gebhart/patrepeval huggingface dataset:
Screening for feature genes associated with hereditary hemochromatosis and functional analysis with DNA microarrays (2013)

The aim of this study was to identify feature genes that are associated with hereditary hemochromatosis (HHC; iron overload) in cardiac and skeletal muscle of mice. First, the expression profile GSE9726 was downloaded from Gene Expression Omnibus database which included 12 samples. Then the differentially expressed genes (DEGs) were identified by R language. Furthermore, the KUPS software was used to identify relationships in interactions among common DEGs in the cardiac and skeletal muscles. We then used the EASE software to obtain enriched pathways in a gene interaction network. Finally, we used the plugins of the Cytoscape software, i.e., Mcode and Bingo, to conduct module analysis. By comparing diseased and normal tissue samples, 5 and 6 genes in the cardiac and skeletal muscles, respectively, were identified as DEGs. We observed that the S100a8 and S100a9 genes were common DEGs in both tissues examined. In addition, we constructed an interaction network with common DEGs and their interacting components, and identified S100a8 and S100a9 as being associated with immune responses. In view of the relationship between the early stage of myelodysplastic syndrome and the immune system, we hypothesize that the expression of the S100a8 and S100a9 genes is a feature that can be used for diagnosis during the early stage of the myelodysplastic syndrome and that the 2 genes could be used as targets in treating this disease.
Individualized margins for prostate patients using a wireless localization and tracking system (2011)

This study investigates the dosimetric benefits of designing patient-specific margins for prostate cancer patients based on 4D localization and tracking. Ten prostate patients, each implanted with three radiofrequency transponders, were localized and tracked for 40 fractions. "Conventional margin" (CM) planning target volumes (PTV) and PTVs resulting from uniform margins of 5 mm (5M) and 7 mm (7M) were explored. Through retrospective review of each patient's tracking data, an individualized margin (IM) design for each patient was determined. IMRT treatment plans with identical constraints were generated for all four margin strategies and compared. The IM plans generally created the smallest PTV volumes. For similar PTV coverage, the IM plans had a lower mean bladder (rectal) dose by an average of 3.9% (2.5%), 8.5% (5.7%) and 16.2 % (9.8%) compared to 5M, 7M and CM plans, respectively. The IM plan had the lowest gEUD value of 23.8 Gy for bladder, compared to 35.1, 28.4 and 25.7, for CM, 7M and 5M, respectively. Likewise, the IM plan had the lowest NTCP value for rectum of 0.04, compared to 0.07, 0.06 and 0.05 for CM, 7M and 5M, respectively. Individualized margins can lead to significantly reduced PTV volumes and critical structure doses, while still ensuring a minimum delivered CTV dose equal to 95% of the prescribed dose.
Information exposure control through data manipulation for ubiquitous computing (2005)

The vision of Ubiquitous Computing [22] creates the world in which information is omnipresent, migrating seamlessly through the environment to be accessible whenever and wherever needed. Such a vision poses substantial challenges to information security and privacy protection.Unlike in traditional, static, execution environments, information in the Ubiquitous world is exposed, throughout its lifetime, to constantly varying security and privacy threats caused by the inherent dynamicity and unpredictability of the new computing environment and its mobility. Existing data protection mechanisms, built for non- or predictably slowly-changing environments, are unable to strike the balance in the information availability vs. security and privacy threat trade-off in the Ubiquitous world thus hindering the feasibility of the overall vision.In this paper, we present our initial work on a novel paradigm for information security and privacy protection in the ubiquitous world. We model security and privacy threats through sets of contextual attributes and mitigate the projected risks through proactive and reactive data format transformations, subsetting and forced migrations while trying to maximize information availability. We also try to make the approach flexible, scalable and infrastructure independent, as required by the very vision of the Ubiquitous Computing.
An advanced bipolar-MOS-I<sup>2</sup>L technology with a thin epitaxial layer for analog-digital VLSI (1985)

A novel Bi-MOS technology, Advanced Bipolar CMOS (ABC), is proposed. Bipolar transistors (n-p-n, p-n-p, I <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> L) and MOS transistors (both n- and p-channel) have been successfully fabricated on the same chip with no decrease in performance by using a 3-µm design rule. Thin epitaxial layer ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\leq 2 \micro</tex> m) is used in order to obtain small-size high-performance (3-GHz) bipolar devices. Device size is reduced by using a shallow junction and self-aligning technique. n-channel MOS transistors are formed in p-well regions designed to reach p-type substrate, and p-channel MOS transistors are formed in epitaxial layer with an n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> buried layer. This technology has the potential for monolithic multifunctional analog-digital VLSI.
Tea and sympathy (2013)

