gebhart/patrepeval huggingface dataset:
Docking and molecular dynamics simulation for therapeutic repurposing in small cell lung cancer (SCLC) patients infected with COVID-19 (2021)

Cancer care has become a challenge with the current COVID-19 pandemic scenario. Specially, cancers like small cell lung cancers (SCLC) are difficult to treat even in the normal situation due to their rapid growth and early metastasis. For such patients, treatment can't be compromised and care must be taken to ensure their minimum exposure to the ongoing spread of COVID-19 infection. For this reason, in-house treatments are being suggested for these patients. Another issue is that symptoms of SCLC match well with that of COVID-19 infection. Hence, the detection of COVID-19 may also get delayed leading to unnecessary complications. Thus, we have tried to investigate if the therapeutics that is currently used in lung cancer treatment can also act against SARS-CoV-2. If it is so, the same treatment protocols can be continued even if the SCLC patient had contracted COVID-19 without compromising the cancer care. For this, RNA dependent RNA polymerase (RdRP) from SARS-CoV-2 has been selected as drug target. Both docking and molecular dynamicssimulation analysis have indicated that Paclitaxel and Dacomitinib may be explored as multi-target drugs for both SCLC and COVID-19.Communicated by Ramaswamy H. Sarma.
Telling experts from spammers (2009)

With a suitable algorithm for ranking the expertise of a user in a collaborative tagging system, we will be able to identify experts and discover useful and relevant resources through them. We propose that the level of expertise of a user with respect to a particular topic is mainly determined by two factors. Firstly, an expert should possess a high quality collection of resources, while the quality of a Web resource depends on the expertise of the users who have assigned tags to it. Secondly, an expert should be one who tends to identify interesting or useful resources before other users do. We propose a graph-based algorithm, SPEAR (SPamming-resistant Expertise Analysis and Ranking), which implements these ideas for ranking users in a folksonomy. We evaluate our method with experiments on data sets collected from Delicious.com comprising over 71,000 Web documents, 0.5 million users and 2 million shared bookmarks. We also show that the algorithm is more resistant to spammers than other methods such as the original HITS algorithm and simple statistical measures.
Softbit-source decoding based on the turbo-principle (2002)

This contribution deals with a robust decoding approach of source codec parameters called softbit-source decoding. It can be considered as an error concealment technique which estimates codec parameters at the receiver utilizing the residual redundancy remaining after source coding and the channel decoder reliability information. We apply the turbo-principle to softbit-source decoding. We derive a formula that shows how different terms of residual redundancy can be transformed into independent extrinsic information utilizable in iterative processes. After introducing a new, iterative approach to softbit-source decoding, we analyze the influences of different bit mappings and of the number of iterations. Finally, the new approach is compared to conventional techniques with respect to performance and complexity.
The “We” Problem in Teaching International Studies (2002)

This article addresses the problems that emerge when students in international studies courses approach the subject matter from the perspective of the first person plural. Whether in terms of “we,”“us,” or “our,” many college students choose to adopt a personal perspective in discussions of international affairs. While it is natural for students to base their analysis of international studies on their personal observations and experiences, this inclination to adopt a collective first person approach detracts from the scholarly neutrality toward which students of global studies should aspire. Furthermore, a first person plural approach to course subject matter creates the false impression among students that they are all in agreement over contentious issues of global interactions and the theories employed to study them. The article concludes with suggestions for remedying the “we” problem, and offers advice for instructors who have encountered it in their own classroom.
Microfluidic Serial Dilution Cell-Based Assay for Analyzing Drug Dose Response over a Wide Concentration Range (2010)

In this paper we report a perfusion culture microchamber array chip with a serial dilution microfluidic network for analyzing drug dose response over a concentration range spanning 6 orders of magnitude, which is required for practical drug discovery applications. The microchamber array chip was equipped with a pressure-driven interface, in which medium and drug solution were added with a micropipet and delivered into the microfluidic network by pneumatic pressure. We demonstrated that the microchamber array chip could be used to estimate the 50% growth inhibitory concentration using the model anticancer drug paclitaxel and the model cancer cell line HeLa. The results obtained by using the microchamber array chip were consistent with those obtained by a conventional assay using microplates. The microchamber array chip, with its simple interface and well-designed microfluidic network, has potential as an efficient platform for high-throughput dose response assays in drug discovery applications.
The Classical Soviet-Type Economy: Nature of the System and Implications for Reform (1991)

Below I will outline the traditional Soviet economic system, developing its logic of institutions and interactions, and pointing out their natural economic consequences. This will lead me to a list of defining characteristics of that system, characteristics that are mutually dependent and supporting and hence must be changed more or less simultaneously if effective reform is to take place. One implication is that step-by-step measures are likely to fail. Instead, complete replacement of the economic system, as apparently intended by many East European reformers, seems necessary for a market-based system to begin functioning. This will be a truly monumental task and nowhere more so than in the Soviet Union.
Release of hyaluronate from eukaryotic cells (1990)

