gebhart/patrepeval huggingface dataset:
Genetic Dissection of Quantitative Resistance to Common Rust (Puccinia sorghi) in Tropical Maize (Zea mays L.) by Combined Genome-Wide Association Study, Linkage Mapping, and Genomic Prediction (2021)

Common rust is one of the major foliar diseases in maize, leading to significant grain yield losses and poor grain quality. To dissect the genetic architecture of common rust resistance, a genome-wide association study (GWAS) panel and a bi-parental doubled haploid (DH) population, DH1, were used to perform GWAS and linkage mapping analyses. The GWAS results revealed six single-nucleotide polymorphisms (SNPs) significantly associated with quantitative resistance of common rust at a very stringent threshold of <i>P-</i>value 3.70 × 10<sup>-6</sup> at bins 1.05, 1.10, 3.04, 3.05, 4.08, and 10.04. Linkage mapping identified five quantitative trait loci (QTL) at bins 1.03, 2.06, 4.08, 7.03, and 9.00. The phenotypic variation explained (PVE) value of each QTL ranged from 5.40 to 12.45%, accounting for the total PVE value of 40.67%. Joint GWAS and linkage mapping analyses identified a stable genomic region located at bin 4.08. Five significant SNPs were only identified by GWAS, and four QTL were only detected by linkage mapping. The significantly associated SNP of S10_95231291 detected in the GWAS analysis was first reported. The linkage mapping analysis detected two new QTL on chromosomes 7 and 10. The major QTL on chromosome 7 in the region between 144,567,253 and 149,717,562 bp had the largest PVE value of 12.45%. Four candidate genes of <i>GRMZM2G328500</i>, <i>GRMZM2G162250</i>, <i>GRMZM2G114893</i>, and <i>GRMZM2G138949</i> were identified, which played important roles in the response of stress resilience and the regulation of plant growth and development. Genomic prediction (GP) accuracies observed in the GWAS panel and DH1 population were 0.61 and 0.51, respectively. This study provided new insight into the genetic architecture of quantitative resistance of common rust. In tropical maize, common rust could be improved by pyramiding the new sources of quantitative resistance through marker-assisted selection (MAS) or genomic selection (GS), rather than the implementation of MAS for the single dominant race-specific resistance gene.
Ss-DNA functionalized array of ALN Contour-Mode NEMS Resonant Sensors with single CMOS multiplexed oscillator for sub-ppb detection of volatile organic chemicals (2011)

This paper reports on the design and experimental verification of the first prototype of a resonant sensing platform based on nanoscaled aluminum nitride Contour-Mode Resonant Sensors (CMR-S) for selective detection of sub-ppb levels of volatile organic chemicals (VOCs). For the first time arrays of 8 nano-CMR-S were fabricated on the same chip and functionalized with two different thiol-terminated ss-DNA sequences. A low noise and low power (as low as 224 μW) CMOS circuit read-out capable of monitoring the responses of each NEMS sensor in a time-multiplexed mode was used. A ss-DNA sequence dependant adsorption of two vapors, such as DNT and DMMP, was recorded. Concentrations of DMMP and DNT as low as 700 part per billion (ppb) and 700 part per trillion (ppt), respectively, were experimentally detected. A limit of detection to mass per unit area as low as ~60 zg/μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> was extracted by noise characterization of the sensor array.
Gene Expression Patterns in Calorically Restricted Mice: Partial Overlap with Long-Lived Mutant Mice (2002)

To gain insight into the pathways by which caloric restriction (CR) slows aging, gene expression levels were assessed for each of 2,352 genes in the livers of 9-month-old CR and control mice. A total of 352 genes were found to be significantly increased or decreased by CR. The distribution of affected genes among functional classes was similar to the distribution of genes within the test set. Surprisingly, a disruption or knockout of the gene for the GH receptor (GHR-KO), which also produces life extension, had a much smaller effect on gene expression, with no more than 10 genes meeting the selection criterion. There was, however, an interaction between the GHR-KO mutation and the CR diet: the effects of CR on gene expression were significantly lower in GHR-KO mice than in control mice. Of the 352 genes altered significantly by CR, 29 had shown a significant and parallel alteration in expression in a previous study of liver gene expression that compared mice of the long-lived Snell dwarf stock (dw/dw) to controls. These 29 genes, altered both by CR and in dwarf mice, provide a list of biochemical features common to both models of delayed aging, and thus merit confirmation and more detailed study.
The Role of Cathepsin D in the Pathophysiology of Heart Failure and its Potentially Beneficial Properties: A Translational Approach (2019)

