gebhart/patrepeval huggingface dataset:
Mutations of Bacterial RNA Polymerase Leading to Resistance to Microcin J25 (2002)

A mutation in the conserved segment of the rpoC gene, which codes for the largest RNA polymerase (RNAP) subunit, beta', was found to make Escherichia coli cells resistant to microcin J25 (MccJ25), a bactericidal 21-amino acid peptide active against Gram-negative bacteria (Delgado, M. A., Rintoul, M. R., Farias, R. N., and Salomon, R. A. (2001) J. Bacteriol. 183, 4543-4550). Here, we report that mutant RNAP prepared from MccJ25-resistant cells, but not the wild-type RNAP, is resistant to MccJ25 in vitro, thus establishing that RNAP is a true cellular target of MccJ25. We also report the isolation of additional rpoC mutations that lead to MccJ25 resistance in vivo and in vitro. The new mutations affect beta' amino acids in evolutionarily conserved segments G, G', and F and are exposed into the RNAP secondary channel, a narrow opening that connects the enzyme surface with the catalytic center. We also report that previously known rpoB (RNAP beta subunit) mutations that lead to streptolydigin resistance cause resistance to MccJ25. We hypothesize that MccJ25 inhibits transcription by binding in RNAP secondary channel and blocking substrate access to the catalytic center.
Finding what's not there (2007)

Neglected conditions are an important but difficult-to-find class of software defects. This paper presents a novel approach to revealing neglected conditions that integrates static program analysis and advanced data mining techniques to discover implicit conditional rules in a code base and to discover rule violations that indicate neglected conditions. The approach requires the user to indicate minimal constraints on the context of the rules to be sought, rather than specific rule templates. To permit this generality, rules are modeled as graph minors of program dependence graphs, and both frequent itemset mining and frequent subgraph mining algorithms are employed to identify candidate rules. We report the results of an empirical evaluation of the approach in which it was used to discover conditional rules and neglected conditions in ~25,000 lines of source code.
The Multidimensional Prognostic Index (MPI), Based on a Comprehensive Geriatric Assessment Predicts Short- and Long-Term Mortality in Hospitalized Older Patients with Dementia (2009)

Aim of this study was to evaluate the usefulness of a Multidimensional Prognostic Index (MPI) based on a Comprehensive Geriatric Assessment (CGA) for predicting mortality risk in older patients with dementia. The present was a retrospective study with a year of follow-up that included 262 patients aged 65 years and older with a diagnosis of dementia. A standardized CGA that included information on clinical, cognitive, functional, and nutritional aspects, as well as comorbidity, medications, and social support network, was used to calculate MPI. The predictive value of the MPI for all-cause mortality over 1 month, 6 months, and 12 months of follow-up was evaluated. Higher MPI values were significantly associated with higher mortality at 1 month (MPI-1, low risk = 0%, MPI-2, moderate risk = 5.2%, MPI-3, severe risk = 13.7%; p < 0.002), 6-months (MPI-1 = 2.7%, MPI-2 = 11.2%, MPI-3 = 28.8%; p < 0.001), and 12-months (MPI-1 = 2.7%, MPI-2 = 18.2%, MPI-3 = 35.6%; p < 0.001) of follow-up. The discrimination of the MPI was also good, with areas under the ROC curves of 0.77 (sensitivity = 82.9%, specificity = 66.0%, with a cut off value > 0.16) at 12-months of follow up. In conclusion, the MPI, calculated from information collected in a standardized CGA, accurately stratified hospitalized elderly patients with dementia into groups at varying risk of short- and long-term mortality.
Effect of Targeted Agents on the Endocrine Response of Breast Cancer in the Neoadjuvant Setting: A Systematic Review (2015)

