gebhart/patrepeval huggingface dataset:
Markov decision process (MDP) framework for optimizing software on mobile phones (2009)

We present a framework based on Markov decision process to optimize software on mobile phones. Unlike previous approaches in literature that focus on energy optimization while meeting a specific task-related time constraint, we model the desired talk-time as an explicit user given parameter and formulate the optimization of resources such as battery-life on a mobile phone as a decision processes that maximizes a user specified application specific reward or utility metric while meeting the talk-time constraint. We propose efficient techniques to solve the optimization problem based on dynamic programming and illustrate how it can be used in the context of realistic applications such as WiFi radio power optimization and email synchronization. We present a design methodology to use the proposed technique and experimental results using the Android platform from Google running on the HTC mobile phone.
Long‐term treatment with Sitagliptin, a dipeptidyl peptidase‐4 inhibitor, reduces colon carcinogenesis and reactive oxygen species in 1,2‐dimethylhydrazine‐induced rats (2013)

Type 2 diabetes mellitus (T2DM) and insulin resistance (IR) increase colon cancer risk. Antidiabetic drugs stabilizing incretin hormones, such as inhibitors of dipeptidyl peptidase‐4 activity (DPP4i), may affect colon carcinogenesis; however, the data remain controversial. Therefore, the authors studied whether long‐term administration of the DPP4i Sitagliptin (SITA) affects 1,2‐dimethylhydrazine (DMH)‐induced colon carcinogenesis. Male F344 rats fed a high‐fat (HF) diet promoting colon carcinogenesis and IR, were induced with DMH (100 mg/kg × 2 times). One week later, the animals were allocated to two groups: one continuing with HF diet (controls; n = 8) and one receiving SITA ( n = 8) mixed in the diet (260 ppm). Body weight, food consumption and glycemia were not affected by SITA. Fifteen weeks after DMH, the number of the precancerous lesions mucin‐depleted foci (MDF) was significantly lower in rats treated with SITA [MDF/colon: 9.5 ± 0.9 and 6.4 ± 0.9 in controls ( n = 8) and SITA groups ( n = 8), respectively; means ± SE, p < 0.05]. Reactive oxygen species in the blood were also significantly lower in the SITA group [6.75 ± 0.69 and 5.63 ± 0.75 (H 2 O 2 in mM) in controls ( n = 5) and SITA ( n = 6), respectively; means ± SE, p < 0.05]. Rats treated with SITA had a lower DPP4 activity in the intestine but not in the plasma. Intestine growth morphometric parameters and colon proliferation, as proliferating cell nuclear antigen expression, were not affected by SITA. In conclusion, the results suggest a protective effect of DPP4i against colon carcinogenesis that could be exploited in chemoprevention trials.
DTM: Deformable template matching (2016)

A novel template matching algorithm that can incorporate the concept of deformable parts, is presented in this paper. Unlike the deformable part model (DPM) employed in object recognition, the proposed template-matching approach called Deformable Template Matching (DTM) does not require a training step. Instead, deformation is achieved by a set of predefined basic rules (e.g. the left sub-patch cannot pass across the right patch). Experimental evaluation of this new method using the PASCAL VOC 07 dataset demonstrated substantial performance improvement over conventional template matching algorithms. Additionally, to confirm the applicability of DTM, the concept is applied to the generation of a rotation-invariant SIFT descriptor. Experimental evaluation employing deformable matching of SIFT features shows an increased number of matching features compared to a conventional SIFT matching.
Application of flow cytometry to rapid microbial analysis in food and drinks industries (1993)

In food and drinks industries, the time required for conventional tests can lead to substantial delays in product release to the market. Flow cytometry (FCM) has been used in conjunction with viability markers for rapid counting of yeast, mould and bacterial cells in food products. A single-parameter flow cytometer has proved applicable to the rapid detection of low numbers of microbial contaminants in finished products. The excellent correlation between FCM results and product quality shelf-life expiry date has allowed the establishment of realistic quality control criteria for rapid positive release of product. Used for the monitoring of microbial biomass during manufacturing processes, flow cytometry allowed a direct assessment of bacterial growth. The reproducibility of the results and the proven correlation with standard plate count method obtained in industrial conditions make FCM a good predictive method for product and process quality control.
Solar Water Oxidation by Composite Catalyst/α-Fe<sub>2</sub>O<sub>3</sub> Photoanodes (2009)

