gebhart/patrepeval huggingface dataset:
Plant pyruvate dehydrogenase complexes (1996)

While there is considerable overall metabolic similarity between plant and animal cells, drastically different anatomy, physiology, and organismal requirements have led to increasing diversity between these two classes of eukaryotes. Analyses of the pyruvate dehydrogenase complex (PDC) in plant cells serve to illustrate both the similarities inherent in pyruvate metabolism and differences dictated by the need to respond to diverse external stimuli. Plants contain two distinct, spatially separated PDCs, one within the mitochondrial matrix and the other in the plastid stroma. Each PDC isoform has characteristic structural, catalytic, and regulatory properties (Miernyk et al., 1985; Randall et al., 1989). The mitochondrial location of PDC is typical of the eukaryotic cell, where it serves as a primary entry point for carbon into the citric acid cycle. The plastid PDC provides the acetyl-CoA and NADH required for fatty acid and isoprenoid biosynthesis. Thus the first and most important mechanism for regulation of plant PDCs is compartmentalization of each of the enzymes.
Protein-Nucleic Acid Interaction (1989)

The book contains articles highlighting the rapidly evolving field of protein-nucleic acid interactions. Individual chapters demonstrate the diversity of biological systems to which protein-nucleic re
Genetic Manipulation of the Rabbit Heart via Transgenesis (2000)

Directed organ-specific expression is feasible in a larger animal with existing reagents, and cardiac-selective transgenic manipulation is possible in the rabbit.
Characterization of PrpC fromBacillus subtilis, a Member of the PPM Phosphatase Family (2000)

We cloned the yloO gene and purified a His-tagged form of its product, the putative protein phosphatase YloO, which we now designate PrpC. This closely resembles the human protein phosphatase PP2C, a member of the PPM family, in sequence and predicted secondary structure. PrpC has phosphatase activity in vitro against a synthetic substrate, p-nitrophenol phosphate, and endogenous Bacillus subtilis proteins. The prkC and prpC genes are adjacent on the chromosome, and the phosphorylated form of PrkC is a substrate for PrpC. These findings suggest that PrkC and PrpC may function as a couple in vivo.
Do salt bridges stabilize proteins? A continuum electrostatic analysis (1994)

The electrostatic contribution to the free energy of folding was calculated for 21 salt bridges in 9 protein X-ray crystal structures using a continuum electrostatic approach with the DELPHI computer-program package. The majority (17) were found to be electrostatically destabilizing; the average free energy change, which is analogous to mutation of salt bridging side chains to hydrophobic isosteres, was calculated to be 3.5 kcal/mol. This is fundamentally different from stability measurements using pKa shifts, which effectively measure the strength of a salt bridge relative to 1 or more charged hydrogen bonds. The calculated effect was due to a large, unfavorable desolvation contribution that was not fully compensated by favorable interactions within the salt bridge and between salt-bridge partners and other polar and charged groups in the folded protein. Some of the salt bridges were studied in further detail to determine the effect of the choice of values for atomic radii, internal protein dielectric constant, and ionic strength used in the calculations. Increased ionic strength resulted in little or no change in calculated stability for 3 of 4 salt bridges over a range of 0.1-0.9 M. The results suggest that mutation of salt bridges, particularly those that are buried, to "hydrophobic bridges" (that pack at least as well as wild type) can result in proteins with increased stability. Due to the large penalty for burying uncompensated ionizable groups, salt bridges could help to limit the number of low free energy conformations of a molecule or complex and thus play a role in determining specificity (i.e., the uniqueness of a protein fold or protein-ligand binding geometry).
Bootstrapping energy debugging on smartphones (2011)

