gebhart/patrepeval huggingface dataset:
Nonalloyed ohmic contacts to <i>n</i>-GaAs by solid-phase epitaxy of Ge (1987)

A low resistance nonalloyed ohmic contact to n-GaAs is formed which utilizes the solid-phase epitaxy of Ge through PdGe. Discussion focuses on the conditions necessary to attain low specific contact resistivity (∼10−6 Ω cm2 on 1018 cm−3 n-GaAs) and on the interfacial morphology between the contact metallization and the GaAs substrate. MeV Rutherford backscattering spectrometry and channeling show the predominant reaction to be that of Pd with amorphous Ge to form PdGe followed by the solid-phase transport and epitaxial growth of Ge on 〈100〉 GaAs. Cross-sectional transmission electron microscopy and lattice imaging show a very limited initial Pd-GaAs reaction and a final interface which is planar and structurally abrupt to within atomic dimensions. The presence of excess Ge over that necessary for PdGe formation and the placement of Pd initially in contact with GaAs are required to result in the lowest contact resistivity. The experimental data suggest a replacement mechanism in which an n+-GaAs surface region is formed when Ge occupies excess Ga vacancies.
Genome-wide methylation profiling reveals Zinc finger protein 516 (<i>ZNF516</i>) and FK-506-binding protein 6 (<i>FKBP6</i>) promoters frequently methylated in cervical neoplasia, associated with HPV status and ethnicity in a Chilean population (2013)

Cervical cancer is a major health concern among women in Latin America due to its high incidence and mortality. Therefore, the discovery of molecular markers for cervical cancer screening and triage is imperative. The aim of this study was to use a genome wide DNA methylation approach to identify novel methylation biomarkers in cervical cancer. DNA from normal cervical mucosa and cervical cancer tissue samples from Chile was enriched with Methylated DNA Immunoprecipitation (MeDIP), hybridized to oligonucleotide methylation microarrays and analyzed with a stringent bioinformatics pipeline to identify differentially methylated regions (DMRs) as candidate biomarkers. Quantitative Methylation Specific PCR (qMSP) was used to study promoter methylation of candidate DMRs in clinical samples from two independent cohorts. HPV detection and genotyping were performed by Reverse Line Blot analysis. Bioinformatics analysis revealed GGTLA4, FKBP6, ZNF516, SAP130, and INTS1 to be differentially methylated in cancer and normal tissues in the Discovery cohort. In the Validation cohort FKBP6 promoter methylation had 73% sensitivity and 80% specificity (AUC = 0.80). ZNF516 promoter methylation was the best biomarker, with both sensitivity and specificity of 90% (AUC = 0.92), results subsequently corroborated in a Prevalence cohort. Together, ZNF516 and FKBP6 exhibited a sensitivity of 84% and specificity of 81%, when considering both cohorts. Our genome wide DNA methylation assessment approach (MeDIP-chip) successfully identified novel biomarkers that differentiate between cervical cancer and normal samples, after adjusting for age and HPV status. These biomarkers need to be further explored in case-control and prospective cohorts to validate them as cervical cancer biomarkers.
InGaAsP/InP buried-heterostructure lasers with concurrent fabrication of the stripes and mirrors (1988)

Concurrent fabrication of InGaAsP/InP buried-heterostructure laser stripes and mirrors has been demonstrated by the use of dry etching and mass transport. In comparison to previous processes in which the laser stripes and mirrors are fabricated separately, this process offers the advantages of simplicity, built-in alignment, and improved control of device dimensions. Lasers with a cylindrical and a flat end mirror have threshold currents as low as 22 mA and differential quantum efficiencies as high as 24% per facet. Beam divergences as narrow as 13° are obtained for the cylindrical mirrors.
Small group multicast: a new solution for multicasting on the Internet (2000)

The Internet's global ubiquity has fostered numerous applications that use many different communications models. Applications like FTP Web browsing, and e-mail employ a unicast model where two parties exchange data over logical point-to-point connections. In other applications, such as multiparty audio/video conferencing and collaborative gaming, a source sends data to multiple parties. One way to support multiparty communications is with unicast connections between the source and all of the receivers. If a group has N parties, then a source must set up N-1 unicast connections and transmit the data N times over the network. When N is large, scalability becomes an issue for the source and the network. IP multicast solves this problem by sending a single copy of the data over a distribution tree that is rooted at the source and that branches out to the various destinations. Because the source transmits a single copy of the data, only one copy of the data appears on the branches in the distribution tree.
Transparent Privacy Control via Static Information Flow Analysis (2011)