Electrodeposition of an amorphous cobalt catalyst layer over a high-surface-area alpha-Fe(2)O(3) photoanode causes a more than 350 mV cathodic shift in the onset potential for photoelectrochemical water oxidation using this anode and simulated solar irradiation. The catalyst layer is shown to deposit conformally onto the mesostructured alpha-Fe(2)O(3), leading to a large contact area at the interface between the two halves of the composite photoanode. Photoelectrochemical measurements show that the photocurrent generated from this composite photoanode still derives from alpha-Fe(2)O(3) excitation but is now accessible at an external bias several hundred millivolts below what is typically required for alpha-Fe(2)O(3) photoanodes alone, indicating a reduced external bias would be needed to drive overall water splitting. These results demonstrate modification of this prototypical photoanode material with a conformal layer of a competent electrocatalyst to separate the tasks of photon absorption and redox catalysis, a strategy that may have important and general ramifications for solar photoelectrochemical hydrogen generation.
Complete Genome Sequence of a Staphylococcus epidermidis Strain with Exceptional Antimicrobial Activity (2017)

<i>Staphylococcus epidermidis</i> is a Gram-positive bacterium that is prevalent on human skin. The species is associated with skin health, as well as with opportunistic infections. Here, we report the complete genome sequence of <i>S. epidermidis</i> 14.1.R1, isolated from human skin. In bacterial interference assays, the strain showed exceptional antimicrobial activity.
Approaches and Challenges of Engineering Implantable Microelectromechanical Systems (MEMS) Drug Delivery Systems for in Vitro and in Vivo Applications (2012)

Despite the advancements made in drug delivery systems over the years, many challenges remain in drug delivery systems for treating chronic diseases at the personalized medicine level. The current urgent need is to develop novel strategies for targeted therapy of chronic diseases. Due to their unique properties, microelectromechanical systems (MEMS) technology has been recently engineered as implantable drug delivery systems for disease therapy. This review examines the challenges faced in implementing implantable MEMS drug delivery systems in vivo and the solutions available to overcome these challenges.
BRENDA in 2015: exciting developments in its 25th year of existence (2014)

The BRENDA enzyme information system (http://www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools. The information is obtained by manual extraction from primary literature, text and data mining, data integration, and prediction algorithms. Approximately 300 million data include enzyme function and molecular data from more than 30,000 organisms. The manually derived core contains 3 million data from 77,000 enzymes annotated from 135,000 literature references. Each entry is connected to the literature reference and the source organism. They are complemented by information on occurrence, enzyme/disease relationships from text mining, sequences and 3D structures from other databases, and predicted enzyme location and genome annotation. Functional and structural data of more than 190,000 enzyme ligands are stored in BRENDA. New features improving the functionality and analysis tools were implemented. The human anatomy atlas CAVEman is linked to the BRENDA Tissue Ontology terms providing a connection between anatomical and functional enzyme data. Word Maps for enzymes obtained from PubMed abstracts highlight application and scientific relevance of enzymes. The EnzymeDetector genome annotation tool and the reaction database BKM-react including reactions from BRENDA, KEGG and MetaCyc were improved. The website was redesigned providing new query options.
Optimal breast cancer diagnostic strategy using combined ultrasound and diffuse optical tomography (2020)

Ultrasound (US)-guided near-infrared diffuse optical tomography (DOT) has demonstrated great potential as an adjunct breast cancer diagnosis tool to US imaging alone, especially in reducing unnecessary benign biopsies. However, DOT data processing and image reconstruction speeds remain slow compared to the real-time speed of US. Real-time or near real-time diagnosis with DOT is an important step toward the clinical translation of US-guided DOT. Here, to address this important need, we present a two-stage diagnostic strategy that is both computationally efficient and accurate. In the first stage, benign lesions are identified in near real-time by use of a random forest classifier acting on the DOT measurements and the radiologists' US diagnostic scores. Any lesions that cannot be reliably classified by the random forest classifier will be passed on to the second stage which begins with image reconstruction. Functional information from the reconstructed hemoglobin concentrations is employed by a Support Vector Machine (SVM) classifier for diagnosis at the end of the second stage. This two-step classification approach which combines both perturbation data and functional features, results in improved classification, as denoted by the receiver operating characteristic (ROC) curve. Using this two-step approach, the area under the ROC curve (AUC) is 0.937 ± 0.009, with a sensitivity of 91.4% and specificity of 85.7%. In comparison, using functional features and US score yields an AUC of 0.892 ± 0.027, with a sensitivity of 90.2% and specificity of 74.5%. Most notably, the specificity is increased by more than 10% due to the implementation of the random forest classifier.
Clinical photography in dermatology using smartphones: An overview (2015)

