gebhart/patrepeval huggingface dataset:
High-Throughput Screening Normalized to Biological Response: Application to Antiviral Drug Discovery (2013)

The process of conducting cell-based phenotypic screens can result in data sets from small libraries or portions of large libraries, making accurate hit picking from multiple data sets important for efficient drug discovery. Here, we describe a screen design and data analysis approach that allow for normalization not only between quadrants and plates but also between screens or batches in a robust, quantitative fashion, enabling hit selection from multiple data sets. We independently screened the MicroSource Spectrum and NCI Diversity Set II libraries using a cell-based phenotypic high-throughput screening (HTS) assay that uses an interferon-stimulated response element (ISRE)-driven luciferase-reporter assay to identify interferon (IFN) signal enhancers. Inclusion of a per-plate, per-quadrant IFN dose-response standard curve enabled conversion of ISRE activity to effective IFN concentrations. We identified 45 hits based on a combined z score ≥2.5 from the two libraries, and 25 of 35 available hits were validated in a compound concentration-response assay when tested using fresh compound. The results provide a basis for further analysis of chemical structure in relation to biological function. Together, the results establish an HTS method that can be extended to screening for any class of compounds that influence a quantifiable biological response for which a standard is available.
CUDAlign 3.0: Parallel Biological Sequence Comparison in Large GPU Clusters (2014)

This paper proposes and evaluates a parallel strategy to execute the exact Smith-Waterman (SW) biological sequence comparison algorithm for huge DNA sequences in multi-GPU platforms. In our strategy, the computation of a single huge SW matrix is spread over multiple GPUs, which communicate border elements to the neighbour, using a circular buffer mechanism. We also provide a method to predict the execution time and speedup of a comparison, given the number of the GPUs and the sizes of the sequences. The results obtained with a large multi-GPU environment show that our solution is scalable when varying the sizes of the sequences and/or the number of GPUs and that our prediction method is accurate. With our proposal, we were able to compare the largest human chromosome with its homologous chimpanzee chromosome (249 Millions of Base Pairs (MBP) x 228 MBP) using 64 GPUs, achieving 1.7 TCUPS (Tera Cells Updated per Second). As far as we know, this is the largest comparison ever done using the Smith-Waterman algorithm.
Hydrogenolysis of Glycerol to 1,3‐propanediol under Low Hydrogen Pressure over WOx‐Supported Single/Pseudo‐Single Atom Pt Catalyst (2016)

Single/pseudo-single atom Pt catalyst was prepared on mesoporous WOx . The large surface area and abundant oxygen vacancies of WOx improve the Pt dispersion and stabilize the Pt isolation. This newly prepared catalyst exhibited outstanding hydrogenolysis activity under 1 MPa H2 pressure with a very high space-time yield towards 1,3-propanediol (3.78 g gPt (-1) h(-1) ) in Pt-W catalysts. The highly isolated Pt structure is thought to contribute to the excellent H2 dissociation capacity over Pt/WOx . The high selectivity towards 1,3-propanediol is attributed to the heterolytic dissociation of H2 at the interface of Pt and WOx (providing specific Brønsted acid sites and the concerted dehydration-hydrogenation reaction) and the bond formation between glycerol and WOx , which favors/stabilizes the formation of a secondary carbocation intermediate as well as triggers the redox cycle of the W species (W(6+) ⇄W(5+) ).
Posterior capsule opacification and capsulotomy rates with taco-style hydrogel intraocular lenses (1996)

The logel lenses led to a high incidence of regeneratory PCO within the gap between the lens and capsule that might be the result of the properties of the lens' hydrogel material rather than its design.
Regulation of Herpes Simplex Virus gB-Induced Cell-Cell Fusion by Mutant Forms of gH/gL in the Absence of gD and Cellular Receptors (2013)