Circulating cathepsin D levels are associated with HF severity and poorer outcome, and reduced levels of cathepsin D may have detrimental effects with therapeutic potential in HF.
Time-Resolved IR Studies of 2-Naphthyl(carbomethoxy)carbene:  Reactivity and Direct Experimental Estimate of the Singlet/Triplet Energy Gap (1999)

To clarify the role of diazocarbonyl excited states in Wolff rearrangement chemistry, time-resolved infrared (TRIR) spectroscopy has been used to study methyl 2-diazo-(2-naphthyl) acetate (1) and the subsequently produced 2-naphthyl(carbomethoxy)carbene (2). TRIR analysis of the growth rate of the ketene rearrangement product following laser excitation of diazoester 1 demonstrates that in this case ketene is formed almost exclusively from the carbene. The absence of reaction from the diazoester excited state is likely due to the highly preferred anti relationship between the diazo and carbonyl groups in 1. In addition, the detection of IR bands from both the singlet and triplet states of spin-equilibrated carbene 2 has allowed a direct experimental estimate of the singlet/triplet energy gap in solution at ambient temperature. This work represents the first TRIR detection and study of a carbene intermediate and demonstrates the potential value of TRIR spectroscopy in structural and mechanistic aspects of carbene chemistry.
Discrete Polyoxopalladates as Molecular Precursors for Supported Palladium Metal Nanoparticles as Hydrogenation Catalysts (2019)

We have used discrete polyoxopalladates(II) (POPs) of the MPd<sub>12</sub>X<sub>8</sub> nanocube- and Pd<sub>15</sub>X<sub>10</sub> nanostar-types (M = central metal ion, X = capping group) as molecular precursors (diameter ca. 1 nm) for the formation of supported (SBA-15) metallic nanoparticles. These materials proved to be highly active in the hydrogenation of o-xylene. The characterization of such hydrogenation catalysts revealed that the average size of the resulting alloy particles is quite uniform with diameters ranging from 1 to 3 nm (indicating little to no agglomeration). The central transition-metal ion M <sup>n+</sup> (Mn<sup>II</sup>, Fe<sup>III</sup>, Co<sup>II</sup>, Ni<sup>II</sup>, Cu<sup>II</sup>, Zn<sup>II</sup>, Pd<sup>II</sup>) in the POP structure and also the nature of the capping group (AsO<sub>4</sub><sup>3-</sup>, SeO<sub>3</sub><sup>2-</sup>, PO<sub>4</sub><sup>3-</sup>, phenyl-AsO<sub>3</sub><sup>2-</sup>) influence the resulting catalytic performance.
A Case Study on User Behavior Based Service Design in case of Communication Failure (2019)

그동안 우리나라는 세계 최고 수준의 통신망을 구 축ᆞ운영하는 국가로 평가되어 왔으나, 2018년 11월 KT 아현국사 통신구 화재로 통신 서비스 장애 시 신 속한 대처가 미비한 것으로 나타났으며 특히“통신장 애 발생 시 이용자 행동요령”의 부재는 이용자의 적 절하고 능동적 대응이 이루어지지 못한 근본적 원인 이 되었다. KT 아현국사 통신구 화재로 인한 통신장애는 아 현동 지역의 KT 가입자인 직접 이해관계자뿐만 아니 라 카드 결제, 주문 등으로 불편을 겪은 다양한 간접 이해관계자를 비롯하여 119 연결 지연으로 신고를 못 해 인명사고를 발생시키는 등 국민 생활에 막대한 영향을 미치는 재해와 같은 피해 상황을 초래했다. 현재 정보통신 분야의 사고 관련 매뉴얼은 주로 정 부 또는 통신 사업자의 시설 복구 측면에 편중되어 있어 이용자 대응 및 보호 조치 활용에는 한계가 있 다. 이에, 서비스디자인 방법론을 통해 이용자의 대응 과 보호 조치를 위한 통신장애 시 이용자 행동요령을 마련하였다. 본 연구는 통신 사업자 ․ 변호사 등의 전문가와 소 비자 단체 ․ 대학생 ․ 일반 국민으로 다양한 이해관계 자를 구성하여, 공동창작인 코-크리에이션(Co-creation) 을 통해 서비스콘셉트를 수립하고 서비스디자인 프로 토타이핑(Prototyping) 방법을 통한 피드백과 공동창 작 반영을 반복 연계하여 통신장애 시 이용자 행동요령을 최종적으로 도출한 사례연구이다.
TRAMS Project: Variability and Reliability of SRAM Memories in sub-22nm Bulk-CMOS Technologies (2011)

