gebhart/patrepeval huggingface dataset:
Antibiotic Therapy for Treatment-Naive Crohnʼs Disease Patients (2016)

Introduction: Anti-inflammatory and immunosuppressive agents have been standard therapy for Crohn's disease (CD). Due to an increasing interest in Mycobacterium avium subspecies paraturberculosis (MAP) as an infective agent in CD, more antibiotic therapy trials have been published. Such trials, including a multi-centre trial of rifabutin, clofazimine and clarithromycin (known as Anti-MAP) currently being conducted (NCT 01951326) have all enrolled participants who received standard CD therapy prior to Anti-MAP treatment. A single treatment-naiveCD patient at our centre was offered Anti-MAP as first line therapy. Rapid mucosal healing was observed while on antibiotics alone. Hence, a further seven treatment-naive patients were offered Anti-MAP as initial, stand-alone therapy. Methods: Anti-MAP treatment was commenced after colonoscopic diagnosis of CD. Final doses of rifabutin [4mg/kg], clofazimine [3.75mg/kg] and clarithromycin [14mg/kg] were achieved after dose escalation over 8-10 weeks. Five of the eight patients were also on ciprofloxacin [12mg/kg] and/or metronidazole [7.5mg/kg] and one patient on ethambutol [15mg/kg]. Patients were monitored by clinical, colonoscopic and blood results. Leucopenia and LFT elevation were avoided by dose escalation. A paired two tailed T-test was used to compare the effect of Anti-MAP on the CDAI scores pre and post-treatment in the eight patients. Results: Mean (x̄) CDAI score decreased significantly from 352.5(SEM 25.0) prior to treatment to 57.4(SEM 9.2, p < 0.001 (CI=95%)) in the eight patients (4 male; 4 female; 12-35 yrs). All patients achieved remission (CDAI < 150) between 4-21 weeks (Table 1). Follow-up colonoscopy showed healed ulcers and mucosa often replaced by fine white scars, disappearance of contact bleeding and histological deep mucosal healing.Table 1: Mean and Standard error of Mean (SEM) Indicators of Crohn's disease healingConclusion: One patient has ceased therapy and remains well. Two patients who had complete resolution of all CD related symptoms independently ceased Anti-MAP therapy, subsequently relapsed after two years then resumed low-dose maintenance treatment. Drug adverse effects were minimal. Clofazimine staining resembling a sun-tan, was seen in all patients. In conclusion, 1. Rapid CD remission with mucosal healing in all patients using antibiotics alone suggests CD is infection-dependent. 2. Results from this study suggest the need for a randomised controlled trial in CD to compare initial therapy with Anti-MAP antibiotics vs current standard-of-care.
Effects of methotrexate on transfected DNA stability in mammalian cells. (1990)

The chromosomal locations, amounts, and level of expression of transfected, amplified c-myc and dihydrofolate reductase sequences were measured in cells cultured in the presence and absence of methotrexate. These studies show that the location and amount of transfected sequences, as well as the level of expression, were more variable when the cells were cultured in methotrexate.
NFκB Signaling in Posthypoxic Endothelial Cells: Relevance to E-Selectin Expression and Neutrophil Adhesion (2001)

Our previous studies have implicated the nuclear transcription factor kappa B (NF kappa B) in the regulation of adhesion molecule expression in endothelial cells exposed to anoxia-reoxygenation (A/R) or a redox imbalance. The objectives of this study were (1) to define the kinetics of NF kappa B activation by examining I kappa B alpha degradation and the nuclear translocation of p65 in response to A/R or redox imbalance (induced by treatment of cells with diamide and buthionine sulfoximine) and (2) to determine whether the signal for I kappa B alpha degradation, nuclear translocation of p65, and E-selectin-mediated neutrophil adhesion is related to the activity of protein tyrosine kinase (PTK), protein tyrosine phosphatase (PTPase) and/or protein kinase C (PKC). The results demonstrate that both A/R and redox imbalance led to I kappa B alpha degradation within 30 min and the concomitant appearance of p65 in the nucleus, consistent with rapid cytosolic activation of NF kappa B and subsequent nuclear translocation of the activated p65 subunit. Inhibition of PKC blocked I kappa B alpha degradation and p65 translocation in A/R-challenged, but not redox-altered, endothelial cells. However, both A/R- and redox-induced NF kappa B activation was blocked by inhibition of PTK. Similarly, A/R-induced E-selectin expression and neutrophil-endothelial cell adhesion were blocked by inhibition of PKC or PTK, while only PTK inhibited the redox-induced adhesion response. Pretreatment of cells with N-acetyl cysteine effectively blocked A/R- or redox-induced I kappa B degradation and significantly attenuated the respective neutrophil adhesion responses. Collectively, these findings indicate that A/R-induced E-selectin expression and neutrophil-endothelial cell adhesion are mediated by both PKC and PTK, which signal rapid activation of NF kappa B. This A/R-induced NF kappa B signaling response appears to be mediated, at least in part, by intracellular redox imbalance.
Expanding the structural analysis capabilities on an Orbitrap-based mass spectrometer for large macromolecular complexes (2017)

