gebhart/patrepeval huggingface dataset:
Images of a lipid bilayer at molecular resolution by scanning tunneling microscopy. (1987)

The molecular structure of a fatty acid bilayer has been recorded with a scanning tunneling microscope operating in air. The molecular film, a bilayer of cadmium icosanoate (arachidate), was deposited onto a graphite substrate by the Langmuir-Blodgett technique. The packing of the lipid film was found to be partially ordered. Along one axis of the triclinic unit cell the intermolecular distance varied randomly around a mean of 5.84 A with a SD of 0.24 A. Along the other axis the mean distance was 4.1 A and appeared to vary monotonically over several intermolecular distances, indicating that a superstructure of longer range may exist. The molecular density was one molecular per 19.4 A2. The surprising ability of the scanning tunneling microscope to image the individual molecular chains demonstrates that electrons from the graphite can be transferred along the molecular chains for a distance of 50 A.
The out of phase 1 Mutant Defines a Role for PHYB in Circadian Phase Control in Arabidopsis (2002)

Arabidopsis displays circadian rhythms in stomatal aperture, stomatal conductance, and CO(2) assimilation, each of which peaks around the middle of the day. The rhythmic opening and closing of stomata confers a rhythm in sensitivity and resistance, respectively, to the toxic gas sulfur dioxide. Using this physiological assay as a basis for a mutant screen, we isolated mutants with defects in circadian timing. Here, we characterize one mutant, out of phase 1 (oop1), with the circadian phenotype of altered phase. That is, the timing of the peak (acrophase) of multiple circadian rhythms (leaf movement, CO(2) assimilation, and LIGHT-HARVESTING CHLOROPHYLL a/b-BINDING PROTEIN transcription) is early with respect to wild type, although all circadian rhythms retain normal period length. This is the first such mutant to be characterized in Arabidopsis. oop1 also displays a strong photoperception defect in red light characteristic of phytochrome B (phyB) mutants. The oop1 mutation is a nonsense mutation of PHYB that results in a truncated protein of 904 amino acids. The defect in circadian phasing is seen in seedlings entrained by a light-dark cycle but not in seedlings entrained by a temperature cycle. Thus, PHYB contributes light information critical for proper determination of circadian phase.
On the design of side-stick controllers in fly-by-wire aircraft (1994)

This paper presents the problem of designing the functional behaviour of the interaction between two side-stick controllers, an autopilot, and a flight control computer in a fly-by-wire aircraft. Two models are developed using the ISO formal description technique LOTOS, and analysed using rigorous abstract testing techniques.
Cytokine inhibition in the treatment of COPD (2014)

Cytokines play an important part in many pathobiological processes of chronic obstructive pulmonary disease (COPD), including the chronic inflammatory process, emphysema, and altered innate immune response. Proinflammatory cytokines of potential importance include tumor necrosis factor (TNF)-α, interferon-γ, interleukin (IL)-1β, IL-6, IL-17, IL-18, IL-32, and thymic stromal lymphopoietin (TSLP), and growth factors such as transforming growth factor-β. The current objectives of COPD treatment are to reduce symptoms, and to prevent and reduce the number of exacerbations. While current treatments achieve these goals to a certain extent, preventing the decline in lung function is not currently achievable. In addition, reversal of corticosteroid insensitivity and control of the fibrotic process while reducing the emphysematous process could also be controlled by specific cytokines. The abnormal pathobiological process of COPD may contribute to these fundamental characteristics of COPD, and therefore targeting cytokines involved may be a fruitful endeavor. Although there has been much work that has implicated various cytokines as potentially playing an important role in COPD, there have been very few studies that have examined the effect of specific cytokine blockade in COPD. The two largest studies that have been reported in the literature involve the use of blocking antibody to TNFα and CXCL8 (IL-8), and neither has provided benefit. Blocking the actions of CXCL8 through its CXCR2 receptor blockade was not successful either. Studies of antibodies against IL-17, IL-18, IL-1β, and TSLP are currently either being undertaken or planned. There is a need to carefully phenotype COPD and discover good biomarkers of drug efficacy for each specific target. Specific groups of COPD patients should be targeted with specific anticytokine therapy if there is evidence of high expression of that cytokine and there are features of the clinical expression of COPD that will respond.
Rolling resistance of articular cartilage due to interstitial fluid flow (1997)