The TRAMS (Terascale Reliable Adaptive MEMORY Systems) project addresses in an evolutionary way the ultimate CMOS scaling technologies and paves the way for revolutionary, most promising beyond-CMOS technologies. In this abstract we show the significant variability levels of future 18 and 13 nm device bulk-CMOS technologies as well as its dramatic effect on the yield of memory cells and circuits.
Identification of a Pegivirus (GB Virus-Like Virus) That Infects Horses (2013)

The recent identification of nonprimate hepaciviruses in dogs and then in horses prompted us to look for pegiviruses (GB virus-like viruses) in these species. Although none were detected in canines, we found widespread natural infection of horses by a novel pegivirus. Unique genomic features and phylogenetic analyses confirmed that the tentatively named equine pegivirus (EPgV) represents a novel species within the Pegivirus genus. We also determined that EPgV causes persistent viremia whereas its clinical significance is undetermined.
Data from BET Inhibitors Suppress ALDH Activity by Targeting <i>ALDH1A1</i> Super-Enhancer in Ovarian Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;The emergence of tumor cells with certain stem-like characteristics, such as high aldehyde dehydrogenase (ALDH) activity due to ALDH1A1 expression, contributes to chemotherapy resistance and tumor relapse. However, clinically applicable inhibitors of ALDH activity have not been reported. There is evidence to suggest that epigenetic regulation of stem-related genes contributes to chemotherapy efficacy. Here, we show that bromodomain and extraterminal (BET) inhibitors suppress ALDH activity by abrogating BRD4-mediated ALDH1A1 expression through a super-enhancer element and its associated enhancer RNA. The clinically applicable small-molecule BET inhibitor JQ1 suppressed the outgrowth of cisplatin-treated ovarian cancer cells both &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;. Combination of JQ1 and cisplatin improved the survival of ovarian cancer–bearing mice in an orthotopic model. These phenotypes correlate with inhibition of &lt;i&gt;ALDH1A1&lt;/i&gt; expression through a super-enhancer element and other stem-related genes in promoter regions bound by BRD4. Thus, targeting the BET protein BRD4 using clinically applicable small-molecule inhibitors, such as JQ1, is a promising strategy for targeting ALDH activity in epithelial ovarian cancer. &lt;i&gt;Cancer Res; 76(21); 6320–30. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
NMR studies of cytochrome P-450scc. Effects of steroid binding on water proton access to the active site of the ferric enzyme (1987)

Water proton relaxation rates of various complexes of cholesterol side chain cleavage cytochrome P-450(P-450_(scc)) were investigated to gain information about the structure and dynamics of the steroid binding site. In all cases bulk water protons were found to be in rapid exchange with protons near the paramagnetic Fe^(3+) center, and the long electron spin relaxation time of the heme iron, T_s~0.3 ns, resulted in fast relaxation rates. For the steroid-free enzyme, the closest approach of exchangeable protons is ~2.5 Å, a distance consistent with a water molecule binding directly to the heme iron or rapidly exchanging with a coordinated ligand. When cholesterol was bound, the distance increased to ~4 Å, indicative of displacement of water from the immediate coordination sphere of the heme but still in close proximity to the active site. For the Complex with (22R)-22-hydroxycholesterol, a distance of ~2.7 Å is observed, suggesting a reorganization of the active site when this intermediate is formed from cholesterol. Complexes of P-450_(scc) with the competitive inhibitors (22R)-22-aminocholesterol, 22-amino-23,24-bisnor-5-cholen-3β-ol, or (20R)-20-phenyl-5-&#13;\npregnene-3β,20-diol, also yielded distances of ~2.5 Å and reveal no effect of side chain size on access of protons to the heme. In the nitrogen-coordinated amino-steroid complexes, the distances observed indicate solvent proton exchange with the heme-bound nitrogen ligand. In contrast to cytochrome P-450_(cam), in which water is excluded from the heme center in the substrate complex [Griffin, B. W., &amp; Peterson, J. A. (1975) J. Biol. Chem. 250, 6445-6451; Philson, S. B., Debrunner, P. G., Schmidt, P. G., &amp; Gunsalus, I. C. (1979) J. Biol. Chem. 254, 10173-10179], protons have rapid access to regions near the active site of several steroid complexes of P-450_(scc). This suggests that the active site of P-450_(scc) may be open to solvent and that solvent water molecules, rather than acid/base groups in the active site, may provide the protons required during the monooxygenation reaction cycle.
Establishing a Fiber-Optic-Based Optical Neural Interface (2014)

