gebhart/patrepeval huggingface dataset:
Use of Genome-Wide Expression Data to Mine the “Gray Zone” of GWA Studies Leads to Novel Candidate Obesity Genes (2010)

To get beyond the "low-hanging fruits" so far identified by genome-wide association (GWA) studies, new methods must be developed in order to discover the numerous remaining genes that estimates of heritability indicate should be contributing to complex human phenotypes, such as obesity. Here we describe a novel integrative method for complex disease gene identification utilizing both genome-wide transcript profiling of adipose tissue samples and consequent analysis of genome-wide association data generated in large SNP scans. We infer causality of genes with obesity by employing a unique set of monozygotic twin pairs discordant for BMI (n = 13 pairs, age 24-28 years, 15.4 kg mean weight difference) and contrast the transcript profiles with those from a larger sample of non-related adult individuals (N = 77). Using this approach, we were able to identify 27 genes with possibly causal roles in determining the degree of human adiposity. Testing for association of SNP variants in these 27 genes in the population samples of the large ENGAGE consortium (N = 21,000) revealed a significant deviation of P-values from the expected (P = 4x10(-4)). A total of 13 genes contained SNPs nominally associated with BMI. The top finding was blood coagulation factor F13A1 identified as a novel obesity gene also replicated in a second GWA set of approximately 2,000 individuals. This study presents a new approach to utilizing gene expression studies for informing choice of candidate genes for complex human phenotypes, such as obesity.
Proteomics of Cerebrospinal Fluid for Biomarker Discovery in Multiple Sclerosis (2013)

The discovery of reliable biomarkers, which are eligible for the prediction of both disease progression and response to treatment, means a great challenge in the management of multiple sclerosis (MS), a devastating disease of the central nervous system. The results of recent proteomic findings from the cerebrospinal fluid of MS patients hold promise of finding ideal biomarkers in the near future.
Altered expression and deletion of RMO1 in osteosarcoma (2004)

In order to increase our understanding of the molecular events underlying osteosarcoma progression, the expression of approximately 950 genes was examined in 24 primary and metastatic osteosarcoma tumor specimens. A gene, RMO1, was isolated with decreased expression in metastatic samples. Real-Time PCR corroborated this pattern, revealing lower expression in the primary sample in 6 of 7 cases for which both primary and metastatic osteosarcoma samples were available from the same patient (p = 0.034). RMO1 is located at 2q33, a region of frequent loss of heterozygosity in cancer, and exhibited loss of heterozygosity in 6 out of 9 primary osteosarcoma tumor samples (67%). Loss of heterozygosity is evident in primary tumors while the decrease in gene expression is seen in the metastatic samples, indicating that these 2 events are separately implicated in cancer progression. Cloning of RMO1 revealed an open reading frame with multiple splice forms with significant homology to GRB7, 10 and 14 and MIG10 in the region containing a Pleckstrin homology domain and a Ras association domain, suggestive of a role in cell signaling and migration. Northern blot analysis indicated that RMO1 mRNA is ubiquitously expressed in tissues except for peripheral blood leukocytes. These data suggest that RMO1 may be a candidate for a protein involved in inhibiting tumor progression.
Anisotropic electrical conductivity in polymer derived ceramics induced by graphene aerogels (2017)

Anisotropic electrical conductivity was introduced into bulk polymer derived ceramics by embedded reduced graphene oxide aerogels.
The Effect of Temperature on the Viability of Deformed Cells (2000)

Abstract Recent studies show that during slow freezing of cells, in addition to chemical damage, the cells may be also injured by mechanical damage induced by ice crystal compression. A new experimental procedure is employed to develop a quantitative understanding of cell destruction by deformation with two parallel surfaces. The viability of deformed cells (prostatic carcinoma cells, 17.5 μm in mean diameter) is measured at 0 °C, 23 °C and 37 °C, and six different nominal gap sizes between 32 μm and 3.5 μm. The relation between measured viability and gap size at 0 °C and 23 °C are identical but the viability decreases at 37 °C. This may suggest that deformation damage is not related to the mechanical properties of the lipid membrane but the deformation of the cytoskeleton.
The PAR2 signal peptide prevents premature receptor cleavage and activation (2019)

