gebhart/patrepeval huggingface dataset:
Structural organization of the human alpha-galactosidase A gene: further evidence for the absence of a 3' untranslated region. (1988)

Human alpha-galactosidase A (alpha-D-galactoside galactohydrolase; EC 3.2.1.22) is a lysosomal hydrolase encoded by a gene localized to the chromosomal region Xq22. The deficient activity of this enzyme results in Fabry disease, an X chromosome-linked recessive disorder that leads to premature death in affected males. For studies of the structure and function of alpha-galactosidase A and for characterization of the genetic lesions in families with Fabry disease, the full-length cDNA was isolated, sequenced, and used to screen human genomic libraries. The 1393-base-pair full-length cDNA had a 60-nucleotide 5' untranslated region and encoded a precursor peptide of 429 amino acids including a signal peptide of 31 residues. Three overlapping lambda clones spanning 32 kilobases were identified that contained the entire approximately equal to 12-kilobase chromosomal gene as well as approximately equal to 9 and approximately equal to 11 kilobases of 5' and 3' flanking sequence, respectively. The gene had seven exons. The genomic exonic and full-length cDNA sequences were identical. All intron-exon splice junctions conformed to the GT/AT consensus sequence. The 5' flanking region of this lysosomal housekeeping gene contained Sp1 and CCAAT box promoter elements as well as sequences corresponding to the activator protein 1 (AP1), octanucleotide ("OCTA"), and "core" enhancer elements. There was an upstream "HTF" island (Hpa II tiny fragments) followed by four direct repeats of the "chorion box" enhancer. The unique lack of a 3' untranslated sequence in the alpha-galactosidase A cDNA was confirmed by sequencing additional cDNA clones and the genomic 3' region.
Label propagation with robust initialization for brain tumor segmentation (2012)

A fully automatic segmentation algorithm based on local and global consistency with robust label initialization is proposed for brain tumor segmentation in multi-parametric MR images. A tumor probability map is first computed using support vector machine (SVM) classification of voxel-wise features, and then aggregated with respect to the image intrinsic structures in a multi-scale manner. Salient candidate tumor regions are extracted from the multi-scale hierarchy by a novel strategy based on perceptually important points. Robust label initialization is finally generated taking into account the information from both SVM classification and salient candidate regions. Validation experiment results on multi-parametric MR images have demonstrated that improved tumor segmentation accuracy can be achieved compared with state-to-the-art methods.
Fabric Phase Sorptive Extraction: Current State of the Art and Future Perspectives (2018)

Fabric phase sorptive extraction (FPSE) is a novel and green sample preparation technique introduced in 2014. FPSE utilizes a natural or synthetic permeable and flexible fabric substrate chemically coated with a sol-gel organic-inorganic hybrid sorbent in the form of ultra-thin coating, which leads to a fast and sensitive micro-extraction device. The flexible FPSE requires no modification of samples and allows direct extraction of analytes. Sol-gel sorbent-coated FPSE media possesses high chemical, solvent, and thermal stability due to the strong covalent bonding between the substrate and the sol-gel sorbent. Therefore, any elution solvent can be used in a small volume, which achieves a high pre-concentration factor without requiring any solvent evaporation and sample reconstitution step. Taking into consideration the complexity of the samples and the need of further minimization and automation, some new, alternative modes of the FPSE have also been developed. Therefore, FPSE has attracted the interest of the scientific community that deals with sample pre-treatment and has been successfully applied for the extraction and determination of many analytes in environmental samples as well as in food and biological samples. The objective of the current review is to present and classify the applications of FPSE according to different sample categories and to briefly show the progress, advantages, and the main principles of the proposed technique.
Measurement of exceptional motion in VR video contents for VR sickness assessment using deep convolutional autoencoder (2018)

