gebhart/patrepeval huggingface dataset:
The anabolic response to a meal containing different amounts of protein is not limited by the maximal stimulation of protein synthesis in healthy young adults (2015)

We have determined whole body protein kinetics, i.e., protein synthesis (PS), breakdown (PB), and net balance (NB) in human subjects in the fasted state and following ingestion of ~40 g [moderate protein (MP)], which has been reported to maximize the protein synthetic response or ~70 g [higher protein (HP)] protein, more representative of the amount of protein in the dinner of an average American diet. Twenty-three healthy young adults who had performed prior resistance exercise (X-MP or X-HP) or time-matched resting (R-MP or R-HP) were studied during a primed continuous infusion of l-[(2)H5]phenylalanine and l-[(2)H2]tyrosine. Subjects were randomly assigned into an exercise (X, n = 12) or resting (R, n = 11) group, and each group was studied at the two levels of dietary protein intake in random order. PS, PB, and NB were expressed as increases above the basal, fasting values (mg·kg lean body mass(-1)·min(-1)). Exercise did not significantly affect protein kinetics and blood chemistry. Feeding resulted in positive NB at both levels of protein intake: NB was greater in response to the meal containing HP vs. MP (P < 0.00001). The greater NB with HP was achieved primarily through a greater reduction in PB and to a lesser extent stimulation of protein synthesis (for all, P < 0.0001). HP resulted in greater plasma essential amino acid responses (P < 0.01) vs. MP, with no differences in insulin and glucose responses. In conclusion, whole body net protein balance improves with greater protein intake above that previously suggested to maximally stimulating muscle protein synthesis because of a simultaneous reduction in protein breakdown.
Local probing of magnetoelectric coupling and magnetoelastic control of switching in BiFeO3-CoFe2O4 thin-film nanocomposite (2013)

We report on the combination of piezoresponse force microscopy (PFM), magnetic force microscopy, and local ferroelectric switching with magnetic field for the study of a thin-film magnetoelectric (ME) nanocomposite. The collection of PFM under an applied variable magnetic field within a polycrystalline perovskite-spinel BiFeO3-CoFe2O4 (BFO-CFO) 0-3 type thin-film nanocomposite enables quantitative and proximal measurement of magnetoelastic strain-driven ME response. Combination of measurement of the as-grown strain state with local measurements of microstructure and macroscopic magnetization permits local mapping of ME coupling.
Human Chromosome 7: DNA Sequence and Biology (2003)

DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. This approach enabled the discovery of candidate genes for developmental diseases including autism.
Interlayer modification and single-layer exfoliation of the Ruddlesden–Popper perovskite oxynitride K2LaTa2O6N to improve photocatalytic H2 evolution activity (2023)

Ethylamine-intercalated H x K 2− x LaTa 2 O 6 N, further modified with a Pt cocatalyst, exhibited 60 times height photocatalytic activity for H 2 evolution under visible light, as compared with the parent layered material.
Impact of allosteric modulation: Exploring the binding kinetics of glutamate and other orthosteric ligands of the metabotropic glutamate receptor 2 (2018)

