gebhart/patrepeval huggingface dataset:
Combined sentinel lymphadenectomy and Mohs micrographic surgery for high-risk cutaneous squamous cell carcinoma (2000)

The combination of Mohs micrographic surgery and sentinel lymphadenectomy is feasible and has theoretical utility in the management of a subset of cutaneous SCCs at high risk for metastasis. The ability of sentinel lymphadenectomy to identify regionally metastatic cutaneous SCC as well as the additive benefit of SLN and Mohs micrographic extirpation in the treatment of high-risk cutaneous SCC remain to be further clarified.
Mutagenesis as a Tool in Plant Genetics, Functional Genomics, and Breeding (2011)

Plant mutagenesis is rapidly coming of age in the aftermath of recent developments in high-resolution molecular and biochemical techniques. By combining the high variation of mutagenised populations with novel screening methods, traits that are almost impossible to identify by conventional breeding are now being developed and characterised at the molecular level. This paper provides a comprehensive overview of the various techniques and workflows available to researchers today in the field of molecular breeding, and how these tools complement the ones already used in traditional breeding. Both genetic (Targeting Induced Local Lesions in Genomes; TILLING) and phenotypic screens are evaluated. Finally, different ways of bridging the gap between genotype and phenotype are discussed.
Kinetic and inhibition studies for the aerobic cometabolism of 1,1,1‐trichloroethane, 1,1‐dichloroethylene, and 1,1‐dichloroethane by a butane‐grown mixed culture (2002)

Batch kinetic and inhibition studies were performed for the aerobic cometabolism of 1,1,1-trichloroethane (1,1,1-TCA), 1,1-dichloroethylene (1,1-DCE), and 1,1-dichloroethane (1,1-DCA) by a butane-grown mixed culture. These chlorinated aliphatic hydrocarbons (CAHs) are often found together as cocontaminants in groundwater. The maximum degradation rates (k(max)) and half-saturation coefficients (K(s)) were determined in single compound kinetic tests. The highest k(max) was obtained for butane (2.6 micromol/mg TSS/h) followed by 1,1-DCE (1.3 micromol/mg TSS/h), 1,1-DCA (0.49 micromol/mg TSS/h), and 1,1,1-TCA (0.19 micromol/mg TSS/h), while the order of K(s) from the highest to lowest was 1,1-DCA (19 microM), butane (19 microM), 1,1,1-TCA (12 microM) and 1,1-DCE (1.5 microM). The inhibition types were determined using direct linear plots, while inhibition coefficients (K(ic) and K(iu)) were estimated by nonlinear least squares regression (NLSR) fits to the kinetic model of the identified inhibition type. Two different inhibition types were observed among the compounds. Competitive inhibition among CAHs was indicated from direct linear plots, and the CAHs also competitively inhibited butane utilization. 1,1-DCE was a stronger inhibitor than the other CAHs. Mixed inhibition of 1,1,1-TCA, 1,1-DCA, and 1,1-DCE transformations by butane was observed. Thus, both competitive and mixed inhibitions are important in cometabolism of CAHs by this butane culture. For competitive inhibition between CAHs, the ratio of the K(s) values was a reasonable indicator of competitive inhibition observed. Butane was a strong inhibitor of CAH transformation, having a much lower inhibition coefficient than the K(s) value of butane, while the CAHs were weak inhibitors of butane utilization. Model simulations of reactor systems where both the growth substrate and the CAHs are present indicate that reactor performance is significantly affected by inhibition type and inhibition coefficients. Thus, determining inhibition type and measuring inhibition coefficients is important in designing CAH treatment systems.
The effects of sertraline on psychopathic traits (2011)

