing antibody did not affect the mitogenic capacity of the oocyte, but completely neutralized TGF beta 1-induced DNA synthesis. This study has characterized a specific GDF9 neutralizing antibody. Our data provide the first direct evidence that the endogenous GDF9 protein is an important oocyte-secreted mitogen, but also show that GDF9 accounts for only part of total oocyte bioactivity.
Alpha-amylase genes (amyR2 and amyE+) from an alpha-amylase-hyperproducing Bacillus subtilis strain: molecular cloning and nucleotide sequences (1983)

amyR2, amyE+, and aroI+ alleles from an alpha-amylase-hyperproducing strain, Bacillus subtilis NA64, were cloned in temperate B. subtilis phage p11, and the amyR2 and amyE+ genes were then recloned in plasmid pUB110, which was designated pTUB4. The order of the restriction sites, ClaI-EcoRI-PstI-SalI-SmaI, found in the DNA fragment carrying amyR2 and amyE+ from the phage genome was also found in the 2.3-kilobase insert of pTUB4. Approximately 2,600 base pairs of the DNA nucleotide sequence of the amyR2 and amyE+ gene region in pTUB4 were determined. Starting from an ATG initiator codon, an open reading frame was composed of a total 1,776 base pairs (592 amino acids). Among the 1,776 base pairs, 1,674 (558 amino acids) were found in the cloned DNA fragment, and 102 base pairs (34 amino acids) were in the vector pUB110 DNA. The COOH terminal region of the alpha-amylase of pTUB4 was encoded in pUB110. The electrophoretic mobility in a 7.5% polyacrylamide gel of the alpha-amylase was slightly faster than that of the parental alpha-amylases. The NH2 termination portion of the gene encoded a 41-amino acid-long signal sequence (Ohmura et al., Biochem. Biophys. Res. Commun. 112:687-683, 1983). The DNA sequence of the mature extracellular alpha-amylase, a potential RNA polymerase recognition site and Pribnow box (TTGATAGAGTGATTGTGATAATTTAAAAT), and an AT-rich inverted repeat structure which has free energy of -8.2 kcal/mol (-34.3 kJ/mol) were identified. The AT-rich inverted repeat structure seemed to correspond to the hyperproducing character. The nucleotide sequence around the region was quite different from the promoter region of the B. subtilis 168 alpha-amylase gene which was cloned in the Escherichia coli vector systems.
Prediction of sensitivity of esophageal tumors to adjuvant chemotherapy by cDNA microarray analysis of gene-expression profiles. (2001)

We applied cDNA microarray analyses of 9216 genes to establish a genetic method for predicting the outcome of adjuvant chemotherapy to esophageal cancers. We analyzed expression profiles of 20 esophageal cancer tissues from patients who were treated with the same adjuvant chemotherapy after removal of tumor by operation, and we attempted to find genes associated with the duration of survival after surgery. By comparing expression profiles of those cancer tissues, we identified by statistical analysis 52 genes that were likely to be correlated with prognosis and possibly with sensitivity/resistance to the anticancer drugs. We also developed a drug response score based on the differential expression of these genes, and we found a significant correlation between the drug response score and individual patients' prognoses. Our results indicated that this scoring system, based on microarray analysis of selected genes, is likely to have great potential for predicting the prognosis of individual cancer patients with the adjuvant chemotherapy.
Ad Hoc Networking (2008)

