gebhart/patrepeval huggingface dataset:
A pentatricopeptide repeat‐containing gene that promotes the processing of aberrant atp6 RNA of cytoplasmic male‐sterile rice (2003)

A fertility restorer gene (Rf-1) of [ms-bo] cytoplasmic male sterility (CMS) in rice has been reported to be responsible for the processing of RNA of aberrant atp6 of mitochondria. We have carried out map-based cloning of the Rf-1 gene and found that a 4.7-kb genomic fragment of a restorer line promoted the processing of aberrant atp6 RNA when introduced into a CMS line. The genomic fragment contained a single open reading frame encoding 18 repeats of the 35 amino acid pentatricopeptide repeat (PPR) motif. The cloned PPR gene is a possible candidate of Rf-1. A non-restoring genotype was identified to have deletions within the coding region.
Introduction of plasmids into whole cells of Clostridium acetobutylicum by electroporation (1988)

A method is presented for the introduction of plasmids into Clostridium acetobutylicum ATCC 8052 by electroporation. A plasmid shuttle vector, pMTL500E, which contains the erythromycin resistance gene and replication machinery of plasmid pAMβ1, was constructed and introduced into C. acetobutylicum by electroporation. The vector was then used to introduce a 2.2 kb ClaI/SphI chromosomal fragment from C. pasteurianum into a leucine requiring mutant of C. acetobutylicum, SBA9, where complementation of auxotrophy was observed. Plasmid DNA indistinguishable from that introduced, on the basis of agarose gel electrophoresis, was observed in transformants containing either plasmid.
Reduced Immune Response to Borrelia burgdorferi in the Absence of γδ T Cells (2011)

Little is known regarding the function of γδ T cells, although they accumulate at sites of inflammation in infections and autoimmune disorders. We previously observed that γδ T cells in vitro are activated by Borrelia burgdorferi in a TLR2-dependent manner. We now observe that the activated γδ T cells can in turn stimulate dendritic cells in vitro to produce cytokines and chemokines that are important for the adaptive immune response. This suggested that in vivo γδ T cells may assist in activating the adaptive immune response. We examined this possibility in vivo and observed that γδ T cells are activated and expand in number during Borrelia infection, and this was reduced in the absence of TLR2. Furthermore, in the absence of γδ T cells, there was a significantly blunted response of adaptive immunity, as reflected in reduced expansion of T and B cells and reduced serum levels of anti-Borrelia antibodies, cytokines, and chemokines. This paralleled a greater Borrelia burden in γδ-deficient mice as well as more cardiac inflammation. These findings are consistent with a model of γδ T cells functioning to promote the adaptive immune response during infection.
Activation of muscarinic K+ current in guinea‐pig atrial myocytes by sphingosine‐1‐phosphate. (1995)

1. Activation of muscarinic K+ current (IK(ACh)) by sphingosine-1-phosphate (Sph-1-P) was studied in isolated cultured guinea-pig atrial myocytes using whole-cell voltage clamp. 2. Sph-1-P caused activation of IK(ACh) with an EC50 of 1.2 nM. The maximal current that could be activated by Sph-1-P amounted to about 90% of the IK(ACh) caused by a saturating concentration of acetylcholine (ACh, 10 microM). Sphingosine (1 microM), which can mimic the signalling effects of Sph-1-P in other cells, failed to cause measurable activation of IK(ACh). 3. IK(ACh) activation by Sph-1-P was completely suppressed in cells treated with pertussis toxin. 4. Desensitization of muscarinic receptors by pre-incubation of the cells with carbachol did not affect the response to Sph-1-P; likewise, pre-incubation of the cells with Sph-1-P resulted in a reduced sensitivity to the phospholipid but not to ACh. In contrast, pre-incubation with either Sph-1-P or a serum phospholipid previously described as activating atrial IK(ACh) resulted in reduced sensitivity to both phospholipids. 5. It is concluded that activation of IK(ACh) by Sph-1-P in atrial myocytes is induced by binding to a novel G protein-coupled phospholipid receptor.
Erweitertes API zum TCOS-Betriebssystem (1998)

