gebhart/patrepeval huggingface dataset:
Recent Advances in Silicon Nanowire Biosensors: Synthesis Methods, Properties, and Applications (2016)

The application of silicon nanowire (SiNW) biosensor as a subtle, label-free, and electrical tool has been extensively demonstrated by several researchers over the past few decades. Human ability to delicately fabricate and control its chemical configuration, morphology, and arrangement either separately or in combination with other materials as lead to the development of a nanomaterial with specific and efficient electronic and catalytic properties useful in the fields of biological sciences and renewable energy. This review illuminates on the various synthetic methods of SiNW, with its optical and electrical properties that make them one of the most applicable nanomaterials in the field of biomolecule sensing, photoelectrochemical conversion, and diseases diagnostics.
Motion synthesis from annotations (2003)

This paper describes a framework that allows a user to synthesize human motion while retaining control of its qualitative properties. The user paints a timeline with annotations --- like walk, run or jump --- from a vocabulary which is freely chosen by the user. The system then assembles frames from a motion database so that the final motion performs the specified actions at specified times. The motion can also be forced to pass through particular configurations at particular times, and to go to a particular position and orientation. Annotations can be painted positively (for example, must run), negatively (for example, may not run backwards) or as a don't-care . The system uses a novel search method, based around dynamic programming at several scales, to obtain a solution efficiently so that authoring is interactive. Our results demonstrate that the method can generate smooth, natural-looking motion.The annotation vocabulary can be chosen to fit the application, and allows specification of composite motions (run and jump simultaneously, for example). The process requires a collection of motion data that has been annotated with the chosen vocabulary. This paper also describes an effective tool, based around repeated use of support vector machines, that allows a user to annotate a large collection of motions quickly and easily so that they may be used with the synthesis algorithm.
Temporal Behavior of Radiation-Pressure-Induced Vibrations of an Optical Microcavity Phonon Mode (2005)

We analyze experimentally and theoretically mechanical oscillation within an optical cavity stimulated by the pressure of circulating optical radiation. The resulting radio frequency cavity vibrations (phonon mode) cause modulation of the incident, continuous-wave (cw) input pump beam. Furthermore, with increasing cw pump power, an evolution from sinusoidal modulation to random oscillations is observed in the pump power coupled from the resonator. The temporal evolution with pump power is studied, and agreement was found with theory. In addition to applications in quantum optomechanics, the present work suggests that radiation-pressure-induced effects can establish a practical limit for the miniaturization of optical silica microcavities.
Recombinant Vaccinia virus-coded interferon inhibitor B18R: Expression, refolding and a use in a mammalian expression system with a RNA-vector (2017)

B18R protein of Vaccinia virus binds to type I interferons and inhibits activation of interferon-mediated signal transduction. Cells which have unimpaired interferon signaling such as primary cell cultures or some industrially important cell lines are capable of development of an antiviral state. An establishment of the antiviral state limits replication of RNA-viruses and can suppress replication of RNA vectors. The interferon inhibitor B18R effectively prevents the establishment of the antiviral state. For this reason, B18R has become a ubiquitous component of protocols for epigenetic reprogramming which use transfections of RNA replicons or mRNA. Despite wide practical applicability, commercially available B18R is predominantly produced in cell cultures and little information has been published on a production and use of bacterially expressed B18R. Objectives of this study were to produce B18R in an E.coli expression system and to confirm the product's biological activity by using it to maintain RNA-vectors in cell cultures capable of the antiviral state. The described method allows the expression and efficient refolding to obtain 10-100 mg of B18R from a small-scale culture and the production process is economically attractive compared to a use of an eukaryotic expression. To check for a presence of the biological activity of bacterially-expressed B18R the protein was used to support persistence of an autonomously replicating RNA-vector in a cell culture which is capable of the antiviral state. A RNA-containing virus, Venezuelan equine encephalitis virus (VEE) can serve as an efficient vector for heterologous expression in cell cultures, although its replication is sensitive to the effects of type I interferons which limit a range of cell lines for a use with this vector. The VEE replicon was utilized to direct an expression of recombinant human granulocyte colony stimulating factor (G-CSF). The producing replicon could persist in HEK293 cells for sufficiently long time only in presence of B18R, whereas addition of B18R not only allowed persistence of the replicon but also increased production from the replicon. A model product granulocyte colony stimulating factor accumulated to 35.5 μg/ml during a 7 day experiment. This work describes efficacious expression and refolding of the viral cytokine inhibitor and demonstrates a utility of bacterially-expressed B18R.
Human Mediator Enhances Activator-Facilitated Recruitment of RNA Polymerase II and Promoter Recognition by TATA-Binding Protein (TBP) Independently of TBP-Associated Factors (2003)