This paper argues that a new class of bugs faced by millions of smartphones, energy bugs or ebugs, have become increasingly prominent that already they have led to significant user frustrations. We take a first look at this emerging important technical challenge faced by the smartphones, ebugs, broadly defined as an error in the system (application, OS, hardware, firmware, external conditions or combination) that causes an unexpected amount of high energy consumption by the system as a whole. We first present a taxonomy of the kinds of ebugs based on mining over 39K posts (1.2M before filtering) from 4 online mobile user forum and mobile OS bug repositories. The taxonomy shows the highly diverse nature of smartphone ebugs. We then propose a roadmap towards developing a systematic diagnosing framework for debugging ebugs on smartphones.
Vitamin D: More Than a “Bone-a-Fide” Hormone (2003)

The vitamin D endocrine system is critical for the proper development and maintenance of mineral ion homeostasis and skeletal integrity. Beyond these classical roles, recent evidence suggests that the bioactive metabolite of vitamin D, 1,25-dihydroxyvitamin D3, functions in diverse physiological processes, such as hair follicle cycling, blood pressure regulation, and mammary gland development. This minireview explores the current progress in unraveling the complexities of the vitamin D endocrine system by focusing on four main areas of research: the resolution of the vitamin D receptor crystal structure, the molecular details of 1,25-dihydroxyvitamin D3-mediated transcription, murine knockout models of key genes in the endocrine system, and alternative vitamin D receptors and ligands.
Calcitonin gene-related peptide triggers migraine-like attacks in patients with migraine with aura (2010)

CGRP triggered migraine-like attacks without aura in patients suffering exclusively from MA. It also triggered a typical aura in 28% of the patients. These data indicate similar neurobiological pathways responsible for triggering migraine headache in MA and MO patients, and suggest differences between MA/MO and FHM.
Risk of recurrence of prolonged pregnancy (2003)

Risk of recurrence of prolonged pregnancyProlonged pregnancy-a pregnancy with a gestational length of 294 days or more-occurs in about 5% of all births.It is associated with a higher frequency of obstetric complications and perinatal morbidity, 1 and little is known about its aetiology. 2 We studied the risk of recurrence of prolonged pregnancy as a function of change in partner or change in social conditions.
Drilling Fluids Approaches for Control of Wellbore Instability in Fractured Formations (2003)

Abstract The presence of microfractures is now recognized as a common cause of severe wellbore instability, particularly in ultra-low permeability rocks such as shales and some limestones. In unstable microfractured formations, it is important to avoid pressurizing the fractures with drilling mud. This paper examines the rock mechanics aspects of wellbore instability in microfractured formations, and identifies drilling fluids and drilling practices that reduce the problem. Improved stability can be achieved by the use of certain drilling fluid additives that seal fractures. Limited success is seen with sized solids, asphalts, gilsonites or conventional lost circulation materials but a recently developed additive for use in oil- or water-based muds appears to prevent much of the instability normally observed. The mechanism of action of this additive is discussed and a recent field case history presented.
Starch Formate (1957)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStarch FormateI. A. Wolff, D. W. Olds, and G. E. HilbertCite this: J. Am. Chem. Soc. 1957, 79, 14, 3860–3862Publication Date (Print):July 1, 1957Publication History Published online1 May 2002Published inissue 1 July 1957https://pubs.acs.org/doi/10.1021/ja01571a063https://doi.org/10.1021/ja01571a063research-articleACS PublicationsRequest reuse permissionsArticle Views144Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The Balancing Act: Combining Symbolic and Statistical Approaches to Language (1996)

Symbolic and statistical approaches to language have historically been at odds -- the former viewed as difficult to test and therefore perhaps impossible to define, and the latter as descriptive but possibly inadequate. At the heart of the debate are fundamental questions concerning the nature of language, the role of data in building a model or theory, and the impact of the competence-performance distinction on the field of computational linguistics. Currently, there is an increasing realization in both camps that the two approaches have something to offer in achieving common goals. The eight contributions in this book explore the inevitable balancing act that must take place when symbolic and statistical approaches are brought together -- including basic choices about what knowledge will be represented symbolically and how it will be obtained, what assumptions underlie the statistical model, what principles motivate the symbolic model, and what the researcher gains by combining approaches. The topics covered include an examination of the relationship between traditional linguistics and statistical methods, qualitative and quantitative methods of speech translation, study and implementation of combined techniques for automatic extraction of terminology, comparative analysis of the contributions of linguistic cues to a statistical word grouping system, automatic construction of a symbolic parser via statistical techniques, combining linguistic with statistical methods in automatic speech understanding, exploring the nature of transformation-based learning, and a hybrid symbolic/statistical approach to recovering from parser failures.
2-(Alkylamino)nicotinic acid and analogs. Potent angiotensin II antagonists (1993)