We examined whether antidepressants alter expression of psychopathic personality traits in patients with major depressive disorder (MDD). Data were collected from a double-blind, placebo-controlled 8-week trial evaluating the efficacy of sertraline (50-200 mg/day) combined with either tri-iodothyronine (T3) or matching placebo in adult outpatients with major depressive disorder. Administration of sertraline was open-label; T3/placebo was double-blind. At the baseline and week 8 visits, patients completed the short form of the Psychopathic Personality Inventory (PPI), a well-validated self-report measure assessing two major factors of psychopathy: Fearless Dominance (PPI-1) and Self-Centered Impulsivity (PPI-2). Change in PPI scores were assessed using paired t-tests for all participants who completed a baseline and postrandomization PPI. Ninety patients (84 completers and six who terminated the trial early) were eligible for the analysis. Both PPI factors changed significantly from baseline to endpoint, but in opposing directions. The mean score on PPI-1 increased significantly during treatment; this change was weakly correlated with change in depression scores. In contrast, the mean score on PPI-2 decreased significantly, but these changes were not correlated with changes in depression scores. Independent of their effects on depression, antidepressants increase adaptive traits traditionally observed in psychopathic individuals, such as social charm and interpersonal and physical boldness. Antidepressants reduce other, more maladaptive, traits associated with psychopathy, including dysregulated impulsivity and externalization.
Development of a Novel Sensorless Longitudinal Road Gradient Estimation Method Based on Vehicle CAN Bus Data (2007)

The availability of road gradient information will have a big impact upon the quality of vehicle control. This paper presents a novel "sensorless" longitudinal road-gradient estimation method, which was developed in two steps starting from a benchmark system design. The gradient benchmark system consists of an inclinometer sensor and an acceleration-based error correction algorithm, which can be used to verify the accuracy of the road gradient obtained using a sensorless estimation method. The sensorless road-gradient estimation algorithm uses the vehicle data currently available on the vehicle controller area network (CAN) bus. The completed gradient estimation algorithm was successfully tested online in variable road conditions and different driving manners. The test results showed that the resulting longitudinal road-gradient estimation algorithm fulfilled the specified accuracy requirement, and provided a cost effective and reliable way for longitudinal road-gradient estimation in real time.
Derivative-free active-RC elliptic filter using cascade of biquads in 28 nm CMOS (2015)

A highly linear, 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> order, active-RC low-pass elliptic filter with Variable Gain Amplifier (VGA) is presented. The new derivative-free biquad topology for an elliptic filter could be easily extended to a higher order filter using a cascade of biquads and it will have a zero capacitive spread when used along with a VGA. It is introduced to minimize the power consumption of an active-RC filter in a radio receiver. The combination of a filter+VGA provides a ripple of just 0.4 dB through 35 MHz pass-band and sharply attenuates out of band carriers by placing a zero at 50 MHz. A Filter+VGA together achieves an IIP3 of 29.91 dBm and integrated input referred noise of 44.96 μVrms consuming 54 mW. The proposed architecture is simulated using 28 nm CMOS technology and verified through extensive spectre simulations.
ChemInform Abstract: Diastereoselective Alkylation of 3‐Aminobutanoic Aicd in the 2‐Position. (1989)

Abstract The enantiomerically pure aminobutanoic acids (IVa) and (IVb) are available starting from the compounds (I) and (II) as shown in the scheme and converted to the derivatives (V).
Sound alters visual evoked potentials in humans (2001)

When a single flash is accompanied by two auditory beeps, the single flash is perceived as two flashes. We investigated whether this crossmodal influence on visual perception occurs at the level of the modality-specific visual pathway or later. We compared the visual evoked potentials (VEPs) in the presence and absence of sound. Activity was modulated extensively and with short latency in trials in which an illusory flash was perceived. In addition, the brain potentials for the illusory flash were qualitatively very similar to those for a physical flash, suggesting that the same mechanism underlies the percept of both illusory and physical flashes. These results suggest that the activity in the visual cortex can be modulated by sound. This implication challenges the general belief that the visual cortical processing is independent of other modalities.
Comparative Evaluation of MS-based Metabolomics Software and Its Application to Preclinical Alzheimer’s Disease (2018)

