gebhart/patrepeval huggingface dataset:
Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE (2011)

Autism is a neurodevelopmental disorder with increasing evidence of heterogeneous genetic etiology including de novo and inherited copy number variants (CNVs). We performed array comparative genomic hybridization using a custom Agilent 1 M oligonucleotide array intended to cover 197 332 unique exons in RefSeq genes; 98% were covered by at least one probe and 95% were covered by three or more probes with the focus on detecting relatively small CNVs that would implicate a single protein-coding gene. The study group included 99 trios from the Simons Simplex Collection. The analysis identified and validated 55 potentially pathogenic CNVs, categorized as de novo autosomal heterozygous, inherited homozygous autosomal, complex autosomal and hemizygous deletions on the X chromosome of probands. Twenty percent (11 of 55) of these CNV calls were rare when compared with the Database of Genomic Variants. Thirty-six percent (20 of 55) of the CNVs were also detected in the same samples in an independent analysis using the 1 M Illumina single-nucleotide polymorphism array. Findings of note included a common and sometimes homozygous 61 bp exonic deletion in SLC38A10, three CNVs found in lymphoblast-derived DNA but not present in whole-blood derived DNA and, most importantly, in a male proband, an exonic deletion of the TMLHE (trimethyllysine hydroxylase epsilon) that encodes the first enzyme in the biosynthesis of carnitine. Data for CNVs present in lymphoblasts but absent in fresh blood DNA suggest that these represent clonal outgrowth of individual B cells with pre-existing somatic mutations rather than artifacts arising in cell culture. GEO accession number GSE23765 (http://www.ncbi.nlm.nih.gov/geo/, date last accessed on 30 August 2011). Genboree accession: http://genboree.org/java-bin/gbrowser.jsp?refSeqId=1868&entryPointId=chr17&from=53496072&to=53694382&isPublic=yes, date last accessed on 30 August 2011.
Mechanism of Poly(A) Signal Transduction to RNA Polymerase II In Vitro (2001)

Termination of transcription by RNA polymerase II usually requires the presence of a functional poly(A) site. How the poly(A) site signals its presence to the polymerase is unknown. All models assume that the signal is generated after the poly(A) site has been extruded from the polymerase, but this has never been tested experimentally. It is also widely accepted that a "pause" element in the DNA stops the polymerase and that cleavage at the poly(A) site then signals termination. These ideas also have never been tested. The lack of any direct tests of the poly(A) signaling mechanism reflects a lack of success in reproducing the poly(A) signaling phenomenon in vitro. Here we describe a cell-free transcription elongation assay that faithfully recapitulates poly(A) signaling in a crude nuclear extract. The assay requires the use of citrate, an inhibitor of RNA polymerase II carboxyl-terminal domain phosphorylation. Using this assay we show the following. (i) Wild-type but not mutant poly(A) signals instruct the polymerase to stop transcription on downstream DNA in a manner that parallels true transcription termination in vivo. (ii) Transcription stops without the need of downstream elements in the DNA. (iii) cis-antisense inhibition blocks signal transduction, indicating that the signal to stop transcription is generated following extrusion of the poly(A) site from the polymerase. (iv) Signaling can be uncoupled from processing, demonstrating that signaling does not require cleavage at the poly(A) site.
Iridescence-free and narrowband perfect light absorption in critically coupled metal high-index dielectric cavities (2017)

Perfect light absorption in the visible and near-infrared (NIR) was demonstrated using metamaterials, plasmonic nanostructures, and thin films. Thin film absorbers offer a simple and low-cost design as they can be produced on large areas and without lithography. Light is strongly absorbed in thin film metal-dielectric-metal (MDM) cavities at their resonance frequencies. However, a major drawback of MDM absorbers is their strong resonance iridescence, i.e., angle dependence. Here, we solve the iridescence problem by achieving angle-insensitive narrowband perfect and near-perfect light absorption. In particular, we show analytically that using a high-index dielectric in MDM cavities is sufficient to achieve angle-insensitive cavity resonance. We demonstrate experimentally angle-insensitive perfect and near-perfect absorbers in the NIR and visible regimes up to ±60°. By overcoming the iridescence problem, we open the door for practical applications of MDM absorbers at optical frequencies.
O23 ‐ Functional effects of an amino‐acid based formula with synbiotics in cow's milk allergic infants (2014)

