gebhart/patrepeval huggingface dataset:
Preimplantation Genetic Diagnosis for Aneuploidy and Translocations Using Array Comparative Genomic Hybridization (2012)

At least 50% of human embryos are abnormal, and that increases to 80% in women 40 years or older. These abnormalities result in low implantation rates in embryos transferred during in vitro fertilization procedures, from 30% in women <35 years to 6% in women 40 years or older. Thus selecting normal embryos for transfer should improve pregnancy results. The genetic analysis of embryos is called Preimplantation Genetic Diagnosis (PGD) and for chromosome analysis it was first performed using FISH with up to 12 probes analyzed simultaneously on single cells. However, suboptimal utilization of the technique and the complexity of fixing single cells produced conflicting results. PGD has been invigorated by the introduction of microarray testing which allows for the analysis of all 24 chromosome types in one test, without the need of cell fixation, and with staggering redundancy, making the test much more robust and reliable. Recent data published and presented at scientific meetings has been suggestive of increased implantation rates and pregnancy rates following microarray testing, improvements in outcome that have been predicted for quite some time. By using markers that cover most of the genome, not only aneuploidy can be detected in single cells but also translocations. Our validation results indicate that array CGH has a 6Mb resolution in single cells, and thus the majority of translocations can be analyzed since this is also the limit of karyotyping. Even for translocations with smaller exchanged fragments, provided that three out of the four fragments are above 6Mb, the translocation can be detected.
Involvement of Early Growth Response Factor Egr-1 in Apolipoprotein AI Gene Transcription (1995)

Liver-specific expression of the apolipoprotein AI (apoAI) gene is mediated by transcription factors bound to three sites (A, B, and C) in the apoAI enhancer. Sites A and C bind various members of the nuclear receptor superfamily, including the orphan nuclear receptor apolipoprotein regulatory protein-1 (ARP-1); site B binds the liver-enriched factor hepatic nuclear factor-3. The immediate early growth response factor (Egr-1), which is transiently expressed in various pathophysiologic states of the liver, activates the apoAI enhancer and overcomes ARP-1-mediated repression of the enhancer in hepatoblastoma HepG2 cells. Deletion mapping analysis revealed two Egr-1 binding sites, E1 and E2, flanking site A. Erg-1 bound efficiently to both E1 and E2. Sp1 in HepG2 nuclear extracts bound to E2 but not E1. In HepG2 cells, E1 functioned as an Egr-1 response element, whereas E2 had high basal activity and was not further induced by Egr-1. Mutations that prevent Egr-1 binding to the apoAI enhancer abolished its responsiveness to Erg-1, while they had only minor effects on its constitutive activity. These mutations also diminished the ability of Egr-1 to overcome ARP-1-mediated repression. Elimination of transcription factor binding to sites A, B, or C reduced enhancer activity without affecting Egr-1-dependent activation. We argue that Egr-1 is recruited to the apoAI enhancer complex under unusual circumstances, such as those prevailing during liver regeneration, to maintain apoAI transcription levels by overriding prior transcriptional controls.
Load Sharing in a Distributed IMS Architecture (2009)

The IP Multimedia Subsystem (IMS) serves as universal platform for fast and standardized creation of mobile services. Typical deployment models for the IMS favor centralized session control and application servers. Furthermore, they rely on sophisticated border elements for, e.g., policy enforcement. One step towards a simpler architecture is the integration of call control, application server, and media functions into border elements. This leads to a distributed IMS architecture with equal processing nodes, which drastically reduces system complexity and scales on functional module instantiation basis. However, the distributed nature of the architecture reduces the statistical gain. In this work, we study a suitable load sharing concept that counters or even over-compensates this problem. In principle, this mechanism realizes one large virtual central server with small control and message overhead. Our simulative evaluation shows the feasibility and performance of our approach.
Structure, Function, and Control of Phosphoinositide-Specific Phospholipase C (2000)