While many orthosteric ligands have been developed for the mGlu<sub>2</sub> receptor, little is known about their target binding kinetics and how these relate to those of the endogenous agonist glutamate. Here, the kinetic rate constants, i.e. k<sub>on</sub> and k<sub>off</sub>, of glutamate were determined for the first time followed by those of the synthetic agonist LY354740 and antagonist LY341495. To increase the understanding of the binding mechanism and impact of allosteric modulation thereon, kinetic experiments were repeated in the presence of allosteric modulators. Functional assays were performed to further study the interplay between the orthosteric and allosteric binding sites, including an impedance-based morphology assay. We found that dissociation rate constants of orthosteric mGlu<sub>2</sub> ligands were all within a small 6-fold range, whereas association rate constants were ranging over more than three orders of magnitude and correlated to both affinity and potency. The latter showed that target engagement of orthosteric mGlu<sub>2</sub> ligands is k<sub>on</sub>-driven in vitro. Moreover, only the off-rates of the two agonists were decreased by a positive allosteric modulator (PAM), thereby increasing their affinity. Interestingly, a PAM increased the duration of a glutamate-induced cellular response. A negative allosteric modulator (NAM) increased both on- and off-rate of glutamate without changing its affinity, while it did not affect these parameters for LY354740, indicating probe-dependency. In conclusion, we found that affinity- or potency-based orthosteric ligand optimization primarily results in ligands with high k<sub>on</sub> values. Moreover, positive allosteric modulators alter the binding kinetics of orthosteric agonists mainly by decreasing k<sub>off</sub>, which we were able to correlate to a lengthened cellular response. Together, this study shows the importance of studying binding kinetics in early drug discovery, as this may provide important insights towards improved efficacy in vivo.
Screening for chemoimmunotherapeutics, success rate and predictivity of models: a five years experience. (1986)

While repository adjuvants are already established drugs for antigen specific immunomodulation, no unspecific active immunomodulator has successfully passed clinical trials in tumor patients in western countries yet. As this is in striking contrast to the effects seen with unspecific immunomodulators in experimental immunological and tumor test systems, the value of those screening models to predict clinical success may be asked for. To improve the success rate, it is recommended to test compounds for their immunomodulatory effects as broad as possible in ex vivo and in vivo test systems. Subsequently, the prophylactic as well as therapeutic potency of selected immunomodulating drugs should be evaluated in various models of aptitude, such as chronic infection, autoimmune diseases and chronic inflammatory reactions. Those diseases are at least to a certain extent influenced by the immune system, in contrast to the uncertainty in case of tumor diseases. In a battery of chronic infection models we could find that different chemoimmunotherapeutics with very similar immunopharmacological activity behaved quite differently. Most compounds were ineffective, a part enhanced chronic diseases and only in a few cases a therapeutic effect could be shown. On the other hand, effectivity in protection against the pathogenicity of subsequently applied, selected microorganisms does not predict the therapeutic potency for the same pathogen. Altogether the data show that activation of cells of the immune system by an immunostimulating drug does not predict its therapeutic potency. Moreover, activation of immune cells may also lead to impairness of the immune resistance.
Protein induced by vitamin K absence or antagonist-II (PIVKA-II) specifically increased in Italian hepatocellular carcinoma patients (2016)

The combination of the two biomarkers, evaluated by the ROC analysis, improved the specificity compared to a single marker. These data suggest that the combined analysis of the two markers could be a useful tool in clinical practice.
Plasma mitochondrial DNA is associated with extrapulmonary sarcoidosis (2019)

Sarcoidosis is an unpredictable granulomatous disease in which African Americans disproportionately experience aggressive phenotypes. Mitochondrial DNA (mtDNA) released by cells in response to various stressors contributes to tissue remodelling and inflammation. While extracellular mtDNA has emerged as a biomarker in multiple diseases, its relevance to sarcoidosis remains unknown. We aimed to define an association between extracellular mtDNA and clinical features of sarcoidosis.Extracellular mtDNA concentrations were measured using quantitative PCR for the human <i>MT-ATP6</i> gene in bronchoalveolar (BAL) and plasma samples from healthy controls and patients with sarcoidosis from The Yale Lung Repository; associations between <i>MT-ATP6</i> concentrations and Scadding stage, extrapulmonary disease and demographics were sought. Results were validated in the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis cohort.Relative to controls, <i>MT-ATP6</i> concentrations in sarcoidosis subjects were robustly elevated in the BAL fluid and plasma, particularly in the plasma of patients with extrapulmonary disease. Relative to Caucasians, African Americans displayed excessive <i>MT-ATP6</i> concentrations in the BAL fluid and plasma, for which the latter compartment correlated with significantly higher odds of extrapulmonary disease.Enrichments in extracellular mtDNA in sarcoidosis are associated with extrapulmonary disease and African American descent. Further study into the mechanistic basis of these clinical findings may lead to novel pathophysiologic and therapeutic insights.
Zero-Knowledge Proofs on Secret-Shared Data via Fully Linear PCPs (2019)