A mechanism which may contribute to the frictional coefficient of diarthrodial joints is the rolling resistance due to hysteretic energy loss of viscoelastic cartilage resulting from interstitial fluid flow. The hypothesis of this study is that rolling resistance contributes significantly to the measured friction coefficient of articular cartilage. Due to the difficulty of testing this hypothesis experimentally, theoretical predictions of the rolling resistance are obtained using the solution for rolling contact of biphasic cylindrical cartilage layers [Ateshian and Wang]. Over a range of rolling velocities, tissue properties and dimensions, it is found that the coefficient of rolling resistance microR varies in magnitude from 10(-6) to 10(-2); thus, it is generally negligible in comparison with experimental measurements of the cartilage friction coefficient (10(-3)-10(-1)) except, possibly, when the tissue is arthritic. Hence, the hypothesis of this study is rejected on the basis of these results.
A Synthetic Arabinose-Inducible Promoter Confers High Levels of Recombinant Protein Expression in Hyperthermophilic Archaeon Sulfolobus islandicus (2012)

Despite major progresses in genetic studies of hyperthermophilic archaea, recombinant protein production in these organisms always suffers from low yields and a robust expression system is still in great demand. Here we report a versatile vector that confers high levels of protein expression in Sulfolobus islandicus, a hyperthermophilic crenarchaeon. Two expression vectors, pSeSD and pEXA, harboring 11 unique restriction sites were constructed. They contain coding sequences of two hexahistidine (6×His) peptide tags and those coding for two protease sites, the latter of which make it possible to remove the peptide tags from expressed recombinant proteins. While pEXA employed an araS promoter for protein expression, pSeSD utilized P(araS-SD), an araS derivative promoter carrying an engineered ribosome-binding site (RBS; a Shine-Dalgarno [SD] sequence). We found that P(araS-SD) directed high levels of target gene expression. More strikingly, N-terminal amino acid sequencing of recombinant proteins unraveled that the protein synthesized from pEXA-N-lacS lacked the designed 6×His tag and that translation initiation did not start at the ATG codon of the fusion gene. Instead, it started at multiple sites downstream of the 6×His codons. Intriguingly, inserting an RBS site upstream of the ATG codon regained the expression of the 6×His tag, as shown with pSeSD-N-lacS. These results have yielded novel insight into the archaeal translation mechanism. The crenarchaeon Sulfolobus can utilize N-terminal coding sequences of proteins to specify translation initiation in the absence of an RBS site.
Endogenous Opioid Peptides Acting at μ-Opioid Receptors in the Dorsal Horn Contribute to Midbrain Modulation of Spinal Nociceptive Neurons (1998)

Activation of neurons in the midbrain periaqueductal gray (PAG) inhibits spinal dorsal horn neurons and produces behavioral antinociception in animals and analgesia in humans. Although dorsal horn regions modulated by PAG activation contain all three opioid receptor classes (mu, delta, and kappa), as well as enkephalinergic interneurons and terminal fields, descending opioid-mediated inhibition of dorsal horn neurons has not been demonstrated. We examined the contribution of dorsal horn mu-opioid receptors to the PAG-elicited descending modulation of nociceptive transmission. Single-unit extracellular recordings were made from rat sacral dorsal horn neurons activated by noxious heating of the tail. Microinjections of bicuculline (BIC) in the ventrolateral PAG led to a 60-80% decrease in the neuronal responses to heat. At the same time, the responses of the same neurons to iontophoretically applied NMDA or kainic acid were not consistently inhibited. The inhibition of heat-evoked responses by PAG BIC was reversed by iontophoretic application of the selective mu-opioid receptor antagonists, D-Phe-Cys-Tyr-D-Trp-Orn-Thr-Pen-Thr-NH2 (CTOP) and D-Phe-Cys-Tyr-D-Trp-Arg-Thr-Pen-Thr-NH2 (CTAP). A similar effect was produced by naloxone; however, naloxone had an excitatory influence on dorsal horn neurons in the absence of PAG-evoked descending inhibition. This is the first demonstration that endogenous opioids acting via spinal mu-opioid receptors contribute to brain stem control of nociceptive spinal dorsal horn neurons. The inhibition appears to result in part from presynaptic inhibition of afferents to dorsal horn neurons.
Group B Streptococcal Pilus Proteins Contribute to Adherence to and Invasion of Brain Microvascular Endothelial Cells (2007)

Surface filamentous structures known as pili have been discovered recently in the gram-positive streptococcal pathogens that cause invasive disease in humans, including group B Streptococcus (GBS). We show that two GBS proteins involved in pilus formation, encoded by pilA and pilB, also facilitate the interaction of this important agent of central nervous system infection with endothelial cells of the human blood-brain barrier.
The ‘Non-Criminal’ Class: Wife-beating in Scotland (c. 1800-1949) (2010)

The nineteenth century has been identified as one in which a ‘new softer patriarchy’ emerged along with a more companionate marriage; a wider acceptance of forms of domestic violence and a hardening of attitudes towards men who inflicted violence on their wives. Using criminal statistics, changes in law and practice and the discursive debates which permeated the Scottish media, this article will highlight how the relationship between provocation, criminal liability and diminished responsibility ensured that attitudes towards men who inflicted violence on their wives reflected greater levels of continuity rather than change in Scotland in the period 1850-1950.
Domain Name System KEY (DNSKEY) Resource Record (RR) Secure Entry Point (SEP) Flag (2004)

