gebhart/patrepeval huggingface dataset:
Common Genetic Variants and Modification of Penetrance of BRCA2-Associated Breast Cancer (2010)

The considerable uncertainty regarding cancer risks associated with inherited mutations of BRCA2 is due to unknown factors. To investigate whether common genetic variants modify penetrance for BRCA2 mutation carriers, we undertook a two-staged genome-wide association study in BRCA2 mutation carriers. In stage 1 using the Affymetrix 6.0 platform, 592,163 filtered SNPs genotyped were available on 899 young (<40 years) affected and 804 unaffected carriers of European ancestry. Associations were evaluated using a survival-based score test adjusted for familial correlations and stratified by country of the study and BRCA2*6174delT mutation status. The genomic inflation factor (λ) was 1.011. The stage 1 association analysis revealed multiple variants associated with breast cancer risk: 3 SNPs had p-values<10(-5) and 39 SNPs had p-values<10(-4). These variants included several previously associated with sporadic breast cancer risk and two novel loci on chromosome 20 (rs311499) and chromosome 10 (rs16917302). The chromosome 10 locus was in ZNF365, which contains another variant that has recently been associated with breast cancer in an independent study of unselected cases. In stage 2, the top 85 loci from stage 1 were genotyped in 1,264 cases and 1,222 controls. Hazard ratios (HR) and 95% confidence intervals (CI) for stage 1 and 2 were combined and estimated using a retrospective likelihood approach, stratified by country of residence and the most common mutation, BRCA2*6174delT. The combined per allele HR of the minor allele for the novel loci rs16917302 was 0.75 (95% CI 0.66-0.86, ) and for rs311499 was 0.72 (95% CI 0.61-0.85, ). FGFR2 rs2981575 had the strongest association with breast cancer risk (per allele HR = 1.28, 95% CI 1.18-1.39, ). These results indicate that SNPs that modify BRCA2 penetrance identified by an agnostic approach thus far are limited to variants that also modify risk of sporadic BRCA2 wild-type breast cancer.
Learning Resource Centre (LRC) – en bibliotekstrend? (2008)

Learning Resource Centre, or LRC, is an international phenomenon and a response to the changing society that came with the development of information technology. The LRC concept spread internationally during the 1990s and began to influence Swedish collage libraries at the end of the decade. The main purpose of this study is to analyze if and how Swedish college libraries have incorporated the LRC concept. Is there a Swedish LRC model? Is the LRC concept still interesting or was it a trend that is now out of date? Interviews with eleven people from six college libraries aim to show how they define the concept LRC and how it has been integrated in to their organisations. In order to explain how these six collage libraries have related to and developed their own LRC concept an organisational theory with a mythical perspective has been used. This perspective is related to an institutional perspective and is presented by the Norwegian professors Tom Christensen, Per Lægreid, Paul G. Roness and Kjell Arne Røvik in Organisationsteori i offentlig sektor. This study concludes that there is no Swedish model, however there are some undeniably Swedish characteristics. The concept LRC is never or seldom used and the activities connected to LRC have become ordinary activities at college libraries. The substance of the LRC remains and has improved the chances for use of and collaboration within the organisation.
A Cationic Smart Copolymer for DNA Binding (2017)

A new block copolymer with a temperature-responsive block and a cationic block was prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization, with good control of its size and composition. The first block is composed by di(ethylene glycol) methyl ether methacrylate (DEGMA) and oligo(ethylene glycol) methyl ether methacrylate (OEGMA), with the ratio DEGMA/OEGMA being used to choose the volume phase transition temperature of the polymer in water, tunable from ca. 25 to above 90 °C. The second block, of trimethyl-2-methacroyloxyethylammonium chloride (TMEC), is positively charged at physiological pH values and is used for DNA binding. The coacervate complexes between the block copolymer and a model single strand DNA are characterized by fluorescence correlation spectroscopy and fluorescence spectroscopy. The new materials offer good prospects for biomedical application, for example in controlled gene delivery.
Test vector generation for parametric path delay faults (2002)