A common problem faced by modern mobile-device platforms is that thirdparty applications in the marketplace may leak private information without notifying users. Existing approaches adopted by these platforms provide little information on what applications will do with the private information, failing to effectively assist users in deciding whether to install applications and in controlling their privacy. To address this problem, we propose a transparent privacy control approach, where an automatic static analysis reveals to the user how private information is used inside an application. This flow information provides users with better insights, enabling them to determine when to use anonymized instead of real information, or to force script termination when scripts access private information. To further reduce the user burden in controlling privacy, our approach provides a default setting based on an extended information flow analysis that tracks whether private information is obscured before escaping through output channels. We built our approach into TouchDevelop, a novel application-creation environment that allows users to write application scripts on mobile devices, share them in a web bazaar, and install scripts published by other users. To evaluate our approach, we plan to study a portion of published scripts in order to evaluate the effectiveness and performance of information flow analysis. We also plan to carry out a user survey to evaluate the usability of our privacy control and guide our future design.
Video-Rhino-Hygrometer (RH) (2006)

Rhinomanometry includes a set of methodologies to diagnose pathological alterations of the nostrils and nasal cavities. Some anatomic variations could cause partial or sub total obstruction of one or both nostrils, leading to insufficient nasal respiration. Rhinomanometry measures the airflow through one nostril at time, while a pad occludes the other. This method has some drawbacks, such as the alteration of airflow in the not-occluded nostril due to the presence of the pad, the low reproducibility, and a reduced patient comfort. In this paper we propose a new methodologies that, we call Video-Rhino- Hygrometer (VRH) and illustrate specific device to perform it. VRH may be considered as an automatized evolution of the classical Glatzel methods, because it infers information on clinical parameters analysing the image produced by the condense of the breath on a suitable surface. Specifically, VRH uses a web-cam to record these images and, after a suitable processing, it is able to compute a set of clinical features useful to perform diagnosis. Encouraging clinical tests show that the proposed approach provides results comparable with classical rhinomanometry tools without using the pad, obtaining reproducibility results, with an higher comfort for the patient and with a reduced examination time.
Highest precision centering error measurement (2007)

The optical imaging quality of objectives is mainly influenced by the errors of the mechanical alignment of the single elements. TRIOPTICS has developed a new technology called MultiLens® in order to measure the centering error of single lenses as well as complete objectives. It is possible to measure the tilt of each single optical surface inside of a mounted objective with highest precision. We achieve accuracies in the range of an arc second. During the measurement the deviation of each centre of curvature with respect to a reference axis is measured. These data are further processed in order to provide the shift and tilt of an individual lens or group of lenses with respect to a given reference axis. The knowledge of the centering error can be used to align actively single optical elements. Applications mainly include the measurement of cell phone and digital camera lenses. However, any type of objective lens from endoscope up to very complex objective lenses used in microlithography can be measured with highest accuracy.
A Novel Liquid Crystal Display : A Randomly Oriented Nematic Liquid Crystal Display (RON-LCD) (1991)

Abstract A novel liquid crystal display: a Randomly-Oriented Nematic Liquid Crystal Display (RON-LCD) is demonstrated and the electro-optical properties are discussed compared with those of a Polymer Network Liquid Crystal Display (PN-LCD). The Homeotropic-RON-LCD with an 8 μm network layer and a 2 μm no-network layer has sufficient opaqueness at off-state and can be driven by lower voltage than the d = 10 μm PN-LCD. The resistivity of RON-LCD is improved by using a liquid crystal PN-011.
A Newly Isolated Thermostable Lipase from Bacillus sp. (2011)

A thermophilic lipolytic bacterium identified as Bacillus sp. L2 via 16S rDNA was previously isolated from a hot spring in Perak, Malaysia. Bacillus sp. L2 was confirmed to be in Group 5 of bacterial classification, a phylogenically and phenotypically coherent group of thermophilic bacilli displaying very high similarity among their 16S rRNA sequences (98.5-99.2%). Polymerase chain reaction (PCR) cloning of L2 lipase gene was conducted by using five different primers. Sequence analysis of the L2 lipase gene revealed an open reading frame (ORF) of 1251 bp that codes for 417 amino acids. The signal peptides consist of 28 amino acids. The mature protein is made of 388 amino acid residues. Recombinant lipase was successfully overexpressed with a 178-fold increase in activity compared to crude native L2 lipase. The recombinant L2 lipase (43.2 kDa) was purified to homogeneity in a single chromatography step. The purified lipase was found to be reactive at a temperature range of 55-80 °C and at a pH of 6-10. The L2 lipase had a melting temperature (Tm) of 59.04 °C when analyzed by circular dichroism (CD) spectroscopy studies. The optimum activity was found to be at 70 °C and pH 9. Lipase L2 was strongly inhibited by ethylenediaminetetraacetic acid (EDTA) (100%), whereas phenylmethylsulfonyl fluoride (PMSF), pepstatin-A, 2-mercaptoethanol and dithiothreitol (DTT) inhibited the enzyme by over 40%. The CD spectra of secondary structure analysis showed that the L2 lipase structure contained 38.6% α-helices, 2.2% ß-strands, 23.6% turns and 35.6% random conformations.
Continuous Enzymatic Synthesis of 2′‐Deoxythymidine‐5′‐(α‐<scp>D</scp>‐glucopyranosyl)diphosphate (1994)