Inhibition of aberrantly activated pathways cross-talking with hormone receptor (HR) improves response to endocrine therapy in patients with HR-positive advanced breast cancer. We performed a Pubmed database systematic review to ascertain the existence of a better clinical response when combining endocrine therapy with targeted agents in the neoadjuvant setting. Preclinical studies or trials evaluating toxicity were excluded. We found nine phase II trials that fulfilled the research criteria. The endocrine agents used were third generation aromatase inhibitors (AIs), anastrozole, letrozole or exemestane. The investigated targeted agents were inhibitors of tyrosine kinase receptors such as gefitinib, imatinib or trastuzumab/lapatinib, inhibitors of mTOR, such as everolimus, inhibitors of COX-2, such as celecoxib, and inhibitors of angiogenesis, such as bevacizumab. The response rate (RR) observed combining endocrine and targeted agents ranged between 36% and 90%. Overall the studies failed to show a remarkable advantage in RR in the combination group compared to historical control subjects receiving AIs alone.
The first aggregation-induced emission fluorophore as a solution processed host material in hybrid white organic light-emitting diodes (2016)

The<bold>CzPATPE</bold>AIE fluorophore for a solution processed host material in hybrid white OLEDs.
Abstract 16941: Questioning the efficacy of Proliferation Signal Inhibitors for established Coronary Artery Disease after Heart Transplant (2014)

Purpose: Cardiac Allograft Vasculopathy (CAV) is one of the major factors limiting long term survival after heart transplantat (HTx). The use of proliferation signal inhibitors (PSIs) such as everolimus and sirolimus has been found to be effective in the prevention of CAV in multicenter studies. There has been 1 study (Mancini et al) that has suggested the use of Sirolimus can decrease the progression of CAV in patients (Pts) long term after Htx. It is not been evaluated in the current era of Tacrolimus (TAC)/Mycophenolate Mofetil (MMF) whether a switch from MMF to PSIs has such an advantage. Methods: Between 1998 and 2010, we evaluated 26 HTx Pts who had developed CAV according to the new ISHLT CAV nomenclature (CAV1, CAV2, CAV3) and were subsequently switched from TAC/MMF to TAC/PSIs. Pts who were maintained on TAC/MMF were served as 1:1 controls. Outcomes for these Pts included worsening of CAV by category at 3 year, subsequent 3-year survival and subsequent 3-year freedom from non-fatal major adverse cardiac events (NF-MACE: Myocardial Infarction, Congestive Heart Failure, angioplasty, pacemaker/ICD and stroke). Results: There were 26 patients in the switched to PSIs group and 23 patients in the maintained on MMF group. All patients were either CAV 1 or CAV 2 at baseline. The average time to switch to PSIs was 5.3 ± 3.3 years. At 3 year follow up, the percentage of patients who had worsened CAV by category were comparable among the two groups. Subsequent 3-year survival and 3-year freedom from NF-MACE were also comparable among the two groups (see Table). Conclusions: In the current era of TAC/MMF, switch from MMF to PSI for patients with established CAV does not appear to be beneficial in preventing progression of disease. A larger number of patients are needed to confirm this finding.
TU-D-224C-01: Effects of Choice of the MLC Material On Neutron Dose Equivalent Outside of the Treatment Field in Proton Therapy (2006)

Purpose: To determine the effects of choice of MLC material on neutron dose equivalent outside of the treatment field in proton therapy.Method and Materials: A four‐dimensional GEANT4 Monte Carlo simulation of a commercially available proton therapy nozzle has been used to calculate the ratio of neutron dose equivalent to therapeuticproton absorbed dose (HN/DP). HN/DP varies significantly with proton beam energy, materials used in the nozzle, treatment technique, and range modulation. Technical specifications of the nozzle have been provided by the vendor. Lateral beam spreading is achieved primarily by binary pre‐scatterer foils and a double contoured scatterer. Modulation is generated by a stepped propeller positioned at nozzle entrance, and pre‐collimation is done by nickel inserts. A preliminary design of a multi‐leaf collimator has been added to the simulation, providing final collimation. Four different data sets have been generated, each one corresponding to a different MLC composition: tungsten, brass, iron and stainless steel. Results: A 200 MeV proton beam is used in order to produce a large circular treatment field with a 10 cm radius, a depth of penetration of approximately 22 cm, and an SOBP width of 10 cm. Neutron dose equivalents are calculated outside the treatment field at three distances from isocenter: 15 cm, 25 cm, and 47 cm (along beam direction). The highest HN/DP ratios are calculated for tungsten, and vary from 10 mSv/Gy at a distance of 15 cm off axis, to 0.7 mSv/Gy at 47.5cm off axis. Corresponding HN/DP ratios for stainless steel are 6.93 mSv/Gy and 0.46 mSv/Gy, representing the lowest calculated values. Conclusion: A steel MLC produces, on average, 45% less secondary neutron dose deposit compared to a tungstenMLC. The result indicates potential for dose reduction in proton therapy when a steel collimator is used instead of a tungstencollimator.
A Phase II Study of Fornix Deep Brain Stimulation in Mild Alzheimer’s Disease (2016)