Selective expression of opsins in genetically defined neurons makes it possible to control a subset of neurons without affecting nearby cells and processes in the intact brain, but light must still be delivered to the target brain structure. Light scattering limits the delivery of light from the surface of the brain. For this reason, we have developed a fiber-optic-based optical neural interface (ONI), which allows optical access to any brain structure in freely moving mammals. The ONI system is constructed by modifying the small animal cannula system from PlasticsOne. The system for bilateral stimulation consists of a bilateral cannula guide that has been stereotactically implanted over the target brain region, a screw cap for securing the optical fiber to the animal's head, a fiber guard modified from the internal cannula adapter, and a bare fiber whose length is customized based on the depth of the target region. For unilateral stimulation, a single-fiber system can be constructed using unilateral cannula parts from PlasticsOne. We describe here the preparation of the bilateral ONI system and its use in optical stimulation of the mouse or rat brain. Delivery of opsin-expressing virus and implantation of the ONI may be conducted in the same surgical session; alternatively, with a transgenic animal no opsin virus is delivered during the surgery. Similar procedures are useful for deep or superficial injections (even for neocortical targets, although in some cases surface light-emitting diodes or cortex-apposed fibers can be used for the most superficial cortical targets).
Kinetic Polymer Arrest in Percolated SWNT Networks (2014)

Particle-polymer attractions in nanocomposites can cause significant heterogeneities in the polymer dynamics and remarkably impact the material properties. Dynamical perturbations are generally expected to be limited to interfacial polymer segments. However, composites with highly anisotropic nanoparticles usually exhibit very low percolation thresholds. In such systems, the overlapping interfacial regions could result in a complex polymer relaxation behavior that is unanticipated from dilute nanoparticle dispersions in polymer matrices. To understand this behavior, we examine a system of percolated single-wall carbon nanotubes (SWNT) in a polymer matrix, PMMA, which is known to have strong interfacial binding. Neutron spectroscopy measurements on the composites reveal not only an interfacial polymer layer that is transiently pinned to the SWNT surface, but suggest that the percolated network forms a kinetic cage that dramatically restricts both local and cooperative relaxations of noninterfacial polymer segments. These findings should help guide theories and simulations of hierarchical polymer dynamics in nanocomposites.
A New and Selective Catalyst for the [5 + 2] Cycloaddition of Vinylcyclopropanes and Alkynes (1998)

