gebhart/patrepeval huggingface dataset:
Transition State Interactions in a Promiscuous Enzyme: Sulfate and Phosphate Monoester Hydrolysis by Pseudomonas aeruginosa Arylsulfatase (2018)

ABSTRACT Pseudomonas aeruginosa arylsulfatase (PAS) hydrolyses sulfate and, promiscuously, phosphate monoesters. Enzyme-catalyzed sulfate transfer is crucial to a wide variety of biological processes, but detailed studies of the mechanistic contributions to its catalysis are lacking. We present an investigation based on linear free energy relationships (LFERs) and kinetic isotope effects (KIEs) of PAS and active site mutants that suggest a key role for leaving group (LG) stabilization. In LFERs wild type PAS has a much less negative Br0nsted coefficient (β leaving group obs-Enz = −0.33) than the uncatalyzed reaction (β leavingroup obs = −1.81). This situation is diminished when cationic active site groups are exchanged for alanine. The considerable degree of bond breaking during the TS is evidenced by an 18 O bridge KIE of 1.0088. LFER and KIE data for several active site mutants point to leaving group stabilization by active-site lysine K375, in cooperation with histidine H211. 15 N KIEs combined with an increased sensitivity to leaving group ability of the sulfatase activity in neat D 2 O (Δβ leaving group H-D = +0.06) suggest that the mechanism for S-O bridge bond fission shifts, with decreasing leaving group ability, from charge compensation via Lewis acid interactions towards direct proton donation. 18 O nonbridge KIEs indicate that the TS for PAS-catalyzed sulfate monoester hydrolysis has a significantly more associative character compared to the uncatalyzed reaction, while PAS-catalyzed phosphate monoester hydrolysis does not show this shift. This difference in enzyme-catalyzed TSs appears to be the major factor favoring specificity toward sulfate over phosphate in this promiscuous hydrolase, since other features are either too similar (uncatalyzed TS) or inherently favor phosphate (charge).
Partial purification of ferredoxin from Ruminococcus albus and its role in pyruvate metabolism and reduction of nicotinamide adenine dinucleotide by H2 (1977)

Extracts of Ruminococcus albus were not able to convert pyruvate to acetyl phosphate, CO2, and H2 after passage through a diethylaminoethyl (DEAE)-cellulose column. Activity was restored by a brown protein fraction eluted from the column with 0.4 M Cl-. The protein was partially purified and shown to have the spectral and biological characteristics of ferredoxin. R. albus ferredoxin, Clostridium pasteurianum ferredoxin, and methyl viologen restored activity for pyruvate decomposition by DEAE-cellulose-treated R. albus extracts. R. albus or C. pasteurianum ferredoxin restored the ability of DEAE-cellulose-treated C. pasteurianum extracts to form H2 and acetyl phosphate from pyruvate. Ferredoxin-free extracts of R. albus reduced nicotinamide adenine dinucleotide (NAD) when supplemented with R. albus or C. pasteurianum ferredoxin or with methyl viologen. These extracts reduced NADP with H2 poorly unless both ferredoxin and NAD were added, which indicates the presence of an NADH:NADP transhydrogenase. Flavin mononucleotide and flavin adenine dinucleotide were rapidly reduced by H2 by ferredoxin-free extracts in the absence of ferredoxin.
Characterization of the Human Homologue of the Yeast Spc98p and Its Association with γ-Tubulin (1998)

A trimeric complex formed by Tub4p, the budding yeast gamma-tubulin, and the two spindle pole body components, Spc98p and Spc97p, has recently been characterized in Saccharomyces cerevisiae. We reasoned that crucial functions, such as the control of microtubule nucleation, could be maintained among divergent species. SPC98-related sequences were searched in dbEST using the BLASTN program. Primers derived from the human expressed sequence tag matching SPC98 were used to clone the 5' and 3' cDNA ends by rapid amplification of cDNA ends (RACE)-PCR. The human Spc98 cDNA presents an alternative splicing at the 3' end. The deduced protein possesses 22% identity and 45% similarity with the yeast homologue. We further report that the human Spc98p, like gamma-tubulin, is concentrated at the centrosome, although a large fraction is found in cytosolic complexes. Sucrose gradient sedimentation of the cytosolic fraction and immunoprecipitation experiments demonstrate that both gamma-tubulin and HsSpc98p are in the same complex. Interestingly, Xenopus sperm centrosomes, which are incompetent for microtubule nucleation before their activation in the egg cytoplasm, were found to contain similar amounts of both Spc98p and gamma-tubulin to human somatic centrosomes, which are competent for microtubule nucleation. Finally, affinity-purified antibodies against Spc98p inhibit microtubule nucleation on isolated centrosomes, as well as in microinjected cells, suggesting that this novel protein is indeed required for the nucleation reaction.
Monitoring an Experimental Reactor Using the Group Method of Data Handling Approach (2005)