Dieser Beitrag zeigt die Anwendung von TCOS, Version 1.2, als Teilnehmerchipkarte bei der Realisierung eines neuen Sicherheitsprotokolls für UMTS (Universal Mobile Telecommunications System), der dritten Generation von Mobilfunksystemen. Dabei steht allerdings nicht das Protokoll im Vordergrund der Ausführungen, sondern die Schnittstelle, über die die User-Applikation auf die verfügbaren Chipkartenroutinen zugreift. Um diese Schnittstelle komfortabel zu gestalten, wurde ein erweitertes TCOS-API implementiert und darauf aufbauend eine Personalisierungsinstanz realisiert. Abschließend folgt eine Analyse der Ausführungszeit, die eine RSA Secret-Key Operation auf der verwendeten Chipkarte erfordert. Hier zeigt sich deutlich, daß nicht die RSA-Prozeßzeit der Karte, sondern die Bandbreite des Übertragungskanals die Ausführungszeit im wesentlichen begrenzt.
TAT conjugated, FITC doped silica nanoparticles for bioimaging applications (2004)

Water-in-oil (w/o) microemulsion synthesis of 70 nm size monodisperse TAT (a cell penetrating peptide, CPP) conjugated, FITC (fluorescein isothiocyanate) doped silica nanoparticles (TAT-FSNPs) is reported; human lung adenocarcinoma (A549) cells (in vitro) and rat brain tissue (in vivo) were successfully labeled using TAT-FSNPs.
Somatic mutations of the β-catenin gene are frequent in mouse and human hepatocellular carcinomas (1998)

Hepatocellular carcinoma (HCC) is the major primary malignant tumor in the human liver, but the molecular changes leading to liver cell transformation remain largely unknown. The Wnt-beta-catenin pathway is activated in colon cancers and some melanoma cell lines, but has not yet been investigated in HCC. We have examined the status of the beta-catenin gene in different transgenic mouse lines of HCC obtained with the oncogenes c-myc or H-ras. Fifty percent of the hepatic tumors in these transgenic mice had activating somatic mutations within the beta-catenin gene similar to those found in colon cancers and melanomas. These alterations in the beta-catenin gene (point mutations or deletions) lead to a disregulation of the signaling function of beta-catenin and thus to carcinogenesis. We then analyzed human HCCs and found similar mutations in eight of 31 (26%) human liver tumors tested and in HepG2 and HuH6 hepatoma cells. The mutations led to the accumulation of beta-catenin in the nucleus. Thus alterations in the beta-catenin gene frequently are selected for during liver tumorigenesis and suggest that disregulation of the Wnt-beta-catenin pathway is a major event in the development of HCC in humans and mice.
Epigenetic Control during Lymphoid Development and Immune Responses (2003)

Methylation of cytosines controls a number of biologic processes such as imprinting and X chromosomal inactivation. DNA hypermethylation is closely associated with transcriptional silencing, while DNA hypomethylation is associated with transcriptional activation. Hypoacetylation of histones leads to compact chromatin with reduced accessibility to the transcriptional machinery. Methyl-CpG binding proteins can recruit corepressors and histone deacetylases; thus, the interplay between these epigenetic mechanisms regulates gene activation. Methylation has been implicated as an important mechanism during immune development, controlling VDJ recombination, lineage-specific expression of cell surface antigens, and transcriptional regulation of cytokine genes during immune responses. Aberrations in epigenetic machinery, either by genetic mutations or by somatic changes such as viral infections, are associated with early alterations in chronic diseases such as immunodeficiency and cancer.
Porcine small intestine submucosa (SIS) is not an acellular collagenous matrix and contains porcine DNA: Possible implications in human implantation (2005)

Porcine small intestinal submucosa (SIS) has been recommended as a cell-free, biocompatible biomaterial for the repair of rotator cuff tendon tear. However, we have observed noninfectious edema and severe pain in patients who have undergone SIS implantation for tendon repair. The aim of this study was to conduct an independent assessment of the safety and efficacy of Restore SIS membrane. The Restore orthobiologic implant was examined by histology and the nested PCR technique using porcine immunoreceptor DAP12 gene to examine if SIS membrane contained porcine cells or DNA, respectively. The material was also implanted into mice and rabbits for the evaluation of biological reaction and inflammatory response. Restore SIS was found to contain multiple layers of porcine cells. Chloroacetate esterase staining showed that some of these cells were mast cells. Nested PCR of the DAP12 gene demonstrated that Restore SIS contained porcine DNA material. Subcutaneous implantation of Restore SIS membrane in mice, and in rabbits for rotator cuff tendon repair, showed that the membrane caused an inflammatory reaction characterized by massive lymphocyte infiltration. In conclusion, Restore SIS is not an acellular collagenous matrix, and contains porcine DNA. Our results contradict the current view that Restore SIS is a cell-free biomaterial, and that no inflammatory response is elicited by its implantation. We suggest that further studies should be conducted to evaluate the clinical safety and efficacy of SIS implant biomaterials.
VAL 201 — An Inhibitor of Androgen Receptor-associated Src and a Potential Treatment of Castration-resistant Prostate Cancer (2012)