The preparation of primary nucleotide sugars like 1 with sucrose synthase, a glycosyl transferase in plants, provides an alternative in enzymatic synthesis to the use of highly specific pyrophosphorylases. In an enzyme membrane reactor a continuous synthesis can be performed on preparative scale.
Ethanol extraction of oil, gossypol and aflatoxin from cottonseed (1994)

Abstract Commercial processing of cottonseed requires hexane to extract and recover edible oil. Gossypol and aflatoxin are not removed from extracted meals. A bench‐top extraction process with 95% (vol/vol) aqueous ethanol (EtOH) solvent has been developed that extracts all three of the above materials with a much less volatile solvent. In this process, cottonseed is pretreated and extracted with ambient 95% EtOH to remove gossypol and then extracted with hot 95% EtOH to extract oil and aflatoxin. Membranes and adsorption columns are used to purify the various extract streams, so that they can be recycled directly. A representative extracted meal contained a total gossypol content of 0.47% (a 70% reduction) and 3 ppb aflatoxin (a 95% reduction). Residual oil content was approximately 2%. Although the process is technically feasible, it is presently not economical unless a mill has a continual, serious aflatoxin contamination problem. However, if a plant cannot meet the hexane emission standards under the Clean Air Act of 1990, this process could provide a safer solvent that may expand the use and increase the value of cottonseed meal as a feed for nonruminants.
Developmental lineage of human pluripotent stem cell‐derived cardiac fibroblasts affects their functional phenotype (2021)

Cardiac fibroblasts (CFBs) support heart function by secreting extracellular matrix (ECM) and paracrine factors, respond to stress associated with injury and disease, and therefore are an increasingly important therapeutic target. We describe how developmental lineage of human pluripotent stem cell-derived CFBs, epicardial (EpiC-FB), and second heart field (SHF-FB) impacts transcriptional and functional properties. Both EpiC-FBs and SHF-FBs exhibited CFB transcriptional programs and improved calcium handling in human pluripotent stem cell-derived cardiac tissues. We identified differences including in composition of ECM synthesized, secretion of growth and differentiation factors, and myofibroblast activation potential, with EpiC-FBs exhibiting higher stress-induced activation potential akin to myofibroblasts and SHF-FBs demonstrating higher calcification and mineralization potential. These phenotypic differences suggest that EpiC-FBs have utility in modeling fibrotic diseases while SHF-FBs are a promising source of cells for regenerative therapies. This work directly contrasts regional and developmental specificity of CFBs and informs CFB in vitro model selection.
User Segment Identification Based on Similarity in Content Consumption (2017)

With the rapid growth of online content consumption, knowing end-users and having actionable content insights has become extremely important for any online content provider. Insights from user segment identification could help in developing a content recommendation as well as new content acquisition. For advertisers, identifying segments could assist in designing ad campaigns with greater target accuracy. In this paper, we propose a new approach of finding user segments based on similarity in content consumption. We have exploited content metadata such as genres for this purpose. However, as many videos have multiple genres, the relative importance of these genres for a movie is not known. To solve this problem, we propose a two-step clustering process. First, we identify movie clusters based on metadata-based similarity. Then, based on these movie clusters, user segments are identified. We also propose a segment based recommendation system. Finally, we demonstrate the effectiveness of our approach through experiments on a large online movie database.
<i>In vivo</i> stabilization of a less toxic asparaginase variant leads to a durable antitumor response in acute leukemia (2022)

