gebhart/patrepeval huggingface dataset:
Cocoonase (1973)

Abstract Prococoonases and cocoonases from three species of silkmoths (Antheraea pernyi, Antheraea polyphemus, and Antheraea mylitta) have been purified and compared to each other and to vertebrate trypsins by tryptic peptide mapping, amino acid and carbohydrate composition, and partial amino acid sequence. Comparison of tryptic peptide maps of two cocoonases with bovine trypsin shows 50% coincidence of peptides. The prococoonases from A. pernyi and A. polyphemus are glycoproteins containing 6 moles of mannose and 2 moles of glucosamine. Proteolytic activation of prococoonase to cocoonase does not involve a loss of any of this carbohydrate. Prococoonase from A. mylitta contains no carbohydrate. Sequence analyses of the NH2 and COOH termini of several cocoonases and A. mylitta prococoonase and the entire active site tryptic peptide from A. polyphemus cocoonase reveals 70% identity with bovine trypsin. The partial structure of A. polyphemus cocoonase is [see PDF for sequence] The active site serine is indicated by the box.
Synthesis and recycling of lead tungstate (2006)

We have developed liquid-phase and solid-state processes for the preparation of tetragonal lead tungstate powder with the stoichiometric PbO: WO3 ratio. Solid-state synthesis has been shown to have a number of significant advantages over the liquid-phase process. In addition, a procedure has been developed for processing PbWO4 crystal growth waste through PbWO4 decomposition in nitric acid, which ensures the preparation of extrapure-grade WO3 and PbO. The WO3 and PbO thus obtained have been used in solid-state synthesis of PbWO4, from which high-quality crystals have been grown.
An Evaluation of a Drop Distribution–Based Polarimetric Radar Rainfall Estimator (2003)

A method for estimating the governing parameters of gamma drop size distributions (DSDs) and associated rainfall rates from polarimetric radar measurements at the S band is examined. The technique uses radar reflectivity at horizontal polarization, differential reflectivity, and an empirical constraining relationship between the DSD shape factor and slope parameter. Retrieved DSD parameters show good agreement with disdrometer observations. Retrieved rainfall estimates are insensitive to drop climatological regime. Comparison with fixed-form power-law estimators reveals that the constrained-gamma method outperforms reflectivity estimators and is roughly equivalent to radar reflectivity–differential reflectivity estimators optimized for local DSDs.
A Lower Limb Prosthesis with Active Alignment for Reduced Limb Loading (2021)

Intracellular protein destruction is a carefully coordinated and timed regulatory mechanism that cells utilize to modulate growth, adaptation to environmental cues, and survival. In <em>Caulobacter crescentus</em>, a bacterium known for studies of bacterial cell division cycle, the response regulator CpdR couples phosphorylation events with the AAA+ protease ClpXP to provide punctuated degradation of crucial substrates involved in cell cycle regulation. CpdR functions like an adaptor to alter substrate choice by ClpXP, however it remains unclear how CpdR influences its multiple targets. In this thesis, we show that, unlike canonical ClpXP adaptors, CpdR alone does not strongly bind its substrate. Instead, CpdR binds the N-terminal domain of ClpX and prepares (primes) the unfoldase for substrate engagement. This priming creates a recruitment interface that docks multiple substrates and additional adaptor components. Interestingly, adaptor-dependent priming of ClpX avoids concentration-dependent inhibition that limits traditional, scaffolding adaptors. Control of proteolysis during the <em>Caulobacter</em> cell cycle occurs through proteins involved in a complex phosphosignaling network. We show that this phosphosignal disrupts the interaction between CpdR and ClpX. This regulatory mechanism is efficient because phosphorylated CpdR that cannot bind ClpX should, theoretically, free ClpXP for interaction with its other substrates and adaptors. When dephosphorylated, CpdR binds ClpX, allowing ClpXP to temporarily gain capability to target a completely different range of proteins. Mutations in the predicted response regulator output face of CpdR yielded CpdR variants that impact ClpX binding to cause ranked-order change in adaptor activity and biological function. Through a suppressor mutant screen of a CpdR variant that is hugely defective in binding ClpX, we discover a non-phosphorylatable activated variant of CpdR. Our data suggest that this CpdR variant may have adopted a Mg<sup>2+</sup>-free conformation, giving us insight to the dynamic states that CpdR can adopt during its regulatory function. Together, these results reveal how a single adaptor can command global changes in proteome composition through priming of a protease.
II. Carbohydrate Metabolizing Enzymes (1991)