Previous research in the field of path delay fault test generation has concentrated on finding tests which test paths regardless of component delay values. Coverage of such tests on benchmark circuits has been shown to be poor so we present a mechanism wherein path delay fault tests are found under the assumption of component delay variations resulting from fabrication process fluctuations. Component delay fault models are built which incorporate fabrication process effects represented in terms of basic process parameter variations. We use a sensitization approach based on signal stabilizing times to get conditions on primary inputs and path delays for which a delay fault is produced at the circuit outputs. A minimal test set is then extracted from these conditions. Results for the ISCAS'89 and Logic synthesis'91 benchmark circuits indicate the feasibility of this approach.
Line patterning for flexible and laterally configured electrochromic devices (2005)

We have applied the line patterning method, which involves printing of patterns on a plastic or paper substrate using a commercial printer followed by coating of the non-printed areas by a conductive polymer, or metal conductor, to build laterally configured polymer and metallic interdigitated electrodes (IDEs) for electrochromic devices (ECDs). Selective deposition of transparent poly(3,4-ethylenedioxythiophene)–poly(styrene sulfonate) (PEDOT–PSS) or electroless gold films resulted in lateral electrode resolution values of ∼30 µm as determined by optical microscopy. These ECDs comprise complementary colored, dioxythiophene based electrochromic polymers deposited on alternating fingers of gold coated IDEs and a viscous electrolyte layer to enable ion transport between the polymers. The devices are switched by stepping the applied voltage between −1.2 V to +1.2 V and pass a maximum of 1.3 mA cm−2 and a switching charge of 1.2 mC cm−2 in ∼3 s to switch the device from a highly reflective gold state to an absorptive blue state. Three IDEs with different anode to cathode distances have been line patterned via electroless gold deposition. Electrochromic switching kinetics of 2-lane, 4-lane, and 6-lane ECDs have been studied by applying potential steps from −1.0 V to +0.8 V and monitoring the reflectance change as a function of time. The switching times to reach 85% of the full contrast are 4.3 s, 1.5 s, and 0.8 s for the 2-lane, 4-lane, and 6-lane devices, respectively. The extent of interdigitation noticeably improves the switching performance of lateral ECDs due to shorter diffusion distances for dopant ions and minimal electrolyte resistance.
Data from CD74-NRG1 Fusions Are Oncogenic <i>In Vivo</i> and Induce Therapeutically Tractable ERBB2:ERBB3 Heterodimerization (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;i&gt;NRG1&lt;/i&gt; fusions are recurrent somatic genome alterations occurring across several tumor types, including invasive mucinous lung adenocarcinomas and pancreatic ductal adenocarcinomas and are potentially actionable genetic alterations in these cancers. We initially discovered &lt;i&gt;CD74-NRG1&lt;/i&gt; as the first &lt;i&gt;NRG1&lt;/i&gt; fusion in lung adenocarcinomas, and many additional fusion partners have since been identified. Here, we present the first CD74-NRG1 transgenic mouse model and provide evidence that ubiquitous expression of the CD74-NRG1 fusion protein &lt;i&gt;in vivo&lt;/i&gt; leads to tumor development at high frequency. Furthermore, we show that ERBB2:ERBB3 heterodimerization is a mechanistic event in transformation by CD74-NRG1 binding physically to ERBB3 and that CD74-NRG1–expressing cells proliferate independent of supplemented NRG1 ligand. Thus, &lt;i&gt;NRG1&lt;/i&gt; gene fusions are recurrent driver oncogenes that cause oncogene dependency. Consistent with these findings, patients with NRG1 fusion-positive cancers respond to therapy targeting the ERBB2:ERBB3 receptors.&lt;/p&gt;&lt;/div&gt;
Research Funding: the Case for a Modified Lottery (2016)

The time-honored mechanism of allocating funds based on ranking of proposals by scientific peer review is no longer effective, because review panels cannot accurately stratify proposals to identify the most meritorious ones. Bias has a major influence on funding decisions, and the impact of reviewer bias is magnified by low funding paylines. Despite more than a decade of funding crisis, there has been no fundamental reform in the mechanism for funding research. This essay explores the idea of awarding research funds on the basis of a modified lottery in which peer review is used to identify the most meritorious proposals, from which funded applications are selected by lottery. We suggest that a modified lottery for research fund allocation would have many advantages over the current system, including reducing bias and improving grantee diversity with regard to seniority, race, and gender.
Insulin-induced serine phosphorylation of IRS-2 via ERK1/2 and mTOR: studies on the function of Ser675and Ser907 (2010)

