gebhart/patrepeval huggingface dataset:
Genetic Map and QTL Analysis of Agronomic Traits in a Diploid Potato Population using Single Nucleotide Polymorphism Markers (2015)

ABSTRACT Genetic maps now can be constructed using thousands of genomewide single nucleotide polymorphisms (SNPs) for identification of markers closely associated with agronomic traits. A diploid mapping population for potato ( Solanum tuberosum L.) was developed from a pseudo‐testcross between a homozygous line S. tuberosum Group Phureja DM 1‐3 516 R44 and a heterozygous outcrossing S. tuberosum Group Tuberosum clone, RH89‐039‐16. The population of 96 individuals was evaluated for seven traits in two consecutive years (2012 and 2013). Yield (total tuber yield [TTY], average tuber weight [ATW], and number of tubers per plant [TS]), food quality (specific gravity [SPGR]), and plant development traits (vigor, maturity [Mat], and tuber end rot [TER]) were studied. Sixteen different quantitative trait loci (QTL) were identified. A QTL with major effects at 11.9 cM corresponding to 3.7 Mb on chromosome V of potato genome assembly explained between 20.3 and 75.7% of variance for TS, ATW, vigor, Mat, and TER. For TTY, ATW and SPGR, the QTL was detected at 6.4 and 12.9 cM. The other 15 QTL were located on chromosomes I, II, III, IV, V, VI, IX, X, and XII. In general, the results confirmed QTL previously identified for yield, SPGR, and Mat in diploid and tetraploid populations. The Infinium 8303 Potato Array provides an efficient means of scoring genomewide markers for constructing high‐resolution genetic maps and thereby facilitates identification of genomic regions closely associated with genes coding for agronomic traits of interest.
The United States and the Discipline of International Relations: "Hegemonic Country, Hegemonic Discipline" (2002)

This paper focuses on the relationship between the way the discipline of International Relations (IR) is studied in the U.S. and U.S. foreign policy itself. Referring to the events of September 11 the paper argues that mainstream U.S. IR defines the appropriate methods of how to study international relations in such a narrow way as to restrict understanding of other cultures and rationalities. By relying on culturally and historically specific distinctions between politics and economics, between private and public, and between domestic and foreign policies, U.S. IR explains a narrow range of world political events and does so from a U.S. perspective. This makes it difficult to account for many of the most pressing inequalities in the world, and thus raises the question of the linkage between academia, the civil society in which it is located, and the role that it should serve in encouraging a wide debate on the motivations and views of those outside the U.S.
Colloidal HgTe Nanocrystals with Widely Tunable Narrow Band Gap Energies:  From Telecommunications to Molecular Vibrations (2006)

A convenient, aqueous-based synthesis of stable HgTe nanocrystals with widely size-tunable room temperature emission between wavelengths of 1.2 to 3.7 mum is demonstrated. By the choice of the thiols, applied as stabilizers, we optimized the growth dynamics, the luminescence quantum yields (up to 40%), and a ligand-exchange procedure, required to transfer the nanocrystals from water to nonpolar organic solvents. The latter is greatly improved and facilitated by the use of mercaptoethylamine as initial stabilizer. The possibility to tune the HgTe nanocrystal sizes from 3 to 12 nm and to control their surface functionalities (hydrophobic and hydrophilic) makes them very promising for the development of infrared optical devices, emitting in the wavelength region between the telecommunications and the molecular vibrations.
Ligand-induced association between the T-cell antigen receptor and two glycoproteins. (1989)

We have identified two cell surface glycoproteins of 34 and 38 kDa (gp34 and gp38) that associate with the T-cell antigen receptor (TCR). The coimmunoprecipitation of these proteins with the TCR is increased by treatment with monoclonal antibodies (mAbs) directed against the TCR prior to cell solubilization and immunoprecipitation. Treatment of T cells with mAbs directed against other cell surface molecules, CD2 or HLA, does not induce the association of these proteins with the TCR. The coimmunoprecipitation of gp34 and gp38 with the TCR requires solubilization in the presence of an alkylating agent, suggesting that subunit alkylation stabilizes the interaction. J.CaM1 and J.CaM2 are signal-transduction mutant cell lines derived from Jurkat. These cell lines fail to activate the inositol phospholipid second messenger pathway in response to anti-TCR mAbs. Treatment with mAb C305 (anti-TCR) induces the association of gp34 and gp38 with the TCR in J.CaM2 cells but not in J.CaM1. J.CaM1 modulates the TCR normally in response to anti-TCR antibody treatment. This observation suggests that gp34 and gp38 are involved in the signal-transduction pathway of the TCR complex rather than receptor internalization. Furthermore, since these proteins do associate with the TCR of J.CaM2, the induced association with the TCR is not a consequence of signal transduction.
Suppression of inducible cyclooxygenase and nitric oxide synthase through activation of peroxisome proliferator‐activated receptor‐γ by flavonoids in mouse macrophages (2001)