The smartphone is one of the biggest revolutions in the era of information technology. Its built in camera offers several advantages. Dermatologists, who handle a specialty that is inherently visual, are most benefited by this handy technology. Here in this article, we attempt to provide an overview of smartphone photography in clinical dermatology in order to help the dermatologist to get the best out of the available camera for clinical imaging and storage.
A Critique of Some Current Assembly Line Balancing Techniques (1987)

This paper briefly reviews the assembly line balancing techniques developed over the last 30 years. It attempts to establish the direction of research, to identify unexplored areas with potential for study and recommends future courses of action.
Oogenesis in <i>Xenopus laevis</i> (Daudin). I. Stages of oocyte development in laboratory maintained animals (1972)

Abstract Oogenesis in the anuran Xenopus laevis can be divided into six stages based on the anatomy of the developing oocyte. Stage I consists of small (50 to 100 μ) colorless oocytes whose cytoplasm is transparent. Their large nuclei and mitochondrial masses are clearly visible in the intact oocyte. Stage II oocytes range up to 450 μ in diameter, and appear white and opaque. Stage I and II are both previtellogenic. Pigment synthesis and yolk accumulation (vitellogenesis) begins during Stage III. Vitellogenesis continues through Stage IV (600 to 1000 μ), the oocytes grow rapidly, and the animal and vegetal hemispheres become differentiated. By Stage V (1000 to 1200 μ) the oocytes have nearly reached their maximum size and yolk accumulation gradually ceases. Stage VI oocytes are characterized by the appearance of an essentially unpigmented equatorial band. They range in size from 1200 to 1300 μ, are postivtellogenic and ready for ovulation. These stages of oocyte development have been correlated with physiological and biochemical data related to oogenesis in Xenopus .
Pharmacokinetics of cysteamine bitartrate following intraduodenal delivery (2012)

Cysteamine is approved for the treatment of cystinosis and is being evaluated for Huntington's disease and non-alcoholic fatty liver disease. Little is known about the bioavailability and biodistribution of the drug. The aim was to determine plasma, cerebrospinal fluid (CSF), and tissue (liver, kidney, muscle) cysteamine levels following intraduodenal delivery of the drug in rats pretreated and naïve to cysteamine and to estimate the hepatic first-pass effect on cysteamine. Healthy male rats (n = 66) underwent intraduodenal and portal (PV) or jugular (JVC) venous catheterization. Half were pretreated with cysteamine, and half were naïve. Following intraduodenal cysteamine (20 mg/kg), serial blood samples were collected from the PV or the JVC. Animals were sacrificed at specific time points, and CSF and tissue were collected. Cysteamine levels were determined in plasma, CSF, and tissue. The Cmax was achieved in 5-10 min from PV and 5-22.5 min from JVC. The PV-Cmax (P = 0.08), PV-AUC0-t (P = 0.16), JVC-Cmax (P = 0.02) and JVC-AUC0-t (P = 0.03) were higher in naive than in pretreated animals. Plasma cysteamine levels returned to baseline in ≤120 min. The hepatic first-pass effect was estimated at 40%. Peak tissue and CSF cysteamine levels occurred ≤22.5 min, but returned to baseline levels ≤180 min. There was no difference in CSF and tissue cysteamine levels between naïve and pretreated groups, although cysteamine was more rapidly cleared in the pretreated group. Cysteamine is rapidly absorbed from the small intestine, undergoes significant hepatic first-pass metabolism, crosses the blood brain barrier, and is almost undetectable in plasma, CSF, and body tissues 2 h after ingestion. Sustained-release cysteamine may provide prolonged tissue exposure.
The Complexities of Communicating Science (2002)

Scientists are always keen to explain their discoveries to the waiting world. But they don't always do it well, or with their critical faculties switched to 'on'.
Analysis of a 69-kb Contiguous Genomic Sequence at a Putative Tumor Suppressor Gene Locus on Human Chromosome 6q27 (1998)