A series of pyridines and other six-membered ring heterocycles connected to a biphenyltetrazole with a -CH2-NR'-link (1) were discovered to be potent angiotensin II antagonists. In the pyrimidine carboxylic acid series (W = CR, X = N, Y = CH, Z = COOH), compounds with an alkyl group (R') on the exocyclic nitrogen were much more potent than compounds with an alkyl group (R) on the heterocyclic ring. The corresponding pyridine, pyridazine, pyrazine, and 1,2,4-triazine carboxylic acids also showed potent in vitro angiotensin II antagonism. The pyridine (W, X, Y = CH, Z = COOH, R' = n-C3H7) demonstrated potent in vitro activity (pA2 = 10.10, rabbit aorta, and Ki = 0.61 nM, receptor binding in rat liver) as well as exceptional oral antihypertensive activity and bioavailability. Any nonacidic replacement for the carboxylic acid was detrimental for activity.
Apolipoprotein E isoform-dependent amyloid deposition and neuritic degeneration in a mouse model of Alzheimer's disease (2000)

Apolipoprotein E (apoE) alleles determine the age-adjusted relative risk (epsilon4 > epsilon3) for Alzheimer's disease (AD). ApoE may affect AD pathogenesis by promoting deposition of the amyloid-beta (Abeta) peptide and its conversion to a fibrillar form. To determine the effect of apoE on Abeta deposition and AD pathology, we compared APP(V717F) transgenic (TG) mice expressing mouse, human, or no apoE (apoE(-/-)). A severe, plaque-associated neuritic dystrophy developed in APP(V717F) TG mice expressing mouse or human apoE. Though significant levels of Abeta deposition also occurred in APP(V717F) TG, apoE(-/-) mice, neuritic degeneration was virtually absent. Expression of apoE3 and apoE4 in APP(V717F) TG, apoE(-/-) mice resulted in fibrillar Abeta deposits and neuritic plaques by 15 months of age and substantially (>10-fold) more fibrillar deposits were observed in apoE4-expressing APP(V717F) TG mice. Our data demonstrate a critical and isoform-specific role for apoE in neuritic plaque formation, a pathological hallmark of AD.
Mass measurement and top-down HPLC/MS analysis of intact monoclonal antibodies on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer (2009)

Mass and top-down analyses of 150-kDa monoclonal immunoglobulin gamma (IgG) antibodies were performed on an Orbitrap analyzer. Three different sample delivery methods were tested including (1) infusion of an off-line desalted IgG sample using nano-electrospray; (2) on-line desalting followed by a step elution with a high percentage of organic solvent; and (3) reversed-phase HPLC separation and on-line mass and top-down analyses of disulfide isoforms of an IgG2 antibody. The accuracy of mass measurements of intact antibody was within +/-2 Da (15 ppm). The glycoforms of intact IgG antibodies separated by 162 Da were baseline resolved. In-source fragmentation of the intact antibodies produced mainly 115 residue fragments including N-terminal variable domains of heavy and light chains. The sequence coverage (the number of cleavages) was greatly increased after reduction of disulfide bonds and HPLC/MS/MS analysis of light and heavy chains using collision-induced dissociation in the ion trap of the LTQ-Orbitrap. This is an attractive alternative to peptide mapping for characterization and monitoring of post-translational modifications attributed to minimal sample preparation, high speed of the mass/top-down analysis, and relatively minor method-induced sample modifications.
Chimera States for Coupled Oscillators (2004)

