gebhart/patrepeval huggingface dataset:
Synthesis of a gene for the protein kinase domain of the epidermal growth factor receptor and its expression in <i>Escherichia coli</i> (1989)

A gene encoding the protein kinase domain of the epidermal growth factor receptor has been chemically synthesised, cloned and expressed in Escherichia coli. The 942-base-pair gene was constructed by enzymatic ligation of 56 oligonucleotides and cloned into an expression vector downstream of the E. coli trp promoter. Production of active gene product was confirmed by means of a protein kinase assay, demonstrating that the enzymatic activity of the protein kinase domain of the epidermal growth factor receptor is retained after expression in E. coli.
TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control (2020)

The HUSH complex represses retroviruses, transposons and genes to maintain the integrity of vertebrate genomes. HUSH regulates deposition of the epigenetic mark H3K9me3, but how its three core subunits - TASOR, MPP8 and Periphilin - contribute to assembly and targeting of the complex remains unknown. Here, we define the biochemical basis of HUSH assembly and find that its modular architecture resembles the yeast RNA-induced transcriptional silencing complex. TASOR, the central HUSH subunit, associates with RNA processing components. TASOR is required for H3K9me3 deposition over LINE-1 repeats and repetitive exons in transcribed genes. In the context of previous studies, this suggests that an RNA intermediate is important for HUSH activity. We dissect the TASOR and MPP8 domains necessary for transgene repression. Structure-function analyses reveal TASOR bears a catalytically-inactive PARP domain necessary for targeted H3K9me3 deposition. We conclude that TASOR is a multifunctional pseudo-PARP that directs HUSH assembly and epigenetic regulation of repetitive genomic targets.
Crosslinkable hole-transporting materials for solution processed polymer light-emitting diodes (2008)

One of the most challenging tasks in fabricating multilayer polymer light-emitting diodes (PLEDs) by solution processes is to avoid the interfacial mixing between different layers because most of the commercially available emissive and charge-transporting materials are soluble in common organic solvents. To overcome this difficulty, extensive efforts have been invested in developing novel crosslinkable hole-transporting materials (HTMs). After thermo- or photo-crosslinking, all these crosslinked HTMs possess very good solvent resistance which greatly facilitates the subsequent processing of the emitting layer. By taking advantage of these HTMs, high efficiency red–green–blue (RGB)-emitting PLEDs, as well as white- and quantum dot based PLEDs, have been realized. This article provides a brief overview of the recent development of crosslinkable HTMs and their unique advantages in enhancing the performance of LEDs.
Mode pattern analysis of gallium nitride-based laser diodes (2009)

In this paper, we present an analysis of gallium nitride (GaN) quantum-well (QW) laser diode (LD) by numerical simulation. Here we discuss three aspects that are crucial to our analysis. First, the transverse mode pattern is studied, and our current GaN diode laser structure is discussed with optical waveguide mode analysis. Then we compare the QW design of the laser and maximize laser modal gain. Finally, we report the influence of the electron block (e-block) layer on lasing performance of our design.
Extension dynamics of discotic nematics of variable order : geodesic flow and viscoelastic relaxation (1994)

Variational methods are used to develop the governing equations that describe the flow of spatially invariant uniaxial discotic nematic liquid crystals of variable order ; since the equations are based on a phenomenological truncated expansion of the entropy production, the equations are approximations. Restrictions in the phenomenological parameters appearing in the governing equations are imposed taking into account the ordering of the discotic phase. Numerical and analytical solutions of the director n and alignment S are presented for a given uniaxial extensional start-up flow. The unit sphere description of the director is used to discuss and analyze the sensitivity of the director trajectories and the coupled alignment relaxation to the initial conditions (${\bf n}_0, S_0$) and to the alignment Deborah number (De). The numerical results are used to characterize the relaxation of the tensor order parameter Q and to compute the steady flow birefringence. When the poles of the unit sphere are along the extension axis and the equator lies in the compression plane of the flow, it is found that the director trajectories belong to the meridians (great circles through the poles) and the dynamics follows a geodesic flow ; when subjected to flow the director follows the shortest path that connects the initial orientation ${\bf n}_0$ and the equator (compression plane). As typical of geodesic flows, there is a strong sensitivity to initial conditions : when ${\bf n}_0$ lies on the poles no predictions on the eventually steady director orientation are possible. If the prior to flow orientation is close to the poles the coupled alignment relaxation along the geodesics is nonmonotonic and for large De the discotic may become temporarily isotropic. The couplings between n and S are captured by the tensor order parameter relaxation. At steady state, the director lies on the equator, and the alignment and birefringence increase with increasing De.
Transcutaneous Electrical Nerve Stimulation (TENS) Improves Circadian Rhythm Disturbances in Alzheimer Disease (1998)

