gebhart/patrepeval huggingface dataset:
Synthesis and proton NMR spectroscopic characterization of trans-[Pt(NH3)2[d(ApGpGpCpCpT)-N7-A(1),N7-G(3)]] (1987)

The reaction of trans-[Pt(NH3)2Cl2] with the sodium salt of [d(ApGpGpCpCpT)]2 in aqueous solution at 37 degrees C was monitored by reversed-phase high-performance liquid chromatography and UV spectroscopy. Two intermediates, most likely monofunctional adducts, were observed, which subsequently formed one predominant single-stranded product, as well as several polymeric species proposed to be interstrand cross-linked products. The single-stranded adduct was structurally characterized by 1H NMR spectroscopy. From the pH dependence of the chemical shifts, two-dimensional homonuclear chemical shift correlation (COSY) spectroscopy, and one- and two-dimensional nuclear Overhauser effect (NOESY) experiments, the platinum(II) moiety was found to be coordinated to the N7 positions of adenine(1) and guanine(3), with the intervening guanine(2) base destacked from its neighboring residues. This intrastrand 1,3 adduct induces changes in the backbone torsion angles and causes the deoxyribose ring of adenine(1) to switch from a C2'-endo to a predominantly C3'-endo conformation. The other deoxyribose rings retain B DNA type conformations. The structure of trans-[Pt(NH3)2[d(ApGpGpCpCpT)-N7-A(1),N7-G(3)]] differs from those previously reported for cis-DDP 1,2- and 1,3-intrastrand oligonucleotide adducts but is consistent with the structures of trans-DDP 1,3-intrastrand adducts of two previously reported trinucleotides.
A Weighted Least Squares Approach to Computer Simulation Factor Screening (1995)

In this paper, we develop a weighted least squares (WLS) approach to computer simulation factor screening. Like frequency domain methodology (FDM), the regression analysis is performed in the frequency domain. However, unlike FDM, where unknown nuisance parameters are eliminated by cancellation in a ratio statistic, the WLS procedure is designed to estimate these parameters (the WLS weights) and incorporate this information into the regression analysis. We propose and compare one- and two-run approaches for estimating the weights in the WLS approach.
Combining gene expression and interaction network data to improve kidney lesion score prediction (2012)

Current method of diagnosing kidney rejection based on histopathology of renal biopsies in form of lesion scores is error-prone. Researchers use gene expression microarrays in combination of machine learning to build better kidney rejection predictors. However the high dimensionality of data makes this task challenging and compels application of feature selection methods. We present a method for predicting lesions using combination of statistical and biological feature selection methods along with an ensemble learning technique. Results show that combining highly interacting genes (Hub Genes) from protein-protein interaction network with genes selected by squared t-test method brings the most accurate kidney lesion score predictor.
Corticotropin/lipotropin common precursor-like material in normal rat extrapituitary tissues. (1983)

A Mr 26,000 corticotropin (ACTH)-like material is present in glacial acetic acid extracts of all normal rat extrapituitary tissues. In the present study, beta-melanotropin (beta-MSH) immunoactivity was detected in glacial acetic acid extracts of normal rat extrapituitary tissues. beta-MSH immunoactivity was also present in all extracts (mean +/- SEM, fmol/mg of protein): brain, 71.0 +/- 16.3; stomach, 11.5 +/- 1.6; kidney, 8.9 +/- 0.8; colon, 8.2 +/- 1.1; small intestine, 6.5 +/- 1.1; liver, 4.3 +/- 0.5; and heart, 3.2 +/- 0.5. Except in brain extracts, beta-MSH and ACTH immunoactivities of tissue extracts were strongly correlated to each other (r = 0.79; n = 42). When tissue extracts (except brain) were passed through a Sephadex G-75 (superfine) column, ACTH and beta-MSH immunoactivities were eluted in a single peak corresponding to Mr 26,000. In contrast, for brain extracts, the MrS of major peaks of ACTH and beta-MSH immunoactivities were 4,500 and 8,000, respectively; a smaller peak of Mr 26,000 ACTH/beta-MSH-like material was also eluted. Specific anti-ACTH immunocolumns, which did not bind purified synthetic beta-MSH, adsorbed both ACTH and beta-MSH immunoactivities of all tissue extracts except those of brain. One-third of the beta-MSH immunoactivity in brain extracts adsorbed to the anti-ACTH immunocolumn, but two-thirds of beta-MSH immunoactivity passed through the column. We conclude that ACTH and beta-MSH immunoactivities are present in all normal rat extrapituitary tissues and exist in most tissues on the same molecule. This Mr 26,000 molecule is closely related to the pituitary ACTH/beta-lipotropin common precursor.
<title>Application of advanced methods for durability assessment of new absorber coatings</title> (1995)