Pre- and probiotics (synbiotics) are suggested to have beneficial effects on human health. This study describes effects of an amino acid based formula (AAF) with synbiotics in infants with cow's milk allergy (CMA). In a prospective, randomized, double-blind controlled study, full term infants with diagnosed IgE and/or non-IgE mediated CMA received a commercially available AAF (NEO; n=56) or an AAF with synbiotics (neutral and acidic oligosaccharides, Bifidobacterium breve M-16V) (NEO-SYN; n=54) for 16 weeks. Primary outcome was growth and formula tolerance; secondary outcomes were dermatological/respiratory allergic characteristics, and stool characteristics recorded in subject diaries and evaluated by a physician. Furthermore, adverse events and concomitant medications used during the study were reported. Average age of infants at inclusion was 4.5±2.4 months. Overall, NEO-SYN and NEO were equally tolerated and both supported normal growth. Both formulas reduced allergic symptoms; SCORAD decreased in both groups with no significant differences in SCORAD change over 16 weeks between both groups. Softer and yellow/brown stools were reported more frequently in the NEO-SYN group compared to more dry and green/dark brown stools in the NEO group (week 0-2, p=0.035; week 2-4, p=0.010 for stool consistency). Furthermore, the NEO-SYN group had less subjects with reported infections (p=0.008) and less subjects receiving medication for functional gastrointestinal disorders (p=0.029) when compared with the NEO group. In addition the NEO-SYN group had a lower number of infants on antibiotics (p=0.049), especially amoxicillin (p=0.004). This study shows that an AAF with synbiotics is equally tolerated, supports normal growth and is similarly effective in the management of CMA symptoms compared to an AAF without synbiotics. Infants taking an AAF with this synbiotic blend have different stool characteristics, less reported infections and less antibiotic use, which suggests that addition of the synbiotics to an AAF improves resistance to infections and reduces specific medication use.
Arctiin blocks hydrogen peroxide-induced senescence and cell death though microRNA expression changes in human dermal papilla cells (2014)

Taken together, our data suggest that arctiin has a protective effect on ROS-induced cell dysfunction in HHDPCs and may therefore be useful for alopecia prevention and treatment strategies.
Competing aggregation pathways for monoclonal antibodies (2014)

Aggregation is mediated by local unfolding to allow aggregation "hot spot(s)" to become solvent exposed and available to associate with a hot spot on another partially unfolded protein. Historically, the unfolding of either the crystallizable fragment (Fc) or the antigen binding fragment (Fab) regions of a given monoclonal antibody (MAb) has been implicated in aggregation, with differing results across different proteins. The present work focuses on separately quantifying the aggregation kinetics of isolated Fc, isolated Fab, and intact MAb as a function of pH under accelerated (high temperature) conditions. The results show that both Fab and Fc are aggregation prone and compete within the same MAb.
Molecular characterization of two galactosemia mutations: correlation of mutations with highly conserved domains in galactose-1-phosphate uridyl transferase. (1991)