The identity of specific serine phosphorylation residues of insulin receptor substrate (IRS)-2 and their impact on insulin signal transduction are largely unknown. Ser(675) and Ser(907) of mouse IRS-2 are adjacent to PI 3-kinase or Grb2 binding domains, respectively. Using monoclonal phosphosite-specific antibodies, we demonstrated the phosphorylation of both serines after stimulation of Fao hepatoma cells with insulin, anisomycin, or phorbol esters. Phosphorylation of both sites was a late and prolonged event during insulin treatment and was also detected in liver tissue of insulin-treated as well as refed mice. Inhibition and siRNA-mediated knockdown of ERK1/2 indicated that the insulin-induced phosphorylation of Ser(907) was ERK dependent. Phosphorylation of Ser(907) did not prevent the insulin-induced association of IRS-2 with Grb2, but phosphorylation of the adjacent Tyr(911) was proved to be crucial in HEK 293 cells expressing IRS-2 Ala mutants. The insulin-induced phosphorylation of Ser(675) was prevented by inhibition and siRNA-mediated knockdown of mTOR but not of p70(S6K1). Mutation of Ser(675) to Ala did not affect downstream insulin signaling but increased the half-life of the protein, suggesting an involvement of phospho-Ser(675) in an accelerated degradation of IRS-2. Moreover, the insulin-induced degradation of IRS-2 was blocked by inhibition of mTOR. We conclude that the two novel insulin-dependent serine phosphorylation sites of IRS-2 were not involved in the regulation of the adjacent PI 3-kinase and Grb2 binding domains but might be implicated in the ERK- and mTOR-mediated negative feedback control.
Use of lumbricides species as biological indicators of environmental pollution with metalodisrupters. (2011)

Based upon the ecological and trophic features of lumbricides, it is demonstrated in studies performed worldwide that these animal species may represent preferential organisms for the process of bioaccumulation of heavy metals. Environmental pollutants such as cadmium (Cd), lead (Pb), manganese (Mn), cobalt (Co), nickel (Ni), copper (Co), zinc (Zn), selenium (Se) and mercury (Hg) were identified in the body of lumbricides using sensitive methods as for example atomic absorption spectrometry (AAS) and inductively coupled plasma mass spectroscopy (ICP-MS). Several tisular biomarkers of exposure to heavy metals have been characterized in lumbricides. Of these, methoxyrheorufin-O-deethylase (MROD), NADH and NADPH cytochrome-reductases, glutathione-S-transferase (GST), cytochrome P-450, catalase (CAT), glutatione-reductase (GR), acethylcholinesterase (AchE), lipide peroxidase (LP), the total glutathione concentration (GSH) and the percent of oxidizied gluthatione (% GSSG) deserve to be mentioned. These biomarkers are sensitive to exposure to metalodisrupters. These observations, evidenced in the majority of lumbricide species studied, may justify the use of lumbricides in environmental quality monitoring with respect to heavy metals pollution.
Studies of dynamic contact of ceramics and alloys for advanced heat engines. Final report (1993)

Advanced materials and coatings for low heat rejection engines have been investigated for almost a decade. Much of the work has concentrated on the critical wear interface between the piston ring and cylinder liner. Simplified bench tests have identified families of coatings with high temperature wear performance that could meet or exceed that of conventional engine materials at today`s operating temperatures. More recently, engine manufacturers have begun to optimize material combinations and manufacturing processes so that the materials not only have promising friction and wear performance but are practical replacements for current materials from a materials and manufacturing cost standpoint. In this study, the advanced materials supplied by major diesel engine manufacturers were evaluated in an experimental apparatus that simulates many of the in-cylinder conditions of a low heat rejection diesel engine. Results include ring wear factors and average dynamic friction coefficients measured at intervals during the test. These results are compared with other advanced materials tested in the past as well as the baseline wear of current engines. Both fabricated specimens and sections of actual ring and cylinder liners were used in the testing. Observations and relative friction and wear performance of the individual materials are provided.
Modeling Interband Transitions in Silver Nanoparticle−Fluoropolymer Composites (2005)