We present the Teahouse, a pilot project for supporting and socializing new Wikipedia editors. Open collaboration systems like Wikipedia must continually recruit and retain new members in order to sustain themselves. Wikipedia's editor decline presents unique exigency for evaluating novel strategies to support newcomers and increase new user retention in such systems, particularly among demographics that are currently underrepresented in the user community. In this paper, we describe the design and deployment of Teahouse, and present preliminary findings. Our findings highlight the importance of intervening early in the editor lifecycle, providing user-friendly tools, creating safe spaces for newcomers, and facilitating positive interactions between newcomers and established community members.
Efficient and Selective Peracetic Acid Epoxidation Catalyzed by a Robust Manganese Catalyst (2008)

A manganese catalyst containing a tetradentate ligand derived from triazacyclononane exhibits high catalytic activity in epoxidation reactions using peracetic acid as oxidant. The system exhibits broad substrate scope and requires small (0.1-0.15 mol %) catalyst loading. The catalyst is remarkably selective toward aliphatic cis-olefins. Mechanistic studies point toward an electrophilic oxidant delivering the oxygen atom in a concerted step.
The network modeling tool: a design aid for large-scale campus networks (1990)

A description is given of the network modeling tool (NetMod), which uses simple analytical models to provide the designers of large interconnected local area networks with an in-depth understanding of the potential performance of these systems. This tool will be useful in either a university, industrial, or governmental campus networking environment with thousands of computer sites. NetMod is implemented in easy-to-use Macintosh software packages, such as Microsoft Excel and HyperCard; a PC version of the tool will also be made available. The objectives of the tool, the analytical models, and its user interface are described in detail, along with its application to an actual campuswide network.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Efficient Training of Conditional Random Fields (2002)

This thesis explores a number of parameter estimation techniques for conditional random fields, a recently introduced probabilistic model for labelling and segmenting sequential data. Theoretical and practical disadvantages of the training techniques reported in current literature on CRFs are discussed. We hypothesise that general numerical optimisation techniques result in improved performance over iterative scaling algorithms for training CRFs. Experiments run on a a subset of a well-known text chunking data set confirm that this is indeed the case. This is a highly promising result, indicating that such parameter estimation techniques make CRFs a practical and efficient choice for labelling sequential data, as well as a theoretically sound and principled probabilistic framework.
Wide‐Range Refractive Index Control of Organic Semiconductor Films Toward Advanced Optical Design of Organic Optoelectronic Devices (2012)

A large refractive index difference of 0.58 is demonstrated in organic semiconductor films toward advanced optical design of organic optoelectronic devices. Efficient control of light propagation is shown by distributed Bragg reflectors (DBRs) consisting of organic semiconductor films. The DBRs also show photoconductivity, indicating the promising possibility of active control of both charges and light by the organic semiconductors themselves.
An analytic visible surface algorithm for independent pixel processing (1984)

An algorithm is presented that solves the visible surface problem at each pixel independently. This allows motion blur and depth of field blurring to be integrated into the algorithm. It also allows parallel processing. The algorithm works on large numbers of polygons. An analytic Gaussian filter is used. The filter can be elongated or scaled differently for each polygon to adjust for its speed or distance from the focal plane. This is achieved by shrinking or scaling the polygon prior to solving the hidden surface problem so that blurring is correctly presented when objects obscure each other.
Performance of a MAC protocol with smart antennas in a multicellular environment (2002)

We present a study of the signal-to-interference-plus-noise ratio and throughput efficiency achievable in a multicellular environment in the presence of smart antennas at the base station receivers. Interference is explicitly taken into account, and different cases are compared. It is seen that the system operates most efficiently with full frequency reuse, even though this requires network-wide synchronism. The effect of lack of synchronization is also studied.
Anterior Femoral Stapling (2001)