Multiple neoplasias including B-cell non-Hodgkin's lymphoma, breast carcinoma, and ovarian carcinoma, have been associated with frequent deletions of the distal region on the long arm of human chromosome 6, suggesting the presence of one or more tumor suppressor gene(s) at this locus. Loss of heterozygosity analysis of breast and ovarian tumors has further restricted the minimal region of loss within 6q27. To further characterize this genomic region for gene content including putative tumor suppressor genes as well as other elements that may contribute to tumorigenesis, a 68940-bp contiguous sequence, encompassing markers D6S193 and D6S297, was generated by random shotgun sequencing of a cosmid, P1, and PAC contig. In addition, exon trapping was performed utilizing a subset of these clones. Sixteen trapped exons, ranging in size from 44 to 399 bp, span this approximately 69-kb region. Many other putative exons have been identified computationally. Further analysis has identified 13 potential promoters and 13 putative polyadenylation sites in the region. Northern analysis identified a transcript mapping within this interval that is expressed in ovarian, breast, and lymphoid-derived tumor cell lines. Consideration of these data, together with the demonstration of several regions of high CpG content, suggests the possibility of several genes at this locus.
Site-Selective Carbene-Induced C–H Functionalization Catalyzed by Dirhodium Tetrakis(triarylcyclopropanecarboxylate) Complexes (2017)

Three types of dirhodium tetrakis(triarylcyclopropanecarboxylate) complexes were generated and shown to adopt disparate high-symmetry structures. These catalysts were evaluated in the intermolecular C–H functionalization of an array of terminally substituted n-alkanes and displayed various site-selectivity as a function of catalyst and substrate structure, which could be correlated through quantitative relationships.
Efficient Crystallization-Induced Dynamic Resolution of α-Substituted Carboxylic Acids (2004)

Herein we present a novel route to enantiomerically enriched chiral alpha-substituted carboxylic acids by crystallization-induced dynamic resolution (CIDR) of their diastereomeric salts with chiral amines. Thus, the racemic alpha-bromo acid 3 is converted reliably with (1R,2S)-2-amino-1,2-diphenylethanol in the presence of a catalytic amount of tetrabutylammonium bromide into its R-enantiomer 4 in 90% yield with 88% ee. Similarly, the racemic alpha-thiobenzoyl acid 5 could be resolved to 90% ee in 74% yield. Further enrichment to enantiomeric homogeneity could be achieved in both cases by crystallization. In a telescoped, two-step process, S-alpha-thiobenzoyl acid 6 (>or=99.6% ee) was prepared from the racemic bromide 3 in 63% yield. State-of-the-art parallel experimentation enabled rapid screening for suitable dynamic resolution conditions. Kinetic studies defined the influence of temperature, tetrabutylammonium bromide concentration, molarity, and solvent polarity on the resolution rate, product yield, and enantiomeric excess.
Quantitative Analysis of Multiple Components in Wine Fermentation using Raman Spectroscopy (2015)

Glucose and ethanol are critical quality control components in the wine fermentation process. In this study, we present a novel method in which Fourier Transform (FT)-Raman spectroscopy and chemometric techniques are used to quantitatively analyze ethanolic beverages produced by fermentation. Chromium (VI) Oxide (CrO<sub>3</sub>) was flame-sealed into a fused silica cuvette and used as external standard. Band ratios between the Raman bands of the target molecule and that of CrO3 were calculated and found to be proportional to the concentration of ethanol and glucose. This method can eliminate factors such as laser power or instrumental effects. After pre-processing the spectra, Principal Component Analysis (PCA) and Partial Least Squares (PLS) were selected as the multivariate calibration models. The prediction models proved to be robust resulting in a desirable mapping between the spectra and output attributes. This method could predict the ethanol and glucose concentrations simultaneously and produced a more linear calibration curve. As a result, there is a great potential to use Raman spectroscopy in wine fermentation process and on line fermentation control.
The BCL-2–like protein CED-9 of <i>C. elegans</i> promotes FZO-1/Mfn1,2– and EAT-3/Opa1–dependent mitochondrial fusion (2009)