This paper presents a reactor-monitoring algorithm using the group method of data handling (GMDH) that creates nonlinear algebraic models for system characterization. The monitoring system was applied to the IEA-R1 experimental reactor at the Instituto de Pesquisas Energéticas e Nucleares (IPEN). The IEA-R1 is a 5-MW pool-type research reactor that uses light water as coolant and moderator and graphite as reflector. The GMDH provides a general framework for characterizing the relationships among a set of state variables of a process system and is used for generating estimates of critical variables in an optimal data-driven model form. The monitoring system developed in this work was used to predict the IEA-R1 reactor environment, using nuclear power, rod position, and coolant temperatures, by combining two variables at a time. The results obtained using the GMDH models agreed very well with the dose rate measurements, with prediction errors of less than 5%. The error was minimal when the dose rate prediction was made using reactor power and coolant temperature.
Post-transcriptional Mechanisms Contribute to the Suppression of the ErbB3 Negative Regulator Protein Nrdp1 in Mammary Tumors (2010)

The ErbB2 and ErbB3 receptor tyrosine kinases act synergistically to promote cellular properties associated with tumor development. Previous studies indicate that endogenous ErbB3 protein is markedly elevated in mouse mammary tumors induced by transgenic ErbB2 overexpression. However, this occurs in the absence of elevated ErbB3 transcript, indicating that post-transcriptional regulatory mechanisms play crucial roles in suppressing ErbB3 protein in normal tissue. Our previous studies also demonstrate that protein levels of Nrdp1, an E3 ubiquitin ligase that targets ErbB3 for degradation, are markedly suppressed in tumors from ErbB2 transgenic animals relative to normal tissue. Here we demonstrate that transgenic expression of Nrdp1 cDNA in the mouse mammary gland is not sufficient to suppress elevated ErbB3 levels or tumor initiation and growth in ErbB2 transgenic mice. Unexpectedly, Nrdp1 protein is absent in tumors from Nrdp1/ErbB2 bigenic mice, and real time PCR analysis indicates that Nrdp1 protein levels are suppressed post-transcriptionally. Nrdp1 protein is more resistant to proteasome-dependent degradation when exogenously expressed in cultured MCF10A nontransformed human breast epithelial cells than in breast tumor cells. These observations indicate that mammary tumors use potent post-transcriptional mechanisms to suppress Nrdp1 protein levels and that protein destabilization may play a central role in Nrdp1 loss in tumors.
Bifurcation and fractal basin boundaries of phase-locked loop circuits (2003)

By drawing exact bifurcation diagrams, it is confirmed that the Melnikov curve of homoclinicity gives a good prediction for the onset of the chaotic attractor bifurcated from the periodic solution of the second type in some region of the external sinusoidal force. It is also confirmed that the Melnikov's curve becomes an onset of the fractal basin boundary of multiple attractors. This is confirmed by drawing various initial condition planes above and below the curve.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A hybrid shape decomposition using hyperquadrics and mathematical morphology (2002)

This paper discusses a hybrid shape decomposition method using hyperquadrics to describe a part, mathematical morphology to find an initial ellipse, and polygonal approximation to find additional terms of the hyperquadrics. We adopt a weighted least square fitting to find hyperquadrics using the Levenberg-Marquardt optimization method. The proposed method is illustrated in decomposing some 2D binary images such as a natural object and a man-made object. It can be easily extended to 3D range data. The experimental results show that our method is a promising approach in shape representation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Diagnostic Fecal Occult Blood Testing in Hospitalized and Emergency Department Patients: Time for Change? (2018)

