gebhart/patrepeval huggingface dataset:
Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion (2005)

The genetic code in a eukaryotic system has been expanded by the engineering of Escherichia coli tyrosyl-tRNA synthetase (TyrRS) with the Y37V and Q195C mutations (37V195C), which specifically recognize 3-iodo-L-tyrosine rather than L-tyrosine. In the present study, we determined the 3-iodo-L-tyrosine- and L-tyrosine-bound structures of the 37V195C mutant of the E. coli TyrRS catalytic domain at 2.0-A resolution. The gamma-methyl group of Val-37 and the sulfur atom of Cys-195 make van der Waals contacts with the iodine atom of 3-iodo-L-tyrosine. The Val-37 and Cys-195 side chains are rigidly fixed by the neighboring residues forming the hydrophobic core of the TyrRS. The major roles of the two mutations are different for the 3-iodo-L-tyrosine-selective recognition in the first step of the aminoacylation reaction (the amino acid activation step): the Y37V mutation eliminates the fatal steric repulsion with the iodine atom, and the Q195C mutation reduces the L-tyrosine misrecognition. The structure of the 37V195C mutant TyrRS complexed with an L-tyrosyladenylate analogue was also solved, indicating that the 3-iodo-L-tyrosine and L-tyrosine side chains are similarly discriminated in the second step (the aminoacyl transfer step). These results demonstrate that the amino acid-binding pocket on the 37V195C mutant is optimized for specific 3-iodo-L-tyrosine recognition.
COMPARISON OF THE HAMBURG WHEEL-TRACKING DEVICE AND THE ENVIRONMENTAL CONDITIONING SYSTEM TO PAVEMENTS OF KNOWN STRIPPING PERFORMANCE. FINAL REPORT (1994)

Moisture damage to hot mix asphalt pavements has been a sporadic but persistent problem in Colorado, even though laboratory testing is performed to identify moisture susceptible mixtures. The laboratory conditioning was often less severe than the conditioning the hot mix pavement encountered in the field. Twenty sites of known field performance with respect to moisture susceptibility, both acceptable and unacceptable, were identified. Materials from these sites were tested using several new and innovative tests: the Hamburg wheel-tracking device, the SHRP Environmental Conditioning System (ECS), and tests of only the aggregate component of the mix. Test results indicated the Hamburg wheel-tracking device has very severe moisture conditioning. By modifying the City of Hamburg specification, the results could accurately identify most sites of known performance. The ECS test procedure has a mild moisture conditioning. By making the test specification more severe, the results could accurately identify most sites of known field performance. A combination of methylene blue/Ridgen voids index may identify reasons some sites had poor performance.
CoP 참여 유형과 조직몰입의 관계에 대한 연구 (2010)

최근 급변하는 환경 속에서 기업의 생존전략으로써 지식경영과 창의적 인적자원개발에 힘을 쓰고 있다. 그러나 이보다 앞선 과제는 직원들의 조직소속감과 애사심을 고양시켜 책임감을 가지고 조직에 몰입․헌신할 수 있는 동기와 태도를 이끌어 내는 것이다. 이것을 위한 대안으로 현재 여러 기업에서 CoP를 도입하고 있다. 이 연구는 한국고용정보원과 연세대학교가 공동 조사한 '대졸 청년층 직장생활 적응능력 향상 연구'의 근로자용 데이터를 분석하여 공식적 CoP와 비공식적 CoP의 참여유형이 조직몰입에 미치는 영향을 검토하였다. CoP참여 유형이 조직몰입에 미치는 영향을 살펴보기 위해 다중회귀분석을 실시한 결과 공식적 CoP의 참여가 계속적 몰입에 유의미한 영향을 주는 것으로 나타났다. 기업에서 지원하는 CoP의 참여는 이직의도를 낮추고, 조직에 계속적으로 머물고자 하는 계속적 몰입에 효과적일 수 있음을 나타낸다. 이 연구는 기업차원에서 직원들을 조직몰입으로 이끌고 전략적으로 CoP를 관리, 지원하는 데 시사점을 제공할 수 있을 것으로 기대한다.
Open data integration (2018)