Arrays of identical oscillators can display a remarkable spatiotemporal pattern in which phase-locked oscillators coexist with drifting ones. Discovered two years ago, such "chimera states" are believed to be impossible for locally or globally coupled systems; they are peculiar to the intermediate case of nonlocal coupling. Here we present an exact solution for this state, for a ring of phase oscillators coupled by a cosine kernel. We show that the stable chimera state bifurcates from a spatially modulated drift state, and dies in a saddle-node bifurcation with an unstable chimera state.
α/β-Peptide Foldamers Targeting Intracellular Protein–Protein Interactions with Activity in Living Cells (2015)

Peptides can be developed as effective antagonists of protein-protein interactions, but conventional peptides (i.e., oligomers of l-α-amino acids) suffer from significant limitations in vivo. Short half-lives due to rapid proteolytic degradation and an inability to cross cell membranes often preclude biological applications of peptides. Oligomers that contain both α- and β-amino acid residues ("α/β-peptides") manifest decreased susceptibility to proteolytic degradation, and when properly designed these unnatural oligomers can mimic the protein-recognition properties of analogous "α-peptides". This report documents an extension of the α/β-peptide approach to target intracellular protein-protein interactions. Specifically, we have generated α/β-peptides based on a "stapled" Bim BH3 α-peptide, which contains a hydrocarbon cross-link to enhance α-helix stability. We show that a stapled α/β-peptide can structurally and functionally mimic the parent stapled α-peptide in its ability to enter certain types of cells and block protein-protein interactions associated with apoptotic signaling. However, the α/β-peptide is nearly 100-fold more resistant to proteolysis than is the parent stapled α-peptide. These results show that backbone modification, a strategy that has received relatively little attention in terms of peptide engineering for biomedical applications, can be combined with more commonly deployed peripheral modifications such as side chain cross-linking to produce synergistic benefits.
Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli (2010)

Toward Microbial Taxol Taxol, a minor chemical constituent of yew tree bark, has provided a potent cancer treatment. Production methods presently rely on plant cell cultures. Ajikumar et al. (p. 70 ; see the Perspective by Liu and Khosla ) engineered Escherichia coli cells to produce a key taxol precursor, in which the polycyclic carbon skeleton is intact. The approach relied on optimizing the relative activity of two pathways, the first of which synthesized isoprenoid building blocks that were then stitched together with the second pathway. Accumulation of indole as a by-product inhibited the isoprenoid pathway—an insight that should facilitate more efficient engineered biosynthesis of a wide range of commercially important isoprenoid derivatives.
Convolutional Neural Network (2017)

The importance of the deep neural network lies in the fact that it opened the door to the complicated non-linear model and systematic approach for the hierarchical processing of knowledge.
Mapping of N6-methyladenosine residues in bovine prolactin mRNA. (1984)

N6-Methyladenosine (m6A) residues, which are found internally in viral and cellular mRNA populations at the sequences Apm6ApC and Gpm6ApC, have been proposed to play a role in mRNA processing and transport. We have developed a sensitive approach to analyze the level and location of m6A in specific purified cellular mRNAs in an attempt to correlate m6A location with function. Polyadenylylated mRNA is hybridized to cDNA clones representing the full size mRNA under study or fragments of it, and the protected RNA is digested and labeled with polynucleotide kinase in vitro. After enrichment for m6A with anti-m6A antibody, the [32P]-pm6A is separated on TLC plates, and compared with the total amount of radiolabeled nucleotides. Using this combination of in vitro RNA labeling and antibody selection, we were able to detect m6A in purified stable mRNAs that cannot be readily labeled in cells with greater sensitivity than was possible by previous techniques. We applied this technique to bovine prolactin mRNA and showed that this mRNA contains m6A. Moreover, all of the m6A residues in this message are found within the 3' two-thirds of the molecule and are highly concentrated (61%) within a sequence of 108 nucleotides at the 3' noncoding region of the message. The nonrandom distribution of m6A in a specific cellular mRNA, as demonstrated for bovine prolactin, will have to be taken into account when designing a model for m6A function.
Reduced protein expression of metastasis‐related genes (nm23, KISS1, KAI1 and p53) in lymph node and liver metastases of gastric cancer (2007)