Native mass spectrometry can provide insight into the structure of macromolecular biological systems. As analytes under investigation get larger and more complex, instrument capabilities need to be advanced. Herein, modifications to an Orbitrap Q Exactive Plus mass spectrometer that increase signal intensity, mass resolution, and maximum m/z measurable are described.
Search for the Standard Model Higgs boson produced in association with a vector boson and decaying to a b-quark pair with the ATLAS detector (2012)

This Letter presents the results of a direct search with the ATLAS detector at the LHC for a Standard Model Higgs boson of mass 110⩽m_H⩽130 GeV produced in association with a W or Z boson and decaying to bb. Three decay channels are considered: ZH → ℓ^+ℓ^- → bb, WH → ℓvbb and ZH → vvbb, where ℓ corresponds to an electron or a muon. No evidence for Higgs boson production is observed in a dataset of 7 TeV pp collisions corresponding to 4.7 fb^(−1) of integrated luminosity collected by ATLAS in 2011. Exclusion limits on Higgs boson production, at the 95% confidence level, of 2.5 to 5.5 times the Standard Model cross section are obtained in the mass range 110–130 GeV. The expected exclusion limits range between 2.5 and 4.9 for the same mass interval.
Structure and biosynthesis of the hydroxy fatty acids of cutin in Vicia faba leaves (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure and biosynthesis of the hydroxy fatty acids of cutin in Vicia faba leavesP. E. Kolattukudy and T. J. WaltonCite this: Biochemistry 1972, 11, 10, 1897–1907Publication Date (Print):May 9, 1972Publication History Published online1 May 2002Published inissue 9 May 1972https://pubs.acs.org/doi/10.1021/bi00760a026https://doi.org/10.1021/bi00760a026research-articleACS PublicationsRequest reuse permissionsArticle Views277Altmetric-Citations48LEARN 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
A Planarized Two-Dimensional Multi-Wavelength Routing Network with 1-to-many Cascaded Fanouts (1998)

Wavelength-division (de)multiplexer (WD(D)M) is a pivotal bandwidth enhancement component in optical fiber communications and optical sensor systems.
Efficient Multicast Schemes Using In-Network Caching for Optimal Content Delivery (2013)

Due to the increasing popularity of video streaming services over Internet, the traffic volume on the transit or the peering links continues to grow. Many recent research activities have addressed the locality of content delivery from network edge by introducing storage module into routers. With a persistent Request-Routing System that can redirect all the requests for the same content to a particular content router in order to consume a single multicast stream only during the prefix length of that content, this letter proposes the hybrid Content Delivery Network (CDN) system, which successfully combines novel content routers in underlay with existing CDN servers in overlay by employing prefix caching and multicast schemes respectively. Given the capacity of CDN server, we evaluate and compare the performance of two multicast schemes for the delivery cost minimization in terms of optimal prefix length with in-network caching in the proposed system.
Serum NT/CT SIRT1 ratio reflects early osteoarthritis and chondrosenescence (2020)

Increased levels of serum NT/CT SIRT1 ratio correlated with moderate OA in both mice and humans, stemming at least in part from non-senescent chondrocyte apoptosis, possibly a result of prolonged inflammatory insult.
Energy efficient computing by redox-based memristive oxide elements (2016)

Redox-Based Resistive Switching Memories (ReRAM), also called nanoionic memories or memristive elements, are widely considered to provide a potential leap beyond the limits of Flash (with respect to write speed, write energies) and DRAM (with respect to scalability, retention times) as well as energy-efficient approaches to neuromorphic concepts[1].
A Scalable Sensor Management Architecture Using BDI Model for Pervasive Surveillance (2014)

Recent world events have amplified the need for improved safety and security to contend with natural and man-made threats. The universality and unpredictability of such threats have stimulated intense interest in smart pervasive surveillance systems. They are built by adopting smart sensor networks that cover large areas and can perform self-contained assessments of situations in the environment. However, such systems rely on a massive number of sensors with diverse capabilities but limited resources, e.g., power, processing, and storage. Thus, successful management of tasks hinges on the systems architecture. Sensor management architectures (SMAs) coordinate the sensor nodes and their resources in a manner that improves system control and situation awareness. This paper introduces a scalable and flexible SMA for many sensor management (SM) applications, particularly, pervasive surveillance. This novel SMA is called the extended hybrid architecture for SM (E-HASM), an architecture that combines the advantages of the holonic, federated, and market-based paradigms. The E-HASM models each node as an intelligent sensor by using the beliefs, desires, and intentions model and defines the interaction and cooperation among the nodes. The simulation results illustrate the performance of the E-HASM over a variety of security threats, background targets, and network sizes. The results prove that the proposed architecture is significantly more scalable and flexible than centralized architectures.
Evaluation of the raw microprocessor: an exposed-wire-delay architecture for ILP and streams (2004)

