gebhart/patrepeval huggingface dataset:
A chromatin localization screen reveals poly (ADP ribose)-regulated recruitment of the repressive polycomb and NuRD complexes to sites of DNA damage (2010)

Many proteins that respond to DNA damage are recruited to DNA lesions. We used a proteomics approach that coupled isotopic labeling with chromatin fractionation and mass spectrometry to uncover proteins that associate with damaged DNA, many of which are involved in DNA repair or nucleolar function. We show that polycomb group members are recruited by poly(ADP ribose) polymerase (PARP) to DNA lesions following UV laser microirradiation. Loss of polycomb components results in IR sensitivity of mammalian cells and Caenorhabditis elegans. PARP also recruits two components of the repressive nucleosome remodeling and deacetylase (NuRD) complex, chromodomain helicase DNA-binding protein 4 (CHD4) and metastasis associated 1 (MTA1), to DNA lesions. PARP plays a role in removing nascent RNA and elongating RNA polymerase II from sites of DNA damage. We propose that PARP sets up a transient repressive chromatin structure at sites of DNA damage to block transcription and facilitate DNA repair.
Blood Tests to Diagnose Fibrosis or Cirrhosis in Patients With Chronic Hepatitis C Virus Infection (2013)

Agency for Healthcare Research and Quality.
An electrolytically actuated micropump (2004)

An electrolytically actuated bubble micropump capable of precise dosing at high pumping speed is discussed. The fluid displacement is achieved by sequentially generating electrolytic gas bubbles directly inside the microfluidic channels. The operation of the pump thus requires no moving mechanical parts. A series of phase-shifted dc voltage pulses (ranging from 3.3 to 4.5 V) were applied to inflate the bubbles. Results show that the liquid displacement and pumping rate can be easily and accurately controlled by adjusting the applied voltage, pulse width, and pulse interval. An optimized pump rate of 24 nl/min, corresponding to a flow velocity of 640 μm/s was achieved for a channel size of 25×25 μm in cross section. The measured volume displacements and pump rates were found to be in close agreement with the Faraday bubble growth mechanism. Results also show that the pump can reliably operate at high backpressure (up to 110.1 kPa), and a decrease in pump rate due to elevated backpressure can be offset simply by a small increase in voltage or pulse width.
Adaptive T-spline surface fitting to z-map models (2005)

Surface fitting refers to the process of constructing a smooth representation for an object surface from a fairly large number of measured 3D data points. This paper presents an automatic algorithm to construct smooth parametric surfaces using T-splines from z-map data. The algorithm begins with a rough surface approximation and then progressively refines it in the regions where the approximation accuracy does not meet the requirement. The topology of the resulting T-spline surface is determined adaptively based on the local geometric character of the input data and the geometry of the control points is obtained by a least squares procedure. The advantage of the approach is that the resulting surface is C2 continuous and the refinement is essentially local, resulting in a small number of control points for the surface.
Predictive Tests for Cancer Chemotherapy (1978)

Elsewhere in this issue of the Journal Salmon and his associates describe an in vitro assay for the effectiveness of antitumor agents that strongly correlates with tumor response in man.The capacity to determine the sensitivity of bacterial pathogens in vitro to antibiotics has had a profound and favorable influence on the selection of effective agents for the treatment of patients with infectious diseases. The stakes are as high, if not higher, in cancer chemotherapy. Thus, for most patients with disseminated cancer, the lack of an antitumor effect with chemotherapeutic agents is followed by a progressive downhill course and death, . . .
A surface on the G protein β-subunit involved in interactions with adenylyl cyclases (1997)