Galactosemia is an autosomal recessive disorder of human galactose metabolism caused by deficiency of the enzyme galactose-1-phosphate uridyl transferase (GALT). The molecular basis of this disorder is at present not well understood. We report here two missense mutations which result in low or undetectable enzymatic activity. First, we identified at nucleotide 591 a transition which substitutes glutamine 188 by arginine. The mutated glutamine is not only highly conserved in evolution (conserved also in Escherichia coli and Saccharomyces cerevisiae), but is also two amino acid residues downstream from the active site histidine-proline-histidine triad and results in about 10% of normal enzymatic activity. The arginine 188 mutation is the most common galactosemia mutation characterized to date. It accounts for one-fourth of the galactosemia alleles studied. Second, we report the substitution of arginine 333 by tryptophan, caused by a transition at nucleotide 1025. The area surrounding this missense mutation is the most highly conserved domain in the homologous enzymes from E. coli, yeast, and humans, and this mutation results in undetectable enzymatic activity, suggesting that this is a severe mutation. This second mutation appears to be rare, since it was found only in the patient we sequenced. Our data provide further evidence for the heterogeneity of galactosemia at the molecular level, heterogeneity which might be related to the variable clinical outcome observed in this disorder.
Power sandbox (2018)

Many apps benefit from knowing their power consumption and adapting their behaviors on the fly. To offer apps power knowledge at run time, an OS often meters system power and divides it among apps. Since the impacts of concurrent apps on system power are entangled, this approach not only makes it difficult to reason about power but also results in power side channels, a serious vulnerability.
Identification of biomarkers for hepatocellular carcinoma by semiquantitative immunocytochemistry (2014)

ASGPR, GPC3, and CK may be valuable HCC biomarkers for CTC detection; the expression of ASGPR and GPC3 might be helpful for understanding patients' OS.
Including Magnetic Saturation in Voltage-Behind-Reactance Induction Machine Model for EMTP-Type Solution (2009)

A voltage-behind-reactance (VBR) machine model has been recently proposed for the electro-magnetic transient programs (EMTP)-type simulation programs. The VBR model greatly improves numerical accuracy and efficiency compared with the traditional <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">qd</i> and phase-domain (PD) models. This paper extends the previous research and presents an approach to include magnetic saturation into the VBR induction machine model. The presented method takes into account the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">qd</i> axes static and dynamic cross saturation, whereas the nonlinear magnetic characteristic is represented using a piecewise-linear method that is suitable for the EMTP solution approach. Case studies verify the new saturable VBR model and show that it has improved numerical stability and accuracy even at large time steps.
Medical robotics — why, what and when (1989)

We have the technology: a DTI‐sponsored initiative is exploring health‐care applications for robots.
Germanium wrap-around photodetectors on Silicon photonics (2015)

We present a novel waveguide coupling scheme where a germanium diode grown via rapid melt growth is wrapped around a silicon waveguide. A 4 fF PIN photodiode is demonstrated with 0.95 A/W responsivity at 1550 nm, 6 nA dark current, and nearly 9 GHz bandwidth. Devices with shorter intrinsic region exhibit higher bandwidth (30 GHz) and slightly lower responsivity (0.7 A/W). An NPN phototransistor is also demonstrated using the same design with 14 GHz f(T).
<title>Putting the media into hypermedia</title> (1995)

This paper discusses the issues involved in putting the media into a hypermedia system. The main argument of the paper is that to-date media representation and underlying link strategies have been too closely tied together in the move from hypertext to hypermedia. We argue that it is necessary to separate the issues of media from link structure, and we present a model which solves some of the problems of genuine media integration in a hypermedia system. At the same time the model provides support for the creation of links between data of different media types in a conceptually meaningful way. The paper describes the design of Microcosm++, and object oriented extensible service-based architecture for building consistent integrated hypermedia systems. It is based on the Microcosm hypermedia system which was developed at Southampton. The current implementation of Microcosm++ demonstrates the flexibility of object-based services for making hypermedia more viable in a working environment. The approach described reduces authoring effort significantly while at the same time increasing the integrity of the link structures and providing a unified model for media integration.
Images - March 2012 (2012)