The mechanism of hyaluronate shedding from eukaryotic cell lines was analysed. All cell lines shed identical sizes of hyaluronate as were retained on the surface. They differed in the amount of hyaluronate synthesized and in the proportions of hyaluronate which were released and retained. A method was developed which could discriminate between shedding due to intramolecular degradation and that due to dissociation as intact macromolecules. This method was applied to B6 and SV3T3 cells in order to study the mechanism of hyaluronate release in more detail. The cells were pulse-labelled to form hyaluronate chains with labelled and unlabelled segments, and the sizes of labelled hyaluronate released into the medium during the pulse extension period were determined by gel filtration. B6 cells released identical sizes of hyaluronate at all labelled segment lengths, indicating that no intramolecular degradation occurred. When chain elongation was blocked by periodate-oxidized UDP-glucuronic acid, hyaluronate release was simultaneously inhibited. These results indicated that B6 cells dissociated hyaluronate as an intact macromolecule. In contrast, SV3T3 cells released hyaluronate of varying molecular mass distributions during extension of the labelled segment, suggesting partial degradation. Exogenous hyaluronate added to SV3T3 cultures was also degraded. This degradation could be prevented by the presence of radical scavengers such as superoxide dismutase and tocopherol. Degradation of endogenous hyaluronate could be inhibited by salicylate. These results led to the conclusion that SV3T3 cells released hyaluronate not only by dissociation, but also by radical-induced degradation.
On the large family of low correlation quaternary sequences S(2) (2002)

The current version of the W-CDMA component of the upcoming third generation (3G) global mobile communication standard IMT-2000 includes the use, as uplink scrambling codes, of a family of low correlation quaternary sequences known as family S(2). A tutorial introduction to this sequence family is provided here.
Manufacturing Task Description for Robotic Welding and Automatic Feature Recognition on Product CAD Models (2017)

In this paper, a novel approach for an ontological representation of continuous-path manufacturing tasks is presented on the example of robotic fillet welding. The representation specifies manufacturing information and product related geometric constraints relevant for automatic program planning in robotic arc welding. The geometric constraints are transformed into simple continuous curve primitives such as lines, circular arcs and B-spline curves supporting the easy integration in robot program planning systems decoupled from a complex CAD environment. It also represents information on welding gaps along the joint geometry. Moreover, a method for automatic feature recognition based on rule- based pattern recognition is presented to automatically retrieve manufacturing information from the CAD model of the product and generate the respective manufacturing task specification. The method is evaluated in several test scenarios for welding product assemblies indicating the usability and effectiveness for automatic program planning in robotic welding.
Evaluation of a Novel Material for Recycling Tires into Artificial Reefs - Final Report (1995)

The purpose of this study was to evaluate, from a biological perspective, a tire-concrete aggregate which uses tire shreds mixed into concrete, as a suitable reef building material. Evaluation consisted of comparing the biological assemblages associated with tire-aggregate reefs to standard gravel-concrete reefs of the same design. Four artificial reefs of concrete, tetrahedron modules were placed off Fort Lauderdale, Florida in seven meters of water, two reefs of each type of aggregate. Each reef contains 25 small (1m/side) and 25 large (1.3m/side) tetrahedrons stacked in a random configuration. The reefs were monitored at monthly, or less, intervals for 28 months. The status of the biological assemblages were assayed by: visual census (fishes); uw-video taping and collection (invertebrates) and scanning electron microscopy (initial microscopic colonizers). The reefs acquired a diverse assemblage of fishes and invertebrates over the course of the study; 105 species of fishes and over 120 taxa of invertebrates were recorded. There were no apparent significant differences among the biological assemblages, between the two types of reefs, that can be readily ascribed to the difference in construction material. Based on these results, it appears that the tire-concrete aggregate is an appropriate material for artificial reef construction, and may be an ecologically positive method of tire disposal.
Electric vehicle charging stations in the workplace with high-resolution data from casual and habitual users (2021)

