gebhart/patrepeval huggingface dataset:
The Proteios Software Environment: An Extensible Multiuser Platform for Management and Analysis of Proteomics Data (2009)

Proteome analysis involves many steps that generate large quantities of data in different formats. This creates a need for automatic data merging and extraction of important features from data. Furthermore, metadata need to be collected and reported to enable critical evaluation of results. Many data analysis tools are developed locally in research laboratories and are nontrivial to adapt for other laboratories, preventing optimal exploitation of generated data. The proteomics field would benefit from user-friendly analysis and data management platforms in which method developers can make their analysis tools available for the community. Here, we describe the Proteios Software Environment (ProSE) that is built around a Web-based local data repository for proteomics experiments. The application features sample tracking, project sharing between multiple users, and automated data merging and analysis. ProSE has built-in support for several quantitative proteomics workflows, and integrates searching in several search engines, automated combination of the search results with predetermined false discovery rates, annotation of proteins and submission of results to public repositories. ProSE also provides a programming interface to enable local extensions, as well as database access using Web services. ProSE provides an analysis platform for proteomics research and is targeted for multiuser projects with needs to share data, sample tracking, and analysis result. ProSE is open source software available at http://www.proteios.org .
Practical application of waveform relaxation method for testing remote protective relays (2015)

Testing of newly designed protective relay logics is essential prior to the installation of the relay hardware in power systems. Real-time simulators (rts) are widely used to simulate the computer models of the power system in real-time to analyze the closed loop performance of the relay. This kind of simulation is expensive because high performance processing units are required for the rts systems. Also, the closed loop simulation results will be inaccurate if there are communication delays between the rts and the relay hardware. In this paper, a new iterative method for the closed loop performance test of protective relays is presented. The approach uses the iterative method of the Waveform Relaxation (WR) with the use of a specialized interface hardware called the Real-Time Player/Recorder (RTPR). The power system model is simulated in an off-line electromagnetic transient (EMT) simulation program and the relay hardware is connected to the RTPR device. The off-line simulation results (waveforms) are recorded and then played back in real-time to the relay through the RTPR device. The RTPR records the relay response (trip signals) accordingly and makes them available to the EMT simulation. The EMT simulation is once again repeated with the new recorded waveforms and the results are compared with those from the previous iteration. If the waveforms are different, the above process is repeated. The converged results represent the closed loop response of the EMT simulation and the relay hardware. The approach is used to test the reclosing function of a commercially available relay (SEL-421). It is shown that some of the relay settings must be adjusted to facilitate this type of simulation. The relay is also tested by a real-time digital simulator for cross-validation of the proposed approach. Very similar results prove the high accuracy of the proposed method.
Mixed-Criticality Scheduling with I/O (2016)

This paper addresses the problem of scheduling tasks with differentcriticality levels in the presence of I/O requests. In mixed-criticalityscheduling, higher criticality tasks are given precedence over those of lowercriticality when it is impossible to guarantee the schedulability of alltasks. While mixed-criticality scheduling has gained attention in recentyears, most approaches typically assume a periodic task model. Thisassumption does not always hold in practice, especially for real-time andembedded systems that perform I/O. In prior work, we developed ascheduling technique in the Quest real-time operating system, which integratesthe time-budgeted management of I/O operations with Sporadic Server schedulingof tasks. This paper extends our previous scheduling approach with support formixed-criticality tasks and I/O requests on the same processing core. Resultsshow that in a real implementation the mixed-criticality scheduling methodintroduced in this paper outperforms a scheduling approach consisting of onlySporadic Servers.
Relation between tag position and degree of visualized cerebrospinal fluid reflux into the lateral ventricles in time-spatial labeling inversion pulse magnetic resonance imaging at the foramen of Monro (2015)

The amount of observed CSF reflux into the lateral ventricles in Time-SLIP MR imaging is dependent on the positioning of the CSF tag with decreasing amount of visualized reflux the further caudal the CSF tag is relative to the free margin of the septum pellucidum.
Probiotic and synbiotic therapy in critical illness: a systematic review and meta-analysis (2016)

Probiotics show promise in reducing infections, including VAP in critical illness. Currently, clinical heterogeneity and potential publication bias reduce strong clinical recommendations and indicate further high quality clinical trials are needed to conclusively prove these benefits.
An improved plaque assay for poor plaque-producing temperate lactococcal bacteriophages (1997)