We introduce and study the notion of fully linear probabilistically checkable proof systems. In such a proof system, the verifier can make a small number of linear queries that apply jointly to the input and a proof vector.
Analysis of polymer surface treated by dielectric barrier discharge (2005)

We investigate polymer surfaces after exposing them to dielectric barrier discharges with different flowing gases (He, CF4) in air. The relationship between the gas characteristics and the surface properties of polypropylene (PP) is determined by contact angle measurement, optical emission spectroscopy and x-ray photoelectron spectroscopy. Experimental results reveal that there is a definite relationship between the surface energy and the surface chemical composition of PP and also indicate that the hydrophilicity of PP in an atmospheric pressure (AP) discharge is more dependent on ionic bombardment than on the atomic oxygen composition at the surface and its hydrophobicity depends on the fluorine composition at the PP surface. In addition, it turns out that in a CF4 discharge at AP, the CF3 molecular band exhibits a continuum band at the orange line in the visible range.
Transferring Biomarker into Molecular Probe: Melanin Nanoparticle as a Naturally Active Platform for Multimodality Imaging (2014)

Developing multifunctional and easily prepared nanoplatforms with integrated different modalities is highly challenging for molecular imaging. Here, we report the successful transfer of an important molecular target, melanin, into a novel multimodality imaging nanoplatform. Melanin is abundantly expressed in melanotic melanomas and thus has been actively studied as a target for melanoma imaging. In our work, the multifunctional biopolymer nanoplatform based on ultrasmall (<10 nm) water-soluble melanin nanoparticle (MNP) was developed and showed unique photoacoustic property and natural binding ability with metal ions (for example, (64)Cu(2+), Fe(3+)). Therefore, MNP can serve not only as a photoacoustic contrast agent, but also as a nanoplatform for positron emission tomography (PET) and magnetic resonance imaging (MRI). Traditional passive nanoplatforms require complicated and time-consuming processes for prebuilding reporting moieties or chemical modifications using active groups to integrate different contrast properties into one entity. In comparison, utilizing functional biomarker melanin can greatly simplify the building process. We further conjugated αvβ3 integrins, cyclic c(RGDfC) peptide, to MNPs to allow for U87MG tumor accumulation due to its targeting property combined with the enhanced permeability and retention (EPR) effect. The multimodal properties of MNPs demonstrate the high potential of endogenous materials with multifunctions as nanoplatforms for molecular theranostics and clinical translation.
Expression of a novel autoantibody defined by the VH3-15 gene in inflammatory bowel disease and Campylobacter jejuni enterocolitis. (1994)

This study newly introduces anti-VH mAbs to assess the role of clonal B cell activity in inflammatory bowel disease. Immunohistochemistry of colonic biopsies in ulcerative colitis (UC) and Crohn's disease (CD), but not unaffected individuals, demonstrated uniform staining of intravascular erythrocytes with BK2, a monoclonal specific for the VH3-15 Ig heavy chain gene product. Staining was caused by erythrocytes opsinized in vivo by anti-erythrocyte Abs present in patient sera and by using the VH3-15 gene product. The erythrocyte Ag was identified by immunoprecipitation as 22- and 28-kDa membrane proteins. A direct flow cytometric assay was developed to measure this serum autoantibody and was tested in 101 individuals with UC, CD, other acute or chronic colitis, and healthy controls. Compared with normal subjects, BK2+ anti-erythrocyte Abs were elevated in most sera from patients with CD and UC (including postcolectomy). BK2+ anti-erythrocyte Abs also were elevated in 10 of 38 noninflammatory bowel disease patients, all of whom had Campylobacter jejuni enterocolitis. These findings suggest that a common immunopathogenetic factor, manifested by VH3-15 B cell activation may be shared in UC, CD, and Campylobacter jejuni enterocolitis.
Real-time scene change detection assisted with camera 3A: auto exposure, auto white balance, and auto focus (2011)