Problems of poor network interoperability in electric vehicle (EV) infrastructure, where data about real-time usage or consumption is not easily shared across service providers, has plagued the widespread analysis of energy used for transportation. In this article, we present a high-resolution dataset of real-time EV charging transactions resolved to the nearest second over a one-year period at a multi-site corporate campus. This includes 105 charging stations across 25 different facilities operated by a single firm in the U.S. Department of Energy Workplace Charging Challenge. The high-resolution data has 3,395 real-time transactions and 85 users with both paid and free sessions. The data has been expanded for re-use such as identifying charging behaviour and segmenting user groups by frequency of usage, stage of adoption, and employee type. Potential applications include but are not limited to simulating and parameterizing energy demand models; investigating flexible charge scheduling and optimal power flow problems; characterizing transportation emissions and electric mobility patterns at high temporal resolution; and evaluating characteristics of early adopters and lead user innovation.
Enolate Ions as β-Activators of Ortho-Metalation:  Direct Synthesis of 3-Aminoindenones (2000)

beta-Ketonitriles derived from a Claisen condensation of benzoate esters with alkyl- or phenylacetonitriles lead to 3-aminoindenones in the presence of excess LDA. This new reaction is also applicable to pyridine carboxylic esters. All of the 3-aminoindenones and their aza analogues can be hydrolyzed by acid to give the corresponding 1,3-indandiones. The mechanism of the reaction falls into the directed-ortho-metalation class in which the initial enolate ion of the keto-nitrile directs self-metalation at an ortho position. The new anion then cyclizes onto the nitrile group to generate an aminoindenone. Surprisingly the simplest member of the series, benzoylacetonitrile, does not undergo cyclization. Mechanistic isotope studies revealed that this substance preferentially and directly forms a dianion on the side chain, which is not further deprotonated at the ortho position of the aromatic ring.
Case-Based Reasoning Approach for Well Failure Diagnostics and Planning (2008)

Abstract Case-based reasoning, also known as computer reasoning by analogy, is a simple and practical technique that solves new problems by comparing them to ones that have already been solved in the past, thus saving time and money. The technique constantly incorporates dynamic data, which empowers the system to learn and adapt from new experiences. A general framework for case-based reasoning is presented, along with a review of the four-step cycle that characterizes the technology: retrieve, reuse, revise and retrain. This paper presents a specific application of case-based reasoning to determine the optimum cleaning technique (bailing, washback, or foaming) for sanded/seized well failures. The methodology extracts only the most relevant information from the historical database, utilizes a rule-based system to make adaptations, and then suggests the most appropriate solution for a given well intervention. This technique was used for production operations as a front end tool for well workover planning and design and was applied to sample data from a large oil field where the main artificial lift system is rod pump. This simple case demonstrates how case-based reasoning can be applied to improve the planning and execution of well interventions, thus reducing cost, rig time, and well turnaround time, while maximizing reliability and production.
Relationships between Tornado Intensity and Various Wind and Thermodynamic Variables (1996)

Statistical relationships between tornado intensity and various stability and wind-related parameters are determined from a dataset of more than 200 tornado proximity soundings. Soundings were obtained from two sources: the University of Missouri and from analyses. The surface to 600 hPa wind shear, streamwise vorticity, storm velocity, and storm-relative environmental helicity are shown to be best correlated with tornado intensity. A multiple regression analysis produced an equation relating tornado intensity to the lifted index and the surface to 600 hPa wind shear. This relationship could be used operationally to predict tornado intensity. Mean temperature, dewpoint temperature, and wind profiles are presented for each tornado intensity category and these may be useful as input to numerical thunderstorm simulations. Progressively cooler temperatures and increasing wind speed and vertical wind shear are evident with increasing tornado intensity. A modified form of the bulk Richardson number is derived to assist the forecasting of isolated supercell thunderstorm occurrence. The modified form uses parameters that are readily available to the operational forecaster.
Acute experimental silicosis. Lung morphology, histology, and macrophage chemotaxin secretion. (1982)

The acute inflammatory reaction in the lungs of guinea pigs produced by the intratracheal injection of silica was assessed by histologic studies and whole-lung lavage 1, 2, 4, 7, and 14 days after the intratracheal instillation of quartz particles or saline. In addition, lavaged macrophages were cultured in vitro, and the media were assayed for chemotactic factors. This exposure to silica produced a neutrophilic inflammatory response around terminal bronchioles that was well developed within 1 day after injection. Four days after injection, neutrophils were replaced by mononuclear cells; and by 7 days, loosely organized granulomas and collagen deposition were detected in the interstitium. The number of neutrophils (PMNs) recovered by lavage from experimental animals was greatest 1 day after injection and was significantly greater (P less than 0.01) than that for controls at all time points. In contrast, the number of macrophages recovered by lavage did not exceed control levels until 7 days after injection and remained elevated thereafter. Thus, the cells recovered by lavage tended to mirror the changes seen in the inflamed lung. In experiments utilizing blind-well chemotactic chambers, both peritoneal exudate neutrophils and macrophages migrated toward supernatants from cultures of alveolar macrophages lavaged from silica-exposed animals in greater numbers (P less than 0.02) than toward supernatant from control animal macrophage cultures at each time point. Migration of normal alveolar macrophages toward supernatants from all cultures was minimal. Thus, exposure to silica in vivo appears to be a potent stimulus for the release of neutrophil and monocyte chemotactic factors by alveolar macrophages in vitro. The correlation between the types of inflammatory cells identified in the lung both microscopically and by lavage and the chemotactic factors released in vitro by alveolar macrophages from these lungs suggests that alveolar macrophages play a role in mediating pulmonary inflammation in this form of experimental silicosis.
Direct Intraventricular Delivery of Drugs to the Rodent Central Nervous System (2013)