Receptor activation of heterotrimeric G proteins dissociates G alpha from the G betagamma complex, allowing both to regulate effectors. Little is known about the effector-interaction regions of G betagamma. We had used molecular modeling to dock a peptide encoding the region of residues 956-982 of adenylyl cyclase (AC) 2 onto Gbeta to identify residues on Gbeta that may interact with effectors. Based on predictions from the model, we synthesized peptides encoding sequences of residues 86-105 (Gbeta 86-105) and 115-135 (Gbeta 115-135) from Gbeta. The Gbeta 86-105 peptide inhibited G betagamma stimulation of AC2 and blocked G betagamma inhibition of AC1 and by itself inhibited calmodulin-stimulated AC1, thus displaying partial agonist activity. Substitution of Met-101 with Asn in this peptide resulted in the loss of both the inhibitory and partial agonist activities. Most activities of the Gbeta 115-135 peptide were similar to those of Gbeta 86-105 but Gbeta 115-135 was less efficacious in blocking G betagamma inhibition of AC1. Substitution of Tyr-124 with Val in the Gbeta 115-135 peptide diminished all of its activities. These results identify the region encoded by amino acids 84-143 of Gbeta as a surface that is involved in transmitting signals to effectors.
Genetic testing and counseling for hereditary forms of colorectal cancer (1999)

The discovery of genes responsible for inherited forms of colorectal cancer have the potential to improve cancer risk assessment and counseling. Germline mutations (nonsense, frameshift) of APC are associated with familial adenomatous polyposis, an autosomal dominant syndrome, clinically characterized by young onset, hundreds of adenomatous polyps in the colon, and increased risk for extracolonic tumors. Mutations in APC are also associated with forms of attenuated familial adenomatous polyposis. Germline mutations in five mismatch repair related genes (hMSH2, hMLH1, hMSH6, hPMS1, and hPMS2) cause hereditary nonpolyposis colorectal cancer and are associated with increased risk of somatic genetic alterations and high DNA microsatellite instability. Hereditary nonpolyposis colorectal cancer is characterized by young onset colorectal cancer, proximal colon location, and increased risk of extracolonic cancers. A missense mutation in APC (I1307K) is associated with some familial colorectal cancer in Ashkenazic Jews. For persons at risk for hereditary forms of colorectal cancer, testing algorithms and gene test interpretations depend on identification of the pedigree germline gene mutation. Careful evaluation of the kindred for characteristic aggregation of tumor types among affected individuals and the availability of affected persons for testing are important issues in implementing genetic testing and follow-up management. Case reports illustrate the importance of genetic counseling as a component of cancer genetic risk assessment. The genetic counseling process includes exploration of patient risk perception, sources of anxiety related to cancer risk, patient education (specific cancer-related issues, prevention/intervention options), discussion of possible gene test options, test limitations, and consequences of various gene test outcomes.
Phase Noise in <i>LC</i> Oscillators: A Phasor-Based Analysis of a General Result and of Loaded $Q$ (2009)

Recent work by Bank, and Mazzanti and Andreani has offered a general result concerning phase noise in nearly-sinusoidal inductance-capacitance ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">LC</i> ) oscillators; namely that the noise factor of such oscillators (under certain achievable conditions) is largely independent of the specific operation of individual transistors in the active circuitry. Both use the impulse sensitivity function (ISF). In this work, we show how the same result can be obtained by generalizing the phasor-based analysis. Indeed, as applied to nearly-sinusoidal LC oscillators, we show how the two approaches are equivalent. We analyze the negative-gm LC model and present a simple equation that quantifies output noise resulting from phase fluctuations. We also derive an expression for output noise resulting from amplitude fluctuations. Further, we extend the analysis to consider the voltage-biased LC oscillator and fully differential CMOS LC oscillator, for which the Bank's general result does not apply. Thus we quantify the concept of loaded <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> .
Lab on upconversion nanoparticles: optical properties and applications engineering via designed nanostructure (2014)