Open data plays a major role in supporting both governmental and organizational transparency. Many organizations are adopting Open Data Principles promising to make their open data complete, primary, and timely. These properties make this data tremendously valuable to data scientists. However, scientists generally do not have a priori knowledge about what data is available (its schema or content). Nevertheless, they want to be able to use open data and integrate it with other public or private data they are studying. Traditionally, data integration is done using a framework called query discovery where the main task is to discover a query (or transformation) that translates data from one form into another. The goal is to find the right operators to join, nest, group, link, and twist data into a desired form. We introduce a new paradigm for thinking about integration where the focus is on data discovery, but highly efficient internet-scale discovery that is driven by data analysis needs. We describe a research agenda and recent progress in developing scalable data-analysis or query-aware data discovery algorithms that provide high recall and accuracy over massive data repositories.
Immunohistochemical localization of the mouse stage-specific embryonic antigen 1 in human tissues and tumors. (1983)

Normal human tissues and various human tumors were surveyed by immunohistochemical techniques for expression of the stage-specific embryonic antigen 1 (SSEA-1). The antibody reacted with many normal and neoplastic human tissues. In most instances, equivalent human and mouse tissues expressed SSEA-1; however, different tissue localization patterns were sometimes seen between these two species. Most SSEA-1-positive tumors originate from tissues that normally expressed this antigen; however, some breast and ovarian tumors are SSEA-1 positive, and these organs are SSEA-1 negative. SSEA-1-positive tumors were composed of both immunoreactive and nonreactive tumor cells. These data show that SSEA-1, initially defined as a mouse embryonic antigen, represents a heterogenetic antigen present in many normal human tissues. It is retained on many but not all neoplastic cells originating in these normal tissues and also appears on the surface of some tumor cells developing in SSEA-1-negative tissues.
Human Protease-Activated Receptor 1 Expression in Malignant Epithelia (2003)

While protease-activated receptors (PARs) play a traditional role in vascular biology, they emerge with surprisingly new assignments in tumor biology. PAR1 expression correlates with the invasion properties of breast carcinoma, whereas human PAR1 antisense reduces their ability to migrate through Matrigel. Part of the molecular mechanism of PAR1 invasion involves the formation of focal contact complexes on PAR1 activation. PAR1 induces angiogenesis in animal models in vivo and exhibits an oncogenic phenotype of enhanced ductal complexity when overexpressed in mouse mammary glands.
Finding fault - Locating a ground fault in low-voltage, high-resistance grounded systems via the single-processor concept for circuit protection (2007)

High-resistance grounded systems have distinct advantages over solidly grounded systems in facilities where very reliable delivery of power to the loads is desirable. Unlike solidly grounded systems, resistance- grounded systems are able to operate continuously with one unintentional ground. However, this is true for only the first ground fault. A second ground fault on another phase and circuit breaker allows a phase-to-phase fault that may be of significant magnitude.
Link-Rank: a graphical tool for capturing BGP routing dynamics (2004)

Failures at the BGP level can have significant impact on the overall Internet. Understanding the behavior of BGP is thus both an important practical challenge and an interesting research problem. To understand the true dynamics, and help interpret the multiple gigabytes of BGP log data, we have developed the "Link-Rank" graphical toolset. Link-Rank weighs the links between autonomous systems by the number of routing prefixes going through each link. Tracing these graphs over time results in a directed graph that shows the weight changes of the logical inter-AS links. From this graph one can easily visualise the complex BGP path changes and also combine views from multiple vantage points, to get a better picture of global routing dynamics. We illustrate the usefulness of Link-Rank by using it to examine BGP routing dynamics in three example cases. These examples show Link-Rank is able to help BGP analysts estimate the scope of routing changes and to reveal important routing dynamics in the presence of superfluous BGP update messages.
Adoptive cellular therapies: the current landscape (2018)