In patients with Alzheimer disease (AD), an irregular day-night rhythm with behavioral restlessness during the night makes a strong demand on caregivers and is among the most important reasons for institutionalization. A dysfunctioning circadian timing system is supposed to underlie the disturbance or at least to contribute to it. The disturbance improves with increased environmental light, which, through the retinohypothalamic tract, activates the suprachiasmatic nucleus (SCN), the biological clock of the brain. Because recent studies have indicated both direct and indirect spinal projections to the SCN, we investigated whether excitation of spinal neurons by means of transcutaneous electrical nerve stimulation (TENS) could also improve circadian rhythm disturbances in AD patients. The actigraphically obtained rest-activity rhythm of 14 AD patients showed an improvement in its coupling to Zeitgeber after TENS treatment but not after placebo treatment.
Evaluation of a New Automated Method for Cyclosporine a Therapeutic Monitoring on Tdx Abbott (1989)

Abstract A new automated method for measuring cyclosporine in plasma has been introduced by Abbott Laboratories, involving the TDx instrumentation and fluorescence polarization immunoassay. We have used currently the Sandoz Ciclosporin RIA for cyclosporine therapeutic monitoring for a long time. In order to find a method that will decrease the labor requirements associated with RIA procedure, we used specimens from 64 transplant patients to compare, both from analytical and clinical points of view, the Abbott assay with the Sandoz Ciclosporin assay. We believe that the Abbott assay offers some analytical advantages over the ciclosporin RIA procedure and can be used with confidence for cyclosporine therapeutic monitoring for kidney, heart and allogeneic bone marrow transplantation.
Rivaroxaban versus Warfarin in Nonvalvular Atrial Fibrillation (2011)

In patients with atrial fibrillation, rivaroxaban was noninferior to warfarin for the prevention of stroke or systemic embolism. There was no significant between-group difference in the risk of major bleeding, although intracranial and fatal bleeding occurred less frequently in the rivaroxaban group. (Funded by Johnson & Johnson and Bayer; ROCKET AF ClinicalTrials.gov number, NCT00403767.).
Inorganic-organic hybrid materials and abrasion resistant coatings based on a sol-gel approach (1993)

Novel inorganic-organic hybrid materials made previously in the laboratory have utilized acids catalysts such as HCI, acetic acid, toluene sulfonic acid and polystyrene sulfonic acid to catalyze the sol-gel reaction. The sol-gel reaction can also be catalyzed under near neutral (i.e. 5 < pH < 7) and basic conditions. The effects of synthesizing hybrid materials under near basic and basic conditions has not been studied. Attempts to synthesize hybrid materials from polytetramethylene oxide (PTMO) end functionalized with triethoxy silyl groups and, tetraethylorthosilicate (TEOS) under basic conditions met with only partial success. The films obtained had low mechanical stability. This was attributed to the low reactivity of the triethoxy species under neutral and basic conditions. In contrast, films with good mechanical stability were obtained when the TEOS was replaced with titanium tetraisopropoxide (TIOPR). The microstructure of the TIOPRlPTMO hybrid synthesized under near neutral conditions was generally similar to the acid catalyzed PTMOffIOPR hybrids.
Advanced Oil Recovery Technologies for Improved Recovery From Slope Clastic Reservoirs, Nash Draw Brushy Canyon Pool, Eddy County, New Mexico (1998)

The overall goal of this project is to demonstrate that an advanced development drilling and pressure maintenance program based on advanced reservoir management methods can significantly improve oil recovery. The plan included developing a control area using standard reservoir management techniques and comparing its performance to an area developed using advanced methods. A key goal is to transfer advanced methodologies to oil and gas producers in the Permian Basin and elsewhere, and throughout the US oil and gas industry.
Electrical, structural and magnetic properties of pure and doped 1T-TaS<sub>2</sub> (1979)