Over the past decade, high-quality lanthanide doped upconverting nanoparticles (UCNPs) have been successfully synthesized with the rapid development of nanotechnology. Due to the unique electron configuration of lanthanide ions, there are rich energy level structures in the near-infrared, visible and ultraviolet spectral range. However, for UCNPs, only a limited number of efficient upconversion excitation and emission have been generated due to the limited number of sensitizer (Yb(3+)) and activator (Tm(3+), Er(3+), and Ho(3+)) ions, and the application is mainly focused on the bio-imaging by using the upconversion luminescence of UCNPs. Recently, more and more researchers have started to focus on tuning of upconversion optical properties and developing of multi-functional UCNPs by using the combination of sub-lattice mediated energy migration, core@shell structural engineering and UCNPs based nanocomposites which greatly expands the range of applications for lanthanide-doped UCNPs. Therefore, a "nanolab" can be created on UCNPs, where the property modulation can be realized via the designed host-dopants combinations, core@shell nanostructure, energy exchange with "alien species" (organic dyes, quantum dots, etc.), and so on. In this paper, we provide a comprehensive survey of the latest advances made in developing lanthanide-doped UCNPs, which include excitation and emission energy levels guided designing of the UCNP nanostructure, the synthesis techniques to fabricate the nanostructure with optimum energy level structure and optical properties, the fabrication of UCNPs-based nanocomposites to extend the applications by introducing the additional functional components, or integrating the functional moiety into one nanocomposite.
Self-Assembly of Collagen-Mimetic Peptide Amphiphiles into Biofunctional Nanofiber (2011)

Molecular assembly of protein and peptide is highly specific and frequently occurs in biological systems. Collagen, which is the most abundant component in extracellular matrix, can assemble into fiber and play an essential role in cell adhesion and growth. Since native collagen is difficult to modify and can engender pathogenic and immunological side effects, its application on tissue regeneration is limited. The preparation of collagen-mimetic materials, hence, is gaining interest in the field of tissue regeneration. Collagen peptides have been synthesized to mimic some properties of collagen, such as its triple helix. However, few studies have been done to prepare artificial collagen fiber to mimic its high-level structure and biofunctions. In this work, a novel collagen-mimetic peptide amphiphile (CPA) was prepared by conjugating a single hydrophobic tail with a collagen-mimetic peptide, supplemented with bioactive glycine-phenylalanine-hydroxyproline-glycine-glutamate-arginine (GFOGER). The physical studies indicated that the CPA had a collagen-mimetic triple-helical conformation and was able to self-assemble into nanofiber. In addition, the CPA conjugated with the integrin-specific GFOGER sequence was shown to promote collagen-mimetic cell adhesion and development. The self-assembled peptide nanofiber was shown to have the ability to structurally and biologically mimic native collagen fiber. We anticipate that this artificial collagen fiber holds great potential as collagen-mimetic materials for tissue regeneration applications.
A behavioral model of A/D converters using a mixed-mode simulator (2002)

A generic nonideal behavioral model of A/D converters that can be characterized from published specifications is described. Three conversion methods (successive approximation, flash, and dual-slope) are modeled. A/D converter architecture may be changed by simple specification of external parameters. The model has been implemented in a mixed mode simulator and simulation results are provided. As an example, characterization has been done for the ADC574A manufactured by Burr-Brown. This is a 12-b A/D converter using the successive approximation method. This behavioral model is characterizable from manufacturers' data sheets, is flexible, provides accurate modeling of nonideal behavior, and has a high simulation speed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Overcurrent protection scheme of BMS for Li-Ion battery used in electric bicycles (2013)

Li-Ion batteries are widely used as the power source supplying the electric drive of electric bicycles. They are sensitive to the operation outside their recommended operating area, which could lead to shortened life-time, damage and explosion risk. A battery management system (BMS) is applied in order to monitor and to protect the battery from the abnormal conditions. In general, the commercial BMSs for Li-Ion batteries in electric bicycles typically focus on only the protection of the battery without consideration of other devices in the system, especially, the switching MOSFETs inside the converter. This paper presents the development of an overcurrent protection scheme for BMS which is capable of not only protecting the battery but also protecting other system components from damages. In addition, it can discriminate temporary fault currents so that unnecessary interrupted operations can be avoided. The developed scheme is designed based on the SOA of MOSFETs and the current-time characteristic of fuses. The proposed scheme was validated by experimental results.
<i>FGFRI</i> and <i>PLAT</i> genes and DNA amplification at 8p 12 in breast and ovarian cancers (1993)