Abstract Unlike closely related GPCRs, protease-activated receptors (PAR1, PAR2, PAR3, and PAR4) have a predicted signal peptide at their N-terminus, which is encoded by a separate exon, suggesting that the signal peptides of PARs may serve an important and unique function, specific for PARs. In this report, we show that the PAR2 signal peptide, when fused to the N-terminus of IgG-Fc, effectively induced IgG-Fc secretion into culture medium, thus behaving like a classical signal peptide. The presence of PAR2 signal peptide has a strong effect on PAR2 cell surface expression, as deletion of the signal peptide (PAR2ΔSP) led to dramatic reduction of the cell surface expression and decreased responses to trypsin or the synthetic peptide ligand (SLIGKV). However, further deletion of the tethered ligand region (SLIGKV) at the N-terminus rescued the cell surface receptor expression and the response to the synthetic peptide ligand, suggesting that the signal peptide of PAR2 may be involved in preventing PAR2 from intracellular protease activation before reaching the cell surface. Supporting this hypothesis, an Arg36Ala mutation on PAR2ΔSP, which disabled the trypsin activation site, increased the receptor cell surface expression and the response to ligand stimulation. Similar effects were observed when PAR2ΔSP expressing cells were treated with protease inhibitors. Our findings indicated that these is a role of the PAR2 signal peptide in preventing the premature activation of PAR2 from intracellular protease cleavage before reaching the cells surface. The same mechanism may also apply to PAR1, PAR3, and PAR4.
High-Specific Impulse Hall Thrusters, Part 2: Efficiency Analysis (2006)

Peer Reviewed
Prop-2-yn-1-yl 2-Bromo-2-methylpropanoate: Identification and Suppression of Side Reactions of a Commonly Used Terminal Alkyne-Functional ATRP Initiator (2015)

The atom transfer radical polymerization (ATRP) of styrene was investigated using the popular alkyne-functional initiator prop-2-yn-1-yl 2-bromo-2-methylpropanoate (PBiB). The polymerization kinetics and evolution of molecular weight as a function of monomer conversion were systematically studied with PBiB and similar initiators with protecting groups at the reactive propargylic and terminal acetylenic sites. These studies were compared to control studies using the nonfunctional initiator ethyl 2-bromoisobutyrate. As confirmed by NMR analysis of a model reaction, the terminal alkynes undergo oxidative alkyne–alkyne coupling under ATRP conditions, resulting in polymers with bimodal molecular weight distributions. This side reaction is significant because it diminishes the orthogonality of ATRP/copper-catalyzed azide–alkyne cycloaddition procedures as well as the control of ATRP.
Genome-wide end-sequenced BAC resources for the NOD/MrkTac☆ and NOD/ShiLtJ☆☆ mouse genomes (2009)

Non-obese diabetic (NOD) mice spontaneously develop type 1 diabetes (T1D) due to the progressive loss of insulin-secreting beta-cells by an autoimmune driven process. NOD mice represent a valuable tool for studying the genetics of T1D and for evaluating therapeutic interventions. Here we describe the development and characterization by end-sequencing of bacterial artificial chromosome (BAC) libraries derived from NOD/MrkTac (DIL NOD) and NOD/ShiLtJ (CHORI-29), two commonly used NOD substrains. The DIL NOD library is composed of 196,032 BACs and the CHORI-29 library is composed of 110,976 BACs. The average depth of genome coverage of the DIL NOD library, estimated from mapping the BAC end-sequences to the reference mouse genome sequence, was 7.1-fold across the autosomes and 6.6-fold across the X chromosome. Clones from this library have an average insert size of 150 kb and map to over 95.6% of the reference mouse genome assembly (NCBIm37), covering 98.8% of Ensembl mouse genes. By the same metric, the CHORI-29 library has an average depth over the autosomes of 5.0-fold and 2.8-fold coverage of the X chromosome, the reduced X chromosome coverage being due to the use of a male donor for this library. Clones from this library have an average insert size of 205 kb and map to 93.9% of the reference mouse genome assembly, covering 95.7% of Ensembl genes. We have identified and validated 191,841 single nucleotide polymorphisms (SNPs) for DIL NOD and 114,380 SNPs for CHORI-29. In total we generated 229,736,133 bp of sequence for the DIL NOD and 121,963,211 bp for the CHORI-29. These BAC libraries represent a powerful resource for functional studies, such as gene targeting in NOD embryonic stem (ES) cell lines, and for sequencing and mapping experiments.
ChemInform Abstract: Phenyl 3‐Aminobenzenesulfonates: New Intermediates for Arylazopyridone Disperse Dyes. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Intratumoral characteristics of tumor and immune cells at baseline and on-treatment correlated with clinical responses to MPDL3280A, an engineered antibody against PD-L1 (2013)