ABSTRACT Herpesvirus entry requires the viral glycoprotein triad of gB and gH/gL to carry out fusion between the virion envelope and a cellular membrane in order to release the nucleocapsid into the target cell. Herpes simplex virus (HSV) also requires glycoprotein gD to initiate the fusion cascade by binding a cell receptor such as nectin 1 or herpesvirus entry mediator (HVEM). While the structure of gB is that of a class III fusion protein, gH/gL has no features that resemble other viral fusion proteins. Instead, it is suggested that gH/gL acts as a regulator of gB. The crystal structure of HSV-2 gH/gL was obtained with a functional protein that had a deletion of 28 residues at the gH N terminus (gHΔ48/gL). Unexplainably, monoclonal antibodies (MAbs) with virus-neutralizing activity map to these residues. To reconcile these two disparate observations, we studied the ability of gHΔ48/gL to regulate fusion. Here, we show that the protein induces low (constitutive) levels of fusion by gB in the absence of gD and/or receptor. However, when gD and receptor are present, this mutant functions as well as does wild-type (wt) gH/gL for fusion. We propose that gHΔ48/gL has an intermediate structure on the pathway leading to full regulatory activation. We suggest that a key step in the pathway of fusion is the conversion of gH/gL to an activated state by receptor-bound gD; this activated gH/gL resembles gHΔ48/gL. IMPORTANCE Herpes simplex viruses (HSVs) cause many human diseases, from mild cold sores to lethal neonatal herpes. As an enveloped virus, HSV must fuse its membrane with a host membrane in order for replication to take place. The virus uses four glycoproteins for this process, gD, gB, and gH/gL, and either of two cell receptors, herpesvirus entry mediator (HVEM) and nectin 1. Although the virus can enter the cell by direct fusion at the plasma membrane or via endocytosis, the same four glycoproteins are involved. The absence of any of these proteins abolishes the entry process. Here, we show that a mutant form of gH/gL, gHΔ48/gL, can induce fusion of gB-expressing cells in the absence of gD and a gD receptor. Our study supports the concept that gB is the HSV fusogen and its activity is regulated by gH/gL.
New Insights into Calorie Restriction Induced Bone Loss (2023)

Caloric restriction (CR) is now a popular lifestyle choice due to its ability in experimental animals to improve lifespan, reduce body weight, and lessen oxidative stress. However, more and more emerging evidence suggests this treatment requires careful consideration because of its detrimental effects on the skeletal system. Experimental and clinical studies show that CR can suppress bone growth and raise the risk of fracture, but the specific mechanisms are poorly understood. Reduced mechanical loading has long been thought to be the primary cause of weight loss-induced bone loss from calorie restriction. Despite fat loss in peripheral depots with calorie restriction, bone marrow adipose tissue (BMAT) increases, and this may play a significant role in this pathological process. Here, we update recent advances in our understanding of the effects of CR on the skeleton, the possible pathogenic role of BMAT in CR-induced bone loss, and some strategies to mitigate any potential side effects on the skeletal system.
Suppression of the commensurate charge density wave phase in ultrathin 1T−TaS2 evidenced by Raman hyperspectral analysis (2019)

Using temperature-dependent and low-frequency Raman spectroscopy, we address the question of how the transition from bulk to a few atomic layers affects the charge density wave (CDW) phases in $1T\text{\ensuremath{-}}\mathrm{Ta}{\mathrm{S}}_{2}$. We find that for crystals with thickness larger than $\ensuremath{\approx}10$ nm the transition temperatures between the different phases as well as the hysteresis that occurs in the thermal cycle correspond to the ones expected for a bulk sample. However, when the crystals become thinner than $\ensuremath{\approx}10$ nm, the low-temperature commensurate CDW phases can be suppressed down to the experimentally accessible temperatures ($\ensuremath{\sim}80$ K) upon cooling at moderate rates $(\ensuremath{\sim}5\phantom{\rule{0.16em}{0ex}}\mathrm{K}\phantom{\rule{0.16em}{0ex}}\mathrm{mi}{\mathrm{n}}^{\ensuremath{-}1})$. In addition, even the near commensurate CDW phase is not accessible in few-layer flakes below $\ensuremath{\approx}4$ nm for even slower cooling rates $(\ensuremath{\sim}1\phantom{\rule{0.16em}{0ex}}\mathrm{K}\phantom{\rule{0.16em}{0ex}}\mathrm{mi}{\mathrm{n}}^{\ensuremath{-}1})$. We employ Raman hyperspectral imaging to statistically confirm these findings and consider the interlayer coupling and its dynamics to play significant roles in determining the properties of CDW systems consisting of a few unit cells in the vertical direction.
A GRAPHICAL EXPLORATION OF THE GENERAL PERFORMANCE INDICES FOR BENDING STIFFNESS DESIGN (2011)