Ad hoc networks are to computing devices what Yahoo Personals are to single people: both help individuals communicate productively with strangers while maintaining security. Under the rules of ad hoc networking--which continue to evolve--your mobile phone can, when placed in proximity to your handheld address book, establish a little network on its own and enable data sharing between the two devices. In Ad Hoc Networking, Charles Perkins has compiled a series of technical papers about networking on the fly from a variety of laboratories and experts. The collection explains the latest thinking on how mobile devices can best discover, identify, and communicate with other devices in the vicinity. In this treatment, ad hoc networking covers a broad swath of situations. An ad hoc network might consist of several home-computing devices, plus a notebook computer that must exist on home and office networks without extra administrative work. Such a network might also need to exist when the people and equipment in normally unrelated military units need to work together in combat. Though the papers in this book are much more descriptive of protocols and algorithms than of their implementations, they aim individually and collectively at commercialization and popularization of mobile devices that make use of ad hoc networking. You'll enjoy this book if you're involved in researching or implementing ad hoc networking capabilities for mobile devices. --David Wall Topics covered: The state-of-the-art in protocols and algorithms to be used in ad hoc networks of mobile devices that move in and out of proximity to one another, to fixed resources like printers, and to Internet connectivity. Routing with Destination-Sequenced Distance Vector (DSDV), Dynamic Source Routing (DSR), Ad hoc On-Demand Distance Vector (AODV), and other resource-discovery and routing protocols; the effects of ad hoc networking on bandwidth consumption; and battery life.
Schizophrenia After Prenatal Exposure to the Dutch Hunger Winter of 1944-1945 (1992)

We tested the hypothesis that first-trimester exposure to acute food deprivation is a risk factor for schizophrenia. A sharp and time-limited decline in the food intake of the Dutch population following a Nazi blockade in 1944 to 1945 created a unique if tragic natural experiment to test this hypothesis in three regions of Holland (west, north, and south). In the west, or famine region, birth cohorts exposed to severe food deprivation (an average daily ration under 4200 kJ) during the first trimester showed a substantial increase in hospitalized schizophrenia for women but not for men. Relative risks for women were 2.17 for "broad" and 2.56 for "restricted" schizophrenia. Moderate food deprivation during the first trimester (average daily ration under 6300 kJ) was not associated with increased risk of schizophrenia in the famine region. In the north and south regions, numbers were smaller and there was no exposure to severe famine. Birth cohorts exposed to moderate food deprivation during the first trimester showed a trend toward increased risk of schizophrenia for women. These findings give plausibility to the proposition that early prenatal nutrition can have a gender-specific effect on the risk of schizophrenia.
HOMOLOGOUS PAIRING AND DNA STRAND-EXCHANGE PROTEINS (1994)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
La documentación en el Patrimonio Nacional (1992)

The Circe Plan programme, an integrated system of computerized documentation and office automation, created by the Patrimonio Nacional in the scope of the conservation and historical chattels management, includes three essential projects: Goya, for the Rojal Collections; Ibis, for the bibliographic heritage, and Clio, for the documentary heritage. The Goya project contains an alphanumeric database and another of colour digitalized images. Both are linked can be on lineoperating together. The alphanumeric information is concentrated in a single record for each object, using an unique record for all kinds of objects, and it can be recovered in a single record for each object, using an unique record for all kinds of objects, and it can be recovered through 129 fields, that cover all the inventory, caraloguing, investigation, restoration and management data. Up to now, 125,000 records has been carried out.
Analysis of a Semitendinosus Autograft in a Rabbit Model (1997)

The purpose of this study was to evaluate the histologic and biomechanical changes that occur between 12 and 52 weeks in an intraarticular, semitendinosus autograft placed through tibial and femoral drill holes in a rabbit model. The results of this study show that, in this rabbit model, the soft tissue graft maintained its biologic fixation in the osseous tunnel when stressed to failure at 1 year. The bony fixation occurred by the formation of an indirect tendon insertion, and this formation was complete by 26 weeks. At 52 weeks, large differences persisted in the strength and stiffness of the graft compared with the normal semitendinosus tendon and anterior cruciate ligament. Based on the results of this study, we support a cautious approach in returning patients to early full activity, including sports, after anterior cruciate ligament reconstruction with a semitendinosus autograft.
Macrophage and retinal pigment epithelium expression of angiogenic cytokines in choroidal neovascularization. (2002)