DBS for AD was safe and associated with increased cerebral glucose metabolism. There were no differences in cognitive outcomes for participants as a whole, but participants aged≥65 years may have derived benefit while there was possible worsening in patients below age 65 years with stimulation.
Nondestructive Performance Characterization Techniques for Module Reliability (2003)

This paper describes nondestructive characterization techniques for module reliability. These techniques include light and dark current versus voltage and related analysis such as resistance, diode quality factor, and dark current. The use of the NREL laser scanner at zero volts and forward bias is also described as a technique to uncover cracks, shunts, and open-circuit regions in a module. Quantum-efficiency measurements of isolated cells or regions in a module are also possible. The interpretation of laser-scanning data is enhanced by hot-spot testing with an infrared camera or thermographic paper. Specialized nondestructive techniques have also been developed to determine the shunt resistance of individual cells in a module by selective shading of cells under sunlight. Ultraviolet fluorescence and reflectivity measurements at NREL have proven useful in evaluating encapsulant stability.
Detecting Suspected Pump Thrombosis in Left Ventricular Assist Devices via Acoustic Analysis (2020)

We showed that the acoustical signatures of LVADs can be an index of mechanical deterioration and, when combined with machine learning algorithms, provide clinical decision support regarding the presence of pump thrombosis.
Nanoscopic Pd Line Arrays Using Nanocontact Printed Dendrimers (2006)

High-density Pd line arrays with 55 nm line-width were obtained using nanocontact-printed dendrimer monolayers. Elastomeric PDMS stamps for nanocontact printing were replicated from silicon master molds which were fabricated by UV nanoimprinting in combination with reactive ion etching. The fabrication method effectively controlled the aspect ratios of high-density lines for resolving the problems encountered in both replicating silicon masters to PDMS stamps and printing with the replicated PDMS stamps. Using the PDMS nanostamp with an optimized aspect ratio, a self-assembled monolayer of dendrimer was patterned on a Pd film via nanocontact printing, which was facilitated by the strong interaction between Pd and amine groups of the dendrimer. The patterned self-assembled monolayer was used as an etch-resist mask against the wet etchant of Pd, leaving behind a high-density Pd line array over large areas. The resulting functional Pd nanopattern is of practical significance in microelectronics and bio- or gas-sensing devices.
Mechanically Tunable Three-Dimensional Elastomeric Network/Air Structures via Interference Lithography (2006)

We show how to employ an interference lithographic template (ILT) as a facile mold for fabricating three-dimensional bicontinuous PDMS (poly(dimethylsiloxane)) elastomeric structures and demonstrate the use of such a structure as a mechanically tunable PDMS/air phononic crystal. A positive photoresist was used to make the ILT, and after infiltration with PDMS, the resist was removed in a water-based basic solution which avoided PDMS swelling or pattern collapse occurring during the ILT removal process. Since the period of the structure is approximately 1 microm, the density of states of gigahertz phonons are altered by the phononic PDMS/air crystal. Brillouin light scattering (BLS) was employed to measure phononic modes of the structure as a function of mechanical strain. The results demonstrate that the phononic band diagram of such structures can be tuned mechanically.
Synchronous and metachronous liver metastases in patients with colorectal cancer. (2018)

not relevant.
Epstein‐barr virus infection of rat lymphocytes expressing human CD21 results in restricted latent viral gene expression and not in immunoblastic transformation (2003)