Peroxisome proliferator-activated receptor (PPAR)gamma transcription factor has been implicated in anti-inflammatory response. Of the compounds tested, apigenin, chrysin, and kaempferol significantly stimulated PPAR gamma transcriptional activity in a transient reporter assay. In addition, these three flavonoids strongly enhanced the inhibition of inducible cyclooxygenase and inducible nitric oxide synthase promoter activities in lipopolysaccharide-activated macrophages which contain the PPAR gamma expression plasmids. However, these three flavonoids exhibited weak PPAR gamma agonist activities in an in vitro competitive binding assay. Limited protease digestion of PPAR gamma suggested these three flavonoids produced a conformational change in PPAR gamma and the conformation differs in the receptor bound to BRL49653 versus these three flavonoids. These results suggested that these three flavonoids might act as allosteric effectors and were able to bind to PPAR gamma and activate it, but its binding site might be different from the natural ligand BRL49653.
VMScatter (2013)

Live virtual machine migration is a technique often used to migrate an entire OS with running applications in a non-disruptive fashion. Prior works concerned with one-to-one live migration with many techniques have been proposed such as pre-copy, post-copy and log/replay. In contrast, we propose VMScatter, a one-to-many migration method to migrate virtual machines from one to many other hosts simultaneously. First, by merging the identical pages within or across virtual machines, VMScatter multicasts only a single copy of these pages to associated target hosts for avoiding redundant transmission. This is impactful practically when the same OS and similar applications running in the virtual machines where there are plenty of identical pages. Second, we introduce a novel grouping algorithm to decide the placement of virtual machines, distinguished from the previous schedule algorithms which focus on the workload for load balance or power saving, we also focus on network traffic, which is a critical metric in data-intensive data centers. Third, we schedule the multicast sequence of packets to reduce the network overhead introduced by joining or quitting the multicast groups of target hosts. Compared to traditional live migration technique in QEMU/KVM, VMScatter reduces 74.2% of the total transferred data, 69.1% of the total migration time and achieves the network traffic reduction from 50.1% to 70.3%.
Redox proteomics: understanding oxidative stress in the progression of age-related neurodegenerative disorders (2008)

Redox proteomics is an approach that can be applied to the brain to delineate mechanisms of pathogenesis of age-related neurodegenerative disorders. In addition, redox proteomics can also play role...
A strategy to discover circulating angiogenesis inhibitors generated by human tumors. (1995)

The phenomenon of inhibition of tumor growth by tumor mass has been studied in many experimental animal systems and has been observed in several clinical scenarios. Not until the recent discovery of angiostatin, a circulating angiogenesis inhibitor generated in the presence of a murine Lewis lung tumor, has a satisfactory mechanism been proposed to explain this phenomenon. Thus far, no other animal or human tumors are known to generate angiostatin. In this study, we utilized a mouse corneal neovascularization model to detect circulating inhibitors of angiogenesis generated by three human tumors grown in immunodeficient mice: (a) the PC-3 human prostate carcinoma; (b) the CCL188 human colon carcinoma; and (c) the UBC urinary bladder carcinoma. Mice bearing these three primary tumors demonstrated significant inhibition of angiogenesis in the cornea induced by a pellet containing basic fibroblast growth factor. Corneas of mice bearing s.c. prostate and colon carcinomas showed significant inhibition of vessel length, clock-hours of neovascularization, and vessel density. However, corneas of mice bearing s.c. bladder carcinomas demonstrated significant inhibition of vessel density only. Three colon carcinomas (clone A, CX-1, and MIP101), the MDA-MB-435S breast carcinoma, the MM-AN melanoma, and the JE-3 choriocarcinoma did not significantly inhibit corneal neovascularization.
5-Hydroxymethylcytosine localizes to enhancer elements and is associated with survival in glioblastoma patients (2016)