Several chromosomal regions are found to be consistently amplified in human breast cancers. For two of these regions, 8p12 and 10q26, we previously reported the amplification of genes encoding FGF receptors, FGFRI/FLG and FGFR2/BEK, in about 12% of breast tumors. The PLAT gene, encoding the tissue-type plasminogen activator, is also located close to or within the 8p12 region. In the present study, we show that both FGFRI and PLAT can be amplified in breast as well as ovarian carcinomas. FGFRI amplification was detected in 14.5% of breast and 7.8% of ovarian tumors, whereas PLAT was found to be amplified in 15.6% and 19.4% of the tumors, respectively. Each gene could be amplified independently of the other. These data raised the question of which gene is selected for amplification at 8p12. In most cases, the levels of expression of FGFRI and PLAT in breast tumors were comparable to their level of expression in normal mammary tissue. However, FGFRI was expressed above the normal level in a certain number of cases. This gene could be a good candidate as "driver" of the 8p12 amplification, but it cannot account for all complex molecular events taking place in this region.
Integrating the Climate Science Modelling Language with geospatial software and services (2009)

Abstract Much consideration is rightly given to the design of metadata models to describe data. At the other end of the data-delivery spectrum much thought has also been given to the design of geospatial delivery interfaces such as the Open Geospatial Consortium standards, Web Coverage Service (WCS), Web Map Server and Web Feature Service (WFS). Our recent experience with the Climate Science Modelling Language shows that an implementation gap exists where many challenges remain unsolved. To bridge this gap requires transposing information and data from one world view of geospatial climate data to another. Some of the issues include: the loss of information in mapping to a common information model, the need to create ‘views’ onto file-based storage, and the need to map onto an appropriate delivery interface (as with the choice between WFS and WCS for feature types with coverage-valued properties). Here we summarise the approaches we have taken in facing up to these problems.
More Than 12 Years of Experience with a Successful Conformance-Control Polymer Gel Technology (2000)

Abstract In this paper, we discuss and describe our extensive exper-ience with the widely applied and quite successful Cr(III)-carboxylate/acrylamide-polymer (CC/AP) gel technology for use in oilfield conformance-control, sweep-improvement, and fluid-shutoff treatments, along with briefly reviewing the gel technology's development. Chromic triacetate is the often-preferred chemical crosslinking agent used in conjunction with this polymer-gel technology. The CC/AP gel technology, which was conceived in late 1984, is characterized as having a robust gel chemistry and as being highly insensitive to petroleum reservoir environments and interferences. This gel technology has been employed in over 1,400 conformance-control treatments worldwide. Highlights of illustrative field applications and results involving the CC/AP conformance-control gel technology are presented. An overview of what a decade-plus of experience in developing and applying the CC/AP gel technology has taught us is discussed. This includes discussion of: classifying and distinguishing conformance problems and treatments, attributes of good candidate wells and well patterns for gel conformance-control treatments, requirements that must be met in candidate wells and well patterns in order to achieve success, gel treatment elements that must be successfully implemented in order to achieve success, guidelines where conformance polymer-gel treatments are most successfully applied, risks and pitfalls of gel conformance treatments, and quality control issues. Introduction The development and application of effective conformance-control treatments have been, until somewhat recently, elusive goals within the oil industry. Broadly speaking, conformance-control treatments include both treatments to improve volumetric sweep efficiency during oil-recovery flooding operations and treatments to reduce excessive and unproductive co-production with oil of such fluids as water and gas. That is, the co-production of other fluids that compete with the production of oil. Conformance-control treatments have at times been referred to, in an overly narrow fashion, as profile-modification treatments. Polymer gels of conformance treatments act as permeability-reducing agents and, as such, act as blocking and plugging agents. The gels of such treatments operate by reducing the fluid-flow capacity within the treated portion of the reservoir.
Soluble Fibrin Complexes: Separation as a Function of pH and Characterization (1977)