Transgenic rats expressing human CD21 gene (hCD21) driven by the mouse immunoglobulin enhancer were generated. hCD21 was expressed in lymphoid tissues, especially in the spleen and in the brain. Flow cytometric analysis indicated that about 20% of spleen cells, most having a B-lymphocyte marker, expressed hCD21. After Epstein-Barr virus (EBV) infection of spleen cells, EBV-determined nuclear antigen (EBNA) was first detected on Day 4 and reached a maximum of 0.3% on Day 5, but the infection was abortive and was not followed by blastogenesis, cellular DNA synthesis or proliferation. Reverse transcription-polymerase chain reaction (RT-PCR) analyses demonstrated that EBV-infected spleen cells expressed EBNA1 and EBV-encoded small RNA (EBER), but not other latent EBV products. EBNA promoter analysis by RT-PCR indicated that the Q promoter was active, whereas C and W promoters were not active. The present findings indicate that human and rat lymphocytes respond to EBV infection differently in vitro.
TRIAXIAL APPARATUS FOR THE STUDY OF THE THERMAL BEHAVIOR OF UNSATURATED SOILS (1990)

The thermal consolidation of unsaturated soils in a thermo-hydro-mechanical framework is studied in a thermal triaxial apparatus described in the paper. The results of the first tests performed, under a given state of stress, on both silty and clayey soils, show some similarities between purely thermal consolidation and mechanical consolidation on saturated soils.
Iron (III)‐catalyzed one‐pot synthesis of fused 4H‐pyran derivatives via Knoevenagel‐Michael‐cyclization reaction (2021)

Abstract A facile and efficient protocol has been developed for the synthesis of fused 4 H ‐pyran derivatives via one‐pot three components combination of aldehydes, 1,1‐ bis (methylthio)‐2‐nitroethylene (BMTNE), and enolketone/dimedone derivatives under the catalysis of FeCl 3 . The target products could be obtained in moderate to good yields.
Prediction of protein secondary structure by the hidden Markov model (1993)

The purpose of this paper is to introduce a new method for analyzing the amino acid sequences of proteins using the hidden Markov model (HMM), which is a type of stochastic model. Secondary structures such as helix, sheet and turn are learned by HMMs, and these HMMs are applied to new sequences whose structures are unknown. The output probabilities from the HMMs are used to predict the secondary structures of the sequences. The authors tested this prediction system on approximately 100 sequences from a public database (Brookhaven PDB). Although the implementation is 'without grammar' (no rule for the appearance patterns of secondary structure) the result was reasonable.
ChemInform Abstract: A Large Accelerating Effect of Tri(tert‐butyl)phosphine in the Rhodium‐Catalyzed Addition of Arylboronic Acids to Aldehydes. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Feature Engineering for Mid-Price Prediction With Deep Learning (2019)

Mid-price movement prediction based on the limit order book data is a challenging task due to the complexity and dynamics of the limit order book. So far, there have been very limited attempts for extracting relevant features based on the limit order book data. In this paper, we address this problem by designing a new set of handcrafted features and performing an extensive experimental evaluation on both liquid and illiquid stocks. More specifically, we present an extensive set of econometric features that capture the statistical properties of the underlying securities for the task of mid-price prediction. The experimental evaluation consists of a head-to-head comparison with other handcrafted features from the literature and with features extracted from a long short-term memory autoencoder by means of a fully automated process. Moreover, we develop a new experimental protocol for online learning that treats the task above as a multi-objective optimization problem and predicts: 1) the direction of the next price movement and; 2) the number of order book events that occur until the change takes place. In order to predict the mid-price movement, features are fed into nine different deep learning models based on multi-layer perceptrons, convolutional neural networks, and long short-term memory neural networks. The performance of the proposed method is then evaluated on liquid and illiquid stocks (i.e., TotalView-ITCH US and Nordic stocks). For some stocks, results suggest that the correct choice of a feature set and a model can lead to the successful prediction of how long it takes to have a stock price movement.
Assessment of durability for RC structures by corrosion monitoring (2000)