This paper proposes a new objective metric of exceptional motion in VR video contents for VR sickness assessment. In VR environment, VR sickness can be caused by several factors which are mismatched motion, field of view, motion parallax, viewing angle, etc. Similar to motion sickness, VR sickness can induce a lot of physical symptoms such as general discomfort, headache, stomach awareness, nausea, vomiting, fatigue, and disorientation. To address the viewing safety issues in virtual environment, it is of great importance to develop an objective VR sickness assessment method that predicts and analyses the degree of VR sickness induced by the VR content. The proposed method takes into account motion information that is one of the most important factors in determining the overall degree of VR sickness. In this paper, we detect the exceptional motion that is likely to induce VR sickness. Spatio-temporal features of the exceptional motion in the VR video content are encoded using a convolutional autoencoder. For objectively assessing the VR sickness, the level of exceptional motion in VR video content is measured by using the convolutional autoencoder as well. The effectiveness of the proposed method has been successfully evaluated by subjective assessment experiment using simulator sickness questionnaires (SSQ) in VR environment.
Development of a therapeutic monoclonal antibody that targets secreted fatty acid–binding protein aP2 to treat type 2 diabetes (2015)

The lipid chaperone aP2/FABP4 has been implicated in the pathology of many immunometabolic diseases, including diabetes in humans, but aP2 has not yet been targeted for therapeutic applications. aP2 is not only an intracellular protein but also an active adipokine that contributes to hyperglycemia by promoting hepatic gluconeogenesis and interfering with peripheral insulin action. Serum aP2 levels are markedly elevated in mouse and human obesity and strongly correlate with metabolic complications. These observations raise the possibility of a new strategy to treat metabolic disease by targeting serum aP2 with a monoclonal antibody (mAb) to aP2. We evaluated mAbs to aP2 and identified one, CA33, that lowered fasting blood glucose, improved systemic glucose metabolism, increased systemic insulin sensitivity, and reduced fat mass and liver steatosis in obese mouse models. We examined the structure of the aP2-CA33 complex and resolved the target epitope by crystallographic studies in comparison to another mAb that lacked efficacy in vivo. In hyperinsulinemic-euglycemic clamp studies, we found that the antidiabetic effect of CA33 was predominantly linked to the regulation of hepatic glucose output and peripheral glucose utilization. The antibody had no effect in aP2-deficient mice, demonstrating its target specificity. We conclude that an aP2 mAb-mediated therapeutic constitutes a feasible approach for the treatment of diabetes.
An improved and convenient procedure for the synthesis of 1-substituted imidazoles. (1983)

1-Protected imidazoles, such as 1-acetyl-and 1-benzoylimidazoles, react with various halides, such as benzyl, allyl, α-keto, and alkyl halides, to give 1-protected-3-substituted imidazolium salts in high yields. The resultant imidazolium salts are easily deprotected by treatment with water or alcohols to give the corresponding 1-substituted imidazoles in excellent yields. In this reaction the yields of 1-substituted imidazoles in excellent yields. In this reaction the yields of 1-substituted imidazoles vary with the kinds of halides used and/or with the protecting groups, and the yields increase in the following order : benzyl halides ≥ allyl halides∼α-keto halides < alkyl halides, and acetyl ≥ benzoyl < ethoxycarbonyl < diethoxymethyl < trimethylsilyl < tosyl.
Fourth-Generation Glucose Sensor with an Advanced Algorithm Featuring No Calibrations and Optional Calibration Modes of Operation (2018)

An advanced algorithm was developed for the Medtronic fourth-generation glucose sensor to eliminate the need for blood glucose meter calibrations. The algorithm uses electrochemical impedance spectroscopy and other measurements to self-calibrate the sensor and adjust CGM system sensitivity over time. Self-calibration adjusts for potential sensor-to-sensor variability, as well as subject-dependent sensitivity changes over time. The new algorithm was designed to not require self-monitored blood glucose (SMBG) input during use, but accepts calibrations at any time to improve CGM system performance. It contains multiple independent sensor glucose (SG) calculation units that implement a distinct dynamic model of interstitial glucose that accounts for differences in response caused by sensor-dependent and time-dependent nonlinearities. This approach is particularly useful during the post-sensor insertion period and during periods of hypoglycemia. Each dynamic model was selected for its unique pattern of strengths, which complement each other to augment overall performance. The output of each model is combined to provide a final SG value and a measure of confidence in the calculated value. Performance was evaluated on 31 subjects with type 1 and type 2 diabetes against SMBG values (2441 points over 80 sensors). Sensors were inserted in the arm. The overall (7-day) mean absolute relative difference was 10.8% with no calibrations, 9.5% with 1 calibration/day. There were 86.7% of points that met the 20% agreement rate with no calibrations, 90.0% with 1 calibration/day. A new advanced algorithm for the fourth-generation glucose sensor enables the CGM system to function with good accuracy without SMBG calibrations. Disclosure T. Engel: Employee; Self; Medtronic MiniMed, Inc. P. Ajemba: Employee; Self; Medtronic. J. Nishida: Employee; Self; Medtronic MiniMed, Inc. K. Nogueira: Employee; Self; Medtronic. B. Grosman: Employee; Self; Medtronic. A. Tsai: None. Y. Lu: None. A. Sullivan: None. A. Varsavsky: Employee; Self; Medtronic MiniMed, Inc..
The role of chemoenzymatic synthesis in advancing trehalose analogues as tools for combatting bacterial pathogens (2020)