Knee flexion deformity has an adverse effect on stride length and cadence, resulting in an inefficient and often uncomfortable gait. The purpose of this study was to introduce anterior stapling of the distal femur as a method to treat mild to moderate fixed flexion deformity of the knee. The authors undertook stapling in 28 patients (47 knees) with flexion deformities resulting from a variety of underlying conditions, including spina bifida, cerebral palsy, SCIWORA, and skeletal dysplasia. The preoperative clinical evaluation included assessment of hamstring contracture, fixed knee flexion deformity, and gait pattern. The technique is minimally invasive, requires no immobilization, and allows immediate resumption of bracing and physical therapy as needed. Preoperative fixed flexion deformities were typically 10 degrees -25 degrees (maximum 45 degrees ), decreasing to 0 degrees -11 degrees after surgery. Except for one patient who extruded a staple within the first postoperative month, there were no complications. The authors conclude that stapling is well tolerated and provides an excellent alternative to osteotomy in the immature patient by allowing gradual correction of fixed flexion deformities via growth manipulation.
Harnessing user-level networking architectures for distributed object computing over high-speed networks (1998)

In a distributed object system such as Distributed Component Object Model (DCOM), legacy transport protocols used for communication limit the performance over high-speed networks. By making use of a lowlatency, high-bandwidth, and low overhead user-level networking architecture such as Virtual Interface (VI) Architecture, this performance bottleneck can be significantly reduced. Since user-level networking architectures provide low-level primitives, the challenge lies in integrating them into high-level applications. This requires a systematic approach. In this paper, a methodology to utilize VI Architecture to improve the performance of DCOM using custom object marshaling is developed. Initial experimental results demonstrate that the latencies of small messages in distributed object computing can be significantly reduced by this methodology.
Functional anatomical studies of explicit and implicit memory retrieval tasks (1995)

Across three experiments, PET scans were obtained while subjects performed different word-stem completion and FIXATION control tasks designed to study the functional anatomy of memory retrieval. During each of three different word-stem completion scans, word-stem cues were visually presented in uppercase letters. The RECALL task required explicit retrieval of study words presented prior to the PET scan. The PRIMING task addressed the implicit effects of the prior study words without requiring intentional recall. The BASELINE task encouraged retrieval of information from a general knowledge store. Across experiments, the similarity between study words and word stems was manipulated by presenting prescan study words in either uppercase letters identical to the stems, in lowercase letters, or auditorily. The PRIMING task was not studied with auditory presentation. Many activations were consistent across experiments. The BASELINE task activated several regions in response to the reading and verbal-response demands of the task (visual, motor, and premotor cortices, cerebellum), as well as a left prefrontal region. The RECALL task additionally activated regions in anterior right prefrontal cortex. Bilateral occipitotemporal regions showed blood flow reductions during the PRIMING task as compared to the BASELINE task. Activation in the right hippocampal/parahippocampal region was observed only in one experiment, and no experiment showed activation in the left medial temporal lobe. These experiments suggest that areas of frontal cortex play a role in explicit recall and that an effect of priming may be to require less activation of perceptual regions for the processing of recently presented information.
Neddylation inhibits CtIP-mediated resection and regulates DNA double strand break repair pathway choice (2015)

DNA double strand breaks are the most cytotoxic lesions that can occur on the DNA. They can be repaired by different mechanisms and optimal survival requires a tight control between them. Here we uncover protein deneddylation as a major controller of repair pathway choice. Neddylation inhibition changes the normal repair profile toward an increase on homologous recombination. Indeed, RNF111/UBE2M-mediated neddylation acts as an inhibitor of BRCA1 and CtIP-mediated DNA end resection, a key process in repair pathway choice. By controlling the length of ssDNA produced during DNA resection, protein neddylation not only affects the choice between NHEJ and homologous recombination but also controls the balance between different recombination subpathways. Thus, protein neddylation status has a great impact in the way cells respond to DNA breaks.
Optical multistability in a silicon-core silica-cladding fiber (2010)

We fabricate a novel silicon-core silica-cladding optical fiber using high pressure chemical fluid deposition and investigate optical transmission characteristics at the telecommunications wavelength of 1550 nm. High thermo-optic and thermal expansion coefficients of silicon give rise to a thermal phase shift of 6.3 rad/K in a 4 mm-long, 6.9 microm diameter fiber acting as a Fabry-Perot resonator. Using both power and wavelength modulation, we observe all-optical bistability at a low threshold power of 15 mW, featuring intensity transitions of 1.4 dB occurring over <0.1 pm change in wavelength. Threshold powers for higher-order multistable states are predicted. Tristability is experimentally confirmed.
Nucleotide sequence of the luxR and luxI genes and structure of the primary regulatory region of the lux regulon of Vibrio fischeri ATCC 7744 (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNucleotide sequence of the luxR and luxI genes and structure of the primary regulatory region of the lux regulon of Vibrio fischeri ATCC 7744Jerry H. Devine, Cari Countryman, and Thomas O. BaldwinCite this: Biochemistry 1988, 27, 2, 837–842Publication Date (Print):January 26, 1988Publication History Published online1 May 2002Published inissue 26 January 1988https://pubs.acs.org/doi/10.1021/bi00402a052https://doi.org/10.1021/bi00402a052research-articleACS PublicationsRequest reuse permissionsArticle Views571Altmetric-Citations81LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing (2011)