The durability of reinforced concrete structures exposed to aggressive environment is studied in order to find reasons for unexpected premature deterioration. The corrosion of reinforcement is considered to be one of the most frequent causes of such premature degradation. In this approach for calculating residual life in concrete reinforcement subjected to corrosive action, the loss in the rebar cross-section is taken to be of high significance for the corrosion rate determination. The rebar corrosion rate is defined by the loss of rebar per unit of surface in time. The remaining bearing capacity and safety of structures can be estimated by means of corrosion rate monitoring and using assumptions that the corrosion is uniform and that the loss in diameter is proportional to the corrosion rate. There are several methods for measuring the true, instantaneous rate of corrosion in accordance with electrochemical principles (linear polarization resistance). This paper describes measuring techniques based on the use of the Gecor 6 measuring device, the application of these techniques, their advantages and disadvantages, and the interpretation of our own measurement results as well as those cited in the literature.
The reorganization of time, space, and relationships in school with the use of active learning methodologies and collaborative tools (2014)

Information and communication technologies (ICTs) in our current networked society are a continuing and irreversible process. Therefore, consideration must be given to the construction of a new education and science model that takes into account complementary dimensions of content, form, and relationships between teachers and students. The aim of this study was to evaluate the impact of Design Thinking, PBL methodology and the use ICTs in school routine of the students from the graduate program in Ethics, Values, and Citizenship in School (EVC). The program was conducted in a blended learning format in which three collaboration technologies were experimentally used (BrainMergeâ¢, TERF and Fishbowlâ¢). At the end, we applied a survey to evaluate the use and impact of these technologies. From the 239 participants (second EVC) 96.8% affirmed that the EVC contributed to their learning routine. The first EVC, 142 participants indicated a similar response distribution, 94.4%. These results may indicate that EVC has a transformative impact on participants: while they prototype, they can see better approaches to solve school problems, they are changing their classes turning them into more interactive activities. The basic and higher education are not untouched by the socio-political economic transformations that the world has undergone. Education needs to re-invent to continue the prominent role that societies have granted it over the past 300 years. Paradoxically, this re-invention depends as much on its capacity for continuation as on its capacity for transformation, to adapt to the new demands of society, culture, and science.
Industrial Application and Processes Forming CO Bonds (2012)

This chapter contains sections titled: Processes Using Lipases Processes Using Glycosyltransferases, Glycosidases, and CarbonOxygen Lyases References
Handbook of Lipid Bilayers, Second Edition (1990)

INTRODUCTION Lipid Classification Nomenclature of Lipids Fatty Acids PHOSPHOLIPIDS Phospholipid Classification and Molecular Weights Fatty Acid Composition of Naturally Occurring Phospholipids and of Membrane Lipids from the Yeast Lipidome Physicochemical Properties of Phospholipids Phospholipid pKas Crystal Structures of Phospholipids Phase Behavior and Hydration Calorimetric Data X-Ray Diffraction Data Densitometric Data Elastic Constants Dynamic Properties Phase Transition Temperatures Phase Diagrams: Binary and Ternary Mixtures Non-Lamellar Phases (Hexagonal and Cubic) Critical Micelle Concentrations and Lipid Transfer Bilayer-Bilayer Interactions Ion-Binding Constants GLYCOLIPIDS Glycolipid Classification and Molecular Weights Fatty Acid Composition of Naturally Occurring Glycolipids Physicochemical Properties of Glycolipids Glycolipid pKas Crystal Structures Phase Behavior and Hydration Calorimetric Data X-Ray Diffraction Data Densitometric Data Elastic Constants Dynamic Properties Phase Transition Temperatures Phase Diagrams: Binary Mixtures Non-Lamellar Phases (Hexagonal and Cubic) Critical Micelle Concentrations and Lipid Transfer Bilayer-Bilayer Interactions Ion-Binding Constants.