Abstract A review of the available electrical and structural data on both pure and doped 1T-TaS2 leads us to propose that the nearly commensurate to commensurate transition at 200 K is accompanied by Mott localization in two dimensions. One electron out of 13 in the Ta plane is localized onto the centre of a star of 13 Ta atoms. The picture helps in understanding the concentration dependence of the low-temperature resistivity in cation-doped samples, particularly the sharp maximum at an atomic fraction x ∼ 0.08 for Ti doping. Examining recent resistivity data by Di Salvo and Graebner (1977) we find that at low temperatures the conduction mechanism assumes a three-dimensional character. The lack of a Curie-type susceptibility in spite of electron localization is ascribed to spin-orbit coupling, according to an earlier suggestion by Geertsma, Haas, Huisman and Jellinek (1972).
Development of Low Cost Nutritional Beverage from Whey (2013)

To establish feasibility and superiority of whey based nutritional beverage using established qualitative and quantitative tests for milk proteins and inclusion of cereal based additives. Additionally ensure that whey produced in processing milk; an important source of nutrition; is utilized to its maximum potential. Commercial milk processing recycles whey to extract soluble nutrients, hence whey discarded by commercial milk processing plants is of little use. On the other hand, domestic and low scale milk processing produces whey that has a higher nutritional content and can be utilized locally to produce nutritional drinks that can serve a variety of purposes from refreshment to dietary supplements. Process Guidelines: The research includes collection of waste whey from dairies, messes and canteens; Determination of the proteins and other nutrients present in the whey and their quantity, Extraction and concentration of whey protein and addition of additives; nutritional benefit and waste reduction. The process described above is to be used on a small scale with limited resources both physical as well as monetary hence the current methods of protein extraction from whey fall short. Scope: Whey based nutritional drinks can be produced locally; at low cost; from discarded whey and can play a vital role in combating deficiencies. Whey-Barley beverage contains important nutritional ingredient to address several health problems the common man is facing at the present time. Whey proteins provide excellent nutritional values, in nutrition foods formulated for kids, adults and old aged people as growth tonic for body health maintenance. Additionally, whey protein may help to reduce appetite, improve some diabetes symptoms, increase muscle mass and strength.
Fluorescence Quenching of Dye Molecules near Gold Nanoparticles: Radiative and Nonradiative Effects (2002)

The radiative and nonradiative decay rates of lissamine dye molecules, chemically attached to differently sized gold nanoparticles, are investigated by means of time-resolved fluorescence experiments. A pronounced fluorescence quenching is observed already for the smallest nanoparticles of 1 nm radius. The quenching is caused not only by an increased nonradiative rate but, equally important, by a drastic decrease in the dye's radiative rate. Assuming resonant energy transfer to be responsible for the nonradiative decay channel, we compare our experimental findings with theoretical results derived from the Gersten-Nitzan model.
Reasons for Dropping Out in Distance Learning (2011)

The reasons why learners withdraw or drop out from their programmes before they finish their first course is often of interest to distance learning institutions. From students' records, the authors found that at the Open University of Hong Kong (OUHK), whether a student passed or failed his or her first course is a crucial determinant for their re-registration in new courses in the process of completing their study programmes. The re-registration rates of two cohorts of students were 83.94 per cent and 71.34 per cent for those who passed their courses, and were 28.81 per cent and 27.17 per cent respectively for those who failed their courses. Reasons or factors affecting students dropping out from their distance learning studies were found in a study carried out in 2007-08 by using group interviews and then a survey questionnaire. Based on the reasons found in focus group interviews, a questionnaire consisting of possible dropout reasons was devised and administered to all 'dropout' students in the two cohorts. The reasons for student dropout found in the questionnaire study were classified into three categories. The first category of reasons is labelled 'not addressable' and is found to predominantly include students' personal reasons. The second category is labelled 'not readily addressable', and they include reasons such as high tuition fees and heavy amount of coursework. The third category is 'addressable' factors, and these include failure to maintain motivation in study, and so forth. Measures to assist in reducing drop out, based on the 'addressable factors' of dropout revealed by students, are proposed for implementation, which led to a second phase of the research and development project.
Competitive Reporter Monitored Amplification (CMA) - Quantification of Molecular Targets by Real Time Monitoring of Competitive Reporter Hybridization (2012)