Accelerated life testing of solar energy materials has been one of the main topics within the former Task X 'Solar Materials Research and Development' of the International Energy Agency (IEA) Solar Heating and Cooling Programme. In the case study of some selective solar absorber coating materials for domestic hot water systems procedures are presented for service time assessment, applicable for example to absorber coating materials. As a continuation of the finalized Task X a working group, 'Materials in Solar Thermal Systems' also in the framework of the International Energy Agency (IEA) 'Solar Heating and Cooling Programme' was initiated. One of the first projects is described here. Its aim is to investigate the conformity of the durability assessment, applied on solar absorber coatings tested by different laboratories. Each lab is working independently, this means there is no information exchange between the labs until the results are on paper. Test samples are delivered by the participants. Four different absorber coatings are identified to be useful for the project. The coating materials as well as the production procedures of the coatings are not relevant for the study, therefore no information is given. The experimental procedures as well as the judgement over the different absorber coatings are described in detail. Some comparisons between individual results of the different labs indicates possible weaknesses and further necessary refinements. Finally, expected costs for the whole procedure are presented.
Pupil dilation as an index of preferred mutual gaze duration (2016)

Most animals look at each other to signal threat or interest. In humans, this social interaction is usually punctuated with brief periods of mutual eye contact. Deviations from this pattern of gazing behaviour generally make us feel uncomfortable and are a defining characteristic of clinical conditions such as autism or schizophrenia, yet it is unclear what constitutes normal eye contact. Here, we measured, across a wide range of ages, cultures and personality types, the period of direct gaze that feels comfortable and examined whether autonomic factors linked to arousal were indicative of people's preferred amount of eye contact. Surprisingly, we find that preferred period of gaze duration is not dependent on fundamental characteristics such as gender, personality traits or attractiveness. However, we do find that subtle pupillary changes, indicative of physiological arousal, correlate with the amount of eye contact people find comfortable. Specifically, people preferring longer durations of eye contact display faster increases in pupil size when viewing another person than those preferring shorter durations. These results reveal that a person's preferred duration of eye contact is signalled by physiological indices (pupil dilation) beyond volitional control that may play a modulatory role in gaze behaviour.
Structure and Three-Dimensional Crystal Packing Preferences for mer-Tris(8-quinolinolato)Indium(III) Vapor-Phase-Grown Crystals (2004)

Evaluation of indium(III) tris(8-quinolinolato) (Inq3) chelate crystals grown slowly from the vapor phase under vacuum (∼10-6 Torr) was compared to the aluminum analogue, Alq3. In both cases, a previously unidentified close π−π interaction is identified, which likely impacts charge conduction. In the case of Inq3, we observe a mixture of both meridianal (mer) and facial (fac) crystals. The larger pseudohexagon mer-Inq3 crystals were analyzed by single-crystal X-ray diffraction and showed average In−N and In−O bond lengths significantly longer (0.22 and 0.26 Å, respectively) than Alq3 and bond angles about the In3+ ion more distorted from an ideal octahedral geometry. The crystalline packing of mer-Inq3 is found to closely resemble the β-Alq3 phase, where both metal chelates are characterized by pairing of symmetry-related mer-optical isomers in three-dimensional π−π stacking interactions (∼3.5 Å or less). The smaller needlelike crystals were determined to be pure fac-Inq3 by powder X-ray diffraction studies. An equivalent is not observed when Alq3 is processed in an identical manner.
Discharge measurement structures (1976)