Meeting abstracts PD-L1, PD-L2 and other immune-related molecules regulate Th1 and Th2 immune responses. Tumor-expressed PD-L1, when bound to PD-1 or B7.1 on activated T cells, can mediate cancer immune evasion. While inhibiting PD-L1 receptor binding represents an attractive strategy to restore
Indium-mediated allylations of unprotected carbohydrates in aqueous media: a short synthesis of sialic acid (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIndium-mediated allylations of unprotected carbohydrates in aqueous media: a short synthesis of sialic acidDana M. Gordon and George M. WhitesidesCite this: J. Org. Chem. 1993, 58, 27, 7937–7938Publication Date (Print):December 1, 1993Publication History Published online1 May 2002Published inissue 1 December 1993https://pubs.acs.org/doi/10.1021/jo00079a050https://doi.org/10.1021/jo00079a050research-articleACS PublicationsRequest reuse permissionsArticle Views681Altmetric-Citations88LEARN 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-Alertsclose Get e-Alerts
Gene Expression of Catalytic Proteasome Subunits and Resistance Toward Proteasome Inhibition of B Lymphocytes from Patients with Primary Sjögren Syndrome (2013)

In pSS, catalytic subunits of the proteasome are upregulated at the mRNA level, while dysregulation of subunit β1i is attributed to B lymphocytes. B cell resistance after proteasome inhibition differs from the classical concept of increased susceptibility toward inhibition in activated cells, supporting the novel notion that susceptibility depends on cellular intrinsic factors and on proteasome activation.
Synthesis of Fused Bicyclic Piperidines: Potential Bioactive Templates for Medicinal Chemistry (2014)

An array of six pyridyl-substituted fused bicyclic piperidines was prepared as novel cores for medicinal chemistry. For maximum diversity, the size of the fused ring varied from three to six atoms and contained up to two oxygen atoms. The pyridine ring was incorporated to improve physicochemical properties and to challenge the robustness of the chemistry. The presence of the pyridine did interfere with our initial approaches to these molecules, and in several instances, a blocking strategy had to be employed. These new scaffolds possess high sp3 character and may prove useful in multiple medicinal chemistry applications.
Phosphorus Incorporation in modified chemical vapor deposition (1988)

Phosphorus doping in vapor phase glass formation in modified chemical vapor deposition (MCVD) is investigated to facilitate understanding the cause of concentration gradients within individual MCVD layers. These inhomogeneities are evident in all MCVD preforms and fibers as slight wiggles in the deposited cladding material. Phosphorus is chosen as a representative dopant with the goal of determining the optimal process conditions to maximize incorporation or reduce the concentration gradients. Possible applications are in the fine tuning of MCVD processes to eliminate perturbations which may be the source of microbending losses and in the fabrication of gradient-index lenses by MCVD techniques. This model is also applicable to the previously demonstrated1 modification of dopant profiles during sintering in the VAD process to achieve a more carefully controlled index profile.
Kinetics of and catalyst decay accompanying the gas phase rearrangement of cyclohexanone‐oxime over a hy ultrastable zeolite (1987)