To examine the use of fecal occult blood testing in inpatients and in those presenting to the emergency department. We retrieved all fecal occult blood tests (FOBTs) conducted over a 3 year period, gastrointestinal endoscopic studies, and diagnoses of digestive-tract malignant neoplasms. Scheduling reasons and procedure results for all gastrointestinal endoscopies scheduled within 30 days after the FOBT result became available were recorded. A total of 5028 FOBTs were obtained during the 3-year period. Half of the diagnostic endoscopic procedures (n = 957) completed within 30 days of FOBT followed a negative test result. The few reasons for scheduling endoscopic procedures included a positive FOBT result. During follow-up, 17 new diagnoses of digestive-tract malignant neoplasms were made, and 8 of 17 patients had 1 or more positive FOBT result. The results of FOBTs, by themselves, are rarely used for patient management. Eliminating the routine diagnostic use of FOBTs in those settings would not compromise patient care.
Developmental responses of bread wheat to changes in ambient temperature following deletion of a locus that includes FLOWERING LOCUS T1 (2018)

FLOWERING LOCUS T (FT) is a central integrator of environmental signals that regulates the timing of vegetative to reproductive transition in flowering plants. In model plants, these environmental signals have been shown to include photoperiod, vernalization, and ambient temperature pathways, and in crop species, the integration of the ambient temperature pathway remains less well understood. In hexaploid wheat, at least 5 FT-like genes have been identified, each with a copy on the A, B, and D genomes. Here, we report the characterization of FT-B1 through analysis of FT-B1 null and overexpression genotypes under different ambient temperature conditions. This analysis has identified that the FT-B1 alleles perform differently under diverse environmental conditions; most notably, the FT-B1 null produces an increase in spikelet and tiller number when grown at lower temperature conditions. Additionally, absence of FT-B1 facilitates more rapid germination under both light and dark conditions. These results provide an opportunity to understand the FT-dependent pathways that underpin key responses of wheat development to changes in ambient temperature. This is particularly important for wheat, for which development and grain productivity are sensitive to changes in temperature.
Image Segmentation using Learning Vector Quantization of Artificial Neural Network (2013)

This paper presents color image segmentation application for road-sign detection and recognition system based on Learning vector Quantization (LVQ). In traffic-sign maintenance and in a visual driver assistance system, road-sign detection and recognition are two of the most important functions. Our system is able to detect and recognize the signs. Road signs provide drivers important information and help them to drive more safely and more easily by guiding and warning them and thus regulating their actions. The RGB images are converted into HSV color space, and segmented using LVQ depending on the hue values of each pixel in the HSV color space. LVQ neural network is used to detect the color from the images and recognize them with high accuracy and speed. The detection and recognition of traffic signs represents an important issue in the field of traffic sign analysis. The paper researches the existing traffic sign detection and recognition methods. Special attention has been given to the methods based on artificial neural networks. Some techniques extracted various features from the images containing traffic signs and used various detectors and classifiers to perform detection and recognition. The following examples of these methods can be mentioned: Histogram of Oriented Gradient (2) or (1) and (6) or Support Vector Machines (SVM) (5). Some authors have also used artificial neural networks (4). This paper, however, uses a method of neural network (NN) which has given successful results. For individual object identification in humans, Color discrimination plays an important role. Image segmentation is the basic and first step regarding image analysis and pattern recognition. In image processing, image segmentation is not only the critical and essential component but also it is a very difficult task. The actual operation of the algorithm determines the accuracy and quality of image analysis. Color segmentation is a process of extracting one or more connected regions from the image domain. These connected regions are satisfying the uniformity (homogeneity) criterion which is derived from the spectral components. These components are then defined with respect to some color spaced model such as RGB model. RGB is the most common model. In RGB model, a color point is defined by the color components of the corresponding pixel which are defined in the form of Red (R), Green (G) and Blue (B). This paper considers a color image segmentation problem as a pixel classification problem. .
Crystal Structure and Mutational Analysis of Heparan Sulfate 3- O -Sulfotransferase Isoform 1 (2021)