Mediator is a general cofactor implicated in the functions of many transcriptional activators. Although Mediator with different protein compositions has been isolated, it remains unclear how Mediator facilitates activator-dependent transcription, independent of its general stimulation of basal transcription. To define the mechanisms of Mediator function, we isolated two forms of human Mediator complexes (Mediator-P.5 and Mediator-P.85) and demonstrated that Mediator-P.5 clearly functions by enhancing activator-mediated recruitment of RNA polymerase II (pol II), whereas Mediator-P.85 works mainly by stimulating overall basal transcription. The coactivator function of Mediator-P.5 was not impaired when TATA-binding protein (TBP) was used in place of TFIID, but it was abolished when another general cofactor, PC4, was omitted from the reaction or when Mediator-P.5 was added after pol II entry into the preinitiation complex. Moreover, Mediator- P.5 is able to enhance TBP binding to the TATA box in an activator-dependent manner. Our data provides biochemical evidence that Mediator functions by facilitating activator-mediated recruitment of pol II and also promoter recognition by TBP, both of which can occur in the absence of TBP-associated factors in TFIID.
Continuous Learning and Inference of Individual Probability of SARS-CoV-2 Infection Based on Interaction Data (2020)

This study presents a new approach to determine the likelihood of asymptomatic carriers of the SARS-CoV-2 virus by using interaction-based continuous learning and inference of individual probability (CLIIP) for contagious ranking. This approach is developed based on an individual directed graph (IDG), using multi-layer bidirectional path tracking and inference searching. The IDG is determined by the appearance timeline and spatial data that can adapt over time. Additionally, the approach takes into consideration the incubation period and several features that can represent real-world circumstances, such as the number of asymptomatic carriers present. After each update of confirmed cases, the model collects the interaction features and infers the individual person's probability of getting infected using the status of the surrounding people. The CLIIP approach is validated using the individualized bidirectional SEIR model to simulate the contagion process. Compared to traditional contact tracing methods, our approach significantly reduces the screening and quarantine required to search for the potential asymptomatic virus carriers by as much as 94%.
Identification of DNA Adducts of Methylglyoxal (2005)

Methylglyoxal (MG) is a sugar degradation product, which is endogenously formed by fragmentation of triose phosphates during glycolysis, ketone body metabolism of acetone, and catabolism of threonine. Food, beverages, and medical products are important exogenous sources with concentrations of up to 100 microM MG. MG is a reactive dicarbonyl compound, which easily modifies amino groups of proteins (glycation reaction) and thereby induces proinflammatory responses. Moreover, increased mutation frequencies in mammalian cells after treatment with MG have been reported, which are caused by stable modifications of DNA bases. Thus far, two types of adducts have been identified, which are formed during the reaction of free guanine or 2'-deoxyguanosine with high MG concentrations. In this study, we investigated the prolonged exposure of DNA to physiological MG concentrations. DNA was incubated with MG, enzymatically hydrolyzed to release the free nucleosides, and then analyzed by LC-MS/MS. We detected four products, which were derived from the reaction of 2'-deoxyguanosine and 2'-deoxyadenosine with 1 and 2 equiv of MG each. The adducts with 1 equiv of MG were identified as N2-(1-carboxyethyl)-2'-deoxyguanosine (CEdG) and N6-(1-carboxyethyl)-2'-deoxyadenosine. LC-MS/MS was optimized for these compounds, and incubation of DNA was repeated using physiological concentrations of 10 microM MG. Thereby, CEdG proved to be the most sensitive and suitable marker for the reaction of DNA with MG (negative MRM mode, three mass transitions [M - 1](-) 338-->178, 338-->106, and 338-->149).
Pre-processing Algorithm for Rectification of Geometric Distortions in Satellite Images (2011)