For many cancer types, the immune system plays an essential role in their development and growth. Based on these rather novel insights, immunotherapeutic strategies have been developed. In the past decade, immune checkpoint blockade has demonstrated a major breakthrough in cancer treatment and has currently been approved for the treatment of multiple tumor types. Adoptive cell therapy (ACT) with tumor-infiltrating lymphocytes (TIL) or gene-modified T cells expressing novel T cell receptors (TCR) or chimeric antigen receptors (CAR) is another strategy to modify the immune system to recognize tumor cells and thus carry out an anti-tumor effector function. These treatments have shown promising results in various tumor types, and multiple clinical trials are being conducted worldwide to further optimize this treatment modality. Most successful results were obtained in hematological malignancies with the use of CD19-directed CAR T cell therapy and already led to the commercial approval by the FDA. This review provides an overview of the developments in ACT, the associated toxicity, and the future potential of ACT in cancer treatment.
Applications of the Zero-Group-Velocity Lamb Mode for Air-Coupled Ultrasonic Imaging (2005)

Airborne ultrasound couples particularly well into plates at the zero‐group‐velocity point of the first order symmetric (S1) Lamb mode. Applications of this mode to ultrasonic imaging of plate‐like structures are discussed. The sensitivity and high Q of this mode makes it ideal for imaging. Images from a wide variety of materials and samples, including composites and honeycomb structures are presented. Transmission at the zero‐group‐velocity frequency is shown to be particularly sensitive to nearby flaws and discontinuities, and is therefore suitable for wide‐area scanning for cracks or manufacturing flaws.
Evidence for Native-Defect Donors in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>n</mml:mi></mml:math>-Type ZnO (2005)

Recent theory has found that native defects such as the O vacancy V(O) and Zn interstitial Zn(I) have high formation energies in n-type ZnO and, thus, are not important donors, especially in comparison to impurities such as H. In contrast, we use both theory and experiment to show that, under N ambient, the complex Zn(I)-N(O) is a stronger candidate than H or any other known impurity for a 30 meV donor commonly found in bulk ZnO grown from the vapor phase. Since the Zn vacancy is also the dominant acceptor in such material, we must conclude that native defects are important donors and acceptors in ZnO.
The Transcription Factor Zfp281 Controls Embryonic Stem Cell Pluripotency by Direct Activation and Repression of Target Genes (2008)

Oct4, Sox2, and Nanog are key components of a core transcriptional regulatory network that controls the ability of embryonic stem cells to differentiate into all cell types. Here we show that Zfp281, a zinc finger transcription factor, is a key component of the network and that it is required to maintain pluripotency. Zfp281 was shown to directly activate Nanog expression by binding to a site in the promoter in very close proximity to the Oct4 and Sox2 binding sites. We present data showing that Zfp281 physically interacts with Oct4, Sox2, and Nanog. Chromatin immunoprecipitation experiments identified 2,417 genes that are direct targets for regulation by Zfp281, including several transcription factors that are known regulators of pluripotency, such as Oct4, Sox2, and Nanog. Gene expression microarray analysis indicated that some Zfp281 target genes were activated, whereas others were repressed, upon knockdown of Zfp281. The identification of both activation and repression domains within Zfp281 suggests that this transcription factor plays bifunctional roles in regulating gene expression within the network. Disclosure of potential conflicts of interest is found at the end of this article.
The antifragile organization (2013)

Embracing failure to improve resilience and maximize availability.
Automatic Identification of Systolic Time Intervals in Seismocardiogram (2016)

Continuous and non-invasive monitoring of hemodynamic parameters through unobtrusive wearable sensors can potentially aid in early detection of cardiac abnormalities, and provides a viable solution for long-term follow-up of patients with chronic cardiovascular diseases without disrupting the daily life activities. Electrocardiogram (ECG) and siesmocardiogram (SCG) signals can be readily acquired from light-weight electrodes and accelerometers respectively, which can be employed to derive systolic time intervals (STI). For this purpose, automated and accurate annotation of the relevant peaks in these signals is required, which is challenging due to the inter-subject morphological variability and noise prone nature of SCG signal. In this paper, an approach is proposed to automatically annotate the desired peaks in SCG signal that are related to STI by utilizing the information of peak detected in the sliding template to narrow-down the search for the desired peak in actual SCG signal. Experimental validation of this approach performed in conventional/controlled supine and realistic/challenging seated conditions, containing over 5600 heart beat cycles shows good performance and robustness of the proposed approach in noisy conditions. Automated measurement of STI in wearable configuration can provide a quantified cardiac health index for long-term monitoring of patients, elderly people at risk and health-enthusiasts.
Somatosensory Evoked Potential Monitoring During Carotid Endarterectomy in Patients with a Stroke (2001)