Prostate cancer is the second leading cause of cancer death in men in the US. The initial treatment of metastatic prostate cancer is androgen deprivation (castration) therapy and this is achieved through either surgical or medical castration, however these therapies are also associated with undesirable side effects including impotence, tumour flare and loss of bone mass. Over time, nearly all patients with metastatic disease become resistant to androgen deprivation, progressing to castration-resistant prostate cancer (CRPC), and at this stage of the disease the prognosis is extremely poor (&lt;50 % survival at two years). Currently there are few treatment options for CRPC. Only four have been found to extend survival and none are curative. Effective treatment of CRPC is a major unmet clinical need, and the identification of alternative therapeutic targets is an active focus of research. In this article we discuss the development of a new agent, Val 201 as a potential future treatment for CRPC. VAL 201 targets the association of androgen receptor with Src, a non-receptor tyrosine kinase signal-transduction protein that is important in tumour cell proliferation, and represents a novel and exciting approach for cancer chemotherapy.
The PTEN/MMAC1 tumor suppressor phosphatase functions as a negative regulator of the phosphoinositide 3-kinase/Akt pathway (1998)

The PTEN/MMAC1 phosphatase is a tumor suppressor gene implicated in a wide range of human cancers. Here we provide biochemical and functional evidence that PTEN/MMAC1 acts a negative regulator of the phosphoinositide 3-kinase (PI3-kinase)/Akt pathway. PTEN/MMAC1 impairs activation of endogenous Akt in cells and inhibits phosphorylation of 4E-BP1, a downstream target of the PI3-kinase/Akt pathway involved in protein translation, whereas a catalytically inactive, dominant negative PTEN/MMAC1 mutant enhances 4E-BP1 phosphorylation. In addition, PTEN/MMAC1 represses gene expression in a manner that is rescued by Akt but not PI3-kinase. Finally, higher levels of Akt activation are observed in human prostate cancer cell lines and xenografts lacking PTEN/MMAC1 expression when compared with PTEN/MMAC1-positive prostate tumors or normal prostate tissue. Because constitutive activation of either PI3-kinase or Akt is known to induce cellular transformation, an increase in the activation of this pathway caused by mutations in PTEN/MMAC1 provides a potential mechanism for its tumor suppressor function.
Physics of the Granular State (1992)

Granular materials display a variety of behaviors that are in many ways different from those of other substances. They cannot be easily classified as either solids or liquids. This has prompted the generation of analogies between the physics found in a simple sandpile and that found in complicated microscopic systems, such as flux motion in superconductors or spin glasses. Recently, the unusual behavior of granular systems has led to a number of new theories and to a new era of experimentation on granular systems.
Gene silencing from plant DNA carried by a Geminivirus (1998)

The geminivirus tomato golden mosaic virus (TGMV) replicates in nuclei and expresses genes from high copy number DNA episomes. The authors used TGMV as a vector to determine whether episomal DNA can cause silencing of homologous, chromosomal genes. Two markers were used to asses silencing: (1) the sulfur allele (su) of magnesium chelatase, an enzyme required for chlorophyll formation; and (2) the firefly luciferase gene (luc). Various portions of both marker genes were inserted into TGMV in place of the coat protein open-reading frame and the constructs were introduced into intact plants using particle bombardment. When TGMV vectors carrying fragments of su (TGMV::su) were introduced into leaves of wild type Nicotiana benthamiana, circular, yellow spots with an area of several hundred cells formed after 3-5 days. Systemic movement of TGMV::su subsequently produced varigated leaf and stem tissue. Fragments that caused silencing included a 786 bp 5' fragment of the 1392 bp su cDNA in sense and anti-sense orientation, and a 403 bp 3' fragment. TGMV::su-induced silencing was propogated through tissue culture, along with the viral episome, but was not retained through meiosis. Systemic downregulation of a constitutively expresse luciferase transgene in plants was achieved following infection with TGMV vectors carrying a 623 bp portion of luc in sense or anti-sense orientation. These results establish that homologous DNA sequences localized in nuclear episomes can modulate the expression of active chromosomal genes.
Angiogenin abolishes cell-free protein synthesis by specific ribonucleolytic inactivation of ribosomes. (1987)