Methods for in-depth characterization of transcriptomes and quantification of transcript levels have emerged as valuable tools for understanding cellular physiology and human disease biology, and have begun to be utilized in various clinical diagnostic applications. Today, current methods utilized by the scientific community typically require RNA to be converted to cDNA prior to comprehensive measurements. However, this cDNA conversion process has been shown to introduce many biases and artifacts that interfere with the proper characterization and quantitation of transcripts. We have developed a direct RNA sequencing (DRS) approach, in which, unlike other technologies, RNA is sequenced directly without prior conversion to cDNA. The benefits of DRS include the ability to use minute quantities (e.g. on the order of several femtomoles) of RNA with minimal sample preparation, the ability to analyze short RNAs which pose unique challenges for analysis using cDNA-based approaches, and the ability to perform these analyses in a low-cost and high-throughput manner. Here, we describe the strategies and procedures we employ to prepare various RNA species for analysis with DRS.
Crystal structure of the catalytic domain of a human thioredoxin‐like protein (2002)

Thioredoxin is a ubiquitous dithiol oxidoreductase found in many organisms and involved in numerous biochemical processes. Human thioredoxin-like protein (hTRXL) is differentially expressed at different development stages of human fetal cerebrum and belongs to an expanding family of thioredoxins. We have solved the crystal structure of the recombinant N-terminal catalytic domain (hTRXL-N) of hTRXL in its oxidized form at 2.2-A resolution. Although this domain shares a similar three-dimensional structure with human thioredoxin (hTRX), a unique feature of hTRXL-N is the large number of positively charged residues distributed around the active site, which has been implicated in substrate specificity. Furthermore, the hTRXL-N crystal structure is monomeric while hTRX is dimeric in its four crystal structures (reduced, oxidized, C73S and C32S/C35S mutants) reported to date. As dimerization is the key regulatory factor in hTRX, the positive charge and lack of dimer formation of hTRXL-N suggest that it could interact with the acidic amino-acid rich C-terminal region, thereby suggesting a novel regulation mechanism.
[A method for morphometry of bone formation using fluorochromes (author's transl)]. (1980)

A reliable morphometric determination of newly formed bone requires a continuous labeling of the tissue of interest. A technique is described which uses the fluorochromes Calcein and Xylenolo-range as bone labels. Image contrast in the fluorescence microscope can be increased by means of special filter combinations to permit data collection by computer-compatible video-systems. This technique offers a wide field of applications in experimental bone biology.
Terminators of Transcription with RNA Polymerase from<i>Escherichia coli:</i>What They Look Like and How to Find Them (1986)

We present here a compilation of prokaryotic transcription terminator sequences (ref. 1-152). The compilation includes 49 independent terminators, 52 speculated independent terminators, 27 sites shown to function in vivo, and some 20 proven or speculated rho-dependent terminators. In addition to the well-known features of independent terminators (dyad symmetry and T-run), two consensus are found: CGGG(C/G) upstream and TCTG downstream of the termination point. A subset of the collection of sequence has been used to construct a computer algorithm to locate independent terminators by sequence analysis.
A Deep Learning-Based Blockchain Mechanism for Secure Internet of Drones Environment (2020)

Drones are equipped with high-vision cameras, advanced sensors, and GPS receivers to deliver diverse services from high altitude thereby creating an airborne network. In this environment, physical things (drones, sensors, etc.,) are controlled using computational algorithms to form a cyber-physical system for the Internet of drones. Although the drones provide manifold benefits still there are many issues (security, privacy, and data integrity) which must be resolved before the usage of drones in smart cyber-physical systems. So, in this paper, a blockchain-based security mechanism for cyber-physical systems is proposed to ensure secure transfer of information among drones. In this mechanism, the miner node is selected using a deep learning-based approach, i.e., a deep Boltzmann machine, using features like computational resources, the available battery power, and flight time of the drone. The proposed mechanism is evaluated based on different performance metrics and the results obtained show the potential benefits of the proposed scheme.