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The Hydrogenation of Ethane on Cobalt Catalysts (1939)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Hydrogenation of Ethane on Cobalt CatalystsEllison Hall. Taylor and Hugh S. TaylorCite this: J. Am. Chem. Soc. 1939, 61, 2, 503–509Publication Date (Print):February 1, 1939Publication History Published online1 May 2002Published inissue 1 February 1939https://pubs.acs.org/doi/10.1021/ja01871a080https://doi.org/10.1021/ja01871a080research-articleACS PublicationsRequest reuse permissionsArticle Views167Altmetric-Citations16LEARN 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
Early-Learning Regularization Prevents Memorization of Noisy Labels (2020)

We propose a novel framework to perform classification via deep learning in the presence of noisy annotations. When trained on noisy labels, deep neural networks have been observed to first fit the training data with clean labels during an "early learning" phase, before eventually memorizing the examples with false labels. We prove that early learning and memorization are fundamental phenomena in high-dimensional classification tasks, even in simple linear models, and give a theoretical explanation in this setting. Motivated by these findings, we develop a new technique for noisy classification tasks, which exploits the progress of the early learning phase. In contrast with existing approaches, which use the model output during early learning to detect the examples with clean labels, and either ignore or attempt to correct the false labels, we take a different route and instead capitalize on early learning via regularization. There are two key elements to our approach. First, we leverage semi-supervised learning techniques to produce target probabilities based on the model outputs. Second, we design a regularization term that steers the model towards these targets, implicitly preventing memorization of the false labels. The resulting framework is shown to provide robustness to noisy annotations on several standard benchmarks and real-world datasets, where it achieves results comparable to the state of the art.
Improvement of Steady State Performance of Voltage Control in Switched Reluctance Generator: Experimental Validation (2022)

This paper presents a voltage control approach to a Switched Reluctance Generator (SRG) using a Proportional Integral (PI) controller. The principle of operation is described and the considerations in the design of controller are discussed. A current loop transfer function of an SRG with power converter has been systematically derived in order to obtain a small-signal model for the generator. The generated voltage is controlled by manipulation of the setpoint of the current control of the generator. The entire voltage loop controller and current control have been simulated and tested with a 250 W SRG prototype. The control law of the control system was implemented on a digital signal processor (TMS320F28379D). To verify the feasibility of the proposed voltage control, the performances are evaluated by numerical simulations and experimental tests with an 8/6 SRG for different rotational speeds and resistive loads. Experimental results demonstrate that the DC output voltage from SRG can be controlled well using a simple linear controller.
GPI0363 inhibits the interaction of RNA polymerase with DNA inStaphylococcus aureus (2019)

We previously reported a therapeutically effective spiro-heterocyclic compound, GPI0363, that inhibits the transcription of <i>Staphylococcus aureus via</i> the primary sigma factor of RNA polymerase, SigA. Here, we demonstrated that GPI0363 shares no cross-resistance with the clinically used RNA polymerase inhibitors rifampicin and fidaxomicin. Furthermore, we found that GPI0363 bound to SigA of both GPI0363-susceptible and resistant strains, and inhibited the interaction of the RNA polymerase holoenzyme with DNA. In addition, the gene expression patterns following GPI0363 treatment were different from those following rifampicin treatment. These findings suggest that GPI0363 has a unique mechanism of action and can serve as a promising lead molecule to develop staphylococcal RNA polymerase inhibitors.
Prevention and treatment of enterohemorrhagicEscherichia coliinfections in humans (2008)