Abstract The kinetics of the rearrangement of cyclohexanone‐oxime has been studied in a fixed bed, glass tubular reactor at atmospheric pressure and temperatures of 240, 270, 300 and 335°C, using ultrastable HY zeolite catalyst. Several kinetic models, including the Langmuir‐Hinshelwood type, have been derived and the best statistical fit has been obtained with a pseudo‐first order kinetic equation. The rate constants and activation energies for the formation of the products caprolactam, cyclohexanone and 5‐cyanopent‐l‐ene have been calculated. Based on the evolution of the selectivity with temperature, and the I.R. spectra of the poisoned catalyst, different decay models have been deduced and discussed.
Chromates Recovery from Cooling Tower Blowdown by Ion Exchange Resins (1975)

For the removal of chromates from cooling tower blowdown, laboratory tests were conducted using a weakly basic anion exchange resin, Lewatit MP 64, and a weakly acidic cation exchange resin, Lewatit CNP 80, and the following results were obtained.(1) High chromate loading capacities of Lewatit MP 64 were obtained on simulated cooling tower blowdowns at relatively low influent pH and low concentration of competing anions.(2) Chromate concentration in the anion resin effluent was dependent on the regeneration levels. When the exchange functional groups were completely converted into hydrochloride form from free base form by using hydrochloric acid after regenerating by sodium hydroxide solution, the effluent chromate leakage was reduced to less than 1.0ppm as CrO42-, and the effluent pH ranged from 3 to 6. When exchange functional groups were left partially in free base form, chromate leakage increased more than 1.0ppm as CrO42- at the beginning of the exhaustion cycle. To reduce the effluent chromate leakage, it was necessary to increase sodium hydroxide regenerant.(3) The weakly acidic cation exchange resin, which preceded anion resin, was effective to remove zinc which was often used in combination with chromate as a formulated corrosion inhibitor and, with the resultant lowered influent pH at a range 3 to 5, to increase chromate loading capacity of anion resin. Based on the results of the above laboratory tests, the first commercial plant was installed at a petrochemical factory and has been successfully operating.
A New Sensing Concept for Tripped Rollovers (2004)

&lt;div class="htmlview paragraph"&gt;This paper describes a new system for early detection of tripped rollover crashes. The main goal of this system is to improve the protection of restraint devices, such as curtain window bags, in these rollover situations. This is achieved by a new rollover sensing (RoSe) algorithm in the airbag controller which produces a very early and robust deployment decision.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Based on the analysis of tripped rollover test data, this paper shows how improved rollover sensing performance can be achieved by considering information about the vehicle's driving state before the rollover occurs. The results of this new approach are discussed in terms of deployment times. Finally a combined active and passive safety system architecture for the realization of the approach is suggested.&lt;/div&gt;
Discovery of a Novel Amino Lipid That Improves Lipid Nanoparticle Performance through Specific Interactions with mRNA (2021)

Abstract Lipid nanoparticles (LNPs) are capable of delivering messenger ribonucleic acid (mRNA) efficiently and systemically as a result of both particle composition and architecture. The particle architecture is determined by how the various components interact with one another to establish a stable equilibrium through self‐assembly. The Coulombic attraction between the anionic oligonucleotide cargo and the ionizable amino lipid within the encapsulation media contributes to the coalescence of the particles, but other interactions are also involved. Prior exploration of amino lipids for mRNA delivery via a traditional medicinal chemistry approach suggests that hydrogen bonding between a hydroxyl headgroup and the mRNA contributes to improved LNP in vivo expression. Herein, expansion of that work culminating in the discovery of a novel squaramide lipid that enables robust LNPs with high levels of expression is described. Molecular dynamics simulations and biophysical evidence both support the hypothesis that the squaramide is making specific interactions with mRNA resulting in particles with a more stable and efficient structure.
Enhanced interfacial thermal transport in pnictogen tellurides metallized with a lead-free solder alloy (2015)