With the Delegation Signer (DS) resource record (RR), the concept of a public key acting as a secure entry point (SEP) has been introduced. During exchanges of public keys with the parent there is a need to differentiate SEP keys from other public keys in the Domain Name System KEY (DNSKEY) resource record set. A flag bit in the DNSKEY RR is defined to indicate that DNSKEY is to be used as a SEP. The flag bit is intended to assist in operational procedures to correctly generate DS resource records, or to indicate what DNSKEYs are intended for static configuration. The flag bit is not to be used in the DNS verification protocol. This document updates RFC 2535 and RFC 3755.
Proliferation of glial cells induced by lithium in the neural lobe of the rat pituitary is enhanced by dehydration (2002)

Rats dehydrated by 6 days of water deprivation had a low level of mitotic activity in the astrocytes ('pituicytes') of the neural lobe of the pituitary. Mitotic activity in the pituicytes was greatly increased when isotonic lithium was administered in the last 3 days of water deprivation. Rehydration on the last day of the experiment produced a further increase in mitoses. Isotonic solutions of sodium, potassium or rubidium chloride did not increase mitoses. This model of cell proliferation is of interest because the mitotic activity is related to a physiological attempt to maintain homeostasis rather than a response to injury or the development of neoplasia.
Reduced CTL Response and Increased Viral Burden in Substance P Receptor-Deficient Mice Infected with Murine γ-Herpesvirus 68 (2003)

One component of the protective host response against mucosal pathogens includes the local production and increased expression of certain neuropeptides and their receptors. The present study further demonstrates this fact by investigating the contribution that substance P receptor expression makes toward immunity against a gamma-herpesvirus infection. Following intragastric inoculation with murine gamma-herpesvirus 68 (gamma HV-68), expression of substance P and its receptor was increased in mucosal and peripheral lymphoid organs in wild-type strains of mice. These results suggested that this receptor/ligand pair might be an important component of the host response against this viral infection. Such a hypothesis was supported by the demonstration that mice, genetically deficient in substance P receptor expression, showed an increased viral burden when compared with syngeneic C57BL/6 mice. Furthermore, substance P receptor-deficient mice showed a reduced CTL response against gamma HV-68, suggesting a mechanism to explain this increased viral burden. Such limitations in the Ag-specific CTL response in substance P receptor-deficient mice could result from lowered expression of IL-12 during viral infection. Consistent with this hypothesis, increases in mRNA encoding IL-12 and secretion of this cytokine into sera of infected, wild-type animals were markedly reduced in substance P receptor-deficient mice. These studies demonstrate that genetic elimination of substance P receptors in mice results in an increased gamma-herpesvirus burden and an altered host response.
(C-f)- Weak Contraction in Cone Metric Spaces (2013)

The purpose of this article  is to introduced the concept of  weak contraction in cone metric space and also establish a coincidence and common fixed point result for  weak contractions in cone metric spaces. Our result proper generalizes the results of Sintunavarat and Kumam [7]. We also give an example in support of our result. Keywords :- Cone metric spaces, weak contraction,  weak contraction, coincidence point, common fixed point.
Recurrent anal fistulae: Limited surgery supported by stem cells (2015)

Stem cells are safe and useful for treating anal fistulae. Healing can be achieved in severe cases, sparing fecal incontinence risk, and improving previous scoring.
Calcium carbonate as a phosphate binder: is there a need to adjust peritoneal dialysate calcium concentrations for patients using CaCO3? (1989)

The widespread use of calcium carbonate as a phosphate binder is limited by its tendency to develop hypercalcemia in some patients using effective dosages needed to control hyperphosphatemia. Most common continuous ambulatory peritoneal dialysis (CAPD) regimens using dialysis solutions containing 3.5 mEq/L of calcium result in net absorption of calcium from the dialysis solution and, hence limit the amount of oral calcium that can be administered. Peritoneal dialysis solutions with reduced calcium levels are needed for effective use of CaCO3 to control hyperphosphatemia in some dialysis patients.
Enhanced HtrA2/Omi Expression in Oxidative Injury to Retinal Pigment Epithelial Cells and Murine Models of Neurodegeneration (2009)

These findings suggest that HtrA2/Omi is related to RPE apoptosis due to oxidative stress, which may play an important role in the integrity of mitochondria and the pathogenesis of AMD.
Improving colorectal cancer screening by using community volunteers (2007)