Asparagine is a non-essential amino acid since it can either be taken up via the diet or synthesized by asparagine synthetase. Acute lymphoblastic leukemia (ALL) cells do not express asparagine synthetase or express it only minimally, which makes them completely dependent on extracellular asparagine for their growth and survival. This dependency makes ALL cells vulnerable to treatment with L-asparaginase, an enzyme that hydrolyzes asparagine. To date, all clinically approved L-asparaginases have significant L-glutaminase co-activity, associated with non-immune related toxic side effects observed during therapy. Therefore, reduction of L-glutaminase co-activity with concomitant maintenance of its anticancer L-asparaginase effect may effectively improve the tolerability of this unique drug. Previously, we designed a new alternative variant of Erwinia chrysanthemi (ErA; Erwinaze) with decreased L-glutaminase co-activity, while maintaining its L-asparaginase activity, by the introduction of three key mutations around the active site (ErA-TM). However, Erwinaze and our ErA-TM variant have very short half-lives in vivo. Here, we show that the fusion of ErA-TM with an albumin binding domain (ABD)-tag significantly increases its in vivo persistence. In addition, we evaluated the in vivo therapeutic efficacy of ABD-ErA-TM in a B-ALL xenograft model of SUP-B15. Our results show a comparable long-lasting durable antileukemic effect between the standard-of-care pegylated-asparaginase and ABD-ErA-TM L-asparaginase, but with fewer co-glutaminase-related acute side effects. Since the toxic side effects of current L-asparaginases often result in treatment discontinuation in ALL patients, this novel ErA-TM variant with ultra-low L-glutaminase co-activity and long in vivo persistence may have great clinical potential.
Flatbed-type Autostereoscopic Display Systems Using Integral Imaging Method (2006)

We have developed a new display technology that allows 3-D images to be viewed on a flatbed display without any need for special glasses. Viewing the display from an angle allows the viewer to experience 3-D images that stand out several centimeters from the surface of the display. By employing the integral imaging method, easy-to-view, natural, and less-fatiguing stereoscopic images were observed. The new technology opens up new areas of application for 3-D displays, including arcade games, e-learning, simulations of buildings and landscapes, and even 3-D menus in restaurants.
Fiber-optic shock position sensor (1993)

This report describes work performed for the development of a fiber-optic shock position sensor used to measure the location of a shock front in the neighborhood of a nuclear explosion. Such a measurement would provide a hydrodynamic determination of nuclear yield. The original proposal was prompted by the Defense Nuclear Agency's interest in replacing as many electrical sensors as possible with their optical counterparts for the verification of a treaty limiting the yield of a nuclear device used in underground testing. Immunity to electromagnetic pulse is the reason for the agency's interest; unlike electrical sensors and their associated cabling, fiber-optic systems do not transmit to the outside world noise pulses from the device containing secret information.
Achromatic GRIN singlet lens design (2013)

Gradient refractive index (GRIN) materials are attractive candidates for improved optical design, especially in compact systems. For GRIN lenses cut from spherically symmetric GRIN material, we derive an analogue of the "lens maker's" equation. Using this equation, we predict and demonstrate via ray tracing that an achromatic singlet lens can be designed, where the chromatic properties of the GRIN counterbalance those of the lens shape. Modeling the lens with realistic materials and realistic fabrication geometries, we predict we can make an achromatic singlet with a 19 mm focal length using a matrix of known polymers.
A Multi-resolution Entropic-Based Image Processing Technique for Diagnostic Analysis of Microcirculation Videos (2010)

Segmentation of microcirculation is a major step in analyzing blood circulatory system. In this study, a method for segmentation of capillaries and small blood vessels in video recordings captured from lingual surface is presented. The main objective is to monitor and quantitatively assess the variations that occur in microcirculation over a period of treatment for diseases or during a resuscitation process. The resulting system will assist physicians and researchers to make diagnostically and therapeutically important decisions such as determination of effectiveness of drug usage and resuscitation process. The algorithm is based on advanced digital image processing methods to detect capillaries and to determine the Functional Capillary Density (FCD) in order to identify the distribution of blood flow for a variety of normal and abnormal cases. The technique consists of four main steps; preprocessing, video stabilization, segmentation and post-processing. This study specifically focuses on minimizing user interaction and improving the accuracy of results. Visual inspection of the results by medical experts indicates that the technique can identify 95% of active capillaries and small blood vessels.
A Generalized Deep Learning-Based Diagnostic System for Early Diagnosis of Various Types of Pulmonary Nodules (2018)

A novel framework for the classification of lung nodules using computed tomography scans is proposed in this article. To get an accurate diagnosis of the detected lung nodules, the proposed framework integrates the following 2 groups of features: (1) appearance features modeled using the higher order Markov Gibbs random field model that has the ability to describe the spatial inhomogeneities inside the lung nodule and (2) geometric features that describe the shape geometry of the lung nodules. The novelty of this article is to accurately model the appearance of the detected lung nodules using a new developed seventh-order Markov Gibbs random field model that has the ability to model the existing spatial inhomogeneities for both small and large detected lung nodules, in addition to the integration with the extracted geometric features. Finally, a deep autoencoder classifier is fed by the above 2 feature groups to distinguish between the malignant and benign nodules. To evaluate the proposed framework, we used the publicly available data from the Lung Image Database Consortium. We used a total of 727 nodules that were collected from 467 patients. The proposed system demonstrates the promise to be a valuable tool for the detection of lung cancer evidenced by achieving a nodule classification accuracy of 91.20%.