Mass spectrometry-based metabolomics has undergone significant progresses in the past decade, with a variety of software packages being developed for data analysis. However, systematic comparison of different metabolomics software tools has rarely been conducted. In this study, several representative software packages were comparatively evaluated throughout the entire pipeline of metabolomics data analysis, including data processing, statistical analysis, feature selection, metabolite identification, pathway analysis, and classification model construction. LC-MS-based metabolomics was applied to preclinical Alzheimer's disease (AD) using a small cohort of human cerebrospinal fluid (CSF) samples (N = 30). All three software packages, XCMS Online, SIEVE, and Compound Discoverer, provided consistent and reproducible data processing results. A hybrid method combining statistical test and support vector machine feature selection was employed to screen key metabolites, achieving a complementary selection of candidate biomarkers from three software packages. Machine learning classification using candidate biomarkers generated highly accurate and predictive models to classify patients into preclinical AD or control category. Overall, our study demonstrated a systematic evaluation of different MS-based metabolomics software packages for the entire data analysis pipeline which was applied to the candidate biomarker discovery of preclinical AD.
Microbial community composition and function in wastewater treatment plants (2002)

Biological wastewater treatment has been applied for more than a century to ameliorate anthropogenic damage to the environment. But only during the last decade the use of molecular tools allowed to accurately determine the composition, and dynamics of activated sludge and biofilm microbial communities. Novel, in many cases yet not cultured bacteria were identified to be responsible for filamentous bulking and foaming as well as phosphorus and nitrogen removal in these systems. Now, methods are developed to infer the in situ physiology of these bacteria. Here we provide an overview of what is currently known about the identity and physiology of some of the microbial key players in activated sludge and biofilm systems.
Long‐range steric effects on rotational barriers in peptide chains (1975)

2 17 kcal/mole"; the quantity in line 7 should read "2.5 kcal/mole."
Northern Squawfish ( PtychocheHus Oregonensis ) for Surimi Production (1995)

ABSTRACT Surimi was made from freshwater Northern squawfish ( Ptychocheilus oregonensis ) and tested for processing characteristics and quality. The surimi yield (two washes) averaged 17.9% with moisture 72.10% and protein content 17.54%. Stress and strain results indicated that it was feasible to produce surimi from squawfish stored in ice for up to 9 days. Fish freshness affected initial surimi gel strength and color and had variable effects on loss of gel strength during frozen storage.
Generation of MeV X-rays with 3-mJ, picosecond laser pulses (2023)

We demonstrate High-Energy X-ray (HEX-ray) generation using 2.8-mJ, 850fs pulses on a liquid metal target in a Laser Plasma X-ray Source (LPXS). The measured HEX-ray spectra reach into the MeV spectral range. The spectra follow Boltzmann energy distributions with a maximum HEX-ray “temperature” of 420 keV. The low laser intensity requirement, orders of magnitude less than previously reported, enables operation with widely available picosecond, millijoule laser systems with hundreds of Watt average laser power. Based on lasers with Yb-doped active media, HEX-ray sources driven with kilowatt average laser power are achievable in the very near future.
Building soft real-time monitors based on software reuse (2002)

This paper proposes an integration framework to develop real-time monitor programs based on software reuse. A custom-made real-time monitor program can be quickly built by integrating existing monitor programs in commercial operating systems, where limited real-time system and programming support is provided. We consider issues related to the software control, output re-processing, data age, and interactivities of program executions. The feasibility of this framework is demonstrated by the construction of an integration environment and a soft real-time monitor program consisting of the existing monitor programs PView NT Task Manager, NT Performance Monitor and NT File System Monitor in the Microsoft Windows operating systems. Our experimental results show that the incurred system overheads of this approach are very limited.
An Illustrative Recovery Approach for Stateful Interaction Failure of Orchestrated Processes (2012)

During a stateful interaction, a partner service may become unavailable because of a server crash or a temporary network failure. Once the failed service becomes available again, the interaction partners do not have any knowledge about each other's state, possibly resulting in errors or deadlocks. This paper proposes an approach to the recovery of stateful interactions based on service interaction patterns and process transformations. Our recovery approach works without a central management node and without additional communication protocols. We also minimize the changes to the description of the service supported by the recovery-enabled process. Our approach allows one partner process to be modified in order to support failures in a way that interaction with the other (unchanged) processes is still possible.
Age-associated changes in human CD4+ T cells point to mitochondrial dysfunction consequent to impaired autophagy (2019)

