gebhart/patrepeval huggingface dataset:
The genomic and transcriptomic landscape of HeLa cells (2013)

HeLa is and always has been the most widely used model cell line for studying human cellular and molecular biology, and has thus defined our current understanding of human cells. However, no genomic or transcriptomic references exist for this cell line, and studies thus far have relied on the undoubtedly different human reference genome. This knowledge is essential to guide the increasing number of molecular and genetic studies being done in this cell line, both for design and interpretation. During my doctoral work, I performed deep DNA and RNA sequencing of a HeLa-Kyoto cell line and analyzed its mutational portfolio and gene expression profile. We generated a comprehensive description of the genomic and transcriptomic landscape of this cell line. A segmentation of the genome according to copy number revealed an astonishingly high level of aneuploidy and numerous large structural variations at unprecedented resolution. Remnants of catastrophic chromosome shattering, known as chromothripsis, were evident. Comparison of the HeLa expression profile to the physiological range of human gene expression reveals that several pathways, including cell cycle and DNA repair mechanisms, are 'abnormally' expressed. These results provide the first detailed account of the extent of variations in the HeLa genome, yielding insight into their impact on gene expression, cellular function, and their origins during the evolution of this cell line. This study demonstrates the importance of accounting for the strikingly aberrant characteristics of HeLa cells when designing and interpreting experiments. The important resources provided will help to reevaluate the way HeLa is used to model human biology.
Persistence of Eggs and Hepatic Fibrosis after Treatment of Schistosoma Mansoni-Infected Mice (1992)

In 1971 we estimated that Schistosoma mansoni eggs in the tissues of mice were destroyed with an approximate half-life of four weeks. Our present results of five experiments suggest that egg destruction is not as rapid, and no significant destruction of eggs was detected for up to 26 weeks after treatment. However, in these experiments, a mean of 60% of the eggs in intestinal tissues were found in the feces at the time of treatment. In previously reported experiments, only 15% of gut eggs were passed in the feces. We now believe that underestimation of the number of eggs passed in the feces led to an overestimation of the number of eggs destroyed in the tissues. We analyzed liver eggs separately because eggs lost from this site are unaffected by eggs passed in the feces. No significant decrease in liver eggs occurred in the present experiments, but reanalysis of previously published data showed significant egg destruction in the liver in several experiments, although at a much slower rate than previously estimated. However, inspection of the data in the previously published and present experiments does not show a convincing difference in the number of eggs in the liver after treatment. The persistence of egg shells is probably not important in the pathogenesis of disease, but is of concern in calculating worm fecundity. Hepatic collagen levels increased markedly two weeks after treatment and subsequently decreased significantly in some, but not all, experiments.
Industrial use of lipases to produce fatty acid esters (2003)

Abstract A wide range of fatty acid esters can be synthesised by esterification and transesterification reactions catalysed by lipases in non‐aqueous systems. As well as modifications to the natural substrate triacylglycerol, many other commercially important substances can be produced using this enzyme technology, as lipases have been shown to have broad substrate specificities and can thus catalyse conversions with many other non‐glycerol based compounds. In mild reaction conditions, emollient esters for use in the personal care industry can be made with excellent quality. Development of economical processes was necessary to commercialise this technology for the manufacture of cosmetic ingredients. Enzymatic production methods had to be established which could compete against standard established chemical synthetic methods. Now relatively simple esters are being produced enzymatically. Extensive purification procedures to clean up products after high temperature reaction steps are not required. Product quality and specifications, such as the acid and hydroxy values of commercial ester products, could be improved. Examples of products manufactured with better purity and yields in economical and ecologically friendly processes are decyl oleate, cetyl ricinoleate, myristyl myristate and decyl cocoate.
Resolving the constitutional question of the Malaysian king and rulers (1995)

(1995). Resolving the constitutional question of the Malaysian king and rulers. Asian Journal of Political Science: Vol. 3, No. 1, pp. 13-31.
Immunizing against fraud (1996)