Heparan sulfate interacts with antithrombin, a protease inhibitor, to regulate blood coagulation. Heparan sulfate 3-O-sulfotransferase isoform 1 performs the crucial last step modification in the biosynthesis of anticoagulant heparan sulfate. This enzyme transfers the sulfuryl group (SO(3)) from 3'-phosphoadenosine 5'-phosphosulfate to the 3-OH position of a glucosamine residue to form the 3-O-sulfo glucosamine, a structural motif critical for binding of heparan sulfate to antithrombin. In this study, we report the crystal structure of 3-O-sulfotransferase isoform 1 at 2.5-A resolution in a binary complex with 3'-phosphoadenosine 5'-phosphate. This structure reveals residues critical for 3'-phosphoadenosine 5'-phosphosulfate binding and suggests residues required for the binding of heparan sulfate. In addition, site-directed mutagenesis analyses suggest that residues Arg-67, Lys-68, Arg-72, Glu-90, His-92, Asp-95, Lys-123, and Arg-276 are essential for enzymatic activity. Among these essential amino acid residues, we find that residues Arg-67, Arg-72, His-92, and Asp-95 are conserved in heparan sulfate 3-O-sulfotransferases but not in heparan N-deacetylase/N-sulfotransferase, suggesting a role for these residues in conferring substrate specificity. Results from this study provide information essential for understanding the biosynthesis of anticoagulant heparan sulfate and the general mechanism of action of heparan sulfate sulfotransferases.
Studies of Ligand Binding to Tubulin by Electron Crystallography (2004)

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.
Energy and Cost Evaluation for the Concentration and Dehydration Process of Bioethanol by Zeolite Membranes (2010)

バイオエタノールの脱水にはPSA法が用いられ省エネルギー化が図られているが，PSA法はプロセス上の制約があるためこれ以上の低コスト化が難しい．一方，ゼオライト素材の膜分離法は一層の省エネルギー化の可能性があり，弱点であった耐水性・耐酸性素材の開発も進められている．本研究では，バイオエタノールの蒸留・膜脱水プロセスについてシミュレーション計算を行い，膜分離法が経済的に優位となる膜特性及び濃縮プロセスについて検討した．透過速度の向上は，真空ポンプに負荷をかけない低エネルギーモード運転を可能にするため消費エネルギーの低減に有効であるが，蒸留塔の消費エネルギーが大きいためその低減比率は微小である．一方，透過速度の向上は膜モジュール本数を削減できるため設備コストの低減が可能になる．分離係数の向上は消費エネルギー，コストにほとんど影響しないが，分離係数の低下によるエタノールの損失を考慮すると10,000程度以上は必要と思われる．蒸留の負荷を下げるため蒸留塔出口濃度を下げると，消費エネルギーを大きく低減できコストも下がる．さらに，蒸留法とPSA法をQ=36 kg·m−2·h−1, α=10,000程度の膜で置き換えればおよそ6 JPY·kg-EtOH−1のコスト削減が可能となる．また，含水エタノール製造においても同様におよそ6 JPY·kg-EtOH−1のコスト削減が可能となる．これらの検討結果から，膜分離法をPSA法のみでなく蒸留法に置き換えることにより経済性に優れたプロセスを構築できることがわかった．
On improving the accuracy of Visible Light Positioning system using deep autoencoder (2020)

International audience
The Jasmonate Pathway Is a Key Player in Systemically Induced Defense against Root Knot Nematodes in Rice (2011)

Complex defense signaling pathways, controlled by different hormones, are involved in the reaction of plants to a wide range of biotic and abiotic stress factors. We studied the ability of salicylic acid, jasmonate (JA), and ethylene (ET) to induce systemic defense in rice (Oryza sativa) against the root knot nematode Meloidogyne graminicola. Exogenous ET (ethephon) and JA (methyl jasmonate) supply on the shoots induced a strong systemic defense response in the roots, exemplified by a major up-regulation of pathogenesis-related genes OsPR1a and OsPR1b, while the salicylic acid analog BTH (benzo-1,2,3-thiadiazole-7-carbothioic acid S-methyl ester) was a less potent systemic defense inducer from shoot to root. Experiments with JA biosynthesis mutants and ET-insensitive transgenics showed that ET-induced defense requires an intact JA pathway, while JA-induced defense was still functional when ET signaling was impaired. Pharmacological inhibition of JA and ET biosynthesis confirmed that JA biosynthesis is needed for ET-induced systemic defense, and quantitative real-time reverse transcription-polymerase chain reaction data revealed that ET application onto the shoots strongly activates JA biosynthesis and signaling genes in the roots. All data provided in this study point to the JA pathway to play a pivotal role in rice defense against root knot nematodes. The expression of defense-related genes was monitored in root galls caused by M. graminicola. Different analyzed defense genes were attenuated in root galls caused by the nematode at early time points after infection. However, when the exogenous defense inducers ethephon and methyl jasmonate were supplied to the plant, the nematode was less effective in counteracting root defense pathways, hence making the plant more resistant to nematode infection.
Advances in understanding gray matter pathology in multiple sclerosis: Are we ready to redefine disease pathogenesis? (2012)