To gain understanding on the mechanisms that drive immunosenescence in humans, we examined CD4<sup>+</sup> T cells obtained from younger (20-39 years-old) and older (70+ years-old) healthy participants of the Baltimore Longitudinal Study on Aging (BLSA). We found that mitochondrial proteins involved in the electron transport chain were overrepresented in cells from older participants, with prevalent dysregulation of oxidative phosphorylation and energy metabolism molecular pathways. Surprisingly, gene transcripts coding for mitochondrial proteins pertaining to oxidative phosphorylation and electron transport chain pathways were underrepresented in older individuals. Paralleling the observed decrease in gene expression, mitochondrial respiration was impaired in CD4<sup>+</sup> T cells from older subjects. Though mitochondrial number in both naïve and memory cells visualized with electron microcopy was similar in older versus younger participants, there were a significantly higher number of autophagosomes, many of them containing undegraded mitochondria, in older individuals. The presence of mitochondria inside the accumulated autophagic compartments in CD4<sup>+</sup> T cells from older individuals was confirmed by immunofluorescence. These findings suggest that older age is associated with persistence of dysfunctional mitochondria in CD4<sup>+</sup> T lymphocytes caused by defective mitochondrial turnover by autophagy, which may trigger chronic inflammation and contribute to the impairment of immune defense in older persons.
Chemical Biology of Leucine-Rich Repeat Kinase 2 (LRRK2) Inhibitors (2015)

There is an urgent need for the development of Parkinson's disease (PD) treatments that can slow disease progression. The leucine-rich repeat kinase 2 (LRRK2) protein has been genetically and functionally linked to PD, and modulation of LRRK2 enzymatic activity has been proposed as a novel therapeutic strategy. In this review, we describe the bioactivity of selected small molecules that have been used to inhibit LRRK2 kinase activity in vitro or in vivo. These compounds are important tools for understanding the cellular biology of LRRK2 and for evaluating the potential of LRRK2 inhibitors as disease-modifying PD therapies.
PGE1 inhibited daunorubicin-induced apoptosis of human leukemia cell line, U937. (1998)

Daunorubicin (DNR), one of the chemotherapeutic agents for the treatment of leukemia, is known to induce apoptotic cell death of leukemia cells. Apoptosis of leukemia cells in vivo accompanies phagocytic response by macrophages, which is now known to produce various mediators including PGE2. In the present study, we studied the effect of PGE1, a PGE2 analog, on the DNR-induced apoptosis of human leukemia cell line, U937.PGE1 itself had no effect on the cell cycle of U937, but it inhibited DNR-induced apoptosis in a dose dependent manner. This inhibitory effect was mimicked by a membrane-permeable cAMP analog, db-cAMP, and forskolin. Furthermore, pretreatment of U937 cells with H-89, a protein kinase A inhibitor, reversed the inhibiting effect of PGE1. When co-cultured with LPS-activated peripheral blood monocytes, DNR-treated U937 cells showed less apoptosis, which was augmented by inhibiting endogenous production of PGE2 from LPS-activated monocytes when they are cultured with indomethacin. Therefore, it suggested that PGE1 inhibited DNR-induced apoptosis through activated cAMP, PKA signaling pathway. These results clearly show that PGE1 inhibition of DNR-induced apoptosis of U937 is mediated by cAMP/PKA signaling pathway and that endogenous production of PGE2 by macrophages, which eliminate apoptotic cells by phagocytosis in vivo, attenuates DNR-induced apoptosis of U937 cells. The present study suggests that administration of cyclooxygenase inhibitor, such as indomethacin, enhances chemotherapeutic effect of DNR-induced apoptosis of leukemia cells.
Intraocular Cannula for Continuous, Chronic Drug Delivery (1985)