Infections with enterohemorrhagic Escherichia coli (EHEC) result in various clinical symptoms and outcomes ranging from watery or bloody diarrhea to the life-threatening hemolytic-uremic syndrome (HUS). Shiga toxins (Stxs) are supposed to play a major role in the pathogenesis of EHEC infections; however, the role of other putative virulence factors is not fully elucidated. So far, there is only supportive therapy available for the treatment of both EHEC-associated diarrhea and HUS. Antibiotic therapy for the treatment of EHEC-associated diarrhea is discussed. In recent years other therapeutic strategies have been developed, including Gb3 receptor analogues, that bind Stx in the gut or in the circulation, passive immunization with Stx-neutralizing monoclonal antibodies, or active immunization with Stx1 And Stx2 toxoids as a preventive procedure. These approaches have been demonstrated to be effective in animal models but clinical trials are lacking.
СНИЖЕНИЕ КОНЦЕНТРАЦИИ ФОСФАТА В СРЕДЕ КЛЕТКАМИ BREVIBACTERIUM CASEI (2007)

Представители рода Brevibacterium, эффективно снижающие концентрацию фосфата в среде, представляют интерес для изучения роли бактерий в круговороте фосфора и для разработки биотехнологических процессов очистки стоков от техногенного фосфорного загрязнения. Показано, что в процессе роста Brevibacterium casei, Brevibacterium linens и Brevibacterium epidermidis концентрация фосфата в среде снижается на 90%  для сред с начальной концентрацией этого компонента 111 мМ. Для клеток B. casei определен состав инкубационной среды, который достаточен для осуществления этого процесса. Процесс происходит в отсутствие глюкозы, однако требует присутствия ионов Mg2+, и -кетоглутарата. Последние два компонента можно заменить аминокислотами, катаболизм которых приводит к образованию и -кетоглутарата: гистидином, аргинином, глутамином, пролином или глутаминовой кислотой. Инкубация в указанных условиях с термически обработанными клетками или выдерживание среды без клеток при рН 78.5 не приводит к образованию нерастворимых солей фосфата.
Racism has no place on our streets (2015)

Two thousand people rallied in Federation Square on April 4 to oppose Reclaim Australia freely spreading racism and fascism on the streets of Melbourne.
Accessing Unsymmetrically Linked Heterocycles through Stereoselective Palladium‐Catalyzed Domino Cyclization (2021)

A palladium-catalyzed strategy is presented to synthesize unsymmetrically linked heterocycles within stereoselective tetrasubstituted olefins. This reaction is proposed to occur via a vinyl-Pd<sup>II</sup> intermediate capable of initiating the cyclization of various alkyne-tethered nucleophiles. Products are formed in up to 96 % yield and excellent stereoselectivities are obtained using low catalyst loadings. This transformation was scalable up to 1 mmol and mechanistic studies suggest a syn-carbopalladation of the carbamoyl chloride followed by Pd<sup>II</sup> -catalyzed cyclization of alkyne-tethered nucleophiles.
Neural Origins of the P300 (2000)

A review of the literature investigating the neural origins of detection behavior in humans reveals two event-related potential components, P3a and P3b, each with a distinct neural organization and cognitive function.The P3a is involved in automatic novelty detection and characterized by a more anterior cortical distribution, whereas the P3b is concerned with volitional target detection and has a more posterior cortical distribution. Intracranial investigation, studies with patients with focal brain lesions, and functional neuroimaging (fMRI) studies converge with scalp-recorded event-related potential (ERP) data in suggesting that a widespread cortical network gives rise to both automatic and controlled detection behavior. The main regions consistently attributed to generating detection-related brain activation include the temporal-parietal junction, medial temporal complex, and the lateral prefrontal cortex. The extant human and animal literature addressing the neural networks, neuropharmacological underpinnings, and behavioral significance of the P300 potential will be reviewed.
Conceptual Design of a Proton Therapy Synchrotron for Loma Linda University Medical Center (1986)