3+1= an affordable bachelor's degree for students... With new educational partnerships between College of DuPage and several prominent universities, students in a growing number of disciplines have streamlined options for earning both an associate's and a bachelor's degree. It's called a 3 + 1 agreement, and for students 3 + 1 adds up to substantial tuition savings and convenience while earning a four year degree. ... meet the Waterleaf restaurant's Executive Chef... Waterleaf is a professionally run, full-service fine dining restaurant, located in the Culinary and Hospitality Center on COD's main campus. Images talks with Executive Chef Nadia Tilkian about her inspiration and the creative flair she brings to the Waterleaf's seasonal cuisine. ... and a new certificate prepares instructors to reach students in the digital classroom... COD offers the new Teaching Online Utilizing Technology Certificate. Educators and trainers gain the essential skills to enhance instruction teaching online and engage students using technology. Plus... the art and science of Geography; Chef Chris Thielman prepares an easy and delicious appetizer; and the Student Services Center has it all.
Copper‐Catalyzed Asymmetric Allylic Alkylation (2008)

Abstract Over the past decade, much effort has been put on designing efficient chiral ligands and screening of the different parameters that govern the main challenges of asymmetric S N 2′ reactions, namely chemo‐, regio‐ and enantioselectivity. This review traces the evolution of the methodologies for creating stereogenic centers through asymmetric copper‐catalyzed allylic alkylation with the use of different organometallic reagents and their subsequent applications. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
Order of Assembly of Human DNA Repair Excision Nuclease (1999)

Human excision nuclease removes DNA damage by concerted dual incisions bracketing the lesion. The dual incisions are accomplished by sequential and partly overlapping actions of six repair factors, RPA, XPA, XPC, TFIIH, XPG, and XPF.ERCC1. Of these, RPA, XPA, and XPC have specific binding affinity for damaged DNA. To learn about the role of these three proteins in damage recognition and the order of assembly of the excision nuclease, we measured the binding affinities of XPA, RPA, and XPC to a DNA fragment containing a single (6-4) photoproduct and determined the rate of damage excision under a variety of reaction conditions. We found that XPC has the highest affinity to DNA and that RPA has the highest selectivity for damaged DNA. Under experimental conditions conducive to binding of either XPA + RPA or XPC to damaged DNA, the rate of damage removal was about 5-fold faster for reactions in which XPA + RPA was the first damage recognition factor presented to DNA compared with reactions in which XPC was the first protein that had the opportunity to bind to DNA. We conclude that RPA and XPA are the initial damage sensing factors of human excision nuclease.
The versatility of automatic mesh generators based on tree structures and advanced geometric constructs (1988)

Abstract The ability of the finite octree and finite quadtree automatic mesh generators to satisfy effectively a wide variety of meshing capabilities is demonstrated. Areas considered include the ability to integrate easily with geometric modelling systems, versatile interactive mesh control functions, the ability to reorder unknowns directly from the finite element data structure and the ability to support automated finite element modelling.
1-V power supply high-speed digital circuit technology with multithreshold-voltage CMOS (1995)

1-V power supply high-speed low-power digital circuit technology with 0.5-/spl mu/m multithreshold-voltage CMOS (MTCMOS) is proposed. This technology features both low-threshold voltage and high-threshold voltage MOSFET's in a single LSI. The low-threshold voltage MOSFET's enhance speed performance at a low supply voltage of 1 V or less, while the high-threshold voltage MOSFET's suppress the stand-by leakage current during the sleep period. This technology has brought about logic gate characteristics of a 1.7-ns propagation delay time and 0.3-/spl mu/W/MHz/gate power dissipation with a standard load. In addition, an MTCMOS standard cell library has been developed so that conventional CAD tools can be used to lay out low-voltage LSI's. To demonstrate MTCMOS's effectiveness, a PLL LSI based on standard cells was designed as a carrying vehicle. 18-MHz operation at 1 V was achieved using a 0.5-/spl mu/m CMOS process.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
XML-based specification for Web services document security (2004)