ADVERTISEMENT RETURN TO ISSUECommunicationNEXTA New and Selective Catalyst for the [5 + 2] Cycloaddition of Vinylcyclopropanes and AlkynesPaul A. Wender and David SperandioView Author Information Department of Chemistry, Stanford University, Stanford, California 94305 Cite this: J. Org. Chem. 1998, 63, 13, 4164–4165Publication Date (Web):June 5, 1998Publication History Received9 March 1998Published online5 June 1998Published inissue 1 June 1998https://pubs.acs.org/doi/10.1021/jo9804240https://doi.org/10.1021/jo9804240rapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views1622Altmetric-Citations105LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Addition reactions,Catalysts,Cyclization,Hydrocarbons,Isomerization Get e-Alerts
Data from Comprehensive Genetic Characterization of Human Thyroid Cancer Cell Lines: A Validated Panel for Preclinical Studies (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Thyroid cancer cell lines are valuable models but have been neglected in pancancer genomic studies. Moreover, their misidentification has been a significant problem. We aim to provide a validated dataset for thyroid cancer researchers.&lt;/p&gt;Experimental Design:&lt;p&gt;We performed next-generation sequencing (NGS) and analyzed the transcriptome of 60 authenticated thyroid cell lines and compared our findings with the known genomic defects in human thyroid cancers.&lt;/p&gt;Results:&lt;p&gt;Unsupervised transcriptomic analysis showed that 94% of thyroid cell lines clustered distinctly from other lineages. Thyroid cancer cell line mutations recapitulate those found in primary tumors (e.g., &lt;i&gt;BRAF&lt;/i&gt;, &lt;i&gt;RAS&lt;/i&gt;, or gene fusions). Mutations in the &lt;i&gt;TERT&lt;/i&gt; promoter (83%) and &lt;i&gt;TP53&lt;/i&gt; (71%) were highly prevalent. There were frequent alterations in &lt;i&gt;PTEN&lt;/i&gt;, &lt;i&gt;PIK3CA&lt;/i&gt;, and of members of the SWI/SNF chromatin remodeling complex, mismatch repair, cell-cycle checkpoint, and histone methyl- and acetyltransferase functional groups. Copy number alterations (CNA) were more prevalent in cell lines derived from advanced versus differentiated cancers, as reported in primary tumors, although the precise CNAs were only partially recapitulated. Transcriptomic analysis showed that all cell lines were profoundly dedifferentiated, regardless of their derivation, making them good models for advanced disease. However, they maintained the BRAF&lt;sup&gt;V600E&lt;/sup&gt; versus RAS-dependent consequences on MAPK transcriptional output, which correlated with differential sensitivity to MEK inhibitors. Paired primary tumor-cell line samples showed high concordance of mutations. Complete loss of p53 function in &lt;i&gt;TP53&lt;/i&gt; heterozygous tumors was the most prominent event selected during &lt;i&gt;in vitro&lt;/i&gt; immortalization.&lt;/p&gt;Conclusions:&lt;p&gt;This cell line resource will help inform future preclinical studies exploring tumor-specific dependencies.&lt;/p&gt;&lt;/div&gt;
An exponentially convergent adaptive algorithm for time-varying IIR filters (2010)

Conditions for exponential stability are established for a class of adaptive algorithms that estimate the parameters of a time-varying linear filter using a basis function approach. These algorithms are useful in situations calling for adaptive filters when the ideal filters vary at rates that cannot be considered slow, such as in the study of renal hemodynamics and for some mobile radio channels. Exponential convergence is established by extending a Lyapunov stability analysis for time-invariant adaptive IIR filters to the time-varying case.
Cooperation between the Hic1 and Ptch1 tumor suppressors in medulloblastoma (2008)

Medulloblastoma is an embryonal tumor thought to arise from the granule cell precursors (GCPs) of the cerebellum. PATCHED (PTCH), an inhibitor of Hedgehog signaling, is the best-characterized tumor suppressor in medulloblastoma. However, <20% of medulloblastomas have mutations in PTCH. In the search for other tumor suppressors, interest has focused on the deletion events at the 17p13.3 locus, the most common genetic defect in medulloblastoma. This chromosomal region contains HYPERMETHYLATED IN CANCER 1 (HIC1), a transcriptional repressor that is a frequent target of epigenetic gene silencing in medulloblastoma. Here we use a mouse model of Ptch1 heterozygosity to reveal a critical tumor suppressor function for Hic1 in medulloblastoma. When compared with Ptch1 heterozygous mutants, compound Ptch1/Hic1 heterozygotes display a fourfold increased incidence of medulloblastoma. We show that Hic1 is a direct transcriptional repressor of Atonal Homolog 1 (Atoh1), a proneural transcription factor essential for cerebellar development, and show that ATOH1 expression is required for human medulloblastoma cell growth in vitro. Given that Atoh1 is also a putative target of Hh signaling, we conclude that the Hic1 and Ptch1 tumor suppressors cooperate to silence Atoh1 expression during a critical phase in GCP differentiation in which malignant transformation may lead to medulloblastoma.
Dispersion slope compensating fibers for L-band WDM systems using NZ-DSF (2002)

Dispersion slope compensating fiber, which upgrades installed NZ-DSF to l-band D-WDM transmission line, was designed and fabricated. Both polarisation mode dispersion (PMD) and bending loss are low enough for moduling. It can compensate the dispersion of +NZ-DSF transmission line within /spl plusmn/0.3ps/nm/km over 1580-1620 nm.
Hypertension, Snoring, and Obstructive Sleep Apnea During Pregnancy (2015)

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