This report summarizes the results from an effort to optimize the double-agar plate assay for visualization of the plaques made by six temperate bacteriophages induced from industrial strains of Lactococcus lactis. Among the several parameters found to influence the plaque assay, the effect of incorporating glycine into the growth medium was most striking, resulting in extensive increase in the plaque size of all of the 13 phage-host pairs tested. Notable effects on the plaque size of other factors such as the procedure for sterilization of the agar medium, the volume and softness of the top and bottom layers, and the number and growth stage of the bacterial cells added to the lawn, were also observed. By exploiting these findings in an optimized procedure for plaque assaying, several indicator strains were identified which were unable to support the development of plaques on standard double-agar plates. Since bacterial hosts usually are identified by their ability to support the development of plaques, this observation suggests that the severe difficulty experienced in identifying lactococcal starter strains that are sensitive towards a temperate phage, partly is a problem of methodology.
Association of a Functional Deficit of the BK <sub>Ca</sub> Channel, a Synaptic Regulator of Neuronal Excitability, With Autism and Mental Retardation (2006)

These results suggest a possible association between a functional defect of the BK(Ca) channel and autistic disorder and raise the hypothesis that deficits in synaptic transmission may contribute to the physiopathology of autism and mental deficiency.
Graphene sponge for efficient and repeatable adsorption and desorption of water contaminations (2012)

Seeking highly-efficient, low-cost and robust methods to disinfect and decontaminate water from source to point-of-use is very much in demand. Here, we developed a new material, graphene sponge (GS), for water treatment, which was assembled with graphene oxide sheets by hydrothermal treatment with the assistance of thiourea. These GSs show a tunable pore structure and surface properties, and are mechanically strong. They show high adsorption ability for various water contaminations such as dyes, oils and many other organic solvents. The adsorption capacity of methylene blue and diesel oil in GSs can reach 184 mg g−1 and 129 g g−1, respectively. Moreover, the GSs can be repeatedly used by simple treatment without obvious structure and performance degradation. Additionally, we studied the relationship between the structure and contamination adsorption performance of GSs. It was found that the dye adsorption performance of GSs strongly depends on their surface charge concentration and specific surface area, but the oil adsorption capacity is mainly related to their specific surface area, indicating the different adsorption mechanism. These findings open up many possibilities for the use of graphene in water cleaning, including disinfection, decontamination, re-use, reclamation and desalination.
Detecting Malicious Behavior Using Critical API-Calling Graph Matching (2009)

The proliferation of new malware in recent years has presented a serious security threat to our society. Research shows that variants of some known ones take a large amount of new malware, so one of the challenges in malware detection is how to find the similarities between known malware and its variants. Since API(Application Programming Interface)functions is used extensively to achieve the function of one program and It is difficult for different malware versions to conceal similarity on the functional flow level, making use of the similarity of their API-calling sequences is an essential detection method. In this paper, we present a new approach of malware detection based on critical API-calling Graph (CAG) matching rather than considering all API calls. More attention is paid on the illustration of how to extract a CAG from a control flow graph (CFG) for each malware to define a malicious behavior and how to detect the behavior in a suspicious executable using the CAG matching. This approach can overcome the drawbacks of two most common techniques adopted by current antivirus in detection of variants and unknown malware, which is demonstrated by the favorable experimental results.
Marine Fish Larvae Feeding: Formulated Diets or Live Prey? (1993)

Abstract In the rearing of larval marine fish, any diet that reduces dependance on live prey production is of technical and economic interest. Weaning juveniles with a completely developed digestive tract to a conventional diet, (i.e., “late weaning”) can be successful in any marine fish species. For example, weaning one‐month‐old sea bass (20 mg) to the study's reference diet, Sevbar, resulted in over 85% survival (40% from hatching) and 1.25 g fish at day 90 (at 19 C) In contrast, “early weaning” of larvae to special microdiets during the first month is still difficult. The best way to reduce live prey utilization in sea bass is to wean larvae at about 3–4 mg in size (day 20). If weaning could be accomplished 15 days earlier, Artemia savings could be as high as 80%. However, this introduces risks relative to growth retardation (30% weight loss) and lower juvenile quality, including greater size variability and skeletal abnormalities. Similar results have been obtained with commercial microparticles (Fry Feed Kyowa) and experimental microbound diets (MBD) made from raw materials (alginate MBD) or preferably from freeze‐dried protein sources (zein MBD). Total replacement of live prey is still impossible in marine fish. Sea bass larvae fed formulated diets exclusively from first feeding (0.3 mg larval wet weight), or even from their second week of life onwards, exhibited low survival and poor growth. Better results can be obtained when formulated diets are used in combination with live prey from first feeding, although the optimal ratio of live prey to formulated diet is still to be specified.
Pharmacological and biological therapeutic strategies for osteogenesis imperfecta (2016)