Phosphoinositide-specific phospholipase C (PLC) subtypes beta, gamma, and delta comprise a related group of multidomain phosphodiesterases that cleave the polar head groups from inositol lipids. Activated by all classes of cell surface receptor, these enzymes generate the ubiquitous second messengers inositol 1,4, 5-trisphosphate and diacylglycerol. The last 5 years have seen remarkable advances in our understanding of the molecular and biological facets of PLCs. New insights into their multidomain arrangement and catalytic mechanism have been gained from crystallographic studies of PLC-delta(1), while new modes of controlling PLC activity have been uncovered in cellular studies. Most notable is the realization that PLC-beta, -gamma, and -delta isoforms act in concert, each contributing to a specific aspect of the cellular response. Clues to their true biological roles were also obtained. Long assumed to function broadly in calcium-regulated processes, genetic studies in yeast, slime molds, plants, flies, and mammals point to specific and conditional roles for each PLC isoform in cell signaling and development. In this review we consider each subtype of PLC in organisms ranging from yeast to mammals and discuss their molecular regulation and biological function.
Morning increase of whole blood viscosity in obstructive sleep apnea syndrome. (2000)

Viscosity of whole blood increases in the morning in OSAS patients but not in healthy controls. This condition may be related to the increased susceptibility to cerebral ischemia in patients affected by OSAS, particularly evident in the early morning.
Arabidopsis Calcium-Dependent Protein Kinase AtCPK32 Interacts with ABF4, a Transcriptional Regulator of Abscisic Acid-Responsive Gene Expression, and Modulates Its Activity (2005)

The phytohormone abscisic acid (ABA) regulates stress-responsive gene expression during vegetative growth. The ABA regulation of many genes is mediated by a subfamily of basic leucine zipper class transcription factors referred to as ABFs (i.e. ABF1-ABF4), whose transcriptional activity is induced by ABA. Here we show that a calcium-dependent protein kinase is involved in the ABA-dependent activation process. We carried out yeast two-hybrid screens to identify regulatory components of ABF4 function and isolated AtCPK32 as an ABF4-interacting protein. AtCPK32 has autophosphorylation activity and can phosphorylate ABF4 in vitro. Mutational analysis indicated that serine-110 of ABF4, which is highly conserved among ABF family members, may be phosphorylated by AtCPK32. The serine-110 residue is essential for ABF4-AtCPK32 interaction, and transient expression assay revealed that it is also required for the normal transcriptional function of ABF4. The expression patterns and subcellular localization of AtCPK32 are similar to those of ABF4. Furthermore, its overexpression affects both ABA sensitivity and the expression of a number of ABF4-regulated genes. Together, our data demonstrate that AtCPK32 is an ABA signaling component that regulates the ABA-responsive gene expression via ABF4.
Loss of stearoyl–CoA desaturase-1 function protects mice against adiposity (2002)

Stearoyl-CoA desaturase (SCD) is a central lipogenic enzyme catalyzing the synthesis of monounsaturated fatty acids, mainly oleate (C18:1) and palmitoleate (C16:1), which are components of membrane phospholipids, triglycerides, wax esters, and cholesterol esters. Several SCD isoforms (SCD1-3) exist in the mouse. Here we show that mice with a targeted disruption of the SCD1 isoform have reduced body adiposity, increased insulin sensitivity, and are resistant to diet-induced weight gain. The protection from obesity involves increased energy expenditure and increased oxygen consumption. Compared with the wild-type mice the SCD1-/- mice have increased levels of plasma ketone bodies but reduced levels of plasma insulin and leptin. In the SCD1-/- mice, the expression of several genes of lipid oxidation are up-regulated, whereas lipid synthesis genes are down-regulated. These observations suggest that a consequence of SCD1 deficiency is an activation of lipid oxidation in addition to reduced triglyceride synthesis and storage.
Pharmacogenomic studies of the anticancer and immunosuppressive thiopurines mercaptopurine and azathioprine (2008)