Trehalose, a disaccharide of glucose, is increasingly recognized as an important contributor to virulence in major bacterial pathogens, such as Mycobacterium tuberculosis, Clostridioides difficile, and Burkholderia pseudomallei. Accordingly, bacterial trehalose metabolic pathways that are not present in humans have gained traction as targets for antibiotic and diagnostic development. Toward this goal, trehalose can be modified through a combination of rational design and synthesis to produce functionalized trehalose analogues, which can be deployed to probe or inhibit bacterial trehalose metabolism. However, the unique α,α-1,1-glycosidic bond and C2 symmetry of trehalose make analogue synthesis via traditional chemical methods very challenging. We and others have turned to the creation of chemoenzymatic synthesis methods, which in principle allow the use of nature's trehalose-synthesizing enzymes to stereo- and regioselectively couple simple, unprotected substrates to efficiently and conveniently generate trehalose analogues. Here, we provide a contextual account of our team's development of a trehalose analogue synthesis method that employs a highly substrate-tolerant, thermostable trehalose synthase enzyme, TreT from Thermoproteus tenax. Then, in three vignettes, we highlight how chemoenzymatic synthesis has accelerated the development of trehalose-based imaging probes and inhibitors that target trehalose-utilizing bacterial pathogens. We describe the role of TreT catalysis and related methods in the development of (i) tools for in vitro and in vivo imaging of mycobacteria, (ii) anti-biofilm compounds that sensitize drug-tolerant mycobacteria to clinical anti-tubercular compounds, and (iii) degradation-resistant trehalose analogues that block trehalose metabolism in C. difficile and potentially other trehalose-utilizing bacteria. We conclude by recapping progress and discussing priorities for future research in this area, including improving the scope and scale of chemoenzymatic synthesis methods to support translational research and expanding the functionality and applicability of trehalose analogues to study and target diverse bacterial pathogens.
An efficient color representation for image retrieval (2001)

A compact color descriptor and an efficient indexing method for this descriptor are presented. The target application is similarity retrieval in large image databases using color. Colors in a given region are clustered into a small number of representative colors. The feature descriptor consists of the representative colors and their percentages in the region. A similarity measure similar to the quadratic color histogram distance measure is defined for this descriptor. The representative colors can be indexed in the three-dimensional (3-D) color space thus avoiding the high-dimensional indexing problems associated with the traditional color histogram. For similarity retrieval, each representative color in the query image or region is used independently to find regions containing that color. The matches from all of the query colors are then combined to obtain the final retrievals. An efficient indexing scheme for fast retrieval is presented. Experimental results show that this compact descriptor is effective and compares favorably with the traditional color histogram in terms of overall computational complexity.
Avian Pneumovirus (APV) RNA from Wild and Sentinel Birds in the United States Has Genetic Homology with RNA from APV Isolates from Domestic Turkeys (2000)