Patients who have had a preoperative stroke may show asymmetry of their cortical baseline somatosensory evoked potential waveforms; however, this does not interfere with the ability to use somatosensory evoked potential as a monitor during surgery.
What Does a 'Good' Teaching Team Look Like in a Middle School Classroom? (2005)

Observations of teams have been made during 3 years of ongoing experiences in several local middle school settings. These observations have occurred in the course of teaching middle school classes as a participant-observer, conducting a single case study of a state P-12 school that established a middle school program (Main. 2003), and undertaking a major study in progress of four teaching teams in three middle schools. These observations have provided a basis for reflecting on the current practice environment for middle school teaching teams. Using teaching teams in middle schooling has been justified in terms of benefits for teacher collegiality, student learning, and creation of a flexible environment. That is, teaming allows the creation of a larger working space and more adaptable working time, which then enables teachers to incorporate virtually any teaching or learning method with any combination of students at any time during the normal timetabled sessions of a school day. However, this flexibility raises questions not only about 'what', 'how', and 'when' to team-teach but also about how teachers manage the process of forming and developing as a team. What does a 'good' teaching team look like?
Study of the interaction of DNA and histones by spin-stretching and droplet evaporation (2011)

Molecular combing is a powerful and simple method for aligning DNA molecules onto a surface. Using this technique combined with fluorescence microscopy, DNA-histone complexes are stretched on a hydrophobic polymethyl methacrylate (PMMA) surface and observed directly. We have developed a new method to stretch single DNA-histone complexes, termed spin-stretching. The results show that the histones markedly enhance DNA binding to the PMMA surface. DNA winds around the histones and therefore decreases in length. The number of histones that bind to each DNA molecule is found to correlate with the histone concentration. The combed DNA-histone complexes are found to depend on two factors: the binding force on the surface and the centrifugal force at its local position. Na+ ions should compete with histones for binding to DNA; however, the observed competitive binding effect of Na+ ions at low concentrations was negligible.
Preliminary Characterization of Carrageenan from the Red Seaweed<i>Halymenia floresii</i> (2011)

Increasing worldwide demand and development of new applications of carrageenan have added urgency to the search for new or additional raw material sources. Native and alkali-treated carrageenan from Halymenia floresii from Yucatán was extracted and preliminarily characterized. Results showed that this species contains a highly sulfated carrageenan, with minor amounts of 3,6-anhydro-galactose. Native sulfated galactan seems to be rheologically and chemically similar to the lambda-family carrageenan with appropriate thickening ability for food applications. Further studies are needed to precisely define the structure of these complex polymers and its potential use as a source of industrial lambda family.
Underdetermined Blind Source Separation Based on Subspace Representation (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> This paper considers the problem of blindly separating sub- and super-Gaussian sources from underdetermined mixtures. The underlying sources are assumed to be composed of two orthogonal components: one lying in the rowspace and the other in the nullspace of a mixing matrix. The mapping from the rowspace component to the mixtures by the mixing matrix is invertible using the pseudo-inverse of the mixing matrix. The mapping from the nullspace component to zero by the mixing matrix is noninvertible, and there are infinitely many solutions to the nullspace component. The latent nullspace component, which is of lower complexity than the underlying sources, is estimated based on a mean square error (MSE) criterion. This leads to a source estimator that is optimal in the MSE sense. In order to characterize and model sub- and super-Gaussian source distributions, the parametric generalized Gaussian distribution is used. The distribution parameters are estimated based on the expectation-maximization (EM) algorithm. When the mixing matrix is unavailable, it must be estimated, and a novel algorithm based on a single source detection algorithm, which detects time-frequency regions of single-source-occupancy, is proposed. In our simulations, the proposed algorithm, compared to other conventional algorithms, estimated the mixing matrix with higher accuracy and separated various sources with higher signal-to-interference ratio. </para>
Variance-Penalized Markov Decision Processes (1989)