The interband transition contributions to the optical properties of silver nanoparticles in fluoropolymer matrices are investigated. For the materials in this study, nanoparticle synthesis within the existing polymer matrix is accomplished using an infusion process that consists of diffusing an organometallic precursor gas into the free volume of the fluoropolymer and decomposing the precursor followed by metal nanoparticle nucleation and growth. The resulting polymer matrix nanocomposite has optical properties that are dominated by the response of the nanoparticles owing to the broadbanded transparency of the fluoropolymer matrix. The optical properties of these composites are compared to Maxwell-Garnett and Mie theory with results indicating that interband transitions excited in the silver nanoparticles affect the optical absorption over a range of frequencies including the surface plasmon resonance. It is shown that calculations of the optical absorption spectrum using published data for the silver dielectric function do not accurately describe the measured material response and that a classical model for bound and free electron behavior can best be used to represent the dielectric function of silver.
Constancy of Perceived Depth from Disparity across Spatial Frequency (2014)

Contrast constancy is observed in the luminance domain: gratings of different spatial frequencies have equal perceived contrast when they have the same physical contrast despite large differences in contrast thresholds. Seeing depth from disparity is quite different from seeing luminance variation. For example, depth from disparity is constrained by lower and upper bounds: lower-disparity thresholds and upper-disparity limits respectively. We investigated constancy in the disparity domain by comparing the perceived depth of disparity corrugations of different spatial frequencies. We presented a standard stimulus at 0.3cpd and a comparison stimulus at other frequencies. We varied the disparity amplitude of the comparison to determine the value yielding the same perceived depth as the standard. When the standard was near its lower-disparity threshold, more disparity was required in the comparison for equal perceived depth. When it was above its lower threshold, equal perceived depth occurred when the comparison had the same disparity; i.e., constancy was observed. When the disparity of the standard approached the upper-disparity limit, its perceived depth dropped precipitously. Equal perceived depth then occurred when the comparison's disparity was less than the standard's. Near the upper-limit the task could not be done with frequencies higher than the standard because these stimuli exceeded the disparity-gradient limit. Thus, depth constancy occurs across a broad range of corrugation frequencies provided that the disparity amplitude is not close to the lower-disparity threshold or upper-disparity limit. Low spatial frequencies avoid the disparity-gradient limit at all but the greatest amplitudes and can convey more apparent depth than other frequencies. Our findings call into question stereo compression algorithms that use lower-disparity thresholds to manipulate disparities in images and video and show that disparities near the upper-disparity limit warrant special consideration when creating stereo content. Meeting abstract presented at VSS 2014
Synthesis of model compounds for coal liquefaction research (1990)

The objectives of this project are to develop feasible synthetic routes to produce (1) 4(4{prime}- hydroxy- 5{prime},6{prime},7{prime},8{prime}- tetrahydro-1{prime}- naphthylmethyl)- 6-methyl dibenzothiophene, and (2) a 1-hydroxy naphthalene- dibenzothiophene polymer. These compounds are thought to be representative of sulfur containing molecules in coal. The program is divided into three tasks, the first of which is a project work plan that we have already submitted. Our experimental work during this quarter concentrated on Task 2: Synthesis of 4(4{prime}- hydroxy- 5{prime},6{prime},7{prime},8{prime}- tetrahydro-1{prime}- naphthylmethyl)- 6-methyldibenzothiophene. 11 refs.
Characterization of electromagnetically induced transparency in Rydberg state of <sup>87</sup>Rb (2015)

We present the direct measurement of highly excited Rydberg state using a ladder-type electromagnetically induced transparency in the 5S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1/2</sub> -5P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3/2</sub> -nL transition of <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">87</sup> Rb atoms in a room-temperature vapor cell.
Omics techniques and biobanks to find new biomarkers for the early detection of acute lymphoblastic leukemia in middle-income countries: a perspective from Mexico (2017)