Immunizing financial organizations against loan and mortgage fraud is a non-trivial problem. It involves the non-trivial identification of valid, novel, potentially useful, and ultimately understandable patterns in very large amounts of data. The critical issue is that we are trying to extract knowledge from data. Depending on the techniques used, the identified knowledge can then be used to: identify fraud in new applications; explain existing fraud; enable logical (as opposed to “graphical”) data visualization to aid humans in discovering deeper fraud patterns. An important issue relating to fraud is that as databases grow, fraud identification directly from their contents by humans becomes more and more difficult. A number of approaches have been developed to aid the human in their task. One such approach involves the use of AI techniques such as neural networks and machine induction. In this paper we describe a system based on metaphors taken from the human immune system. This system (referred to as the Artificial Immune System) is a general purpose computer-based learning system which has been applied to applications such as loan and mortgage fraud. (4 pages)
Visible InGaP/InGaAlP quantum well top surface emitting laser diodes (1993)

Vertical cavity top surface emitting lasers emitting near 0.67 μm visible spectral region were fabricated by one-step low pressure metalorganic vapor phase deposition technique. The lasers used four 80-Å-thick InGaP/InGaAlP quantum wells active region, sandwiched between two Al0.5Ga0.5As/AlAs distributed Bragg reflectors. Room temperature pulsed threshold current was 10 mA for 15 μm diam devices.
π-Allyl Derivatives of Transition Metals (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTπ-Allyl Derivatives of Transition MetalsW. R. McClellan, H. H. Hoehn, H. N. Cripps, E. L. Muetterties, and B. W. HowkCite this: J. Am. Chem. Soc. 1961, 83, 7, 1601–1607Publication Date (Print):April 1, 1961Publication History Published online1 May 2002Published inissue 1 April 1961https://pubs.acs.org/doi/10.1021/ja01468a013https://doi.org/10.1021/ja01468a013research-articleACS PublicationsRequest reuse permissionsArticle Views734Altmetric-Citations197LEARN 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
Complex Shape Evolution of Electromigration-Driven Single-Layer Islands (2005)

The shape evolution of two-dimensional islands through periphery diffusion biased by an electromigration force is studied numerically using a continuum approach. We show that the introduction of crystal anisotropy in the mobility of edge atoms induces a rich variety of migration modes, which include oscillatory and irregular behavior. A phase diagram in the plane of anisotropy strength and island size is constructed. The oscillatory motion can be understood in terms of stable facets that develop on one side of the island, and which the island then slides past. The facet orientations are determined analytically.
InverseRenderNet: Learning single image inverse rendering (2018)

We show how to train a fully convolutional neural network to perform inverse rendering from a single, uncontrolled image. The network takes an RGB image as input, regresses albedo and normal maps from which we compute lighting coefficients. Our network is trained using large uncontrolled image collections without ground truth. By incorporating a differentiable renderer, our network can learn from self-supervision. Since the problem is ill-posed we introduce additional supervision: 1. We learn a statistical natural illumination prior, 2. Our key insight is to perform offline multiview stereo (MVS) on images containing rich illumination variation. From the MVS pose and depth maps, we can cross project between overlapping views such that Siamese training can be used to ensure consistent estimation of photometric invariants. MVS depth also provides direct coarse supervision for normal map estimation. We believe this is the first attempt to use MVS supervision for learning inverse rendering.
Cleavage of the thrombin receptor: identification of potential activators and inactivators (1996)