The system presented in this paper enables simultaneous detection and quantification of multiple targets. Moreover, the presented fluorescence background displacement technique provides a generic solution for real time monitoring of binding events of fluorescently labelled ligands to surface immobilized probes. With the model assay for the detection of human immunodeficiency virus type 1 and 2 (HIV 1/2), we have been able to observe the amplification kinetics of five targets simultaneously and accommodate two additional hybridization controls with a simple instrument set-up. The ability to accommodate multiple controls and targets into a single assay and to perform the assay on simple and robust instrumentation is a prerequisite for the development of novel molecular point of care tests.
Intercellular Adhesion-Dependent Cell Survival and ROCK-Regulated Actomyosin-Driven Forces Mediate Self-Formation of a Retinal Organoid (2016)

In this study we dissected retinal organoid morphogenesis in human embryonic stem cell (hESC)-derived cultures and established a convenient method for isolating large quantities of retinal organoids for modeling human retinal development and disease. Epithelialized cysts were generated via floating culture of clumps of Matrigel/hESCs. Upon spontaneous attachment and spreading of the cysts, patterned retinal monolayers with tight junctions formed. Dispase-mediated detachment of the monolayers and subsequent floating culture led to self-formation of retinal organoids comprising patterned neuroretina, ciliary margin, and retinal pigment epithelium. Intercellular adhesion-dependent cell survival and ROCK-regulated actomyosin-driven forces are required for the self-organization. Our data supports a hypothesis that newly specified neuroretina progenitors form characteristic structures in equilibrium through minimization of cell surface tension. In long-term culture, the retinal organoids autonomously generated stratified retinal tissues, including photoreceptors with ultrastructure of outer segments. Our system requires minimal manual manipulation, has been validated in two lines of human pluripotent stem cells, and provides insight into optic cup invagination in vivo.
Enhanced wear resistance of orthopaedic bearing due to the cross‐linking of poly(MPC) graft chains induced by gamma‐ray irradiation (2007)

We assumed that the extra energy supplied by gamma-ray irradiation produced cross-links in 2-methacryloyloxyethyl phosphorylcholine (MPC) polymer grafted cross-linked polyethylene (CLPE-g-MPC) and investigated its effects on the tribological properties of CLPE-g-MPC. In this study, we found that the gamma-ray irradiation produced cross-links in three kinds of regions of CLPE-g-MPC: poly(MPC) layer, CLPE-MPC interface, and CLPE substrate. The dynamic coefficient of friction of CLPE-g-MPC slightly increased with increasing irradiation doses. After the simulator test, both the nonsterilized and gamma-ray sterilized CLPE-g-MPC cups exhibited lower wear than the untreated CLPE ones. In particular, the gamma-ray sterilized CLPE-g-MPC cups showed extremely low and stable wear. As for the nonsterilized CLPE-g-MPC cups, the weight change varied with each cup. When the CLPE surface is modified by poly(MPC) grafting, the MPC graft polymer leads to a significant reduction in the sliding friction between the surfaces that are grafted because water thin films formed can behave as extremely efficient lubricants. Such a cross-link of poly(MPC) slightly increases the friction of CLPE by gamma-ray irradiation but provides a stable wear resistant layer on the friction surface. The cross-links formed by gamma-ray irradiation would give further longevity to the CLPE-g-MPC cups.
Phase separation provides a mechanism to reduce noise in cells (2020)