Thiopurine methyltransferase variant alleles were associated with a preferential metabolism away from 6-methylmercaptopurine nucleotides (P = 0.008 in ALL patients, P = 0.038 in IBD patients) favouring 6-thioguanine nucleotides (6-TGNs) (P = 0.021 in ALL patients). Interestingly, carriers of inosine triphosphatase IVS2+21A-->C variants among ALL and IBD patients had significantly higher concentrations of the active cytotoxic metabolites, 6-TGNs (P = 0.008 in ALL patients, P = 0.047 in IBD patients). The study confirmed the association of thiopurine methyltransferase heterozygosity with leucopenia and neutropenia in ALL patients and reported a significant association between inosine triphosphatase IVS2+21A-->C variants with thrombocytopenia (P = 0.012). CONCLUSIONS; Pharmacogenetic polymorphisms in the 6-MP pathway may help identify patients at risk for associated toxicities and may serve as a guide for dose individualization.
DNA sequence variation in a negative control region 5' to the beta- globin gene correlates with the phenotypic expression of the beta s mutation (1992)

The clinical diversity of sickle cell anemia is strongly related to the degree of intracellular hemoglobin S (Hb S) polymerization, which in turn is dependent on the intracellular concentration of Hb S. We have recently defined a region of DNA approximately 500 bp 5′ to the human beta-globin gene that acts as a silencer for the transcription of this gene and have shown that a polymorphism in this sequence is associated with a thalassemic phenotype of the beta-globin gene. In this work we have examined the correlation of DNA sequence polymorphisms in this silencer with binding of a previously identified putative repressor protein, BP1, and with the expression of Hb S in individuals heterozygous for the beta s allele. It was found that specific configurations of the motif, (AT)x(T)y, are homogeneous for the major haplotypes of the beta-globin gene cluster described on beta s chromosomes. Binding of BP1 was measured to DNA of three haplotypes: Indian, Benin, and Bantu. BP1 binds most tightly to DNA of the Indian haplotype, and these patients produce less beta s protein than Benin patients, whose DNA exhibits weaker affinity for BP1. Binding of BP1 is the weakest to DNA of the Bantu haplotype, which is associated with clinically more severe sickle cell symptoms. These data are consistent with the hypothesis that these polymorphisms may not be neutral and that the DNA sequence at this site may affect the expression of the beta s gene. Such an effect may be synergistic with other genetic variables, such as fetal hemoglobin levels, F-cell numbers, and the number of alpha-globin genes, in determining intracellular polymerization and, thus, the severity of the sickle cell syndromes.
The pH Response and Sensing Mechanism of n-Type ZnO/Electrolyte Interfaces (2009)

Ever since the discovery of the pH-sensing properties of ZnO crystals, researchers have been exploring their potential in electrochemical applications. The recent expansion and availability of chemical modification methods has made it possible to generate a new class of electrochemically active ZnO nanorods. This reduction in size of ZnO (to a nanocrystalline form) using new growth techniques is essentially an example of the nanotechnology fabrication principle. The availability of these ZnO nanorods opens up an entire new and exciting research direction in the field of electrochemical sensing. This review covers the latest advances and mechanism of pH-sensing using ZnO nanorods, with an emphasis on the nano-interface mechanism. We discuss methods for calculating the effect of surface states on pH-sensing at a ZnO/electrolyte interface. All of these current research topics aim to explain the mechanism of pH-sensing using a ZnO bulk- or nano-scale single crystal. An important goal of these investigations is the translation of these nanotechnology-modified nanorods into potential novel applications.
Frequency and diversity of p53 mutations in childhood rhabdomyosarcoma. (1992)

The p53 gene was examined in primary or metastatic tumors from six patients with rhabdomyosarcoma (RMS) and in five RMS cell lines by screening methods including single-strand conformation polymorphism analysis, the RNase protection assay, sequencing of complementary DNA subclones, and Southern blotting. Six original tumors were of embryonal histology, four alveolar, and one mixed. p53 mutations were identified in four of the six tumors or cell lines derived from tumors with embryonal histology and in one of the four with alveolar histology. Consistent with p53 allele loss, each mutation was found in the homo- or hemizygous state. One tumor showed a G to C transversion at p53 codon 213 (arginine to proline), and another showed deletion of the entire gene. The p53 mutations in cell lines included a codon 248 C to T transition (arginine to tryptophan) in RD and a codon 280 A to T transversion (arginine to serine) in RH30. The cell line CTR contained a 4-base pair deletion at codons 219/220 in exon 6 with resultant frame shift and premature termination in exon 7. These data support the role of diverse types of p53 mutations in the pathogenesis and/or progression of a significant proportion of cases of childhood RMS.
Chemical control of bacterial epibiosis on ascidians (1994)