An indwelling cannula for drug delivery was implanted in rabbit eyes. Rabbits were followed up for as long as 1 1/2 years after surgery. They showed almost no adverse effects as a result of the implantation, and cannula patency was demonstrated by the injection of fluorescein sodium through the cannula at various times following surgery. Histopathologic studies using light and electron microscopy were performed at various times to determine the effect of cannula implantation on the eye. Cellular proliferation along the cannula after 1 1/2 years was limited to the region immediately adjacent to the wound and rarely extended to the surrounding retina or ciliary body. The proliferative tissue at the wound site originated mainly from the episclera; the retina and the choroid at the posterior fundus remained intact. Photoreceptor cell metabolism was studied by light microscopic autoradiography following intraocular injection of tritiated leucine to assess photoreceptor outer-segment renewal. Autoradiography showed normal receptor uptake of leucine. A broad band of radioactive labeling of the outer segments resulted from continuous, chronic drug delivery, while a narrow band of labeling resulted from a single intravitreous injection. These data indicate that the cannula system continuously delivered tritiated leucine into the vitreous cavity. We believe that the implanted intraocular cannula, which allows continuous drug delivery on a relatively long-term basis, will be a valuable technique for research and possibly clinical studies.
Role of water hyacinth-mediated phytoremediation in waste water purification at east Calcutta wetland (2008)

Abstract This research note is an attempt to understand the role of water hyacinth vis-à-vis metal removal mechanism operating in “Bheris” – the shallow flat bottom waste water fed fisheries, which are unique ecosystems found in West Bengal, India. This study approaches the question by analysing the extent of heavy metal accumulation in water bodies of varied origin and geographic location in and around east Calcutta wetland as well as in different parts of water hyacinth obtained from these locations. Wastewater fed fish ponds are found to have lesser metal accumulation compared to rainwater ponds. This may be partly due to strong bioremediation operating in the wastewater ponds as a result of the existing microbes as well as plankton community. The phenomenon of heavy metal accumulation at a site thus depends on the soil condition, ground water level and the biotic population inhabiting that site.
Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome (2023)

Spaceflight presents a multifaceted environment for plants, combining the effects on growth of many stressors and factors including altered gravity, the influence of experiment hardware, and increased radiation exposure. To help understand the plant response to this complex suite of factors this study compared transcriptomic analysis of 15 Arabidopsis thaliana spaceflight experiments deposited in the National Aeronautics and Space Administration's GeneLab data repository. These data were reanalyzed for genes showing significant differential expression in spaceflight versus ground controls using a single common computational pipeline for either the microarray or the RNA-seq datasets. Such a standardized approach to analysis should greatly increase the robustness of comparisons made between datasets. This analysis was coupled with extensive cross-referencing to a curated matrix of metadata associated with these experiments. Our study reveals that factors such as analysis type (i.e., microarray versus RNA-seq) or environmental and hardware conditions have important confounding effects on comparisons seeking to define plant reactions to spaceflight. The metadata matrix allows selection of studies with high similarity scores, i.e., that share multiple elements of experimental design, such as plant age or flight hardware. Comparisons between these studies then helps reduce the complexity in drawing conclusions arising from comparisons made between experiments with very different designs.
Packaged hybrid integrated phased-array multi-wavelengthlaser (2000)

A hybrid integration technology has been developed which only involves the use of InP components. A six-channel multi-wavelength laser has been realised using this approach. The chips were bonded using a UV-curable epoxy and packaged in a commercial laser module. A 1.6 GHz 3 dB bandwidth and a linewidth of &lt; 1 MHz were measured.
Synthesis of Fluoroalkylated β-Aminophosphonates and Pyridines from Primary β-Enaminophosphonates (2008)

A simple and efficient stereoselective synthesis of fluorine containing beta-aminophosphonates by reduction of beta-enaminophosphonates is described. Reduction with sodium cyanborohydride in the presence of zinc chloride and the catalytic hydrogenation of beta-enaminophosphonates gives beta-aminophosphonates. beta-Enaminophosphonates are also used as intermediates for the regioselective synthesis of fluoroalkyl-substituted pyridines.
Battery Performance of ADEOS (Advanced Earth Observing Satellite) and Ground Simulation Test Results (1997)

The Advanced Earth Observing Satellite (ADEOS) is developed with the aim of establishment of platform technology for future spacecraft and inter-orbit communication technology for the transmission of earth observation data. ADEOS uses 5 batteries, consists of two packs. This paper describes, using graphs and tables, the ground simulation tests and results that are carried to determine the performance of the ADEOS batteries.