The kinetic parameters were determined for the hydrolysis of a peptide based on the activation site of the thrombin receptor (residues 38-60) by thrombin and 12 other proteases. The kcat and Km values for the cleavage of this peptide (TR39-40) by thrombin were 107 s-1 and 1.3 microM; the kcat/Km of TR39-40 is among the highest observed for thrombin. A model is presented that reconciles the parameters for cleavage of the peptide with the concentration dependence of cellular responses to thrombin. Cleavage of TR39-40 was not specific for thrombin. The pancreatic proteases trypsin and chymotrypsin hydrolysed TR39-40 efficiently (kcat/Km > 10(6) M-1.s-1). Whereas trypsin cleaved TR39-40 at the thrombin activation site (Arg41-Ser42), chymotrypsin hydrolysed the peptide after Phe43. This chymotryptic cleavage would result in inactivation of the receptor. The efficient cleavage of TR39-40 by chymotrypsin (kcat/Km approximately 10(6) M-1.s-1) was predominantly due to a low Km value (2.8 microM). The proteases factor Xa, plasmin, plasma kallikrein, activated protein C and granzyme A also hydrolysed TR39-40 at the Arg41-Ser43 bond, but exhibited kcat/Km values that were at least 10(3)-fold lower than that observed with thrombin. Both tissue and urokinase plasminogen activators as well as granzyme B and neutrophil elastase were unable to cleave TR39-60 at appreciable rates. However, neutrophil cathepsin G hydrolysed the receptor peptide after Phe55. Like the chymotryptic cleavage, this cleavage would lead to inactivation of the receptor, but the cathepsin G reaction was markedly less efficient; the kcat/K(m) value was almost four orders of magnitude lower than that for thrombin. In addition to the above cleavage sites, a secondary site for thrombin and other arginine-specific proteases was identified at Arg46, but the cleavage at this site only occurred at very low rates and is unlikely to be significant in vivo.
Solid-Phase Radioimmunoassay for Digoxin (1973)

Abstract Anti-digoxin serum was conjugated to agarose or to organo-functional glass beads. The immunoadsorbents were compared to each other and to the soluble antibody, with respect to coupling efficiency and retention of immunological activity. We found that the antisera coupled to a glass-isothiocyanate retained about 50% of its immunological activity upon attachment. This derivative was superior to one prepared by coupling to CNBr-activated agarose, in which the attached protein retained 7% of its activity; and one prepared by coupling the protein to alkylamino glass using a water soluble carbodiimide, in which the attached antiserum retained only 1.5% of its original activity.
Substrate guided-wave-based optical interconnects for multiwavelength routing and distribution networks (1999)

A two-dimensional (2-D) wavelength division demultiplexing (WDDM) device is demonstrated to separate and to distribute multiwavelength optical signals by employing substrate-guided wave optical interconnects. Working principle and power budget issues are analyzed. In this planarized architecture, stacked/multiplexed input holographic gratings and arrays of output holographic gratings are designed to be fabricated on the same waveguiding plate to steer multiwavelength optical signals into different routing directions, to zigzag within a waveguiding substrate, and then to be surface-normally coupled out of the substrate. A dual-wavelength routing and distribution network is demonstrated in experiment at 780 nm and 790 nm. The crosstalk is measured to be >-30 dB. The fan-out energy fluctuation is within /spl plusmn/10% for each wavelength. We also demonstrate a planar three wavelength optical network to separate and distribute three wavelengths at 760, 790, and 820 nm. It is feasible for this structure to be used as high capacity wavelength division demultiplexing and routing networks at center wavelengths of 800, 1330, and 1550 nm.
A 25μm pitch LWIR focal plane array with pixel-level 15-bit ADC providing high well capacity and targeting 2mK NETD (2010)

CEA Leti has recently developed a new readout IC (ROIC) with pixel-level ADC for cooled infrared focal plane arrays (FPAs). It operates at 50Hz frame rate in a snapshot Integrate-While-Read (IWR) mode. It targets applications that provide a large amount of integrated charge thanks to a long integration time. The pixel-level analog-to-digital conversion is based on charge packets counting. This technique offers a large well capacity that paves the way for a breakthrough in NETD performances. The 15 bits ADC resolution preserves the excellent detector SNR at full well (3Ge-). These characteristics are essential for LWIR FPAs as broad intra-scene dynamic range imaging requires high sensitivity. The ROIC, featuring a 320x256 array with 25μm pixel pitch, has been designed in a standard 0.18μm CMOS technology. The main design challenges for this digital pixel array (SNR, power consumption and layout density) are discussed. The IC has been hybridized to a LWIR detector fabricated using our in-house HgCdTe process. The first electro-optical test results of the detector dewar assembly are presented. They validate both the pixel-level ADC concept and its circuit implementation. Finally, the benefit of this LWIR FPA in terms of NETD performance is demonstrated.
Synthesis and Properties of a Lead-Free Hybrid Double Perovskite: (CH<sub>3</sub>NH<sub>3</sub>)<sub>2</sub>AgBiBr<sub>6</sub> (2017)