Osteogenesis imperfecta (OI) is a connective tissue disorder characterized by bone fragility, low bone mass, and bone deformities. The majority of cases are caused by autosomal dominant pathogenic variants in the COL1A1 and COL1A2 genes that encode type I collagen, the major component of the bone matrix. The remaining cases are caused by autosomal recessively or dominantly inherited mutations in genes that are involved in the post-translational modification of type I collagen, act as type I collagen chaperones, or are members of the signaling pathways that regulate bone homeostasis. The main goals of treatment in OI are to decrease fracture incidence, relieve bone pain, and promote mobility and growth. This requires a multi-disciplinary approach, utilizing pharmacological interventions, physical therapy, orthopedic surgery, and monitoring nutrition with appropriate calcium and vitamin D supplementation. Bisphosphonate therapy, which has become the mainstay of treatment in OI, has proven beneficial in increasing bone mass, and to some extent reducing fracture risk. However, the response to treatment is not as robust as is seen in osteoporosis, and it seems less effective in certain types of OI, and in adult OI patients as compared to most pediatric cases. New pharmacological treatments are currently being developed, including anti-resorptive agents, anabolic treatment, and gene- and cell-therapy approaches. These therapies are under different stages of investigation from the bench-side, to pre-clinical and clinical trials. In this review, we will summarize the recent findings regarding the pharmacological and biological strategies for the treatment of patients with OI. © 2016 Wiley Periodicals, Inc.
INFORMATION SECURITY AND OPEN SOURCE SOFTWARE (2011)

In times of increasing dependence on computer systems, information security emerges as an important issue for public administrations. Many governments have made a transition to open source software; the reason being not just financial, but connected to increasing numbers of operating systems security issues. Having more control over the systems is also key. Some researchers speak in favour of proprietary software, others in favour of open source software. Data shows, however, that open source software leads over proprietary software in security mechanisms, although it is not without its limitations. This is the reason that states transitioning to open source software must take precautions in doing so.
HYDRODYNAMIC DAMPING DUE TO POROUS PLATES. (2004)

Abstract:- This paper studies the damping coefficients of solid and porous disks in the context of their use as heave dampers in offshore structures. Results from forced heave oscillation experiments obtained in this study are compared with previously published data. While results for a solid disk agree reasonably with published data, the agreement with porous disks shows some discrepancies which need to be studied further. Damping coefficients for all disks are found to increase linearly with increasing amplitude of oscillation. The maximum damping coefficient corresponds to a disk of 10 % porosity where the heave damping is increased by a factor of 2.4 compare to a solid disk. An envelope is created for a range of porosity from 0 % to 10 % to maximise heave response.
One Atom Makes All the Difference: Getting a Foot in the Door between SOS1 and KRAS (2021)

KRAS, the most common oncogenic driver in human cancers, is controlled and signals primarily through protein-protein interactions (PPIs). The interaction between KRAS and SOS1, crucial for the activation of KRAS, is a typical, challenging PPI with a large contact surface area and high affinity. Here, we report that the addition of only one atom placed between Y884<sup>SOS1</sup> and A73<sup>KRAS</sup> is sufficient to convert SOS1 activators into SOS1 inhibitors. We also disclose the discovery of <b>BI-3406</b>. Combination with the upstream EGFR inhibitor afatinib shows <i>in vivo</i> efficacy against KRAS<sup>G13D</sup> mutant colorectal tumor cells, demonstrating the utility of <b>BI-3406</b> to probe SOS1 biology. These findings challenge the dogma that large molecules are required to disrupt challenging PPIs. Instead, a "foot in the door" approach, whereby single atoms or small functional groups placed between key PPI interactions, can lead to potent inhibitors even for challenging PPIs such as SOS1-KRAS.
Min/max on-chip inductance models and delay metrics (2001)

This paper proposes an analytical inductance extraction model for characterizing min/max values of typical on-chip global intercon-nect structures, and a corresponding delay metric that can be used to provide RLC delay prediction from physical geometries. The model extraction and analysis is efficient enough to be used within optimization and physical design exploration loops. The analytical min/max inductance approximations also provide insight into the effects caused by inductances.
Inducible RNA Interference-Mediated Gene Silencing Using Nanostructured Gene Delivery Arrays (2007)

RNA interference (RNAi) has become a powerful biological tool over the past decade. In this study, a tetracycline-inducible small hairpin RNA (shRNA) vector system was designed for silencing cyan fluorescent protein (CFP) expression and delivered alongside the yfp marker gene into Chinese hamster ovary cells using impalefection on spatially indexed vertically aligned carbon nanofiber arrays (VACNFs). The VACNF architecture provided simultaneous delivery of multiple genes, subsequent adherence and proliferation of interfaced cells, and repeated monitoring of single cells over time. Following impalefection and tetracycline induction, 53.1% +/- 10.4% of impalefected cells were fully silenced by the inducible CFP-silencing shRNA vector. Additionally, efficient CFP silencing was observed in single cells among a population of cells that remained CFP-expressing. This effective transient expression system enables rapid analysis of gene-silencing effects using RNAi in single cells and cell populations.
Focusing characteristics of symmetrically configured bootlace lenses (1978)