This study shows that RPE cells express MCP, a cytokine involved with macrophage recruitment, and that macrophages express TF in CNV. Macrophages and RPE express VEGF, thus perpetuating angiogenesis. TF is involved with fibrin formation and provides a scaffold effect for growth of the CNV complex. CNV likely represents a dynamic process with inflammatory active and inflammatory inactive (involutional) stages.
Increased gene transfer into human hematopoietic progenitor cells by extended in vitro exposure to a pseudotyped retroviral vector (1994)

Retroviral-mediated gene transfer is the most attractive modality for gene transfer into hematopoietic stem cells. However, transduction efficiency has been low using amphotropic Moloney murine leukemia virus (MoMLV) vectors. In this study, we investigated modifications of gene transfer using amphotropic MoMLV vectors in cell-free supernatant for their ability to increase the currently low transduction of both committed hematopoietic progenitors, granulocyte-macrophage colony-forming units (CFU-GMs), and their precursors, long-term culture-initiating cells (LTC-IC). First, based on the observation that bone marrow cells express more gibbon ape leukemia virus (GALV) receptor (Glvr-1) than amphotropic receptor (Ram-1), PG13/LN, which is a MoMLV vector pseudotyped with the GALV envelope, was compared with the analogous amphotropic envelope vector (PA317/LN). Second, progenitor cell transduction efficiency was compared between CD34 enriched and nonenriched progenitor populations. Third, the duration of transduction in vitro was extended to increase the proportion of progenitor cells that entered cell cycle and could thereby integrate vector cDNA. In 20 experiments, 1 x 10(6) marrow or peripheral blood mononuclear cells (PBMCs)/mL were exposed to identical titers of pseudotyped PG13/LN vector or PA317/LN vector in the presence of recombinant human interleukin-1 (IL-1), IL-3, IL-6, and stem cell factor (SCF; c-kit ligand) for 5 days. 50% of fresh vector supernatant was refed daily. Hematopoietic progenitor cells as measured by G418-resistant granulomonocytic colony (CFU-GM) formation were transduced more effectively with PG13/LN (19.35%) than with PA317/LN (11.5%, P = .012). In 11 further experiments, enrichment of CD34 antigen positive cells significantly improved gene transfer from 13.9% G418-resistant CFU-GM in nonenriched to 24.9% in CD34-enriched progenitor cells (P < .01). To analyze gene transfer after extended growth factor-supported long-term culture, 1 x 10(6) marrow cells/mL were cultured with IL-1, IL-3, IL-6, and SCF (50 ng/mL each) for 1, 2, and 3 weeks. Fifty percent of PG13/LN supernatant with growth factors was refed on 5 days per week. Five percent of marrow CFU-GM and 67% of LTC-IC were G418 resistant at 1 week (n = 4), 60% of CFU-GM and 100% of LTC-IC were resistant at 2 weeks (n = 2) and 74% of CFU-GM (n = 4) and 82% of LTC-IC (n = 2) were resistant at three weeks.(ABSTRACT TRUNCATED AT 400 WORDS)
FIRE: FInding Rogue nEtworks (2009)

For many years, online criminals have been able to conduct their illicit activities by masquerading behind disreputable Internet service providers (ISPs). For example, organizations such as the Russian business network (RBN), Atrivo (a.k.a., Intercage), McColo, and most recently, the triple fiber network (3FN) operated with impunity, providing a safe haven for Internet criminals for their own financial gain. What primarily sets these ISPs apart from others is the significant longevity of the malicious activities on their networks and the apparent lack of action taken in response to abuse reports. Interestingly, even though the Internet provides a certain degree of anonymity, such ISPs fear public attention. Once exposed, rogue networks often cease their malicious activities quickly, or are de-peered (disconnected) by their upstream providers. As a result, the Internet criminals are forced to relocate their operations. In this paper, we present FIRE, a novel system to identify and expose organizations and ISPs that demonstrate persistent, malicious behavior. The goal is to isolate the networks that are consistently implicated in malicious activity from those that are victims of compromise. To this end, FIRE actively monitors Botnet communication channels, drive-by-download servers, and phishing Web sites. This data is refined and correlated to quantify the degree of malicious activity for individual organizations. We present our results in real-time via the Web site maliciousnetworks.org. These results can be used to pinpoint and to track the activity of rogue organizations, preventing criminals from establishing strongholds on the Internet. Also, the information can be compiled into a null-routing blacklist to immediately halt traffic from malicious networks.
Extensible language-aware merging (2003)