Two CO-occurring ascidians of the Pacific subtidal, Polyclinum planum and Cystodytes lobatus, were found to exhlbit remarkably different numbers of surface bacteria. On average, epibactenal densities on P. planum were 140 times greater than those on C. lobatus as measured by platecounting methods. Organic extracts of both ascidian species were tested for antimicrobial activities and effects on bacterial settlement. Bacterial settlement was measured using a new bioassay described in this paper. The results of the settlement bioassay clearly demonstrate that extracts of the littlecolonized C, lobatus deter bacterial settlement while extracts of the heavily colonized P. planum induce settlement relative to the control. In addition to reduclng bacterial settlement, extracts of C. lobatus colonies exhibited varylng, but generally low, levels of antimicrobial acbvity against, on average, onehalf of the 36 strains of marine bactena tested. On an interspecific level, including 11 ascldian species screened in a pilot study, fouling-deterring activities were correlated with epibacterial abundances while antimicrobial activity was not. It is concluded that the chemical control of bacterial settlement, possibly complemented by antimicrobial toxicity, provides an accurate model to explain the dramatically different bacterial abundance on the surfaces of the ascidian species studied. This investigation presents evidence that non-toxic metabolltes influence bacterial settlement and, in this way, may function to regulate bacterial epibiosis on the surfaces of some marine invertebrates.
Unsupervised information extraction approach using graph mutual reinforcement (2006)

Information Extraction (IE) is the task of extracting knowledge from unstructured text. We present a novel unsupervised approach for information extraction based on graph mutual reinforcement. The proposed approach does not require any seed patterns or examples. Instead, it depends on redundancy in large data sets and graph based mutual reinforcement to induce generalized "extraction patterns". The proposed approach has been used to acquire extraction patterns for the ACE (Automatic Content Extraction) Relation Detection and Characterization (RDC) task. ACE RDC is considered a hard task in information extraction due to the absence of large amounts of training data and inconsistencies in the available data. The proposed approach achieves superior performance which could be compared to supervised techniques with reasonable training data.
Evidence for transcriptional repression of SPARC-like 1, a gene downregulated in human lung tumors. (2004)

SPARCL1 mRNA was shown to be downregulated in NSCLC as well as in prostate, colon, and bladder carcinomas. Therefore, SPARCL1 was suggested to be a tumor suppressor gene. By microsatellite analysis, real-time quantitative PCR, and sequence analysis of all exons including the intron-exon junctions and a part of the putative promoter region, we could not find any deletion or mutation that might be responsible for the downregulation of SPARCL1 in NSCLC. We conclude that SPARCL1 is therefore not a classical tumor suppressor gene with a deletion or mutation in one allele and another mutation in the second allele. To test whether SPARCL1 could be downregulated by repression of transcription we performed luciferase reporter gene assays with 10 different SPARCL1 promoter constructs. These experiments revealed that the presence of exon 1 is able to cause a reduction in luciferase activity. Furthermore, we show that the inhibitory activity of exon 1 can be transferred to a heterologous promoter. This indicates that SPARCL1 downregulation might be mediated (at least in part) through transacting factors that bind to exon 1.
Augmenting IoT networks with backscatter-enabled passive sensor tags (2016)

The sensing modalities available in an Internet-of-Things (IoT) network are usually fixed before deployment, when the operator selects a suitable IoT platform. Retrofitting a deployment with additional sensors can be cumbersome, because it requires either modifying the deployed hardware or adding new devices that then have to be maintained. In this paper, we present our vision and work towards passive sensor tags: battery-free devices that allow to augment existing IoT deployments with additional sensing capabilities without the need to modify the existing deployment. Our passive sensor tags use backscatter transmissions to communicate with the deployed network. Crucially, they do this in a way that is compatible with the deployed network's radio protocol, and without the need for additional infrastructure. We present an FPGA-based prototype of a passive sensor tag that can communicate with unmodified 802.15.4 IoT devices. Our initial experiments with the prototype support the feasibility of our approach. We also lay out the next steps towards fully realizing the vision of passive sensor tags.
Electron spin ensemble strongly coupled to a three-dimensional microwave cavity (2011)