Many scene change detection techniques have been developed for scene cuts, fade in and fade out by analyzing video encoder input signals. For real time scene change detection, sensor input signals provide first-hand information which can be used for scene change detection. In this paper, by analyzing camcorder front end sensor input signals with our proposed algorithms based on camera 3A (auto exposure, auto white balance and auto focus), a novel scene change detection technique is described. Camera 3A based scene change detection algorithm can detect scene changes in a timely manner and therefore fits well for real time scene change detection applications. Experimental results show that this algorithm can detect scene changes with good accuracy. The proposed algorithm is computationally efficient and easy to implement.
Vagueness as closeness (2005)

Abstract This paper presents and defends a definition of vagueness, compares it favourably with alternative definitions, and draws out some consequences of accepting this definition for the project of offering a substantive theory of vagueness. The definition is roughly this: a predicate 'F' is vague just in case for any objects a and b, if a and b are very close in respects relevant to the possession of F, then 'Fa' and 'Fb' are very close in respect of truth. The definition is extended to cover vagueness of many-place predicates, of properties and relations, and of objects. Some of the most important advantages of the definition are that it captures the intuitions which motivate the thought that vague predicates are tolerant, without leading to contradiction, and that it yields a clear understanding of the relationships between higher-order vagueness, sorites susceptibility, blurred boundaries, and borderline cases. The most notable consequence of the definition is that the correct theory of vagueness must countenance degrees of truth.
Regularity and strict identifiability in MIMO systems (2002)

We study finite impulse response (FIR) multi-input multi-output (MIMO) systems with additive noise, treating the finite-length sources and channel coefficients as deterministic unknowns, considering both regularity and identifiability. In blind estimation, the ambiguity set is large, admitting linear combinations of the sources. We show that the Fisher information matrix (FIM) is always rank deficient by at least the number of sources squared and develop necessary and sufficient conditions for the FIM to achieve its minimum nullity. Tight bounds are given on the required source data lengths to achieve minimum nullity of the FIM. We consider combinations of constraints that lead to regularity (i.e., to a full-rank FIM and, thus, a meaningful Cramer-Rao bound). Exploiting the null space of the FIM, we show how parameters must be specified to obtain a full-rank FIM, with implications for training sequence design in multisource systems. Together with constrained Cramer-Rao bounds (CRBs), this approach provides practical techniques for obtaining appropriate MIMO CRBs for many cases. Necessary and sufficient conditions are also developed for strict identifiability (ID). The conditions for strict ID are shown to be nearly equivalent to those for the FIM nullity to be minimized.
Electrically-pumped, broad-area, single-mode photonic crystal lasers (2007)

Planar broad-area single-mode lasers, with modal widths of the order of tens of microns, are technologically important for high-power applications and improved coupling efficiency into optical fibers. They may also find new areas of applications in on-chip integration with devices that are of similar size scales, such as for spectroscopy in microfluidic chambers or optical signal processing with micro-electromechanical systems. An outstanding challenge is that broad-area lasers often require external means of control, such as injection-locking or a frequency/spatial filter to obtain single-mode operation. In this paper, we propose and demonstrate effective index-guided, large-area, edge-emitting photonic crystal lasers driven by pulsed electrical current injection at the optical telecommunication wavelength of 1550 nm. By suitable design of the photonic crystal lattice, our lasers operate in a single mode with a 1/e(2) modal width of 25 microm and a length of 600 microm.
ChemInform Abstract: Synthesis of 13C‐Dilabeled 4‐Coumaroylspermidines. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
IC‐P‐194: DETECTION OF INCREASED MAGNETIC SUSCEPTIBILITIES IN THE CEREBRAL CORTEX IN PATIENTS WITH ALZHEIMER'S DISEASE: COMPARISON OF QUANTITATIVE SUSCEPTIBILITY MAPPING BETWEEN CONVENTIONAL AND BRAIN SURFACE CORRECTION METHOD (2018)