Parallel development has become standard practice in software development and maintenance. Though almost every revision control and configuration management system provides some form of merging for combining changes made in parallel, these mechanisms often yield unsatisfactory results. The authors present a new merging algorithm, that uses a fast differencing algorithm and renaming analysis to provide better merge results. The system is language aware, but not language dependent and does not require a special editor so it can be easily integrated in current development environments.
Continuously active interferometer stabilization and control for time-bin entanglement distribution (2015)

We describe a new method enabling continuous stabilization and fine-level phase control of time-bin entanglement interferometers. Using this technique we demonstrate entangled photon transmission through 50 km of standard single-mode fiber. This technique reuses the entangled-pair generation pump which is co-propagated with the transmitted entangled photons. The co-propagating pump adds minimal noise to the entangled photons which are characterized by measuring a two-photon interference fringe.
The Compensatory Reserve For Early and Accurate Prediction Of Hemodynamic Compromise (2016)

Shock is deadly and unpredictable if it is not recognized and treated in early stages of hemorrhage. Unfortunately, measurements of standard vital signs that are displayed on current medical monitors fail to provide accurate or early indicators of shock because of physiological mechanisms that effectively compensate for blood loss. As a result of new insights provided by the latest research on the physiology of shock using human experimental models of controlled hemorrhage, it is now recognized that measurement of the body's reserve to compensate for reduced circulating blood volume is the single most important indicator for early and accurate assessment of shock. We have called this function the "compensatory reserve," which can be accurately assessed by real-time measurements of changes in the features of the arterial waveform. In this paper, the physiology underlying the development and evaluation of a new noninvasive technology that allows for real-time measurement of the compensatory reserve will be reviewed, with its clinical implications for earlier and more accurate prediction of shock.
Active Learning in Approximately Linear Regression Based on Conditional Expectation of Generalization Error (2006)

The goal of active learning is to determine the locations of training input points so that the generalization error is minimized. We discuss the problem of active learning in linear regression scenarios. Traditional active learning methods using least-squares learning often assume that the model used for learning is correctly specified. In many practical situations, however, this assumption may not be fulfilled. Recently, active learning methods using importance-weighted least-squares learning have been proposed, which are shown to be robust against misspecification of models. In this paper, we propose a new active learning method also using the weighted least-squares learning, which we call ALICE (Active Learning using the Importance-weighted least-squares learning based on Conditional Expectation of the generalization error). An important difference from existing methods is that we predict the conditional expectation of the generalization error given training input points, while existing methods predict the full expectation of the generalization error. Due to this difference, the training input design can be fine-tuned depending on the realization of training input points. Theoretically, we prove that the proposed active learning criterion is a more accurate predictor of the single-trial generalization error than the existing criterion. Numerical studies with toy and benchmark data sets show that the proposed method compares favorably to existing methods.
A synonymous mutation in TCOF1 causes Treacher Collins syndrome due to mis‐splicing of a constitutive exon (2009)

Interpretation of the pathogenicity of sequence alterations in disease-associated genes is challenging. This is especially true for novel alterations that lack obvious functional consequences. We report here on a patient with Treacher Collins syndrome (TCS) found to carry a previously reported mutation, c.122C > T, which predicts p.A41V, and a novel synonymous mutation, c.3612A > C. Pedigree analysis showed that the c.122C > T mutation segregated with normal phenotypes in multiple family members while the c.3612A > C was de novo in the patient. Analysis of TCOF1 RNA in lymphocytes showed a transcript missing exon 22. These results show that TCS in the patient is due to haploinsufficiency of TCOF1 caused by the synonymous de novo c.3612A > C mutation. This study highlights the importance of clinical and pedigree evaluation in the interpretation of known and novel sequence alterations.