This paper evaluates the Raw microprocessor. Raw addresses the challenge of building a general-purpose architecture that performs well on a larger class of stream and embedded computing applications than existing microprocessors, while still running existing ILP-based sequential programs with reasonable performance in the face of increasing wire delays. Raw approaches this challenge by implementing plenty of on-chip resources - including logic, wires, and pins - in a tiled arrangement, and exposing them through a new ISA, so that the software can take advantage of these resources for parallel applications. Raw supports both ILP and streams by routing operands between architecturally-exposed functional units over a point-to-point scalar operand network. This network offers low latency for scalar data transport. Raw manages the effect of wire delays by exposing the interconnect and using software to orchestrate both scalar and stream data transport. We have implemented a prototype Raw microprocessor in IBM's 180 nm, 6-layer copper, CMOS 7SF standard-cell ASIC process. We have also implemented ILP and stream compilers. Our evaluation attempts to determine the extent to which Raw succeeds in meeting its goal of serving as a more versatile, general-purpose processor. Central to achieving this goal is Raw's ability to exploit all forms of parallelism, including ILP, DLP, TLP, and Stream parallelism. Specifically, we evaluate the performance of Raw on a diverse set of codes including traditional sequential programs, streaming applications, server workloads and bit-level embedded computation. Our experimental methodology makes use of a cycle-accurate simulator validated against our real hardware. Compared to a 180nm Pentium-III, using commodity PC memory system components, Raw performs within a factor of 2/spl times/ for sequential applications with a very low degree of ILP, about 2/spl times/ to 9/spl times/ better for higher levels of ILP, and 10/spl times/-100/spl times/ better when highly parallel applications are coded in a stream language or optimized by hand. The paper also proposes a new versatility metric and uses it to discuss the generality of Raw.
Rapid prototyping for orthopaedic surgery (1998)

The revision of an orthopaedic procedure can present surgeons with the challenge of a complex reconstructive process. Orthopaedic surgery can also face considerable challenges in cases presenting extensive primary injuries with multiple bone fragmentation, as well as in cases presenting bone deformities. Radiographs are used routinely for orthopaedic surgical planning, yet they provide inadequate information on the precise three-dimensional extent of bone defects. Three-dimensional reconstructions from X-ray computed tomography offer superior visualization but are not portable for consultation or readily available in the operating theatre for guidance during a procedure. A physical model manufactured from X-ray computed tomography data can offer surgeons a clear understanding of complex anatomical detail, by providing an intuitive physical relationship between patient and model. Rapid prototyping was used for the construction of an anatomical model in a case presenting with a complex shoulder injury. The model provided a definitive interpretation of joint pathology and enabled a full assessment of the degree of injury.
Gravity Drainage of Activated Sludge on Reed Beds (2010)

Activated sludge is a by-product from waste water treatment plants, and the water content in the sludge is high (&gt; 90%). Among several methods to remove the water, sludge drying reed beds are often used to dewater the sludge by drainage. There is, however, no well-defined criterion for design and operation of reed beds and the efficiencies are often lower than predicted. One reason is that the sludge quality varies from plant to plant and even within plants from time to time. No good method exists for measuring the sludge quality with respect to drainage characteristics. A new experimental method has therefore been developed to measure relevant quality parameters: specific cake resistance, settling velocity and cake compressibility. It has been found that activated sludge form highly compressible cake even at the low compressive pressures obtained during drainage. Numerical simulation shows that the compressibility has a high influence on the drainage process especially during the start-up phases where the volumetric load on the sludge bed is critical. The load has to be low in order to ensure that the drainage properties of the bed are not destroyed. The data also shows that transport of activated sludge from the wastewater treatment plant to the red beds may destroy the sludge structure and thereby reduces the dewaterability of sludge. Both the mechanical stress during pumping and anaerobic microbial activity affects the sludge quality. The quality of the sludge can be improved if I) the drying reed beds are placed close to the wastewater treatment plant, II) anaerobic condition is avoid e.g. by adding calcium nitrate, and III) the sludge structure is rebuild before it is poured on the reed bed e.g. by adding calcium carbonate
VisualHints: A Visual-Lingual Environment for Multimodal Reinforcement Learning (2020)