We consider a Markov decision process with both the expected limiting average, and the discounted total return criteria, appropriately modified to include a penalty for the variability in the stream of rewards. In both cases we formulate appropriate nonlinear programs in the space of state-action frequencies (averaged, or discounted) whose optimal solutions are shown to be related to the optimal policies in the corresponding “variance-penalized MDP.” The analysis of one of the discounted cases is facilitated by the introduction of a “Cartesian product of two independent MDPs.”
Estimated SARS-CoV-2 Seroprevalence in the US as of September 2020 (2020)

This cross-sectional study found that as of September 2020, most persons in the US did not have serologic evidence of previous SARS-CoV-2 infection, although prevalence varied widely by jurisdiction. Biweekly nationwide testing of commercial clinical laboratory sera can play an important role in helping track the spread of SARS-CoV-2 in the US.
Merging Organocatalysis and Gold Catalysis—A Critical Evaluation of the Underlying Concepts (2012)

While both organocatalysis and gold catalysis have their roots deeply entrenched in the landscape of modern organic chemistry, an exciting trend in the complementary merging of organocatalysis and especially Au(I) catalysis has emerged in the last four years. This niche area has been developing rapidly and this minireview serves to pin-point the fundamental concepts guiding reaction design in these binary catalytic systems. Moreover, the proven synthetic utility of organo/Au(I) multicatalytic systems in accessing molecular frameworks, previously a challenge to single catalytic systems, has resulted in this new concept permeating numerous areas of organocatalysis, such as primary/secondary amine, Brønsted acid, hydrogen-bonding as well as N-heterocyclic carbene (NHC) catalysis. The first detailed account of these recent developments is systematically presented.
Nanoparticle Mediated Tumor Vascular Disruption: A Novel Strategy in Radiation Therapy (2015)

More than 50% of all cancer patients receive radiation therapy. The clinical delivery of curative radiation dose is strictly restricted by the proximal healthy tissues. We propose a dual-targeting strategy using vessel-targeted-radiosensitizing gold nanoparticles and conformal-image guided radiation therapy to specifically amplify damage in the tumor neoendothelium. The resulting tumor vascular disruption substantially improved the therapeutic outcome and subsidized the radiation/nanoparticle toxicity, extending its utility to intransigent or nonresectable tumors that barely respond to standard therapies.
SaaS Authentication Middleware for Mobile Consumers of IaaS Cloud (2013)

The mobile terrain is rapidly establishing itself as the reliable node for accessing cloud hosted data. Today, commodity cloud providers especially from the Infrastructure-as-a-Service (IaaS) cloud expose their service APIs which facilitates the "app-ification" of enterprise workflows on mobile devices. However, these IaaS providers require the customer (i.e., the data consumer) to submit multiple security credentials which are computation intensive for the purposes of authentication and authorization. As a result, the authentication process introduces undesired delays in a mobile network when consuming enterprise data due to the increasing computational demand and the voluminous HTTP header that is transported across the wireless bandwidth.This paper introduces an application called MiLAMob that is a middleware-layer that handles the authentication process on behalf of the consumer devices in real time and with minimal HTTP traffic. The middleware currently supports mobile consumption of data on IaaS clouds such as Amazon S3, Dropbox, and MEGA. Further, the middleware employs the OAuth 2.0 technique (E.g. Facebook, Google+, and Personal Login) to identify the mobile end-user and uses security tokens to handle the tedious authentication with the IaaS cloud. Also, the deployment of the middleware enforces additional data protection because the security credentials and the IaaS abstractions are shielded from the mobile application domain and the end users.