Angiogenin is a potent inhibitor of cell-free protein synthesis. When incubated with rabbit reticulocyte lysate at a concentration of 40-60 nM, it completely abolishes the capacity of the lysate to support protein synthesis. The inhibition appears to be due to its ribonucleolytic activity since it (i) generates limited cleavage products from reticulocyte RNA and (ii) is prevented from both cleaving RNA and inhibiting protein synthesis by placental RNase inhibitor. The ribonucleolytic activity of angiogenin toward the reticulocyte RNA system is highly specific. Thus, under conditions where angiogenin totally abolishes protein synthesis, an equivalent concentration of pancreatic RNase A inhibits it only partially. In contrast, RNase A is a much more effective enzyme than angiogenin using isolated RNA as substrate. Angiogenin inhibits protein synthesis by cleaving rRNA, thereby inactivating the protein synthesis machinery. Addition of isolated reticulocyte ribosomes to an angiogenin-treated lysate restores the capacity for protein synthesis, whereas addition of tRNA or mRNA does not. This potent effect on protein synthesis suggests a possible physiological function of angiogenin whose overall relevance and implications should become evident as the mechanisms of neovascularization are deciphered. The use of angiogenin may also further elucidate ribosome structure and its role in protein synthesis.
Smooth Muscle Tissues Express a Major Dominant Negative Splice Variant of the Type 3 Ca2+ Release Channel (Ryanodine Receptor) (2003)

It is well known that the type 3 Ca(2+) release channel (ryanodine receptor, RyR3) exhibits strikingly different pharmacological and functional properties depending on the tissues in which it resides. To investigate the molecular basis for this tissue-dependent heterogeneity, we examined the primary structure of RyR3 from various tissues by reverse transcription polymerase chain reaction and DNA sequence analysis. As many as seven alternatively spliced variants of RyR3 were detected. Ribonuclease protection assays revealed that one of these splice variants, RyR3 (AS-8a), which lacks a 29-amino acid fragment (His(4406)-Lys(4434)) encompassing a predicted transmembrane helix, was highly expressed in smooth muscle tissues, but not in skeletal muscle, the heart, or the brain. Although the RyR3 (AS-8a) splice variant did not form a functional Ca(2+) release channel when expressed alone in HEK293 cells, it was able to form functional heteromeric channels with reduced caffeine sensitivity when co-expressed with the wild type RyR3. Interestingly, this RyR3 splice variant was also able to form heteromeric channels with and suppress the activity of the type 2 ryanodine receptor (RyR2). Tissue-specific expression of RyR3 splice variants is therefore likely to account for some of the pharmacological and functional heterogeneities of RyR3. These observations also reveal a novel mechanism by which a splice variant of one RyR isoform (RyR3) can suppress the activity of another RyR isoform (RyR2) via a dominant negative effect.
Impaired Thermosensation in Mice Lacking TRPV3, a Heat and Camphor Sensor in the Skin (2005)

Environmental temperature is thought to be directly sensed by neurons through their projections in the skin. A subset of the mammalian transient receptor potential (TRP) family of ion channels has been implicated in this process. These "thermoTRPs" are activated at distinct temperature thresholds and are typically expressed in sensory neurons. TRPV3 is activated by heat (>33 degrees C) and, unlike most thermoTRPs, is expressed in mouse keratinocytes. We found that TRPV3 null mice have strong deficits in responses to innocuous and noxious heat but not in other sensory modalities; hence, TRPV3 has a specific role in thermosensation. The natural compound camphor, which modulates sensations of warmth in humans, proved to be a specific activator of TRPV3. Camphor activated cultured primary keratinocytes but not sensory neurons, and this activity was abolished in TRPV3 null mice. Therefore, heat-activated receptors in keratinocytes are important for mammalian thermosensation.
Telomere length, oxidative damage, antioxidants and breast cancer risk (2008)