The discovery of lead-free hybrid double perovskites provides a viable approach in the search for stable and environmentally benign photovoltaic materials as alternatives to lead-containing systems such as MAPbX3 (X = Cl, Br, or I). Following our recent reports of (MA)2KBiCl6 and (MA)2TlBiBr6, we have now synthesized a hybrid double perovskite, (MA)2AgBiBr6, that has a low band gap of 2.02 eV and is relatively stable and nontoxic. Its electronic structure and mechanical and optical properties are investigated with a combination of experimental studies and density functional theory calculations.
CCXXX.—Effects induced by the phenyl group. Part I. The addition of polar reagents to styrene and the behaviour of the halogenated ethylbenzenes (1928)

F. Ashworth and G. N. Burkhardt, J. Chem. Soc., 1928, 1791 DOI: 10.1039/JR9280001791
Activation of epitope-specific memory cytotoxic T lymphocyte responses by synthetic peptides (1996)

Cytotoxic T lymphocytes (CTL) recognize antigens as short peptides selected for presentation by their ability to bind to MHC class I molecules. Polyclonal Epstein-Barr virus (EBV)-specific memory CTL responses, reactivated from blood lymphocytes of HLA-A11-positive individuals by stimulation with the autologous EBV-transformed lymphoblastoid cell line (LCL), are often dominated by reactivites directed to the peptide epitope IVTDFSVIK (IVT), corresponding to amino acids 416-424 of EBV nuclear antigen-4 (EBNA4). We now report the selective activation of IVT-specific CTL by stimulation of lymphocytes with the corresponding synthetic peptide. A more than 10-fold increase in frequency of CTL clones with this specificity (from 8% to 96%) was obtained when the peptide was presented by HLA-A11-transfected T2 cells (T2/A11). Titration of synthetic peptide in cytotoxic assay demonstrated that clones activated under these conditions are as efficient as clones activated by conventional LCL stimulations. Induction of memory CTL responses required low surface density of MHC: peptide complexes, since reactivation was achieved by stimulation with T2/A11 cells pulsed with concentrations of peptide that are suboptimal for induction of target cell lysis. This protocol of activation revealed the presence of IVT-specific CTL precursors in a donor that failed to mount an IVT-specific response upon stimulation with the autologous B95.8 virus-transformed LCL. The results suggest that stimulation with synthetic peptide epitopes can be efficiently used for induction of memory CTL responses, and may be particularly helpful for the selective expansion of subdominant CTL specificities.
Parallel execution of hash joins in parallel databases (1997)

We explore two important issues, processor allocation and the use of hash filters, to improve the parallel execution of hash joins. To exploit the opportunity of pipelining for hash join execution, a scheme to transform a bushy execution tree to an allocation tree is first devised. In an allocation tree, each node denotes a pipeline. Then, using the concept of synchronous execution time, processors are allocated to the nodes in the allocation tree in such a way that inner relations in a pipeline can be made available at approximately the same time. Also, the approach of hash filtering is investigated to further improve the parallel execution of hash joins. Extensive performance studies are conducted via simulation to demonstrate the importance of processor allocation and to evaluate various schemes using hash filters. It is experimentally shown that processor allocation is, in general, the dominant factor of performance, and the effect of hash filtering becomes more prominent as the number of relations in a query increases.
miR-30 Promotes Thermogenesis and the Development of Beige Fat by Targeting RIP140 (2015)

Members of the microRNA (miR)-30 family have been reported to promote adipogenesis and inhibit osteogenesis, yet their role in the regulation of thermogenesis remains unknown. In this study, we show that miR-30b/c concentrations are greatly increased during adipocyte differentiation and are stimulated by cold exposure or the β-adrenergic receptor activator. Overexpression and knockdown of miR-30b and -30c induced and suppressed, respectively, the expression of thermogenic genes such as UCP1 and Cidea in brown adipocytes. Forced expression of miR-30b/c also significantly increased thermogenic gene expression and mitochondrial respiration in primary adipocytes derived from subcutaneous white adipose tissue, demonstrating a promoting effect of miRNAs on the development of beige fat. In addition, knockdown of miR-30b/c repressed UCP1 expression in brown adipose tissue in vivo. miR-30b/c targets the 3'-untranslated region of the receptor-interacting protein 140 (RIP140), and overexpression of miR-30b/c significantly reduced RIP140 expression. Consistent with RIP140 as a target of miR-30b/c in regulating thermogenic gene expression, overexpression of RIP140 greatly suppressed the promoting effect of miR-30b/c on the expression of UCP1 and Cidea in brown adipocytes. Taken together, the data from our study identify miR-30b/c as a key regulator of thermogenesis and uncover a new mechanism underlying the regulation of brown adipose tissue function and the development of beige fat.
Influence of molecular structure on the degradation mechanism of degradable polymers: <i>In vitro</i> degradation of poly(trimethylene carbonate), poly(trimethylene carbonate‐<i>co</i>‐caprolactone), and poly(adipic anhydride) (1995)