Nasal turbinates or swabs were collected from wild ducks, geese, owls, sparrows, swallows, and starlings and from sentinel ducks placed next to turkey farms experiencing avian pneumovirus (APV) infections and were analyzed for APV genome and infectious particles. APV RNA was detected in samples examined from geese, sparrows, and starlings. APV RNA and antibodies were also detected in two different groups of sentinel ducks. Infectious APV was recovered from sentinel duck samples. The APV M gene isolated from the wild birds had over 96% predicted amino acid identity with APV/Minnesota 2A, which was isolated earlier from domestic turkeys showing respiratory illness, suggesting that wild birds may be involved in spreading APV infection.
Fluorescent Brighteners Can Enhance or Inhibit the Nucleopolyhedrovirus of the Diamondback Moth (Lepidoptera: Plutellidae)2 (2004)

The nucleopolyhedrovirus of the diamondback moth, Plutella xylostella (L.), (PxMNPV) was the most potent of three viruses tested against this insect. The potency of PxMNPV could be increased by the addition of certain diaminostilbene disulfonic acid-derived fluorescent brighteners, including Blankophor P167® at a concentration of 1%. Other fluorescent brighteners, including Blankophor HRS® at 1%, reduced the activity of PxMNPV, though lower concentrations of Blankophor HRS (0.25 to 0.5%) enhanced activity. In contrast, Blankophor HRS at 1% enhanced the nucleopolyhedrovirus of the celery looper, Anagrapha falcifera (Kirby), (AfMNPV) against the diamondback moth. Similar results were found in the corn earworm, Helicoverpa zea (Boddie), and the beet armyworm, Spodoptera exigua (Hübner), which are also susceptible to both PxMNPV and AfMNPV. Consumption of foliage treated with Blankophor HRS (0.5 to 1.0%) did not differ from that of foliage treated with similar concentrations of Blankophor P167. These results indicate a negative effect of higher concentrations of Blankophor HRS on PxMNPV, rather than on the host insect.
Model adaptation methods for speaker verification (2002)

Model adaptation methods for a text-dependent speaker verification system are evaluated. The speaker verification system uses a discriminant model and a statistical model to represent each enrolled speaker. These modeling approaches consist of a neural tree network and Gaussian mixture model. Adaptation methods are evaluated for both modeling approaches. We show that the overall system performance with adaptation is comparable to that obtained by training the model with the additional information. However, the adaptation can be performed within a fraction of the time required to retrain a model. Additionally, we have evaluated the adapted and non-adapted models with data recorded six months after the initial enrolment. The adaptation reduced the error rate for the aged data by 40%.
Temporal Bottleneck Attention for Video Recognition (2021)

This work introduces temporal bottleneck (TBoT) attention for video-based human action recognition (VHAR). TBoT is a mechanism that aims to build short key-frame sequences from long videos and create more valuable representations for convolution-based models. These compact video clips demonstrate two benefits. First, video recognition models can benefit from compact inputs by learning and modeling the data distribution more quickly and accurately. Second, a network trained on short but informative clips can take advantage of longer sequences when predicting human actions which can improve recognition accuracy. We also propose a multi-head mechanism combining pooling and residual self-attentions that can integrate easily on top of a 2D CNN backbone (ResNet50) and build compelling contexts for human action recognition. We assess the performance of the TBoTNet on several ablation experiments on the Kinetics-400 dataset and compared our results with state-of-the-art architectures on RGB inputs.
Patterning Graphene Film by Magnetic-assisted UV Ozonation (2017)

Developing an alternative method for fabricating microscale graphene patterns that overcomes the obstacles of organic contamination, linewidth resolution, and substrate damaging is paramount for applications in optoelectronics. Here we propose to pattern chemical vapor deposition grown graphene film through a stencil mask by magnetic-assisted ultraviolet (UV) ozonation under irradiation of a xenon excimer lamp. In this process, the paramagnetic oxygen molecules and photochemically generated oxygen radicals are magnetized and attracted in an inhomogenous external magnetic field. As a consequence, their random motions convert into directional, which can greatly modify or enhance the quality of graphene patterns. Using a ferromagnetic steel mask, an approximately vertical magnetic-field-assisted UV ozonation (B<sub>Z</sub> = 0.31 T, ∇B<sub>Z</sub> = 90 T · m<sup>-1</sup>) has a capability of patterning graphene microstructures with a line width of 29 μm and lateral under-oxidation less than 4 μm. Our approach is applicable to patterning graphene field-effect transistor arrays, and it can be a promising solution toward resist-free, substrate non-damaging, and cost effective microscale patterning of graphene film.
Nonhereditary Enhancement of Progeny Growth (2002)