This book presents instructions, standards, and procedures for the selection, design, and use of structures, which measure or regulate the flow rate in open channels. It is intended to serve as a guide to good practice for engineers concerned with the design and operation of such structures. It is hoped that the book will serve this purpose in three ways: (i) by giving the hydraulic theory related to discharge measurement structures; (ii) by indicating the major demands made upon the structures; and (iii) by providing specialized and technical knowledge on the more cornrnon types of structures now being used throughout the world. The text is addressed to the designer and operator of the structure and gives the hydraulic dimensions of the structure. Construction methods are only given if they influence the hydraulic performance of the structure. Otherwise, no methods of construction nor specifications of materials are given since they vary greatly from country to country and their selection will be influenced by such factors as the availability of materials, the quality of workmanship, and by the number of structures that need to be built.
Synthesis and structural characterization of a novel C3-chiral triamine and its trilithium triamide (2001)

The novel C3-chiral tripodal amine HC(SiMe2NHR*)3 (1) and the corresponding trilithium triamide HC(SiMe2N(Li)R*) (2) [R* = (R)-tetrahydronaphthyl] have been synthesized and characterized by X-ray diffraction; the latter was found to have a central adamantoid cage structure in which the two-coordinate Li atoms are internally solvated by the peripheral aryl groups.
[Telepsychiatry--psychiatric advice on the Internet]. (2004)

Psychiatrists on the Internet may expect an increase of electronic mail applicability in psychiatric advising. There is a need of medical, legal and ethical regulations of by-Internet doctor-patient relationship. Electronic mail may be treated as a source of knowledge on psychopathological symptoms and epidemiology of mental disturbances amongst the internet users.
Supplemental Tables S1-S12 from Genomic and Transcriptomic Analysis of Relapsed and Refractory Childhood Solid Tumors Reveals a Diverse Molecular Landscape and Mechanisms of Immune Evasion (2023)

&lt;p&gt;Table S1. Extended Cohort Annotations. Table S2. Mutational Signatures. Table S3. GISTIC Copy Number Analysis. Table S4. Somatic Variants in Relapsed/Refractory Childhood Solid Tumors (n=184 Patients with T/N WES). Table S5. Clinvar Pathogenic and Likely Pathogenic Germline Variants in Relapsed/Refractory Childhood Solid Tumors(n=184 Patients with T/N WES). Table S6. Gene Lists. Table S7. Log2(TPM+1) Values for the 2,199 Most Variable Genes Expressed Across the Cohort of Relapsed/Refractory Childhood Solid Tumors with RNA-seq (n=245). Table S8. Differential Expression Analysis of 2,199 Most Variable Genes Among Clusters. Table S9. Genes Filtered for COSMIC, Transcription Factors and Potential Drug Targets from Table S8 with log2FC greater than or equal to 2. Table S10. Differential Expression Analysis Among C3a, C3b, and C3c Subclusters. Table S11. Samples Falling in Clusters C3a-C3c and Genes that are Uniformly Highly Expressed in the Clusters. Table S12. Longitudinal Samples.&lt;/p&gt;
2 x 500Mb/s transmission across 25m of 1mm step-index PMMA POF with angular mode group diversity multiplexing (2006)

Angular Mode Group Diversity Multiplexing (AMGDM) is based on the principle that the axial angle of light propagating in a step-index multimode fiber is preserved for relatively short distances. By launching light from two laser diodes, each at a different angle, into a standard step-index Plastic Optical Fiber (POF), two different angular mode groups are excited, thereby creating two independent transmission channels in a single step-index POF. Moreover, these individual channels will experience less modal dispersion because fewer modes are present in each channel, leading to higher bandwidths. Using a demultiplexing setup consisting of two lenses and a concentric mirror, these two angular channels can be separated and detected properly at the receive side. Simultaneous transmission at a bit-rate of 500 Mb/s per channel with BER &amp;lt;10-10 is shown, resulting in a total bit-rate of 1 Gb/s over 25 m of standard SI-PMMAPOF.
Age-associated increase in rat cardiac opioid production (1993)