The Internet and related technologies have seen tremendous growth in distributed applications such as medicine, education, e-commerce, and digital libraries. As demand increases for online content and integrated, automated services, various applications employ Web services technology for document exchange among data repositories. Web services provide a mechanism to expose data and functionality using standard protocols, and hence to integrate many features that enhance Web applications. XML, a well-established text format, is playing an increasingly important role in supporting Web services. XML separates data from style and format definition and allows uniform representation, interchange, sharing, and dissemination of information content over the Internet. XML and Web services provide a simplified application integration framework that drives demand for models that support secure information interchange. Providing document security in XML-based Web services requires access control models that offer specific capabilities. Our XML-based access control specification language addresses a new set of challenges that traditional security models do not address.
Integrated optical detector array, waveguide, and modulator based on silicon technology (1977)

An integrated optical (IO) hybrid circuit consisting of a photodetector array, waveguide, and acousto-optic modulator on a common silicon substrate has been fabricated. This IO hybrid circuit is a major step in the development of a combination optical-electronic processing system. In this device an array of p-n junction photodiodes was fabricated on a 2-in silicon wafer and a 7059 glass waveguide film sputtered over an SiO/SUB 2/ insulating layer on the wafer. Another SiO/SUB 2/ layer was deposited under the transducer electrode. The transducer was a 40-MHz lithium niobate rotated Y-cut crystal. A prism was used to couple in the light beam from a 5 mW He-Ne laser. The guided light beam was directed at one of the diodes in the array and pulsed RF signals were applied to the transducer. Oscillator frequencies of 40 MHz and 120 MHz were separately applied. Modulation depths of greater than 25 percent were produced. The fabrication of the optical guide photodiode and electrical interconnections on a single silicon wafer utilized standard IC fabrication techniques.
Surface Functionalization of Glass and Polymeric Substrates via Graft Copolymerization of Viologen in an Aqueous Medium (2002)

Surface functionalization of low-density polyethylene (LDPE), silanized glass, and free-standing polyaniline (PANI) films via UV-induced graft copolymerization with 1,1‘-bis(4-vinyl-benzyl)-4,4‘-bipyridinium dichloride (VBV) was carried out. The vinyl group containing viologen was synthesized by the double Anderson reaction using 4,4‘-bipyridine and vinyl benzyl chloride and characterized by elemental analysis, FTIR spectrum, and X-ray photoelectron spectroscopy. The graft copolymerization of VBV was carried out by placing the plasma-pretreated substrate in contact with an aqueous solution of VBV under UV irradiation. The effects of the plasma-pretreatment time of the substrate, UV-induced graft copolymerization time, and monomer concentration on the VBV-graft copolymer concentration were investigated. The responses of the VBV-graft-copolymerized LDPE films and silanized glass slides to photoirradiation were monitored. In both cases, intensely blue viologen radical cations were formed after 10 min of UV irradiation in a vacuum and bleaching occurred when the substrate was exposed to air upon termination of the irradiation. VBV-graft-copolymerized PANI films with good conductivity can be prepared, and these films may have possible applications as active templates in biosensors where the viologen groups may serve as electron transfer mediators from the electrode surface to the active site of biomaterials. This method of surface functionalization of viologen moieties offers a number of advantages over a previously developed technique.
Three-Dimensional Printable Origami Twisted Tower: Design, Fabrication, and Robot Embodiment (2017)

This letter presents a novel robotic mechanism inspired by origami and its fabrication method using three-dimensional (3D) printing. The selected twisted tower design shows unique structural and geometrical properties that enable bending and linear motions, and therefore, can be suitable for various robotic applications. However, fabrication of this origami design requires a complex sequence of paper folding and assembling by hand, which cannot be automated by existing manufacturing technologies. To fabricate this structure via 3D printing, the twisted tower is reconstructed in a computer aided design (CAD) model. The CAD model is then 3D printed using two different materials-a flexible material for creases and a rigid material for surfaces. The printed structure preserves the geometrical properties of the original tower. Associated kinematics and workspace analysis are also presented in this letter. The 3D printed tower is embodied into a robotic arm to physically demonstrate its potential utility.