Glioblastomas exhibit widespread molecular alterations including a highly distorted epigenome. Here, we resolve genome-wide 5-methylcytosine and 5-hydroxymethylcytosine in glioblastoma through parallel processing of DNA with bisulfite and oxidative bisulfite treatments. We apply a statistical algorithm to estimate 5-methylcytosine, 5-hydroxymethylcytosine and unmethylated proportions from methylation array data. We show that 5-hydroxymethylcytosine is depleted in glioblastoma compared with prefrontal cortex tissue. In addition, the genomic localization of 5-hydroxymethylcytosine in glioblastoma is associated with features of dynamic cell-identity regulation such as tissue-specific transcription and super-enhancers. Annotation of 5-hydroxymethylcytosine genomic distribution reveal significant associations with RNA regulatory processes, immune function, stem cell maintenance and binding sites of transcription factors that drive cellular proliferation. In addition, model-based clustering results indicate that patients with low-5-hydroxymethylcytosine patterns have significantly poorer overall survival. Our results demonstrate that 5-hydroxymethylcytosine patterns are strongly related with transcription, localizes to disease-critical genes and are associated with patient prognosis.
Biochemical and hormonal changes induced by one week of administration of rIGF‐I to patients with Laron type dwarfism (1991)

IGF-I mimics the biochemical and hormonal changes described after administration of hGH. The administration of IGF-I in patients with Laron type dwarfism is devoid of side-effects and warrants assessment in long-term studies.
Catalysis of the electrochemical reduction of carbon dioxide (2012)

The direct and catalyzed electrochemistry of CO(2) partake in the contemporary attempts to reduce this inert molecule to fuels by means of solar energy, either directly, after conversion of light to electricity, or indirectly in that all elements of comprehension derived from electrochemical experiments can be used in the design and interpretation of photochemical experiments. Following reviews of the activity in the field until 2007-2008, the present review reports more recent findings even if their interpretation remains uncertain. It also develops useful notions that allow analyzing and comparing more rigorously the performances of existing catalysts when the necessary data are available. Among the general trends that transpire presently and are likely to be the object of active future work emphasis is put on the favorable role of acid addition in homogeneous catalytic systems and on the crucial chemical role of the electrode material in heterogeneous catalysis.
Silencing of the E-cadherin invasion-suppressor gene by CpG methylation in human carcinomas. (1995)

E-Cadherin, a cell adhesion molecule, which plays a key role in maintaining the epithelial phenotype, is regarded as an invasion-suppressor gene in light of accumulating evidence from in vitro experiments and clinical observations. In an attempt to clarify the mechanism responsible for inactivation of this gene in carcinomas, we investigated the methylation state around the promoter region by digestion of DNA with the methylation-sensitive restriction enzyme Hpa II, as CpG methylation of the promoter has been postulated to be a mechanism of transcriptional inactivation of some genes. We found that E-cadherin expression-negative carcinoma cell lines were accompanied by the hypermethylation state, whereas E-cadherin-positive cell lines were not. Furthermore, treatment of E-cadherin-negative carcinoma cells with the demethylating agent 5-azacytidine resulted in reexpression of the gene and reversion of scattered spindle-shaped cells to cells with epithelial morphology. These results suggest that hypermethylation around the promoter may be a mechanism of E-cadherin inactivation in human carcinomas and that treatment of E-cadherin-inactivated cells with a demethylating agent may cause gene expression reversion leading to epithelial morphogenesis with acquisition of the homophilic cell-cell adhesive property.
Tumor-targeted IL-2 amplifies T cell-mediated immune response induced by gene therapy with single-chain IL-12 (1999)