Effects of light on carbohydrate levels and certain carbon metabolizing enzyme activities were studied during the early development of tomato (Lycopersicon esculentum) fruit. Sucrose levels were low and continued to decline during development and were unaffected by light. Starch was significantly greater in light. Invertase activity was similar in both light- and dark-grown fruit. Sucrose synthase activity was much lower than invertase and showed a slight decrease in light-grown fruit between days 21 and 28. Light-grown fruit also had higher ADP glucose pyrophosphorylase activity than dark-grown fruit, which was correlated with higher starch levels. The rapidly decreasing activity of ADP glucose pyrophosphorylase during early fruit development in the dark in conjunction with reduced starch levels and rates of accumulation indicates that ADP glucose pyrophosphorylase is crucial for carbon import and storage in tomato. The differential stimulation of ADP glucose pyrophosphorylase activity from lightand dark-grown tissue by 3-phosphoglycerate suggests that this enzyme may be allosterically altered by light. Tomato (Lycopersicon esculentum) quality and yield are mainly dependent upon sugar import and accumulation in the fruit. The composition of stored carbohydrate in tomato is associated with certain key enzymes responsible for sucrose metabolism (12). Invertase and sucrose synthase, catalyzing the breakdown of sucrose, have been correlated with reducing sugar levels and rate of carbon translocation into tomato fruit
Enzymes in preparative mono- and oligo-saccharide synthesis (2004)

This review covers advances/developments in the use of enzymes in synthetic mono-/oligo-saccharide chemistry published in the literature between January 2001 and June 2003. Particular attention is paid to the use of aldolases, ketolases, glycosidases, glycosynthases, lipases, esterases and coupled multi-enzyme biotransformations and 132 references are cited.
An identified PfHMGB1 promotes microcystin-LR-induced liver injury of yellow catfish (Pelteobagrus fulvidraco) (2020)

Microcystin-LR (MC-LR) is a potent hepatotoxin that can cause liver inflammation and injury. However, the mode of action of related inflammatory factors is not fully understood. PfHMGB1 is an inflammatory factor induced at the mRNA level in the liver of juvenile yellow catfish (Pelteobagrus fulvidraco) that were intraperitoneally injected with 50 μg/kg MC-LR. The PfHMGB1 mRNA level was highest in the liver and muscle among 11 tissues examined. The full-length cDNA sequence of PfHMGB1 was cloned and overexpressed in E. coli, and the purified protein rPfHMGB1 demonstrated DNA binding affinity. Endotoxin-free rPfHMGB1 (6-150 μg/mL) also showed dose-dependent hepatotoxicity and induced inflammatory gene expression of primary hepatocytes. PfHMGB1 antibody (anti-PfHMGB1) in vitro reduced MC-LR (30 and 50 μmol/L)-induced hepatotoxicity, suggesting PfHMGB1 is important in the toxic effects of MC-LR. In vivo study showed that MC-LR upregulated PfHMGB1 protein in the liver. The anti-PfHMGB1 blocked its counterpart and reduced ALT/AST activities after MC-LR exposure. Anti-PfHMGB1 partly neutralized MC-LR-induced hepatocyte disorganization, nucleus shrinkage, mitochondria, and rough endoplasmic reticula destruction. These findings suggest that PfHMGB1 promotes MC-LR-induced liver damage in the yellow catfish. HMGB1 may help protect catfish against widespread microcystin pollution.
Prognostic Significance of a Scoring System Combining p16, Smoking, and Drinking Status in a Series of 131 Patients with Oropharyngeal Cancers (2021)

This study confirmed that the overexpression of the p16 protein could be viewed as a factor of good prognosis for RFS and OS of OSCC patients. The prognostic significance of a scoring system combining p16 expression, smoking, and drinking status was evaluated and concluded to be a more effective tool to determine therapeutic orientations based on the risk factors for better treatment relevance and survival.
Meta-analysis of the effects of dietary inclusion of sericea lespedeza (Lespedeza cuneata) forage on performance, digestibility, and rumen fermentation of small ruminants (2021)