A symmetrically configured class of bootlace lenses (also known as Gent or Rotman lenses) is analyzed. These trifocal lenses are used to feed haft-wave spaced linear arrays to form a set of multiple beams. The lens dimensions are scaled' so that all lenses have transmission characteristics equivalent to those of a Butler matrix with the same number of ports. The relationship between the focusing characteristics and the lens dimensions is calculated, and it is shown that these symmetrically configured lenses form a one-parameter family. Design equations are derived, and a design procedure is described. It is found that, for a wavefront tolerance of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\pm\lambda/16</tex> , the maximum usable array length varies from <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">20 \lambda</tex> to <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">200 \lambda</tex> as the ratio of lens width to array length varies from one to 1.6.
Design and Evaluation Criteria for Development of Toxic Wicks for Rodent Control (1983)

Research suggests the feasibility of using wicks to deliver toxicants for rodent control, with subsequent rodent ingestion of the toxicant through grooming. Such wicks may overcome disadvantages of more conventional control materials, such as toxic baits and tracking powders for such applications as sites with little space or access for conventional baiting, with attractive alternative food sources, or where potential hazard and contamination are of particular concern. Several innovations for developing and evaluating toxic wicks for rodent control are described. These methods are devised to determine optimum wick systems based on considerations of outer device construction, wick configuration and composition, and the nature and concentration of the toxicant in the device. Further, the delivery system to the rodent in relation to rodent susceptibility and behavior, wick placement, longevity, and safety are explored. Although the techniques illustrated involve a brodifacoum-containing wick device for commensal house mouse control, similar considerations and test procedures would have application in developing other toxicants and wick devices for rodent control.
Astragalus (Leguminosae): nomenclatural proposals and new taxa (1998)

As part of an ongoing summary revision of Astragalus for the Flora North America project, several nomenclatural changes are indicated. Nomenclatural proposals include A. molybdenus var. shultziorum (Barneby) Welsh, comb. nov.; A. australis var. aboriginorum (Richardson) Welsh, comb. nov.; A. australis var. cottoni (M.E. Jones) Welsh, comb. nov.; A. australis var. lepagei (Hulten) Welsh, comb. nov.; A. australis var. muriei (Hulten) Welsh, comb. nov.; A. subcinereus var. sileranus (M.E. Jones) Welsh, comb. nov.; A. tegetarioides var. anxius (Meinke & Kaye) Welsh, comb. nov.; A. ampullarioides (Welsh) Welsh, comb. nov.; A. cutleri (Barneby) Welsh, comb. nov.; and A. laccoliticus (M.E. Jones) Welsh, comb. nov. Proposals of new taxa included Astragualus sect. Scytocarpi subsect. Microcymbi Welsh, subsect. nov., and A. sabulosus var. vehiculus Welsh, var. nov. A lectotype is selected for Phaca australis L.
Tazarotene 0.1% cream for the treatment of photodamage. (2004)

Tazarotene (Tazorac, Allergan) has been shown to be effective in reducing the effects of photoaging in short term studies. To determine its effectiveness in the longer term, a 24-week multicenter, double-blind, randomized, vehicle controlled intervention study of 562 patients with facial photodamage was carried out followed by a 28-week open label extension. Patients were treated with one daily application of tazarotene 0.1% cream or vehicle cream to the face for 24 weeks, then tazarotene 0.1% cream for another 28 weeks. At week 24, when compared to vehicle, tazarotene resulted in a significantly greater incidence of patients achieving treatment success (over 50 percent greater improvement) and at least a 1 grade improvement in fine wrinkling, mottled pigmentation, pore size, lentigines, elastosis, irregular depigmentation, tactile roughness, coarse wrinkling and overall integrated assessment of photodamage. Additional clinical improvement occurred with continued tazarotene treatment and had not plateaued by week 52.
Retinopathy of Prematurity, Intraventricular Hemorrhage, and Oxidative Damage (1986)

To the Editor.— Hittner et al1 and Speer et al2 have recently reported that supplementation of vitamin E in premature infants reduces the incidence of retinopathy of prematurity and intraventricular hemorrhage, respectively. Ensuing correspondence3,4 has been primarily concerned with the potentially toxic effects of vitamin E. (It should be noted that, in contrast, Phelps5 found no evidence that the use of vitamin E reduced the incidence of intraventricular hemorrhage.) However, we believe that the most significant aspect of these papers1,2 is their support of the hypothesis that both retinopathy of prematurity and intraventricular hemorrhage are manifestations of oxidative damage caused by oxygen-derived free radicals.