Induction, maintenance, and amplification of tumor-protective immunity after cytokine gene therapy is essential for the clinical success of immunotherapeutic approaches. We investigated whether this could be achieved by single-chain IL-12 (scIL-12) gene therapy followed by tumor-targeted IL-2 using a fusion protein containing a tumor-specific recombinant anti-ganglioside GD(2) antibody and IL-2 (ch14.18-IL-2) in a poorly immunogenic murine neuroblastoma model. Herein, we demonstrate the absence of liver and bone marrow metastases after a lethal challenge with NXS2 wild-type cells only in mice (five of six animals) vaccinated with scIL-12-producing NXS2 cells and given a booster injection of low-dose ch14.18-IL-2 fusion protein. This tumor-protective immunity was effective 3 months after initial vaccination, in contrast to control animals treated with a nonspecific fusion protein or an equivalent mixture of antibody and IL-2. Only vaccinated mice receiving the tumor-specific ch14.18-IL-2 fusion protein revealed a reactivation of CD8(+) T cells and subsequent MHC class I-restricted tumor target cell lysis in vitro. The sequential increase in the usage of TCR chains Vbeta11 and -13 in mouse CD8(+) T cells after vaccination and amplification with ch14.18-IL-2 suggests that the initial polyclonal CD8(+) T cell response is effectively boosted by targeted IL-2. In conclusion, we demonstrate that a successful boost of a partially protective memory T cell immune response that is induced by scIL-12 gene therapy could be generated by tumor-specific targeting of IL-2 with a ch14.18-IL-2 fusion protein. This approach could increase success rates of clinical cancer vaccine trials.
Bacteraemia in patients admitted to an urban hospital in West Africa (2007)

In The Gambia, those with bacteraemia are more likely than those without to die in hospital and to have a raised peripheral blood WCC. S. pneumoniae is the most common organism isolated. Introduction of a pneumococcal conjugate vaccine can be expected to lead to a reduction in disease incidence.
Synthesis and Optical Properties of Gold Nanodecahedra with Size Control (2006)

Regular gold nanodecahedra (pentagonal bipyramids) are obtained in high yield through ultrasound-induced reduction of HAuCl4 by dimethylformamide on presynthesized seeds (see figure). A dependence of the final morphology on the crystalline structure of the seeds is demonstrated by growing gold on single-crystal platinum nanoparticles, which yields uniform octahedra. Resolution of Maxwell's equations for bicones shows good agreement with experimental optical properties. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2006/c0475_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Spectral-domain phase microscopy (2005)

Broadband interferometry is an attractive technique for the detection of cellular motions because it provides depth-resolved phase information via coherence gating. We present a phase-sensitive technique called spectral-domain phase microscopy (SDPM). SDPM is a functional extension of spectral-domain optical coherence tomography that allows for the detection of nanometer-scale motions in living cells. The sensitivity of the technique is demonstrated, and its calibration is verified. A shot-noise limit to the displacement sensitivity of this technique is derived. Measurement of cellular dynamics was performed on spontaneously beating cardiomyocytes isolated from chick embryos.
The human platelet alloantigens, PlA1 and PlA2, are associated with a leucine33/proline33 amino acid polymorphism in membrane glycoprotein IIIa, and are distinguishable by DNA typing. (1989)

The human platelet alloantigens, PlA1 and PlA2, comprise a diallelic antigen system located on a component of the platelet fibrinogen receptor, membrane glycoprotein (GP) IIIa. Of the known platelet alloantigens, PlA1, which is carried by 98% of the caucasian population, appears to be the alloantigen that most often provokes neonatal alloimmune thrombocytopenic purpura and posttransfusion purpura. The structural features of the GPIIIa molecule responsible for its antigenicity are as yet unknown. Using the polymerase chain reaction (PcR), we amplified the NH2-terminal region of platelet GPIIIa mRNA derived from PlA1 and PlA2 homozygous individuals. Nucleotide sequence analysis of selected amplified cDNA products revealed a C in equilibrium T polymorphism at base 196 that created a unique Nci I restriction enzyme cleavage site in the PlA2, but not the PlA1 form of GPIIIa cDNA. Subsequent restriction enzyme analysis of cDNAs generated by PcR from 10 PlA1/A1, 5 PlA2/A2, and 3 PlA1/A2 individuals showed that Nci I digestion permitted clear discrimination between the PlA1 and PlA2 alleles of GPIIIa. All PlA2/A2 individuals studied contain a C at base 196, whereas PlA1 homozygotes have a T at this position. This single base change results in a leucine/proline polymorphism at amino acid 33 from the NH2-terminus, and is likely to impart significant differences in the secondary structures of these two allelic forms of the GPIIIa molecule. The ability to perform DNA-typing analysis for PlA phenotype may have a number of useful clinical applications, including fetal testing and determination of the phenotype of severely thrombocytopenic individuals.
Synthesis of NM23 and P53 protein in renal cell carcinoma and its clinical significance (1998)