Summary 1. The influence of the pH on the separation of high molecular weight derivatives obtained by a limited action of thrombin on fibrinogen was studied by agarose gel chromatography. When the pH of the elution buffer was 8.5, non crosslinked associations were easily separated in two peaks eluted prior to the fibrinogen peak: one contained a dimer, the other several high polymers. At pH 6.5, only the fibrinogen peak appeared: the fibrinogen molecule proteolysed by thrombin formed no stable associations at this pH and was eluted with the intact fibrinogen molecule. In the presence of factor XIII and Ca++, numerous associations were obtained which are independant of the pH. 2. The polypeptide chain composition of the different species separated at pH 8.5 was studied by SDS-polyacrylamide gel electrophoresis. This technic showed Aα, Bβ and γ chains in the fibrinogen peak, whereas in the chromatographic fractions containing the dimer four bands corresponding to Aα, α, Bβ and γ chains were found. In the peak containing the high polymers, only the presence of α, Bβ and γ chains was demonstrated. 3. These experimental results concerning the effect of pH on the formation of soluble complexes showed that the presence of fibrin monomers in fibrinogen solution was not sufficient to promote any associations. The formation of such derivatives is strongly dependent on the pH of the solution. This obviously can be explained by an influence of the pH either on the ionization of polymerisation sites and the intermolecular bonds between the complex units or on the unmasking of the polymerisation sites by a hypothetical pH induced conformational change of the fibrinogen molecule.
<i>Helicobacter</i> <i>pylori</i> <b>-</b> Specific CD4 <sup>+</sup> CD25 <sup>high</sup> Regulatory T Cells Suppress Memory T-Cell Responses to <i>H</i> . <i>pylori</i> in Infected Individuals (2003)

Helicobacter pylori colonizes the gastric and duodenal mucosa. The infection normally persists for life and causes peptic ulcers and gastric cancer in a subset of infected individuals. We hypothesized that the inability to clear the infection may be a consequence of H. pylori-specific regulatory T cells that actively suppress T-cell responses. Therefore, we characterized the T-cell responses to H. pylori in H. pylori-infected individuals without any subjective symptoms and in uninfected control subjects and investigated the role of regulatory CD4+ CD25(high) T cells during infection. The stimulation of CD4+ peripheral blood T cells with monocyte-derived dendritic cells pulsed with a membrane preparation of H. pylori resulted in proliferation and gamma interferon production in both infected and uninfected individuals. Sorted memory cells from infected individuals responded less than cells from uninfected subjects, and the unresponsiveness could be abolished by depletion of CD4+ CD25(high) regulatory T cells or the addition of interleukin 2. Furthermore, CD4+ CD25(high) T cells suppressed H. pylori-induced responses in cocultures with CD25(low/-) cells. Tetanus toxoid induced comparable responses in memory cells from infected and uninfected individuals in both the presence and the absence of regulatory T cells, suggesting that the suppression was H. pylori specific. In conclusion, we have shown that H. pylori-infected individuals have impaired memory CD4+ T-cell responses to H. pylori that are linked to the presence of H. pylori-specific regulatory T cells that actively suppress the responses.
Relevance of microRNAs in normal and malignant development, including human testicular germ cell tumours (2007)

The dogma of genome functionality has recently been challenged by identification of non-protein-encoding RNAs, including mi(cro)RNAs. These relatively small sequences interact with mRNA and in the mammalian system, are involved in fine-tuning the process of translation. miRNAs have been found to be of crucial importance for normal development, including stem cell formation. Recent interesting fundamental observations will be discussed in this paper, as well as their impact on the genesis of human germ cell tumours (GCTs), in particular those of the adult testis, seminomas and non-seminomas (type II), and spermatocytic seminomas (type III). miRNA cluster 371-373 is specifically involved in inhibition of cellular senescence induced by oncogenic stress in the type II GCTs. This explains the unusual presence of wild type P53, characteristic of this type of solid cancer. Specific sets of differentiating miRNA were found to characterize the various differentiation lineages within the GCTs, which simulate normal embryonic development.