Our investigations revealed a tendency of reduced protein expression of metastasis suppressor genes nm23, KISS1 and KAI1 in gastric cancer with the progress of metastasis. This means that the progression theory is an important determinant of metastatic efficiency.
Predictors of decreased libido in women during the late reproductive years (2004)

Decreased libido in the late reproductive years is associated with a pronounced fluctuation in total testosterone over time. Other independent risk factors for decreased libido include vaginal dryness, depression, and living with children. Sexual dysfunction is a complex disorder, related to physiological and psychosocial factors, requiring further investigation.
Cell Senescence in the Aging Kidney (2010)

Pedigree genetics and environment modulate the biological process of aging. The permanent and irreversible growth arrest of cell senescence is a central paradigm of aging. Various pathophysiologic pressures such as oxidative stress and mitochondrial injury can also induce senescence. Senescent cells secrete altered levels of growth factors, show increased susceptibility to apoptosis, and associate with delayed repair and regeneration in the aging kidney. Here we discuss new progress in understanding renal aging, focusing on mechanisms of cell senescence and possible interventions to modulate age-related organ damage.
Split-Detector Computed Tomography: A Preliminary Report (1978)

A split-detector system, consisting of a thin CaF2 scintillator followed by a thick Nal crystal, was installed in an EMI Mark I scanner. Energy discrimination is possible because the CaF2 crystal responds primarily to low-energy photons; dual-energy images can be obtained from only one scan. Calculations and preliminary experiments show that the split-detector separates energies better than the 100-140 kVp method. It was possible with the split detector to differentiate between two weak solutions of CaCI2 and KI which had the same computed tomography number (44 H), under normal scanning conditions.
RNA polymerase II elongation complex. Elongation complexes purified using an anti-RNA antibody do not contain initiation factor alpha (1991)

Gene expression in eukaryotes can be regulated by controlling the efficiency of transcript elongation by RNA polymerase II. The composition of the elongation complex is, however, poorly understood. Previous work has identified DNA sequences which block RNA polymerase II transcription and factors which stimulate RNA chain elongation. Here, I have purified elongation complexes arrested at discrete template locations. Complexes were rapidly and efficiently precipitated from in vitro transcription reactions using a monoclonal antibody that binds RNA. The isolated complexes remained transcriptionally active. This technique enables the facile manipulation of transcription elongation complexes. Using this approach, I show that transcription initiation factor alpha is not associated with a RNA polymerase II elongation complex. Since others have shown that alpha associates stoichiometrically with DNA, RNA polymerase II, and other required factors in an initiation complex, this work suggests that alpha departs from the transcription complex after nucleotides are required but before extensive RNA chain synthesis. In this regard alpha resembles the bacterial promoter-recognition factor sigma.
Improving fairness, efficiency, and stability in HTTP-based adaptive video streaming with FESTIVE (2012)

Many commercial video players rely on bitrate adaptation logic to adapt the bitrate in response to changing network conditions. Past measurement studies have identified issues with today's commercial players with respect to three key metrics---efficiency, fairness, and stability---when multiple bitrate-adaptive players share a bottleneck link. Unfortunately, our current understanding of why these effects occur and how they can be mitigated is quite limited.
A Sunflower Helianthinin Gene Upstream Sequence Ensemble Contains an Enhancer and Sites of Nuclear Protein Interaction (1989)

Juan Jordano, , Terry L. Thomas, A Sunflower Helianthinin Gene Upstream Sequence Ensemble Contains an Enhancer and Sites of Nuclear Protein Interaction, The Plant Cell, Vol. 1, No. 9 (Sep., 1989), pp. 855-866