Abstract Relationships between molecular structure and the degradation mechanism of degradable polymers are of special interest for temporary medical applications. The in vitro degradation study of three aliphatic polymers—poly(trimethylene carbonate) (PTMC), poly(trimethylene carbonate‐ co ‐caprolactone) (PTMC‐PCL), and poly(adipic anhydride) (PAA)—revealed that these polymers exhibit degradation times from several years (PTMC) to 1 day (PAA). PTMC degraded unexpectedly slow, accompanied by very small changes in weight loss, molecular weight (SEC), and in morphology (DSC, SEM). The degradation was independent of initial molecular weight, ionic strength of the water solution, temperature, and shaking motions. The copolymer PTMC‐PCL showed a higher degradation rate compared to PTMC, with preferential degradation of amorphous parts leading to an increase in % crystallinity. The surprisingly rapid degradation of PAA showed characteristics typical for a surface‐like eroding system in contrast to PTMC and PTMC‐PCL. The degradation products corresponded to the repeating unit of the polymers. The hydrolysis rate increases in the order carbonate, ester, anhydride, and by combining different molecular structures we achieve specific degradation behavior. A change in hydrolysis rate of the labile bond is predicted by altering the electronegativity of groups near the carbonyl‐oxygen region. © 1995 John Wiley & Sons, Inc.
Effect of Magnesium Diphosphate and Zirconium Diphosphate Additions on Sintering of Magnesium Oxide (1980)

酸化マグネシウムに二リン酸マグネシウム又は二リン酸ジルコニウムを0.1-3.0mol%添加したときの焼結について, 昇温法 (昇温速度10℃・min-1, 室温-1300℃) 及び定温法 (1200℃及び1300℃, 300min) によって検討した. 昇温法では熱膨張計で収縮率を測定し, 定温法では焼結体のかさ密度を求めた.昇温法による結果は定温法の結果とほぼ一致した. 定温法による焼結過程は初期 (0-約30min) 及び後期過程 (約30-300min) に区別された. Mg2P2O7添加の場合では, 初期過程において1.0mol%以下の添加でMgOのち密化を促進し, 後期過程では1.0mol%が最もち密化を促進した. しかしながら, ZrP2O7添加の場合は用いたすべての濃度で全過程にわたってMgOの焼結を阻害した. 添加物を加えたときのMgO粒子は1200℃で急速に成長し始め, 1300℃では微量の液相の生成によって粒成長が更に促進された. 添加物のMgOの粒成長に及ぼす効果はZrP2O7の方がMg2P2O7に比べて大であった.以上の結果はMgOと添加物との反応生成物及びその生成量に影響され, 特に安定相であるMg3(PO4)2が多量に生成する場合はMgOの焼結を阻害することが認められた.
Predicting user traits from a snapshot of apps installed on a smartphone (2014)

Third party apps are an integral component of the smartphone ecosystem. In this paper, we investigate how user traits can be inferred by observing only a single snapshot of installed apps. Using supervised learning methods and minimal external information we show that user traits such as religion, relationship status, spoken languages, countries of interest, and whether or not the user is a parent of small children, can be easily predicted. Using data collected from over 200 smartphone users, specifically the list of installed apps and the corresponding ground truth traits of the users, we show that for most traits we can achieve over 90% precision. Our inference method can be used to provide services such as personalized content delivery or recommender systems for users. We also highlight privacy loss that can occur from unrestricted access to the app lists in popular smartphone operating systems.