Several lines of evidence suggest that opioid peptide production in the heart may increase during aging from adulthood through senescence. We tested the hypothesis that cardiac opioid peptides and preproenkephalin (PNK) mRNA would increase with advancing age. Ventricles and atria from male Wistar rats, aged 2, 6, 18, and 22-24 mo of age, were acid extracted and assayed for methionine enkephalin (ME) and leucine enkephalin (LE). Total RNA was extracted from hearts of age-matched rats and probed for PNK mRNA by Northern blot analysis using a cDNA probe. ME and LE peptides were significantly elevated with advancing age in both ventricles [P < 0.001; by analysis of variance (ANOVA)]. Ventricular ME concentration exhibited a biphasic increase with approximately twofold higher peaks at 6 and 22-24 mo of age compared with the 2 mo value of 1.04 +/- 0.05 (SE) pmol/g wet wt. In contrast, ventricular LE concentration was largely unchanged until 22-24 mo of age when it increased approximately threefold over the 2-mo value of 2.19 +/- 0.14 pmol/g wet wt. Left ventricular PNK mRNA increased approximately fivefold between 2 and 18 mo of age (P < 0.01; ANOVA). Thus both enkephalins and the mRNA coding for them were increased in hearts of older vs. younger rats. Because opioid receptor stimulation can negatively modulate several characteristics of cardiac myocyte contraction, these results may have important functional implications for the senescent heart.
Genes affecting foliage color in watermelon (1986)

Journal Article Genes affecting foliage color in watermelon Get access B. B. Rhodes B. B. Rhodes The author is associate professor of horticulture, Clemson University, Edisto Experiment Station, Blackville, South Carolina 29817. Technical contribution no. 2432, South Carolina Agricultural Experiment Station, Clemson, SC 29631. Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Heredity, Volume 77, Issue 2, March 1986, Pages 134–135, https://doi.org/10.1093/oxfordjournals.jhered.a110190 Published: 01 March 1986
Regulation of Src tumor activity by its N-terminal intrinsically disordered region (2021)

ABSTRACT The membrane anchored Src tyrosine kinase is involved in numerous pathways and its deregulation is involved in human cancer. Our knowledge on Src regulation relies on crystallography, which revealed intramolecular interactions to control active Src conformations. However, Src contains a N-terminal intrinsically disordered unique domain (UD) whose function remains unclear. Using NMR, we reported that UD forms an intramolecular fuzzy complex involving a conserved region with lipid-binding capacity named Unique Lipid Binding Region (ULBR), which could modulate Src membrane anchoring. Here we show that the ULBR is essential for Src’s oncogenic capacity. ULBR inactive mutations inhibited Src transforming activity in NIH3T3 cells and in human colon cancer cells. It also reduced Src-induced tumor development in nude mice. An intact ULBR was required for MAPK signaling without affecting Src kinase activity nor sub-cellular localization. Phospho-proteomic analyses revealed that, while not impacting on the global tyrosine phospho-proteome in colon cancer cells, this region modulates phosphorylation of specific membrane-localized tyrosine kinases needed for Src oncogenic signaling, including EPHA2 and Fyn. Collectively, this study reveals an important role of this intrinsically disordered region in malignant cell transformation and suggests a novel layer of Src regulation by this unique region via membrane substrate phosphorylation.
Clinical and Proteomic Correlates of Plasma ACE2 (Angiotensin-Converting Enzyme 2) in Human Heart Failure (2020)

ACE2 (angiotensin-converting enzyme 2) is a key component of the renin-angiotensin-aldosterone system. Yet, little is known about the clinical and biologic correlates of circulating ACE2 levels in humans. We assessed the clinical and proteomic correlates of plasma (soluble) ACE2 protein levels in human heart failure. We measured plasma ACE2 using a modified aptamer assay among PHFS (Penn Heart Failure Study) participants (n=2248). We performed an association study of ACE2 against ≈5000 other plasma proteins measured with the SomaScan platform. Plasma ACE2 was not associated with ACE inhibitor and angiotensin-receptor blocker use. Plasma ACE2 was associated with older age, male sex, diabetes mellitus, a lower estimated glomerular filtration rate, worse New York Heart Association class, a history of coronary artery bypass surgery, and higher pro-BNP (pro-B-type natriuretic peptide) levels. Plasma ACE2 exhibited associations with 1011 other plasma proteins. In pathway overrepresentation analyses, top canonical pathways associated with plasma ACE2 included clathrin-mediated endocytosis signaling, actin cytoskeleton signaling, mechanisms of viral exit from host cells, EIF2 (eukaryotic initiation factor 2) signaling, and the protein ubiquitination pathway. In conclusion, in humans with heart failure, plasma ACE2 is associated with various clinical factors known to be associated with severe coronavirus disease 2019 (COVID-19), including older age, male sex, and diabetes mellitus, but is not associated with ACE inhibitor and angiotensin-receptor blocker use. Plasma ACE2 protein levels are prominently associated with multiple cellular pathways involved in cellular endocytosis, exocytosis, and intracellular protein trafficking. Whether these have a causal relationship with ACE2 or are relevant to novel coronavirus-2 infection remains to be assessed in future studies.
Roles of pgaABCD Genes in Synthesis, Modification, and Export of the Escherichia coli Biofilm Adhesin Poly-β-1,6- N -Acetyl- d -Glucosamine (2008)