A number of algorithms have been reported to process and remove geometric distortions in satellite images. Ortho-correction, geometric error correction, radiometric error removal, etc are a few important examples. These algorithm require supplementary meta-information of the satellite images such as ground control points and correspondence, sensor orientation details, elevation profile of the terrain, etc to establish corresponding transformations. In this paper, a pre-processing algorithm has been proposed which removes systematic distortions of a satellite image and thereby removes the blank portion of the image. It is an input-to-output mapping of image pixels, where the transformation computes the coordinate of each output pixel corresponding to the input pixel of an image. The transformation is established by the exact amount of scaling, rotation and translation needed for each pixel in the input image so that the distortion induced during the recording stage is corrected.Defence Science Journal, 2011, 61(2), pp.174-179, DOI:http://dx.doi.org/10.14429/dsj.61.421
Abnormalities in Glucose Uptake and Metabolism in Imatinib-Resistant Human BCR-ABL–Positive Cells (2009)

The development of imatinib resistance has become a significant therapeutic problem in which the etiology seems to be multifactorial and poorly understood. As of today, clinical criteria to predict the development of imatinib resistance in chronic myelogenous leukemia (CML), other than rebound of the myeloproliferation, are under development. However, there is evidence that the control of glucose-substrate flux is an important mechanism of the antiproliferative action of imatinib because imatinib-resistant gastrointestinal stromal KIT-positive tumors reveal highly elevated glucose uptake in radiologic images. We used nuclear magnetic resonance spectroscopy and gas chromatography mass spectrometry to assess (13)C glucose uptake and metabolism (glycolysis, TCA cycle, and nucleic acid ribose synthesis) during imatinib treatment in CML cell lines with different sensitivities to imatinib. Our results show that sensitive K562-s and LAMA84-s BCR-ABL-positive cells have decreased glucose uptake, decreased lactate production, and an improved oxidative TCA cycle following imatinib treatment. The resistant K562-r and LAMA84-r cells maintained a highly glycolytic metabolic phenotype with elevated glucose uptake and lactate production. In addition, oxidative synthesis of RNA ribose from (13)C-glucose via glucose-6-phosphate dehydrogenase was decreased, and RNA synthesis via the nonoxidative transketolase pathway was increased in imatinib-resistant cells. CML cells which exhibited a (oxidative/nonoxidative) flux ratio for nucleic acid ribose synthesis of >1 were sensitive to imatinib. The resistant K562-r and LAMA84-r exhibited a (oxidative/nonoxidative) flux ratio of <0.7. The changes in glucose uptake and metabolism were accompanied by intracellular translocation of GLUT-1 from the plasma membrane into the intracellular fraction in sensitive cells treated with imatinib, whereas GLUT-1 remained located at the plasma membrane in LAMA84-r and K562-r cells. The total protein load of GLUT-1 was unchanged among treated sensitive and resistant cell lines. In summary, elevated glucose uptake and nonoxidative glycolytic metabolic phenotype can be used as sensitive markers for early detection of imatinib resistance in BCR-ABL-positive cells.
The location stack: a layered model for location in ubiquitous computing (2003)

Based on five design principles extracted from a survey of location systems, we present the location stack, a layered software engineering model for location in ubiquitous computing. Our model is similar in spirit to the seven-layer Open System Interconnect (OSI) model for computer networks. We map two existing ubiquitous computing systems to the model to illustrate the leverage the location stack provides. By encouraging system designers to think of their applications in this way, we hope to drive location-based computing toward a common vocabulary and standard infrastructure, permitting members of the ubiquitous computing community to easily evaluate and build on each other's work.
Serum marker combinations in human breast cancer (review). (1994)