We demonstrate the strong coupling between an electron spin ensemble and a three-dimensional cavity in a reflection geometry. We also find that an anticrossing in the cavity/spin spectrum can be observed under conditions that the collective coupling strength gc is smaller than the spin linewidth γs or the cavity linewidth. We identify a ratio of gc to γs (gc/γs&amp;gt;0.64) as a condition to observe a splitting in the cavity frequency. Finally, we confirm that gc scales with N, where N is the number of polarized spins.
TMEM196acts as a novel functional tumour suppressor inactivated by DNA methylation and is a potential prognostic biomarker in lung cancer (2015)

Epigenetic silencing of tumour suppressors contributes to the development and progression of lung cancer. We recently found that TMEM196 was hypermethylated in lung cancer. This study aimed to clarify its epigenetic regulation, possible roles and clinical significance. TMEM196 methylation correlated with loss of protein expression in chemical-induced rat lung pathologic lesions and human lung cancer tissues and cell lines. 5-aza-2'-deoxycytidine restored TMEM196 expression. Moreover, TMEM196 hypermethylation was detected in 61.2% of primary lung tumours and found to be associated with poor differentiation and pathological stage of lung cancer. Functional studies showed that ectopic re-expression of TMEM196 in lung cancer cells inhibited cell proliferation, clonogenicity, cell motility and tumour formation. However, TMEM196 knockdown increased cell proliferation and inhibited apoptosis and cell-cycle arrest. These effects were associated with upregulation of p21 and Bax, and downregulation of cyclin D1, c-myc, CD44 and β-catenin. Kaplan-Meier survival curves showed that TMEM196 downregulation was significantly associated with shortened survival in lung cancer patients. Multivariate analysis showed that patients with TMEM196 expression had a better overall survival. Our results revealed for the first time that TMEM196 acts as a novel functional tumour suppressor inactivated by DNA methylation and is an independent prognostic factor of lung cancer.
Mobile computing with the Rover toolkit (1997)

Rover is a software toolkit that supports the construction of both mobile-transparent and mobile-aware applications. The mobile-transparent approach aims to enable existing applications to run in a mobile environment without alteration. This transparency is achieved by developing proxies for system services that hide the mobile characteristics of the environment from applications. However, to excel, applications operating in the harsh conditions of a mobile environment must often be aware of and actively adapt to those conditions. Using the programming and communication abstractions present in the Rover toolkit, applications obtain increased availability, concurrency, resource allocation efficiency, fault tolerance, consistency, and adaptation. Experimental evaluation of a suite of mobile applications demonstrates that use of the toolkit requires relatively little programming overhead, allows correct operation, substantially increases interactive performance, and dramatically reduces network utilization.
Cytokine secretion effected by synergism of the immunomodulator AS101 and the protein kinase C inducer bryostatin. (1990)

AS101, a synthetic organotellurium compound, was found to have immunomodulating properties by initiation of cytokine production in vitro and in vivo. Phase I/II clinical trials currently in progress on AIDS and cancer patients treated with AS101 show significant increases in various immunological parameters, with minimal toxicity. Recently, AS101 and the protein kinase C (PKC) inducer, phorbol myristate acetate (PMA), were shown to synergize in the secretion of interleukin-2 (IL-2) and colony-stimulating factor (CSF) in vitro, by human and mouse lymphoid cells. The bryostatins, a group of natural macrocyclic lactones isolated from marine invertebrates (Bugula neritina) have been reported to be potent PKC activators with no tumour promoting activity. In this study, we investigated the synergistic effect of AS101 and a partially purified preparation of bryostatin on the production of several cytokines. Our data confirm the presence of synergism, which greatly enhances cell proliferation, IL-2, tumour necrosis factor (TNF) and interferon-gamma (IFN-gamma) secretion by human mononuclear cells (MNC) and the production of IL-2 and TNF by mouse cells. The absence of tumour-promoting activity of the bryostatins makes them particularly good candidates, in combination with AS101, for immunomodulation in vivo in clinically immunosuppressed conditions.