The im electroporated injection of a protease-resistant GH-releasing hormone cDNA into rat dams at 16 d gestation resulted in enhanced long-term growth of the F(1) offspring. The offspring were significantly heavier by 2 wk of age, and the difference was sustained to 10 wk of age. Consistent with their augmented growth, the plasma IGF-I concentration of the F(1) progeny was increased significantly. The pituitary gland of the offspring was significantly heavier and contained an increased number of somatotrophs and PRL-secreting cells, which is indicative of modification of cell lineage differentiation. These unique findings demonstrate that enhanced GH-releasing hormone expression in pregnant dams can result in intergenerational growth promotion by altering development of the pituitary gland in the offspring.
Examination of hole mobility in ultra-thin body SOI MOSFETs (2003)

This paper presents an experimental examination of hole mobility in ultra-thin body (UTB) SOI MOSFETs, covering wide ranges of T/sub SOI/ (between /spl sim/3.7 nm and /spl sim/50 nm), and temperature (between /spl sim/79 K and /spl sim/320 K). This paper addresses the observed strong degradation of hole mobility at extremely thin T/sub SOI/, proposing an additional surface roughness scattering mechanism for the thinnest samples due to the perturbation of the conducting band potential stemming from spatial confinement.
Solid Immersion Microscope for Real-Time Near Field Imaging (1991)

We have demonstrated a new type of near‐field microscope based on the principles of the liquid immersion real‐time confocal scanning optical microscope, with the liquid replaced by a solid material of high refractive index. By using this microscope as a real‐time near field imaging system, a factor of two improvement in the edge response over a confocal microscope has been obtained. The system should also have the advantage that it can image inside a material of high refractive index with a better definition than in air.
A conversational interface to web automation (2010)

This paper presents CoCo, a system that automates web tasks on a user's behalf through an interactive conversational interface. Given a short command such as "get road conditions for highway 88," CoCo synthesizes a plan to accomplish the task, executes it on the web, extracts an informative response, and returns the result to the user as a snippet of text. A novel aspect of our approach is that we leverage a repository of previously recorded web scripts and the user's personal web browsing history to determine how to complete each requested task. This paper describes the design and implementation of our system, along with the results of a brief user study that evaluates how likely users are to understand what CoCo does for them.
High Energy Ultrafast Fiber Lasers Based on Coherent Pulse Stacking Amplification (2018)

Coherent pulse stacking amplification extends ultrashort pulse energies from a fiber amplifier by approximately two orders of magnitude compared to CPA, and can lead to compact coherently-combined laser systems with TW-peak and kW-average powers.
Thermal conductivity of diamond between 170 and 1200 K and the isotope effect (1993)

Measurements on the thermal conductivity of natural and synthetic single-crystal diamond are presented over a wide temperature range. The large isotope effect reported previously has been confirmed. The data have been analyzed using both the Debye model of thermal conductivity, which ignores the N processes, and the Callaway model in the limit that the N processes dominate the phonon scattering. It is found that the observed isotope effect can be accounted for by including the N processes alone, without having to postulate the existence of additional defects.
Recognition of Different Toxoplasma Antigens by IgM and IgG Antibodies in Mothers and Their Congenitally Infected Newborns (1985)

The protein-blotting technique was used to determine the antigens of Toxoplasma gondii that were recognized by IgG and IgM antibodies in sera of congenitally infected newborns and their mothers. Patterns of IgG and IgM blots with sera from newborns revealed antigen-antibody reactions (bands) that were not present in the respective blots obtained with sera from their mothers. This was true for 50% of 24 congenitally infected newborns. In contrast, such a difference was noted in only one (5%) of 21 newborns who were not congenitally infected but whose mothers had serological evidence of acute infection with T. gondii acquired during gestation. Our results suggest that the protein-blotting method or an adaptation may be valuable for study of the immune response of the mother, fetus, and newborn to various antigens of infectious organisms and for diagnosis of congenital infections in the newborn.