For more than 20 years, the nutraceutical forage sericea lespedeza ‘AU-grazer’ (SL; Lespedeza cuneata) has been used as an alternative to anthelmintic drugs for controlling gastrointestinal parasites in small ruminants, but with little attention to animal performance. Thus, the objective of this study was to evaluate the effects of dietary inclusion of SL on performance, digestibility, and rumen fermentation of small ruminants using a meta-analytic approach. A total of 24 peer-reviewed manuscripts (sheep = 6 and goats = 18) from 2000 to 2020 met the inclusion criteria for the analysis. Raw mean differences between dietary SL and control treatments weighted by inversed variance were compared with a robust variance estimation. Diet characteristics like crude protein content, NDF content, condensed tannin (CT) content, and inclusion level of SL in the diet (0% to 100%) were used as covariates in a metaregression and subgrouping analysis. Compared to the control, dietary inclusion of SL decreased (P < 0.05) total-tract digestibility by 12% (DMD) and average daily gain (ADG) by 17.7%, but no effects were observed in dry matter intake. Likewise, dietary SL reduced (P < 0.05) molar proportion of acetate (68.88 vs 71.8%), but increased butyrate (10.3 vs 9.2%) and propionate (17.9 vs 16.8%) molar proportions in the rumen. Consequently, dietary SL reduced CH4 emissions by 38% compared to the control. Despite the high heterogeneity in the response variables (I2 > 50), no significant bias was detected (funnel test; P > 0.05). The dose-response analysis revealed that SL-based diets should not include more than 60% in the diet to prevent negative effects in DMD and ADG. Likewise, low inclusion level of SL in the diet (from 30 to 40%) linearly increased propionate concentrations in the rumen but reduced CH4 emissions. In addition to the nutraceutical benefits of this forage, SL inclusion improved rumen fermentation (increased propionate, reduced CH4) at low rates of inclusion, but reduced ADG in small ruminants at higher rates, with these effects minimized if dietary inclusion rate for SL is 60% or less. Further research is needed to determine the optimum inclusion rate to balance nutritional and pharmaceutical effects of SL in the diet of small ruminants.
In Vivo DNA Electrotransfer in Skeletal Muscle (2004)

Appropriate electric pulses can reversibly permeabilize living cells both in vitro and in vivo. Since the pioneering work of E. Neumann and colleagues (1), cell electroporation (also often termed cell electropermeabilization) has become the most frequent method for cell transfection. Indeed, it easily applies in vitro to bacteria, yeast, animal, and plant cells. In vivo, the use of the DNA electrotransfer method is rapidly expanding because of its simplicity and efficiency. First attempts to transfer DNA in vivo to muscle cells were published in 1998 (2,3). This led in 1999 to an extended study on the determination of optimal conditions for DNA electrotransfer in skeletal muscle in mice, rats, rabbits, and even primates using a reporter gene (4). The same year, the first “therapeutic” gene (the erythropoïetin gene) was transferred to mouse muscle in vivo by Rizzuto and colleagues (5). In the last 2 years, several publications have used the conditions described in ref. (4) and have shown the wide applicability of this method for the electrotransfer of a large number of genes in different muscles (6-8). DNA electrotransfer to skeletal muscle could lead to broad potential applications in the therapeutic field (metabolic disorders correction, vaccination, systemic secretion of angiogenic or antiangiogenic factors, etc.) and for physiological, pharmacological, and developmental studies.
Prolonged catheter‐induced coronary artery spasm mimicking fixed stenosis (1997)

Two cases of prolonged catheter-induced right coronary artery spasm, mimicking fixed stenoses, are presented. In one case, the spasm appeared at the same place in sequential catheterizations. This angiographic finding may be easily misinterpreted as a fixed lesion, leading to unnecessary attempts at angioplasty. Cathet. Cardiovasc. Diagn. 41:170–173, 1997. © 1997 Wiley-Liss, Inc.
Measurement of stopping power of 240 MeV argon ions in partially ionized helium discharge plasma (2000)

An energy loss of 240 MeV argon ions in a Z -pinch helium plasma has been for the first time observed throughout the entire pinching process. Standard Stark broadening analysis gives an electron density ranging from 4 to 6 × 10 17 cm −3 during the pinch. To deduce stopping power from the energy loss, the target thickness of the helium plasma has been evaluated assuming the mean charge of helium based on thermal equilibrium. The observed electron density and the mean charge of helium give a target thickness of 30 ± 3 μg cm −2 from 1 μs to 1.8 μs after the discharge ignition. The measured stopping power exceeds a tabulated value for cold helium gas by a factor of 2 to 3 around the time of the first pinch. The experimental stopping power is compared with theoretical values calculated using an equation of stopping power for a partially ionized plasma.
Experimental study online testing of acenaphthylene and trichlorobenzene in fluegas (2007)