Several studies of quantitative susceptibility mapping (QSM) have reported increased magnetic susceptibilities in the brain of Alzheimer's disease (AD) patients, which reflect pathological iron accumulation in senile plaques. However, QSM analysis of the brain surface is typically difficult because of the artifact from large susceptibility differences and signal void of the bone and air. The present study compared conventional QSM analysis and our newly developed method of brain surface correction, in AD patients and cognitively normal (CN) subjects. Eleven AD patients and 40 CN subjects were included in this study. Magnetic resonance imaging was performed using a 3-tesla scanner. QSM images were created using a conventional and novel method of brain surface correction. The conventional method was implemented by regularization enabled sophisticated harmonic artifact reduction for phase data (RESHARP). Moreover, the novel method was implemented by constrained RESHARP with a brain-surface background field calculated by local polynomial approximation. Region of interest analysis was performed with an automated anatomical labeling template for 120 regions. Relative susceptibility values to the frontal white matter were compared between the AD and CN groups with analysis of covariance, in which age was used for covariance. In the conventional method, significant increases were observed in susceptibility in AD patients compared with that in CN subjects in only five regions (Fig. 1), namely the right putamen (p = 0.003), left lateral orbitofrontal cortex (p = 0.003), right transverse temporal gyrus (p = 0.024), right amygdala (p = 0.028), and left putamen (p = 0.042). Contrastingly, 21 regions (Fig. 2) showed significant increases in the susceptibility in AD patients with the novel method, including the left anterior orbitofrontal cortex (p = 0.002), left lateral orbitofrontal cortex (p = 0.004), left inferior occipital gyrus (p = 0.007), right parahippocampal gyrus (p = 0.015), and right medial orbital gyrus (p = 0.017).
PCLs: Geometry-aware Neural Reconstruction of 3D Pose with Perspective Crop Layers (2021)

Yu F, Salzmann M, Fua P, Rhodin H. PCLs: Geometry-aware Neural Reconstruction of 3D Pose with Perspective Crop Layers. In: &lt;em&gt;Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition&lt;/em&gt;. 2021: 9064-9073.
Logarithmic sensing in Bacillus subtilis aerotaxis (2017)

Aerotaxis, the directed migration along oxygen gradients, allows many microorganisms to locate favorable oxygen concentrations. Despite oxygen's fundamental role for life, even key aspects of aerotaxis remain poorly understood. In <i>Bacillus subtilis,</i> for example, there is conflicting evidence of whether migration occurs to the maximal oxygen concentration available or to an optimal intermediate one, and how aerotaxis can be maintained over a broad range of conditions. Using precisely controlled oxygen gradients in a microfluidic device, spanning the full spectrum of conditions from quasi-anoxic to oxic (60 n mol/l-1 m mol/l), we resolved <i>B. subtilis'</i> 'oxygen preference conundrum' by demonstrating consistent migration towards maximum oxygen concentrations ('monotonic aerotaxis'). Surprisingly, the strength of aerotaxis was largely unchanged over three decades in oxygen concentration (131 n mol/l-196 μ mol/l). We discovered that in this range <i>B. subtilis</i> responds to the logarithm of the oxygen concentration gradient, a rescaling strategy called 'log-sensing' that affords organisms high sensitivity over a wide range of conditions. In these experiments, high-throughput single-cell imaging yielded the best signal-to-noise ratio of any microbial taxis study to date, enabling the robust identification of the first mathematical model for aerotaxis among a broad class of alternative models. The model passed the stringent test of predicting the transient aerotactic response despite being developed on steady-state data, and quantitatively captures both monotonic aerotaxis and log-sensing. Taken together, these results shed new light on the oxygen-seeking capabilities of <i>B. subtilis</i> and provide a blueprint for the quantitative investigation of the many other forms of microbial taxis.