Breast cancer markers (TM) are mainly useful for monitoring the course of disease after diagnosis and first line treatment with the control options of primary treatments early recognition of reactivation and efficiency control of palliative treatment. The best single and established marker is a polymorphic epithelial mucin of the MUC-1 family the prototype of which is CA 15-3 (successive markers: MCA, CA-549, TAG-12, CAM 26/29) followed by CEA with lower diagnostic sensitivity and specificity and TPA/TPS reflecting more the proliferative activity. Besides former TM combinations of CEA with one or more less specific markers (e.g. PAM, CRP, beta 2m, ferritin, GCDFP, HCG, total or boney AP, gamma GT), more recent studies recommend the use of fewer markers such as TPA/TPS + CEA or CA 15-3, CA 15-3 + CEA or MCA, CA M26 + CA M29, TAG12 + CA 15-3 + MCA and CEA + CA 15-3 + ESR.
Planar type vapor-phase epitaxial In<sub>0.53</sub>Ga<sub>0.47</sub>As photodiode (1980)

A punch-through type planar photodiode with low dark current and high speed response was fabricated from low carrier density In <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</inf> Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.47</inf> As grown by vapor-phase epitaxy. Dark current density was 3.1 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-5</sup> A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> at 10 V bias. Rise time and full width at half maximum were 82 and 126 psec, respectively, at a bias above 4 V.
TRANSPORT MECHANISM OF BASIC FIBROBLAST GROWTH FACTOR (bFGF) THROUGH THE BLOOD-BRAIN BARRIER (2000)

This study was carried out to investigate the transport mechanism of basic fibroblast growth factors (bFGF) through blood-brain barriers (BBB). Following an internal carotid artery perfusion, 125I-bFGF was transcytosed through the BBB from blood into brain parenchyma. The saturable binding of 125I-bFGF to the isolated bovine brain capillaries (Kd = 40 nM, and Bmax = 200 pmol/mg) was significantly inhibited by unlabelled bFGF, poly-L-lysine, heparin and glycosaminoglycans with a sulfate residue. The heparin-resistant binding of 125I-bFGF to the conditionally immortalized mouse brain capillary endothelial cell lines (TM-BBB) was saturable and showed significant dependence on temperature and medium osmolarity. This binding was effectively inhibited in cells treated with heparinase, sodium chlorate and an antibody specific to perlecan, a HSPG. Finally, RT-PCR analysis revealed expression of perlecan, and FGF receptors (FGFR1 and FGFR2) mRNA in TM-BBB. These results are consistent with the conclusions, 1) 125I-bFGF is transcytosed through the BBB, and 2) transport of 125I-bFGF through the BBB may be, in part, ascribed to endocytosis mechanism that is triggered by binding to HSPG.
Cytosolic Ca<sup>2+</sup> and the regulation of secretion in parathyroid cells (1986)

The concentration of intracellular Ca2+ [( Ca2+]i) was measured in dissociated bovine parathyroid cells loaded with quin-2 or fura-2. In quin-2-loaded cells, increases in the concentration of extracellular Ca2+ elicited slow, monophasic increases in [Ca2+]i, whereas in fura-2-loaded cells, extracellular Ca2+ evoked rapid, transient increases which were followed by lower, yet sustained increases in [Ca2+]i. Cytosolic Ca2+ transients arose from the mobilization of cellular Ca2+ and could be evoked by a variety of divalent cations. Transient, but not sustained increases in [Ca2+]i were associated with an inhibition of hormone secretion. Secretion was still inhibited, however, when cytosolic Ca2+ transients were blocked by buffering with quin-2, suggesting that changes in [Ca2+]i might not be the essential factor regulating secretion in parathyroid cells.
Radioimmunodetection of Cutaneous T-Cell Lymphoma with<sup>111</sup>In-Labeled T101 Monoclonal Antibody (1986)