Although CRC screening rates were not significantly better after the intervention, there was a positive change in beliefs about screening and intention to be screened. The results suggest that the dissemination of an evidence-based behavioral intervention may require a longer duration to engage hard-to-reach populations and change behaviors.
Energy Transfer. A System with Relatively Fixed Donor-Acceptor Separation (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnergy Transfer. A System with Relatively Fixed Donor-Acceptor SeparationS. A. Latt, H. T. Cheung, and E. R. BloutCite this: J. Am. Chem. Soc. 1965, 87, 5, 995–1003Publication Date (Print):March 1, 1965Publication History Published online1 May 2002Published inissue 1 March 1965https://pubs.acs.org/doi/10.1021/ja01083a011https://doi.org/10.1021/ja01083a011research-articleACS PublicationsRequest reuse permissionsArticle Views737Altmetric-Citations138LEARN 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
Oxidative stress in β-thalassaemia and sickle cell disease (2015)

Sickle cell disease and β-thalassaemia are inherited haemoglobinopathies resulting in structural and quantitative changes in the β-globin chain. These changes lead to instability of the generated haemoglobin or to globin chain imbalance, which in turn impact the oxidative environment both intracellularly and extracellularly. The ensuing oxidative stress and the inability of the body to adequately overcome it are, to a large extent, responsible for the pathophysiology of these diseases. This article provides an overview of the main players and control mechanisms involved in the establishment of oxidative stress in these haemoglobinopathies.
3D Visualization of the Temporal and Spatial Spread of Tau Pathology Reveals Extensive Sites of Tau Accumulation Associated with Neuronal Loss and Recognition Memory Deficit in Aged Tau Transgenic Mice (2016)

3D volume imaging using iDISCO+ was applied to observe the spatial and temporal progression of tau pathology in deep structures of the brain of a mouse model that recapitulates the earliest stages of Alzheimer's disease (AD). Tau pathology was compared at four timepoints, up to 34 months as it spread through the hippocampal formation and out into the neocortex along an anatomically connected route. Tau pathology was associated with significant gliosis. No evidence for uptake and accumulation of tau by glia was observed. Neuronal cells did appear to have internalized tau, including in extrahippocampal areas as a small proportion of cells that had accumulated human tau protein did not express detectible levels of human tau mRNA. At the oldest timepoint, mature tau pathology in the entorhinal cortex (EC) was associated with significant cell loss. As in human AD, mature tau pathology in the EC and the presence of tau pathology in the neocortex correlated with cognitive impairment. 3D volume imaging is an ideal technique to easily monitor the spread of pathology over time in models of disease progression.
Segmentation of X‐ray computed tomography images of porous materials: A crucial step for characterization and quantitative analysis of pore structures (2009)

Nondestructive imaging methods such as X‐ray computed tomography (CT) yield high‐resolution, three‐dimensional representations of pore space and fluid distribution within porous materials. Steadily increasing computational capabilities and easier access to X‐ray CT facilities have contributed to a recent surge in microporous media research with objectives ranging from theoretical aspects of fluid and interfacial dynamics at the pore scale to practical applications such as dense nonaqueous phase liquid transport and dissolution. In recent years, significant efforts and resources have been devoted to improve CT technology, microscale analysis, and fluid dynamics simulations. However, the development of adequate image segmentation methods for conversion of gray scale CT volumes into a discrete form that permits quantitative characterization of pore space features and subsequent modeling of liquid distribution and flow processes seems to lag. In this paper we investigated the applicability of various thresholding and locally adaptive segmentation techniques for industrial and synchrotron X‐ray CT images of natural and artificial porous media. A comparison between directly measured and image‐derived porosities clearly demonstrates that the application of different segmentation methods as well as associated operator biases yield vastly differing results. This illustrates the importance of the segmentation step for quantitative pore space analysis and fluid dynamics modeling. Only a few of the tested methods showed promise for both industrial and synchrotron tomography. Utilization of local image information such as spatial correlation as well as the application of locally adaptive techniques yielded significantly better results.
Structural Analysis of the Binding of Type I, I1/2, and II Inhibitors to Eph Tyrosine Kinases (2014)

We have solved the crystal structures of the EphA3 tyrosine kinase in complex with nine small-molecule inhibitors, which represent five different chemotypes and three main binding modes, i.e., types I and I1/2 (DFG in) and type II (DFG out). The three structures with type I1/2 inhibitors show that the higher affinity with respect to type I is due to an additional polar group (hydroxyl or pyrazole ring of indazole) which is fully buried and is involved in the same hydrogen bonds as the (urea or amide) linker of the type II inhibitors. Overall, the type I and type II binding modes belong to the lock-and-key and induced fit mechanism, respectively. In the type II binding, the scaffold in contact with the hinge region influences the position of the Phe765 side chain of the DFG motif and the orientation of the Gly-rich loop. The binding mode of Birb796 in the EphA3 kinase does not involve any hydrogen bond with the hinge region, which is different from the Birb796/p38 MAP kinase complex. Our structural analysis emphasizes the importance of accounting for structural plasticity of the ATP binding site in the design of type II inhibitors of tyrosine kinases.