Telomeres play a critical role in maintaining the integrity and stability of the genome, and are susceptible to oxidative damage after telomere shortening to a critical length. In the present study, we explored the role of white blood cell DNA telomere length on breast cancer risk, and examined whether urinary 15-F(2)-isoprostanes (15-F(2t)-IsoP) and 8-oxo-7,8-dihydrodeoxyguanosine (8-oxodG) or dietary antioxidant intake modified the relationship between telomere length and breast cancer risk. A population-based case-control study-the Long Island Breast Cancer Study Project-was conducted among 1,067 cases and 1,110 controls. Telomere length was assessed by quantitative PCR. Overall, the mean levels of telomere length (T/S ratio), 15-F(2t)-IsoP and 8-oxodG were not significantly different between cases and controls. Among premenopausal women only, carrying shorter telomeres (Q3 and Q4), as compared with the longest (Q1), was associated with significantly increased breast cancer risk. Age-adjusted OR and 95% CI were 1.71 (1.10-2.67) and 1.61 (1.05-2.45). The 5-F(2t)-IsoP and 8-oxodG biomarkers did not modify the telomere-breast cancer association. A moderate increase in breast cancer risk was observed among women with the shortest telomeres (Q4) and lower dietary and supplemental intake of beta-carotene, vitamin C or E intake [OR (95% CI) = 1.48 (1.08-2.03), 1.39 (1.01-1.92) and 1.57 (1.14-2.18), respectively], although the trend test exhibited statistical significance only within the lower vitamin E intake subgroup (p(trend) = 0.01). These results provided the strongest evidence to date that breast cancer risk may be affected by telomere length among premenopausal women or women with low dietary intake of antioxidants or antioxidant supplements.
An integrated color pixel in 0.18μm CMOS technology (2002)

A method for controlling photodetector wavelength responsivity via metal layer patterns is demonstrated in a standard 0.18/spl mu/m CMOS technology. Responsivities suitable for RGB integrated color pixels, peaking at 450nm, 575nm and 750nm, are measured. Over 100% uncovered area transmittances are measured. We discuss possible theoretical explanations for the observed high transmittance.
In vitro antigen challenge of human antibody libraries for vaccine evaluation: the human immunodeficiency virus type 1 envelope (1996)

Human antibody responses, or versions thereof, can be cloned as phage display libraries. In vaccine evaluation, the possibility therefore exists of challenging the human response in vitro, rather than in vivo, in order to assist in establishing the most promising vaccine leads. The characteristics of the antibodies retrieved directly indicate the strengths and weaknesses of the vaccine at the molecular level. We applied this approach to compare recombinant and native human immunodeficiency virus type 1 envelope preparations. We conclude that recombinant gp160, gp140, and, to a lesser extent, gp120 present epitopes around the CD4 binding site in a conformation different from that of the native multimer and contrary to expected vaccine requirements. Antibodies to the potently neutralizing b12 epitope were selected preferentially from an immune library by purified human immunodeficiency virus type 1 virions. This suggests that b12 is a major epitope on the virions, in contrast to recombinant envelope preparations, in which related, weakly neutralizing epitopes predominate. Although the majority of virions in the preparation used are expected to be noninfective, it appears that they predominantly express a native envelope configuration and would be able to elicit potent neutralizing antibodies.
Multiple page size modeling and optimization (2005)

With the growing awareness that individual hardware cores will not continue to produce the same level of performance improvement, there is a need to develop an integrated approach to performance optimization. In this paper we present a paradigm for continuous program optimization (CPO), whereby automatic agents monitor and optimize application and system performance. The monitoring data is used to analyze and create models of application and system behavior. Using this analysis, we describe how CPO agents can improve the performance of both the application and the underlying system. Using the CPO paradigm, we implemented cooperating page size optimization agents that automatically optimize large page usage. An offline agent uses vertically integrated performance data to produce a page size benefit analysis for different categories of data structures within an application. We show how an online CPO agent can use the results of the predictive analysis to automatically improve application performance. We validate that the predictions made by the CPO agent reflect the actual performance gains of up to 60% across a range of scientific applications including the SPEC-cpu2000 floating point benchmarks and two large high performance computing (HPC) applications.