Expression of proteins inside cells is noisy, causing variability in protein concentration among identical cells. A central problem in cellular control is how cells cope with this inherent noise. Compartmentalization of proteins through phase separation has been suggested as a potential mechanism to reduce noise, but systematic studies to support this idea have been missing. In this study, we used a physical model that links noise in protein concentration to theory of phase separation to show that liquid droplets can effectively reduce noise. We provide experimental support for noise reduction by phase separation using engineered proteins that form liquid-like compartments in mammalian cells. Thus, phase separation can play an important role in biological signal processing and control.
Synthesis and Glycosidase Inhibitory Activities of 5‐(1′,4′‐Dideoxy‐1′,4′‐imino‐<scp>D</scp>‐erythrosyl)‐2‐methyl‐3‐furoic Acid (=5‐[(3<i>S</i>,4<i>R</i>)‐3,4‐Dihydroxypyrrolidin‐2‐yl]‐2‐methylfuran‐3‐carboxylic Acid) Derivatives: New Leads as Selective <i>α</i>‐<scp>L</scp>‐Fucosidase and <i>β</i>‐Galactosidase Inhibitors (2003)

Abstract The García‐González reaction of D ‐glucose and ethyl acetoacetate generated ethyl 5‐[(1′ S )‐ D ‐erythrosyl]‐2‐methyl‐3‐furoate ( 5 ), which was converted to ethyl 5‐[(1′ R )‐1′,4′‐dideoxy‐1′,4′‐imino‐ D ‐erythrosyl]‐2‐methyl‐3‐furoate ( 3c ) and to ethyl 5‐[(1′ S )‐1′,4′‐dideoxy‐1′,4′‐imino‐ D ‐erythrosyl]‐2‐methyl‐3‐furoate ( 4c ). Similar methods were developed to generate other carboxylic acid derivatives such as methyl (see 3e and 4e ), isopropyl (see 3f ), and butyl esters (see 3g ), S ‐phenyl (see 3a ) and S ‐ethyl thioesters (see 3m ), N ‐benzylcarboxamides 3b and 4b , glycine‐derived amide 3h , and N ‐phenyl (see 3i ), N ‐isopropyl (see 3j and 4j ), N , N ‐diethyl‐ (see 3k and 4k ), and N ‐ethyl‐carboxamides (see 3l ). All the new 5‐(1′,4′‐dideoxy‐1′,4′‐imino‐ D ‐erythrosyl)‐3‐furoic acid (=5‐[(3 S ,4 R )‐3,4‐dihydroxypyrrolidin‐2‐yl)furan‐3‐carboxylic acid) derivatives 3 and 4 were assayed for inhibitory activity towards 25 commercially available glycosidases. Derivative 3a with a S ‐phenyl thioester group is a good and selective α ‐ L ‐fucosidase inhibitor ( K i =2–4 μ M ), whereas 4b (with a N ‐benzylcarboxamide group) is a good β ‐galactosidase inhibitor.
Study to the image denoising algorithm based on multiwavelet transforms (2007)

Compared to the scalar wavelet, the multiwavelet has the properties of orthogonality, short support, real symmetry, high order vanishing moment and so on, however, it does not work well in image denoising techniques, primarily due to not making full use of the characteristic property of images in the multiwavelet domain. By transforming the noisy images to the multiwavelet domain, and applying a special difference scheme of the Laplacian operator and also considering of the image’s fractal dimension of high frequency ubband in the multiwavelet domain, the paper proposes an adaptive multiwavelets thresholding algorithm AMT algorithm, which can automatically determine the wavelet shrinkage thresholding in the multiwavelet domain without a priori knowledge of image, for instance, the variance of image noise. The result of the simulation experiment indicates, that the effect of the AMT algorithm is perfectly well, especially for high degraded images.
Pedestrian Detection at Day/Night Time with Visible and FIR Cameras: A Comparison (2016)

Despite all the significant advances in pedestrian detection brought by computer vision for driving assistance, it is still a challenging problem. One reason is the extremely varying lighting conditions under which such a detector should operate, namely day and nighttime. Recent research has shown that the combination of visible and non-visible imaging modalities may increase detection accuracy, where the infrared spectrum plays a critical role. The goal of this paper is to assess the accuracy gain of different pedestrian models (holistic, part-based, patch-based) when training with images in the far infrared spectrum. Specifically, we want to compare detection accuracy on test images recorded at day and nighttime if trained (and tested) using (a) plain color images; (b) just infrared images; and (c) both of them. In order to obtain results for the last item, we propose an early fusion approach to combine features from both modalities. We base the evaluation on a new dataset that we have built for this purpose as well as on the publicly available KAIST multispectral dataset.