Time-of-flight mass spectrometer(TOF-MS) was utilized for online monitoring polycyclic aromatic hydrocarbons(PAHs) acenaphthylene(AcPy) and dioxin precursor trichlorobenzene(TCB) in model flue gas from combustion process.Experimental results showed that TOF-MS has good response capability to the acenaphthylene in the flue gas,and the online test signal intensity showed good relativity with the offline analysis results.The mass calibration was done preliminary by fitting between online test signal intensity and offline analysis results.Strong response appeared with little interference in the online test of dioxin precursor 1,2,3-Trichlorobenzene by TOF-MS.Experimental results stated the possibility of online measurement of AcPy,TCB,and other organic pollutants in real flue gas.The results supplied the feasibility to investigate the online monitoring method of dioxin-like trace organic pollutants.
Watch-n-patch: Unsupervised understanding of actions and relations (2015)

We focus on modeling human activities comprising multiple actions in a completely unsupervised setting. Our model learns the high-level action co-occurrence and temporal relations between the actions in the activity video. We consider the video as a sequence of short-term action clips, called action-words, and an activity is about a set of action-topics indicating which actions are present in the video. Then we propose a new probabilistic model relating the action-words and the action-topics. It allows us to model long-range action relations that commonly exist in the complex activity, which is challenging to capture in the previous works. We apply our model to unsupervised action segmentation and recognition, and also to a novel application that detects forgotten actions, which we call action patching. For evaluation, we also contribute a new challenging RGB-D activity video dataset recorded by the new Kinect v2, which contains several human daily activities as compositions of multiple actions interacted with different objects. The extensive experiments show the effectiveness of our model.
Cutoff frequency of experimentally generated noise: A Melnikov approach (1996)

The motion of an overdamped particle excited by colored noise in a bistable potential is discussed in chaotic dynamics terms. A Melnikov approach is used to determine an appropriate cutoff frequency of experimentally generated noise as a function of noise correlation time. \textcopyright{} 1996 The American Physical Society.
Individual Reduction Potentials of the Iron Ions in Fe2S2and High-Potential Fe4S4Ferredoxins (1996)

The DelPhi program package has been used to confirm that the span in reduction potentials among high-potential Fe(4)S(4) ferredoxins must be mainly ascribed to the net protein charges arising from acidic and basic residues. Subsequently, the order of the individual reduction potentials of the iron ions in Fe(2)S(2) ferredoxins as found from NMR spectroscopy was explained mainly on the basis of different solvation contributions to the electrostatic potential. The individual reduction potentials of the iron ions in high-potential Fe(4)S(4) ferredoxins, again available from NMR spectroscopy, are only qualitatively reproduced. It is proposed that the protein triggers a distortion in the cluster which would be a further contribution to the electrochemical inequivalence of the individual iron ions.
Structural and Optical Properties of Axial and Radial Heterostructure Ill-V Nanowires Grown by Metalorganic Chemical Vapour Deposition (2006)

We have investigated the structural properties and photoluminescence of novel axial and radial heterostructure III-V nanowires, fabricated by metalorganic chemical vapour deposition. Segments of InGaAs have been incorporated within GaAs nanowires, to create axial heterostructure nanowires which exhibit strong photoluminescence. Photoluminescence is observed from radial heterostructure nanowires (core-shell nanowires), consisting of GaAs cores with AlGaAs shells. Core-multishell nanowires, of GaAs cores clad in several alternating layers of thick AlGaAs barrier shells and thin GaAs quantum well shells, exhibit a blue-shifted photoluminescence peak arising from quantum confinement effects.
Thermosetting Poly(imide silsesquioxane)s Featuring Reduced Moisture Affinity and Improved Processability (2013)