T101 monoclonal antibody recognizes a pan-T-cell antigen present on normal T cells and also found in high concentrations in cutaneous T-cell lymphoma. We used this antibody, radiolabeled with 111In, in gamma-camera imaging to detect sites of metastatic cutaneous T-cell lymphoma in 11 patients with advanced disease. In all patients, [111In]T101 concentrated in pathologically or clinically detected nodes, including those in several previously unsuspected nodal regions. Concentrations (per gram of tissue) ranged from 0.01 to 0.03 percent of the injected dose and were consistently 10 to 100 times higher than previously reported on radioimmunodetection. Focal uptake was seen in skin tumors and heavily infiltrated erythroderma but not in skin plaques. The specificity of tumor targeting was documented by control studies with [111In]chloride or [111In]9.2.27 (anti-melanoma) monoclonal antibody. Increasing the T101 dose (1 to 50 mg) altered distribution in nontumor tissues. These studies suggest that imaging with [111In]T101 may be of value in identifying sites of cutaneous T-cell lymphoma. In contrast to the targeting of solid tumors, the mechanism of localization appears to be related to binding to T cells, which can then carry the radioactivity to involved sites.
Using Global Illumination in Volume Visualization of Rheumatoid Arthritis CT Data (2014)

Proper lighting in rendering is essential for visualizing 3D objects, but most visualization software tools still employ simple lighting models. The advent of hardware-accelerated advanced lighting suggests that volume visualization can be truly usable for clinical work. Researchers studied how volume rendering incorporating global illumination impacted perception of bone surface features captured by x-ray computed-tomography scanners for clinical monitoring of rheumatoid arthritis patients. The results, evaluated by clinical researchers familiar with the disease and medical-image interpretation, indicate that interactive visualization with global illumination helped the researchers derive more accurate interpretations of the image data. With clinical needs and the recent advancement of volume visualization technology, this study is timely and points the way for further research.
Future agents and treatment directions in multiple myeloma (2013)

The development of bortezomib and immunomodulatory agents resulted in a revolution in the treatment of multiple myeloma (MM). Moreover, second-generation proteasome inhibitors (carfilzomib) and immunomodulatory agents (pomalidomide) have recently been approved. Nevertheless, the incurability of this disease requires other drugs with different mechanisms of action to either prolong the survival of patients refractory to current therapies, or achieve cure. Active research has been done exploring the pathogenesis of MM and searching for novel, druggable targets. In this regard, some of these novel agents seem promising, such as monoclonal antibodies (anti-CD38 - daratumumab or anti-CS1 - elotuzumab) or the kinesin protein inhibitor Arry-520. Other agents under investigation are kinase inhibitors, signaling pathways inhibitors or deacetylase inhibitors. With so many novel agents under investigation, future therapy in MM will probably involve the combined use of the already approved drugs with some of those newly discovered.
Microbial degradation of tetrachloromethane: mechanisms and perspectives for bioremediation (2010)

Toxic man-made compounds released into the environment represent potential nutrients for bacteria, and microorganisms growing with such compounds as carbon and energy sources can be used to clean up polluted sites. However, in some instances, microorganisms contribute to contaminant degradation without any apparent benefit for themselves. Such cometabolism plays an important part in bioremediation, but is often difficult to control. Microbial degradation of tetrachloromethane (carbon tetrachloride, CCl(4)), a toxic ozone-depleting organic solvent mainly of anthropogenic origin, is only known to occur by cometabolic reduction under anoxic conditions. Yet no microbial system capable of using CCl(4) as the sole carbon source has been described. Microbial growth based on CCl(4) as a terminal electron acceptor has not been reported, although corresponding degradation pathways would yield sufficient energy. Known modes for the biodegradation of CCl(4) involve several microbial metabolites, mainly metal-bound coenzymes and siderophores, which are produced by facultative or strictly anaerobic bacteria and methanogenic Archaea. Recent reports have demonstrated that CCl(4) dechlorination rates are enhanced by redox-active organic compounds such as humic acids and quinones, which act as shuttles between electron-providing microorganisms and CCl(4) as a strong electron acceptor. The key factors underlying dechlorination of CCl(4), the practical aspects and specific requirements for microorganism-associated degradation of CCl(4) at contaminated sites and perspectives for future developments are discussed.