This document is the report of a conceptual design study of a proton synchrotron for medical therapy. The study has been sponsored by the Loma Linda University Medical Center and carried out by a group at the Fermi National Accelerator Laboratory. This report discusses the conceptual design of a synchrotron and of the associated treatment facilities. The goal of a conceptual design study is to uncover and solve design problems and to demonstrate the feasibility of a complete design. The design presented here meets these goals. We present solutions to the design problems of the accelerator and show that it is feasible to meet the performance specifications given in the table above. No claim is made that the design is optimized; it is an example and further work is needed before construction begins. A great deal of attention has been paid in the design to safety, flexibility, and reliability, because the facility discussed here is a clinical facility suitable for treatment of large numbers of patients, with large numbers of treatment rooms, not a research facility to treat small numbers of patients with beams limited in energy or adaptability. We consider this accelerator equivalent to the Harvard Cyclotron Laboratory, but with many more treatment facilities, more advanced beam control, and the availability of different energies to treat different depths in tissue.
Solid-Phase Synthesis of Carbocyclic Nucleosides (2000)

[formula: see text] An efficient solid-phase synthesis of carbocyclic nucleosides has been developed. The key step is the palladium-catalyzed coupling of a purine derivative to a resin-bound allylic benzoate. The resulting products may be further functionalized on the solid phase. Acidic cleavage affords carbocyclic nucleosides, a class of compounds with demonstrated biological activity and substantial current interest.
Decentralized routing controller design for networks with more than two overlapping subnetworks (2002)

A decentralized dynamic routing controller design strategy is proposed for large-scale traffic networks. The strategy is based on the overlapping decompositions method and can be used for large-scale networks which have more than two overlapping subnetworks and/or have more than one node in the overlapping part. The controller obtained by the proposed approach is decentralized in the sense that all online computations can be done locally at the individual nodes without any information transfer from the other nodes. The controller satisfies all the routing control constraints and it avoids any looping. The controller also clears the queues in finite time in the absence of external arrivals and it keeps the queue lengths bounded in the presence of external arrival rates which do not exceed a certain maximum rate.
A telecommunications framework for real-time monitoring of dangerous goods transport (2009)

Monitoring and tracking of fleets can represent a great improvement in security and safety when transporting hazardous goods by road. In this paper we propose a complete monitoring and tracking solution for truck fleets, which is able to check at the same time the position and the mechanical status of the vehicle, as well as the conditions in the cargo bay. The system exploits battery-powered environmental sensors (temperature, humidity, pressure, gas concentration and ionising radiation levels), connected by a ZigBee-based Wireless Sensor Network. This approach guarantees flexibility, ease of deployment and low power consumption. Collected data is then sent from the vehicle to a remote server via a GPRS link. The GPS positioning system is integrated by the use of an Inertial Navigation System, which guarantees a precise estimate of the position also when the GPS signal is weak or temporarily lost. The proposed solution has been deployed in a real environment, and some performance evaluation tests have been carried out.
Study and Development of a Fluorescence Based Sensor System for Monitoring Oxygen in Wine Production: The WOW Project (2018)

The importance of oxygen in the winemaking process is widely known, as it affects the chemical aspects and therefore the organoleptic characteristics of the final product. Hence, it is evident the usefulness of a continuous and real-time measurements of the levels of oxygen in the various stages of the winemaking process, both for monitoring and for control. The WOW project has focused on the design and the development an innovative device for monitoring the oxygen levels in wine. This system is based on the use of an optical fiber to measure the luminescent lifetime variation of a reference metal/porphyrin complex, which decays in presence of oxygen. The developed technology results in a high sensitivity and low cost sensor head that can be employed for measuring the dissolved oxygen levels at several points inside a wine fermentation or aging tank. This system can be complemented with dynamic modeling techniques to provide predictive behavior of the nutrient evolution in space and time given few sampled measuring points for both process monitoring and control purposes. The experimental validation of the technology has been first performed in a controlled laboratory setup to attain calibration and study sensitivity with respect to different photo-luminescent compounds and alcoholic or non-alcoholic solutions, and then in an actual case study during a measurement campaign at a renown Italian winery.