We present VisualHints, a novel environment for multimodal reinforcement learning (RL) involving text-based interactions along with visual hints (obtained from the environment). Real-life problems often demand that agents interact with the environment using both natural language information and visual perception towards solving a goal. However, most traditional RL environments either solve pure vision-based tasks like Atari games or video-based robotic manipulation; or entirely use natural language as a mode of interaction, like Text-based games and dialog systems. In this work, we aim to bridge this gap and unify these two approaches in a single environment for multimodal RL. We introduce an extension of the TextWorld cooking environment with the addition of visual clues interspersed throughout the environment. The goal is to force an RL agent to use both text and visual features to predict natural language action commands for solving the final task of cooking a meal. We enable variations and difficulties in our environment to emulate various interactive real-world scenarios. We present a baseline multimodal agent for solving such problems using CNN-based feature extraction from visual hints and LSTMs for textual feature extraction. We believe that our proposed visual-lingual environment will facilitate novel problem settings for the RL community.
Dehydroepiandrosterone metabolism in fresh human prostate: A feasibility study. (2014)

225 Background: Understanding adrenal androgen metabolism in the prostate provides the opportunity to better define mechanisms of resistance for patients with prostate cancer. This is especially important with men who have a recurrence after their initial treatment (e.g., surgery or radiation) and are subsequently treated with androgen deprivation therapy by chemical or surgical castration. Unfortunately, these patients tend to progress to castrate resistant prostate cancer. With the contribution of adrenal androgens in mind, we sought to determine the feasibility of characterizing the metabolites of dehydroepiandrosterone (DHEA) in the human prostate. Methods: With institutional review board approval, tissue procurement occurred via the Department of Pathology at the Cleveland Clinic. We obtained prostate tissue from patients immediately after radical prostatectomy. The tissue was processed in culture withserum free medium in triplicate and was treated with tritiated-DHEA ([ 3 H]-DHEA; 100 nM, 300,000–600,000cpm; PerkinElmer). Media was collected at specific time intervals (6, 24, 48, and 72 hours). Once all the time points were collected, they were treated with a β-glucuronidase and steroids were extracted. These samples were processed and analyzed with high-performance liquid chromatography (HPLC) and a radioactivity detector for comparison with known standards (DHEA, androstenedione, 5α-androstanedione, testosterone, and dihydrotestosterone). Results: Evaluation of the HPLC tracings showed metabolism of [ 3 H]-DHEA to downstream androgen products and correlated with standard peaks. These tracings were reproducible and consistent with each sample’s triplicate and from specimen to specimen. Conclusions: It is feasible to consistently determine the products of DHEA metabolism in fresh prostate tissues. By obtaining a better understanding of how androgen metabolites are formed we can dissect how response and resistance to hormonal therapy are regulated.
Toward machine-guided design of proteins (2018)

Abstract Proteins—molecular machines that underpin all biological life—are of significant therapeutic and industrial value. Directed evolution is a high-throughput experimental approach for improving protein function, but has difficulty escaping local maxima in the fitness landscape. Here, we investigate how supervised learning in a closed loop with DNA synthesis and high-throughput screening can be used to improve protein design. Using the green fluorescent protein (GFP) as an illustrative example, we demonstrate the opportunities and challenges of generating training datasets conducive to selecting strongly generalizing models. With prospectively designed wet lab experiments, we then validate that these models can generalize to unseen regions of the fitness landscape, even when constrained to explore combinations of non-trivial mutations. Taken together, this suggests a hybrid optimization strategy for protein design in which a predictive model is used to explore difficult-to-access but promising regions of the fitness landscape that directed evolution can then exploit at scale.
An Experimental Study on the Blood Pressure Cuff as a Transducer for Oscillometric Blood Pressure Measurements (2020)

Noninvasive blood pressure (BP) measurements still rely on empirical interpretation of arterial oscillations recorded via cuff-based oscillometric methods. Extensive effort has dedicated to establishing a theoretical basis for oscillometry, aiming at more accurate BP estimations and measurement of additional hemodynamic parameters. However, oscillometry is still a heuristic method for BP inference. Goal: This study is focused on improving our understanding of the expression of arm volume pulsations in oscillometric signals. The aim is to identify the main factors that determine the transfer function of arm volume to cuff pressure oscillations for existing cuff devices-this being an essential step in establishing a theoretical basis for oscillometry. Methods: The effects of air compression within the cuff and the influence of viscoelastic cuff material properties on the transfer function are studied by an experimental setup. Mechanical numerical modeling is used to interpret the results. Results: Air compression is found to be of adiabatic nature in the frequency range of interest. The cuff material exhibits viscous characteristics which is the cause of cuff response dependence on inflation speed, tightness of wrapping, time passed since previous measurement, and heart rate. Conclusion: It was found that typical cuffs used in clinical practice exhibit complex behavior. Cuff hardware needs to be improved to enable practical translation of pressure to arm volume oscillations. The presented characterization method contributes to standardized development of new cuff prototypes and to identification of designs, techniques, and materials with improved properties for enabling BP measurement accuracy and extraction of additional hemodynamic information.