Controlling thermal transport across metal–thermoelectric interfaces is essential for realizing high efficiency solid-state refrigeration and waste-heat harvesting power generation devices. Here, the authors report that pnictogen chalcogenides metallized with bilayers of Sn96.5Ag3Cu0.5 solder and Ni barrier exhibit tenfold higher interfacial thermal conductance Γc than that obtained with In/Ni bilayer metallization. X-ray diffraction and x-ray spectroscopy indicate that reduced interdiffusion and diminution of interfacial SnTe formation due to Ni layer correlates with the higher Γc. Finite element modeling of thermoelectric coolers metallized with Sn96.5Ag3Cu0.5/Ni bilayers presages a temperature drop ΔT ∼ 22 K that is 40% higher than that obtained with In/Ni metallization. Our results underscore the importance of controlling chemical intermixing at solder–metal–thermoelectric interfaces to increase the effective figure of merit, and hence, the thermoelectric cooling efficiency. These findings should facilitate the design and development of lead-free metallization for pnictogen chalcogenide-based thermoelectrics.
ULSI reliability through ultraclean processing (1993)

The importance of ultraclean processing in establishing advanced process technologies for deep submicron ULSI fabrication is discussed. The most essential requirement for the process technologies is the simultaneous fulfilment of the three principles of ultraclean technology: ultraclean wafer surface, ultraclean processing environment, and perfect process-parameter control. The growth of high-crystallinity silicon epitaxial layers at temperatures as low as 250 degrees C with accompanying in situ impurity doping as a result of optimizing pertinent process parameters in a low-kinetic-energy particle process is described. Advanced copper metallization for large-current driving interconnect formation is discussed. Ultraclean oxidation, which is characterized by native-oxide-free and surface-microroughness-free oxidation, is confirmed to form high-quality very thin oxide films ranging from 5 to 10 nm with complete uniformity. A low-temperature annealing ion implantation that makes practical a metal gate self-aligned MOS LSI, which is crucial for high-speed CMOS having high current driving capability, is described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evaluation of Insecticides for Japanese Beetle and Soldier Beetle Control on Raspberry, 1989 (1990)

Abstract The experiment was conducted at the Rock Springs Research Farm. The study was laid out as a completely randomized design with 7 treatments each replicated 4 times. Treatments consisted of 5 plants, spaced 3 feet apart. Data were obtained from samples taken from the center section of plots. The total number of Japanese and soldier beetles/plot were counted. On 16 Jun, treatments were applied using a CO2 Precision Boom Sprayer that delivered 72 gal/acre at 35 psi. The spray boom was equipped with twin fan nozzles (T.J. 60-1104 vs). On 18 Jul treatments were applied using a Meyers Boom Sprayer that was adjusted to deliver 72 gal/acre traveling 3 mph. Treatments in parentheses were applied previously on 25 May.
Intramolecular [2+2] Cycloaddition of N‐Allylcinnamamines and N‐Allylcinnamamides by Visible‐Light Photocatalysis (2019)

The visible light‐promoted intramolecular [2+2] cycloaddition of N ‐allylcinnamamines and N ‐allylcinnamamides in the presence of catalytic amounts of [Ir{dF(CF 3 )ppy} 2 (dtbpy)]PF 6 is reported. Low energy visible light and a high triplet energy iridium‐photosensitizer were efficient at promoting the cycloaddition reaction of N ‐allylcinnamamides and N ‐allylcinnamamines to the corresponding aryl‐3‐azabicyclo[3.2.0]heptanones and aryl‐3‐azabicyclo[3.2.0]heptanes, respectively, with high diastereoselectivity and under mild conditions. Azabicyclic fused rings have been employed as surrogates for piperidine motifs in drug discovery. Functional groups useful for deployment and/or elaboration in drug discovery campaigns were all shown to be tolerated, including halides, CF 3 , cyanide, ester, acetamide, acetate, CH 3 O, pyridyl, furan, carbamate, tosyl, benzyl, and benzoate.