Aim:To study the relationship between nm23 and p53 gene expression and the carcinogenesis and the development of human renal cell carcinoma (RCC) Methods:Synthesis of NM23 and P53 protein in the cancerous tissues of 55 patients with RCC and 42 pericancerous tissues were studied with immunohistochemical methodResults:The positive rates of NM23 and P53 protein in RCC were 672% and 302% respectively There was significant negative correlation between NM23 and P53 protein positive degree(r′s=-0461,P005)Synthesis of NM23 and P53 protein wasn′t associated with size, clinical stage and pathological classification of the tumor, but was correlated with histological differention degree of the RCC and prognostic evaluation of the patients Conclusions:The results show that nm23 and p53 gene may play some roles in occuring and development of the RCC They may be useful in judging malignance of the RCC and evaluating prognosis of the patients
Signalling to cancer cell invasion through PAK family kinases (2010)

Cancer cell metastasis involves a series of changes in cell behaviour, driven by oncogenic transformation, that leads to local tissue invasion, migration through extracellular matrix, entry into the vascular or lymphatic system and colonisation of distant sites. It is well established that the Rho family GTPases Rho, Rac and Cdc42 orchestrate many of the processes required during metastasis. The Rho family GTPases regulate cellular behaviour through their interaction with downstream effector proteins. The p-21 activated kinases (PAKs), effector proteins for Rac and Cdc42, are known to be important regulators of cell migration and invasion. There are six mammalian PAKs which can be divided into two groups: group I PAKs (PAK1-3) and group II PAKs (PAK4-6). Although the two PAK groups are architecturally similar there are differences in their mode of regulation suggesting their cellular functions are likely to be different. This review will focus on the latest evidence relating to the role of PAK family kinases in the cell signalling pathways that drive cancer cell migration and invasion.
Technical Overview of the Common Language Runtime (2001)

The functionality of the recently announced Microsoft .NET system is founded on the capabilities of the Common Language Infrastructure (CLI). Unlike some other recent systems based on virtual machines, the CLI was designed from the start to support a wide range of programming languages. It is also expected that ECMA standardization will make the CLI available on a wide range of computing platforms. This combination of multi-language capability and multiplatform implementation make the CLI an important target for future language compilers.
Transforming Growth Factor (TGF-β)-specific Signaling by Chimeric TGF-β Type II Receptor with Intracellular Domain of Activin Type IIB Receptor (1997)

of the transforming growth factor- (TGF-) superfamily signal via different heteromeric complexes of two sequentially acting serine/threonine kinase receptors, i.e. type I and type II receptors. We generated two different chimeric TGF- superfamily receptors, i.e. TR-I/BMPR-IB, containing the extracellular domain of TGF- type I receptor (TR-I) and the intracellular domain of bone morphogenetic protein type IB receptor (BMPR-IB), and TR-II/ActR-IIB, containing the extracellular domain of TGF- type II receptor (TR-II) and the intracellular domain of activin type IIB receptor (ActR-IIB). In the presence of TGF-1, TR-I/BMPR-IB and TR-II/ActR-IIB formed heteromeric complexes with wild-type TR-II and TR-I, respectively, upon stable transfection in mink lung epithelial cell lines. We show that TR-II/ActR-IIB restored the responsiveness upon transfection in mutant cell lines lacking functional TR-II with respect to TGF--mediated activation of a transcriptional signal, extracellular matrix formation, growth inhibition, and Smad phosphorylation. Moreover, TR-I/BMPR-IB and TR-II/ActR-IIB formed a functional complex in response to TGF- and induced phosphorylation of Smad1. However, complex formation is not enough for signal propagation, which is shown by the inability of TR-I/BMPR-IB to restore responsiveness to TGF- in cell lines deficient in functional TR-I. The fact that the TGF-1-induced complex between TR-II/ActR-IIB and TR-I stimulated endogenous Smad2 phosphorylation, a TGF--like response, is in agreement with the current model for receptor activation in which the type I receptor determines signal specificity.