The linear homopolymer poly-beta-1,6-N-acetyl-D-glucosamine (beta-1,6-GlcNAc; PGA) serves as an adhesin for the maintenance of biofilm structural stability in diverse eubacteria. Its function in Escherichia coli K-12 requires the gene products of the pgaABCD operon, all of which are necessary for biofilm formation. PgaC is an apparent glycosyltransferase that is required for PGA synthesis. Using a monoclonal antibody directed against E. coli PGA, we now demonstrate that PgaD is also needed for PGA formation. The deletion of genes for the predicted outer membrane proteins PgaA and PgaB did not prevent PGA synthesis but did block its export, as shown by the results of immunoelectron microscopy (IEM) and antibody adsorption assays. IEM also revealed a conditional localization of PGA at the cell poles, the initial attachment site for biofilm formation. PgaA contains a predicted beta-barrel porin and a superhelical domain containing tetratricopeptide repeats, which may mediate protein-protein interactions, implying that it forms the outer membrane secretin for PGA. PgaB contains predicted carbohydrate binding and polysaccharide N-deacetylase domains. The overexpression of pgaB increased the primary amine content (glucosamine) of PGA. Site-directed mutations targeting the N-deacetylase catalytic activity of PgaB blocked PGA export and biofilm formation, implying that N-deacetylation promotes PGA export through the PgaA porin. The results of previous studies indicated that N-deacetylation of beta-1,6-GlcNAc in Staphylococcus epidermidis by the PgaB homolog, IcaB, anchors it to the cell surface. The deletion of icaB resulted in release of beta-1,6-GlcNAc into the growth medium. Thus, covalent modification of beta-1,6-GlcNAc by N-deacetylation serves distinct biological functions in gram-negative and gram-positive species, dictated by cell envelope differences.
GHOST: global hepatitis outbreak and surveillance technology (2017)

GHOST enables automatic extraction of timely and relevant public health information suitable for guiding effective intervention measures. It is designed as a virtual diagnostic system intended for use in molecular surveillance and outbreak investigations rather than in research. The system produces accurate and reproducible information on HCV transmission clusters for all users, irrespective of their level of bioinformatics expertise. Improvement in molecular detection capacity will contribute to increasing the rate of transmission detection, thus providing opportunity for rapid, accurate and effective response to outbreaks of hepatitis C. Although GHOST was originally developed for hepatitis C surveillance, its modular structure is readily applicable to other infectious diseases. Worldwide availability of GHOST for the detection of HCV transmissions will foster deeper involvement of public health researchers and practitioners in hepatitis C outbreak investigation.
Tutorial: model predictive control technology (1999)

This paper provides a brief tutorial on model predictive control (MPC) theory for linear and nonlinear models. The discussion of MPC with linear models covers the topics of steady-state target calculation, infinite horizon receding horizon regulation, resolving infeasibilities caused by constraints, and state estimation and disturbance models. The section on nonlinear models briefly discusses what is desirable from a theoretical perspective and what is possible from an implementation perspective and focuses on some current efforts to bridge this gap. The paper concludes with a brief outlook for future developments in the areas of nonlinear MPC, robustness, moving horizon state estimation and MPC of hybrid systems.
Modeling structured environments by a single moving camera (2003)

We address the problem of the recovery of motion and a 3D model of environment with moving monocular vision. The vision sensor developed here is able to model structured environments in real time. Features such as corners and straight lines are tracked from image sequences. Their location and the motion of the camera are estimated with Kalman filters. Unlike in the conventional solution, these estimations are separated. There is a Kalman filter for each feature of the model. With this separation, it is simple to insert new objects into the environment model as they appear in the camera view. In addition, it is possible to use several separate modelers that update the common environment model. It is shown with several tests that motion estimation works well even with rather difficult real world scenes, but to obtain better 3D models, centers and straight lines are not discriminating enough to model such scenes.