The purpose of this special issue in BMC Neurology is to summarize advances in our understanding of the pathological, immunological, imaging and clinical concepts of gray matter (GM) pathology in patients with multiple sclerosis (MS). Review articles by Lucchinetti and Popescu, Walker and colleagues, Hulst and colleagues and Horakova and colleagues summarize important recent advances in understanding GM damage and its implications to MS pathogenesis. They also raise a number of important new questions and outline comprehensive approaches to addressing those questions in years to come. In the last decade, the use of immunohistochemistry staining methods and more advanced imaging techniques to detect GM lesions, like double inversion recovery, contributed to a surge of studies related to cortical and subcortical GM pathology in MS. It is becoming more apparent from recent biopsy studies that subpial cortical lesions in early MS are highly inflammatory. The mechanisms responsible for triggering meningeal inflammation in MS patients are not yet elucidated, and they should be further investigated in relation to their role in initiating and perpetuating the disease process. Determining the role of antigens, environmental and genetic factors in the pathogenesis of GM involvement in MS is critical. The early involvement of cortical and subcortical GM damage in MS is very intriguing and needs to be further studied. As established in numerous cross-sectional and longitudinal studies, GM damage is a better predictor of physical disability and cognitive impairment than WM damage. Monitoring the evolution of GM damage is becoming an important marker in predicting future disease course and response to therapy in MS patients.
Duodenal bicarbonate secretion ‐ the prostaglandin receptor involved is EP4 (2005)

‘Duodenal bicarbonate secretion is an important mechanism protecting the organism from acid–base disturbances secondary to the gastric acid secretion. The duodenal secretion of bicarbonate in humans is in part mediated via prostaglandin receptors of the EP4 type’ The gastrointestinal (GI) tract is from a functional point of view faced with a seemingly unsolvable problem. On the one hand, the major GI function is to absorb essential nutrients. On the other hand, the single layered epithelium of the GI tract represents an outer surface exposed to ingested unknown, possibly harmful, compounds and/or microorganisms. One physiological mechanism that limits the number of microorganisms in the GI tract is the acid environment in the stomach, the gastric proton concentration being up to 100 000 times higher than that of the extracellular space. To buffer the acid reaching the duodenum, its mucosa produces bicarbonate ions. The duodenal secretion of bicarbonate increases upon exposure to acid. This mechanism is, at least in part, evoked by prostaglandins E2 (PGE2) presumably released from the duodenal epithelial cells upon acidification. In the current report Larsen et al. investigate in human biopsies, which G protein-coupled receptor (EP1–4) that is involved in this response using an Ussing chamber. This technique implies that changes of the transepithelial electrogenic transport are monitored. Adding PGE2 evoked an increase of short circuit current, suggesting that prostaglandin evoked an increased secretion of negatively charged ions. Experiments with receptor antagonists for the various EP receptor subtypes indicated that the receptor involved in the response was of the EP4 type.
Temperature effect on redox voltage in LixCo[Fe(CN)6]y (2017)

The electrochemical thermoelectric (TE) coefficient (SEC≡∂V∂T; V and T are the redox potential and temperature, respectively) is a significant material parameter, because it enable us to convert heat into electricity. Here, we systematically investigated the TE properties of cobalt hexacyanoferrate (Co-HCF), LixCo[Fe(CN)6]y, against the Li concentration (x). |SEC| is higher than the Seebeck coefficient (= 0.2 mV/K at room temperature) of Bi2Te3 and distributes from 0.2 to 0.8 mV/K. We further observed a sign reversal behavior of SEC: SEC is negative at y =0.71 while it is negative (positive) at x≤0.3 (x≥0.6) at y =0.90. Based on the ionic model, we qualitatively reproduced the sign reversal behavior by including the volume expansion effect. These arguments suggest that SEC in solid is mainly governed by the electrostatic energy.
Sleep Disturbances, Daytime Sleepiness, and Quality of Life in Adults with Growth Hormone Deficiency (2010)

GHD is associated with sleep disorders that may be caused by specific hormonal alterations as well as with poor subjective sleep quality and daytime sleepiness. Disturbed sleep is likely to be partly responsible for increased tiredness, a major component of quality of life in GHD.