Due to an inability to cross the blood brain barrier, certain drugs need to be directly delivered into the central nervous system (CNS). Our lab focuses specifically on antisense oligonucleotides (ASOs), though the techniques shown in the video here can also be used to deliver a plethora of other drugs to the CNS. Antisense oligonucleotides (ASOs) have the capability to knockdown sequence-specific targets (1) as well as shift isoform ratios of specific genes (2). To achieve widespread gene knockdown or splicing in the CNS of mice, the ASOs can be delivered into the brain using two separate routes of administration, both of which we demonstrate in the video. The first uses Alzet osmotic pumps, connected to a catheter that is surgically implanted into the lateral ventricle. This allows the ASOs to be continuously infused into the CNS for a designated period of time. The second involves a single bolus injection of a high concentration of ASO into the right lateral ventricle. Both methods use the mouse cerebral ventricular system to deliver the ASO to the entire brain and spinal cord, though depending on the needs of the study, one method may be preferred over the other.
Comparison of triple quadrupole, hybrid linear ion trap triple quadrupole, time‐of‐flight and LTQ‐Orbitrap mass spectrometers in drug discovery phase metabolite screening and identification <i>in vitro</i> – amitriptyline and verapamil as model compounds (2010)

Liquid chromatography in combination with mass spectrometry (LC/MS) is a superior analytical technique for metabolite profiling and identification studies performed in drug discovery and development laboratories. In the early phase of drug discovery the analytical approach should be both time- and cost-effective, thus providing as much data as possible with only one visit to the laboratory, without the need for further experiments. Recent developments in mass spectrometers have created a situation where many different mass spectrometers are available for the task, each with their specific strengths and drawbacks. We compared the metabolite screening properties of four main types of mass spectrometers used in analytical laboratories, considering both the ability to detect the metabolites and provide structural information, as well as the issues related to time consumption in laboratory and thereafter in data processing. Human liver microsomal incubations with amitriptyline and verapamil were used as test samples, and early-phase 'one lab visit only' approaches were used with all instruments. In total, 28 amitriptyline and 69 verapamil metabolites were found and tentatively identified. Time-of-flight mass spectrometry (TOFMS) was the only approach detecting all of them, shown to be the most suitable instrument for elucidating as comprehensive metabolite profile as possible leading also to lowest overall time consumption together with the LTQ-Orbitrap approach. The latter however suffered from lower detection sensitivity and false negatives, and due to slow data acquisition rate required slower chromatography. Approaches with triple quadrupole mass spectrometry (QqQ) and hybrid linear ion trap triple quadrupole mass spectrometry (Q-Trap) provided the highest amount of fragment ion data for structural elucidation, but, in addition to being unable to produce very high-important accurate mass data, they suffered from many false negatives, and especially with the QqQ, from very high overall time consumption.
Distance estimation using a single computational camera with dual off-axis color filtered apertures (2013)

In this paper, we present a novel computational imaging system using a dual off-axis color filtered aperture (DCA) for distance estimation in a single-camera framework. The DCA consists of two off-axis apertures that are covered by red and cyan color filters. The two apertures generate misaligned color channels in which the amount of misalignment of points in the image plane are a function of the distance from the camera of the corresponding points in the object plane. The primary contribution of this paper is the derivation of a mathematical model of the relationship between the color shifting values and distance of an object from the camera when the camera parameters and the baseline distance between the two apertures in the DCA are given. The proposed computational imaging system can be implemented simply by inserting an appropriately sized DCA into any general optical system. Experimental results show that the DCA camera is able to estimate the distances of objects within a single-camera framework.
ISA system architecture (1993)

From the Publisher:
An invaluable tool and reference on ISA architecture and time reading it is time well spent. You might just end up wondering how you ever got along without it!
-David Greenberg, Dell Computer Corporation
I
Virtual Database technology, XML, and the Evolution of the Web. (1998)

We describe Junglee’s Virtual Database (VDB) technology, which makes the World Wide Web and other external data sources behave as an extension of an enterprise’s relational database (RDBMS) system. We provide examples of powerful applications enabled by the technology. We then consider XML, a new markup language standard; we conjecture how XML will transform the web, and the role that will be played by Virtual Database technology in this transformation.