Acute lymphoblastic leukemia (ALL) affects the quality of life of many children in the world and particularly in Mexico, where a high incidence has been reported. With a proper financial investment and with well-organized institutions caring for those patients, together with solid platforms to perform high-throughput analyses, we propose the creation of a Mexican repository system of serum and cells from bone marrow and blood samples derived from tissues of pediatric patients with ALL diagnosis. This resource, in combination with omics technologies, particularly proteomics and metabolomics, would allow longitudinal studies, offering an opportunity to design and apply personalized ALL treatments. Importantly, it would accelerate the development of translational science and will lead us to further discoveries, including the identification of new biomarkers for the early detection of leukemia. La leucemia linfoblástica aguda (LLA) afecta la calidad de vida de una gran cantidad de individuos en edad pediátrica en todo el mundo; particularmente en México, donde se ha reportado una alta incidencia. Con un apropiado fondo de inversión financiera, así como instituciones adecuadamente organizadas al cuidado de los pacientes con LLA, en conjunto con plataformas sólidas para llevar a cabo análisis globales y de alto rendimiento, se propone la creación de un repositorio para la conservación de suero y células provenientes de médula ósea y sangre derivadas de pacientes pediátricos con LLA al diagnóstico. Estos recursos, en combinación con las tecnologías ómicas, en particular la proteómica y la metabolómica, podrían permitir el establecimiento de estudios longitudinales y ofrecer una oportunidad para el diseño y aplicación de tratamientos personalizados para la LLA. Esta estrategia permitiría acelerar el desarrollo de la ciencia traslacional, favoreciendo el hallazgo de importantes descubrimientos, incluyendo la identificación de nuevos biomarcadores para la detección temprana de la leucemia.
Light-activation of gene function in mammalian cells viaribozymes (2008)

A ribozyme based gene control element enabled the spatio-temporal regulation of gene function in mammalian cell culture with light.
Training safer surgeons: How do patients view the role of simulation in orthopaedic training? (2015)

There is also a clear public consensus for this method of training to be more widely utilised and it would enhance public perception of safer training of orthopaedic surgeons. This study of public perception provides a mandate to increase investment and infrastructure in orthopaedic simulation as part of promoting clinical governance.
Carbonated water injection (CWI)–A productive way of using CO2 for oil recovery and CO2 storage (2011)

The main advantage of CO2 is that at most reservoir conditions it is a supercritical fluid which is likely to develop miscibility with the oil. In reservoirs that miscibility cannot be achieved, CO2 injection can lead to additional oil recovery by mixing with the oil and favourably modifying the flow properties of the oil. Displacement and recovery of oil by CO2 injection has been studied and applied in the field extensively in the past three decades. Concerns over the environmental impact of CO2 have led to a resurgence of interest in CO2 injection in oil reservoirs. The injection of CO2 can enhance oil recovery from these reservoirs and at the same time help mitigating the problem of increased CO2 concentrations in the atmosphere by storing large quantities of CO2 for a long period of time. CO2 injection projects so far have been mainly limited geographically to oil fields located in areas where large quantities of CO2 have been available mainly from natural resources. Various CO2 injection strategies e.g. cyclic injection, continuous CO2 flood, alternating (WAG) or simultaneous injection of CO2 and water have been applied in these fields. With the new global interest in CO2 injection, many other reservoir settings and scenarios are being considered for CO2 injection in oil reservoirs. This may require injection strategies other than those conventionally used for CO2 injection especially for offshore reservoirs or in cases where the supply of CO2 can be variable or limited. An alternative CO2 injection strategy is carbonated (CO2-enriched) water injection. In carbonated water, CO2 exists as a dissolved phase as opposed to a free phase eliminating the problems of gravity segregation and poor sweep efficiency, which are characteristics of a typical CO2 injection project. In fact, both viscosity and density of water increase as a result of the dissolution of CO2 in water. In terms of CO2 storage, through carbonated water injection, large volumes of CO2 can be injected into the reservoir without the risk of leakage of CO2 through caprock. Using the results of a series of high-pressure flow visualisation experiments, we reveal the underlying physical processes taking place during CWI. The results show that CWI, compared to conventional water injection, improves oil recovery in both secondary (pre-waterflood) and tertiary (post-waterflood) injection modes. Several key mechanisms taking place at the pore level during CWI leading to additional recovery are presented and discussed. Both conventional (light) oil and viscous oil was used in the experiments.