With the goal of improving the moisture resistance of thermosetting polyimides, a thermally stable, polyhedral oligomeric silsesquioxane (POSS) dianiline, which features an aromatic periphery, was co-oligomerized with 4,4′-(hexafluoroisopropylidene)diphthalic anhydride (6-FDA), 4,4′-diaminodiphenyl ether (ODA), and phenylethynylphthalic anhydride (PEPA) to form thermosetting oligomers of a prescribed number of repeat units. The resultant oligomers were characterized for their chemical architecture, rheological characteristics, and cure behavior. POSS regioisomerism provided a unique opportunity to study the effects of monomer architecture on properties. The type of isomer affects rheological and cure characteristics but was found to have no discernible influence on cured state properties. The benefits of POSS co-oligomerization are 3-fold in that processability, thermal stability, and moisture resistance are each improved. Cured glass transition temperature is reduced, however, for a fixed number of repeat units, due to increased length and molecular weight between cross-links concomitant with POSS co-oligomerization.
Abstract 5436: Targeting oncoproteins via disruption of proteostasis: Identification of oncoprotein destabilizing agents using luciferase tagged oncoproteins (2015)

Abstract Since many oncoproteins are considered undruggable targets, we have developed and validated a new screening strategy to identify small molecules that inhibit oncoprotein activity by causing their degradation. Recently, the mechanism of action for the class of drugs known as immunomodulators (IMiDs; e.g. thalidomide, lenalidomide and pomalidomide) has uncovered a novel oncogene targeting strategy. IMiDs commandeer an E3 ligase complex that contains the E3 recognition subunit cereblon and divert its activity toward two transcription factors IKZF1 and IKZF3, which play critical roles in hematopoietic cells. This mechanism explains the efficacy of IMiDs in multiple myeloma and may translate into a general approach to target traditionally undruggable oncoproteins. We generated cell lines stably expressing IKZF1as a firefly luciferase fusion protein with coexpression of Renilla luciferase. A pilot HTS campaign was run to uncover novel drugs that can mimic the effects of IMiDs. A cell line expressing the MYC-firefly fusion protein was used for counter-screening. We used pomalidomide as our positive control and it reduced firefly luciferase signal ≈75% with no change in the renilla luciferase signals. This control resulted in a Z prime value typically &amp;gt;0.5. The pilot screen of 3,850 compounds resulted in 39 “hits” that reduced firefly luciferase &amp;gt;35%. More importantly, both thalidomide and lenalidomide were found to be active in the screen. Confirmation testing revealed that 75% of “hits” repeated, but also had activity in the MYC-firefly cell line. Actives were tested in western blots for their ability to decrease fusion protein abundance. Many active compounds did not reduce protein levels in western blots and represent nonspecific hits (e.g. luciferase inhibitor). In conclusion, we present a screening paradigm with the potential to uncover novel proteostasis disruptors by expressing luciferase tagged oncoproteins. Citation Format: Richard E. Middleton, Greg Olsen, Russell McSweeney, Gang Lu, Wenhua Gao, Justin Roberts, Michael R. McKeown, Mark A. Bittinger, Kwok-Kin Wong, James E. Bradner, William G. Kaelin. Targeting oncoproteins via disruption of proteostasis: Identification of oncoprotein destabilizing agents using luciferase tagged oncoproteins. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5436. doi:10.1158/1538-7445.AM2015-5436
Antenatal Malaria Parasitaemia And Haemoglobin Profile Of Pregnant Mothers In Awka, Anambra State, Southeast Nigeria (2009)

2 Abstract: Three hundred and two women comprising 242 pregnant women attending antenatal clinic and 60 non pregnant women that served as control group, were tested for malaria parasites using Giemsa stained thick films. The haemoglobin concentration of the mothers were also tested and matched with their infection status. The findings show that malaria parasitaemia and intensity are dependent on pregnancy and parity of pregnancy (p < 0.05). It demonstrated that anaemia is a common feature of malaria infection, more severe during pregnancy especially in the first pregnancy. There was a downward gradation in the prevalence of low haemoglobin levels from primiparae to the control group in both infected and uninfected populations. Over 70% of primigravid mothers, 45% of the multiparae and only 22% of the control group recorded haemoglobin levels lower than the World Health Organization benchmark (11.0g/dl). Anaemia was therefore dependent on infection status, pregnancy status and parity of pregnancy (p <0.05). The effects of malaria and its clinical features (especially anaemia) on the mother and foetus was again re-stressed with emphasis on availability, affordability and sustainability of malaria control efforts especially for the most vulnerable populations. The study will be of immense value as a public health tool for planning, delivery, monitoring and evaluation of interventions.