The mammalian dynamin-related guanosine triphosphatases Mfn1,2 and Opa1 are required for mitochondrial fusion. However, how their activities are controlled and coordinated is largely unknown. We present data that implicate the BCL-2-like protein CED-9 in the control of mitochondrial fusion in Caenorhabditis elegans. We demonstrate that CED-9 can promote complete mitochondrial fusion of both the outer and inner mitochondrial membrane. We also show that this fusion is dependent on the C. elegans Mfn1,2 homologue FZO-1 and the C. elegans Opa1 homologue EAT-3. Furthermore, we show that CED-9 physically interacts with FZO-1 in vivo and that the ability of CED-9 to interact with FZO-1 is important for its ability to cause mitochondrial fusion. CED-9-induced mitochondrial fusion is not required for the maintenance of mitochondrial morphology during embryogenesis or in muscle cells, at least under normal conditions and in the absence of stress. Therefore, we propose that the BCL-2-like CED-9 acts through FZO-1/Mfn1,2 and EAT-3/Opa1 to promote mitochondrial fusion in response to specific cellular signals.
Role of the CD40‐CD40 ligand interaction in CD4<sup>+</sup> T cell contact‐dependent activation of monocyte interleukin‐1 synthesis (1994)

Most studies of the induction of cytokine synthesis in monocytes have employed an exogenous triggering agent such as lipopolysaccharide. However, in nonseptic inflammatory responses (e.g. rheumatoid arthritis) monocyte activation occurs as a result of T cell-generated signals. In previous reports, we and others have demonstrated that contact-dependent T cell-generated signals are capable of contributing to macrophage activation. We have shown that plasma membranes from anti-CD3 activated purified peripheral CD4+ T cells (TmA) but not from resting CD4+ cells (TmR) induce monocytes to synthesize interleukin (IL)-1 in the absence of co-stimulatory cytokines. Studies to determine the expression kinetics of the molecule(s) unique to activated CD4+ T cells which interact with monocytes to induce IL-1 revealed that optimal expression occurred at 6 h post activation. This matched the previously reported kinetics of expression of CD40 ligand (CD40L) on activated peripheral T cells, implicating the CD40-CD40L interaction as a candidate for the initiator of the IL-1 signaling event. The ability of TmA to induce IL-1 synthesis in resting monocytes could be markedly reduced by addition of a monoclonal anti-CD40L antibody, 5c8. In addition, a monoclonal anti-CD40 IgM (BL-C4) proved dramatic in its ability to induce resting monocytes to synthesize IL-1. In summary, these results demonstrate that the CD40-CD40L interaction provides a critical component of CD4+ T cell contact-dependent activation of monocyte IL-1 synthesis.
Advantages of an antagonist: bicuculline and other<scp>GABA</scp>antagonists (2013)

The convulsant alkaloid bicuculline continues to be investigated more than 40 years after the first publication of its action as an antagonist of receptors for the inhibitory neurotransmitter GABA. This historical perspective highlights key aspects of the discovery of bicuculline as a GABA antagonist and the sustained interest in this and other GABA antagonists. The exciting advances in the molecular biology, pharmacology and physiology of GABA receptors provide a continuing stimulus for the discovery of new antagonists with increasing selectivity for the myriad of GABA receptor subclasses. Interesting GABA antagonists not structurally related to bicuculline include gabazine, salicylidene salicylhydrazide, RU5135 and 4-(3-biphenyl-5-(4-piperidyl)-3-isoxazole. Bicuculline became the benchmark antagonist for what became known as GABAA receptors, but not all ionotropic GABA receptors are susceptible to bicuculline. In addition, not all GABAA receptor antagonists are convulsants. Thus there are still surprises in store as the study of GABA receptors evolves.
[Action in vitro of disodium ethylenediaminetetraacetic acid (Na2EDTA) and antibiotics on resistant strains of staphylococcus aureus]. (1993)

The investigation of action of Na2EDTA and doxycycline on strains of staphylococci resistant to doxycycline was performed by two methods: serial dilutions of tested substances in the fluid and solid medium. MIC values for Na2EDTA, doxycycline and both substances together were determined. Both methods resulted in an observation that for majority of tested doxycycline-resistant strains, application of various concentrations of doxycycline together with Na2EDTA resulted in a change of sensitivity of bacteria to the antibiotic by lowering concentration needed for bacterial growth inhibition. It seems that in further studies laborious and time-consuming method of serial dilutions in the fluid medium, should be replaced by more convenient and easier to perform method of serial dilutions of drugs in solid agar medium.