gebhart/patrepeval huggingface dataset:
Acylcarnitine Metabolomic Profiles Inform Clinically-Defined Major Depressive Phenotypes (2019)

Abstract Background Acylcarnitines have important functions in mitochondrial energetics and β-oxidation, and have been implicated to play a significant role in metabolic functions of the brain. This retrospective study examined whether plasma acylcarnitine profiles can help biochemically distinguish the three phenotypic subtypes of major depressive disorder (MDD)—(core depression (CD+), anxious depression (ANX+), and neurovegetative symptoms of melancholia (NVSM+))—following treatment with a selective serotonin reuptake inhibitor (SSRI). Methods Depressed outpatients (n=240) from the Mayo Clinic Pharmacogenomics Research Network were treated with citalopram or escitalopram for eight weeks. Plasma samples collected at baseline and eight weeks post-treatment were profiled for multiple-, short-, medium- and long-chain acylcarnitine levels using AbsoluteIDQ ® p180-Kit and LC-MS. Linear mixed effects models were used to examine whether acylcarnitine levels discriminate the clinical phenotypes at baseline or eight weeks post-treatment, and whether temporal changes in acylcarnitine profiles differ between groups. Results At baseline, significantly lower concentrations of short- and long-chain acylcarnitines were found in CD+ and NVSM+ compared to ANX+, and the short-chain acylcarnitines remained lower after eight weeks. At eight weeks, the medium- and long-chain acylcarnitines were significantly lower in NVSM+ compared to ANX+. Regarding changes baseline to week eight, short-chain acylcarnitine levels significantly increased in CD+ and ANX+, and medium- and long-chain acylcarnitines significantly decreased in NVSM+ and CD+. Conclusions In depressed patients treated with SSRIs, β-oxidation and mitochondrial energetics as evaluated by levels and changes in acylcarnitines may provide the biochemical basis of the clinical heterogeneity of MDD, especially when combined with clinical characteristics.
Psoriasis disease severity measures: comparing efficacy of treatments for severe psoriasis (2003)

Measurement of psoriasis disease severity and effectiveness of treatment involves both objective and subjective assessments.1 Comparing the efficacy of different treatments is complicated by the use of different metrics for measuring outcomes.2 Because these measures are not used routinely in clinical practice, interpreting these data, in particular assessing the degree of clinically meaningful improvement, is difficult. The drug approval process and product labeling reflect historical changes in standards of efficacy measurement.3 This paper reviews the metrics used to evaluate psoriasis treatment and compares available information on approved treatments for severe psoriasis. It further attempts to elucidate the value of these metrics and provide some guidance in properly evaluating the relative efficacy of current proven therapy with new treatments. While clinical trials are somewhat artificial, they provide proof that a drug is more effective than placebo. Efficacy in clinical practice, however, may be very different from the clinical trial setting. Comparison of efficacy under the current circumstances of varying evaluative metrics scales is possible with proper knowledge of the functionality of these methods.
Development of small size 3D LIDAR (2014)

We have developed a new type of 3D LIDAR, which is small, light weight and low cost. The size and weight are important factors of the aimed sensor to use with wide range of robot vehicles, helicopters and airplane, and small vehicles. To achieve compact size and light weight construction the sensor has single pair of laser transmitter and receiver, and scanning motor on which a vibrating mirror is placed. The mirror is driven by the resonant frequency current supplied through contactless power supply unit. Experimental results of the prototype shows that the sensor of comparable size and weight with recent 2D sensors can obtain 3D range data of 8000 points in 20 Hz with 270 degree horizontal and 40 degree vertical views both in indoor and outdoor.
2D-IR Spectroscopy Shows that Optimized DNA Minor Groove Binding of Hoechst33258 Follows an Induced Fit Model (2017)

The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced noncovalent interactions between the ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a suboptimal alternating A-T sequence. Results from two-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of the minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region. This induced fit maximizes favorable ligand-DNA enthalpic contributions in the optimal binding case and demonstrates that controlling the molecular details that induce subtle changes in DNA structure may hold the key to designing next-generation DNA-binding molecules.
Phosphorylation of C8 and C9 Subunits of the Multicatalytic Proteinase by Casein Kinase II and Identification of the C8 Phosphorylation Sites by Direct Mutagenesis (1996)

Two 29 kDa subunits of the multicatalytic proteinase (proteasome) complex, the C8 and C9 components, are phosphorylated in vivo and can be phosphorylated in vitro by casein kinase II (CKII). The major phosphate acceptor is the C8 subunit being phosphorylated in serine, both in vivo and in vitro. The phosphopeptides generated by Glu-C endoprotease digestion from the in vivo 29 kDa labeled subunit and from the in vitro phosphorylation of the recombinant C8 subunit with CKII are identical, suggesting that CKII is likely responsible for the in vivo phosphorylation of the C8 subunit. The in vitro stoichiometry of phosphorylation of the proteasome complex and the recombinant C9 and C8 subunits by CKII is 2-2.5, 0.2, and 2 mol of phosphate per mole, respectively. Several C8 protein constructs allow the location of the CKII phosphorylation sites to be the COOH terminal portion of the protein, and direct mutational analyses show that Ser-243 and Ser-250 are the residues of the C8 subunit phosphorylated by CKII. The in vitro phosphorylation of the proteasome by CKII does not affect its proteolytic activity (on proteins or fluorogenic synthetic peptides), therefore suggesting its involvement in the interaction of the proteasome with other cellular proteins, i.e. in the formation of the 26S complex and/or in the interaction with the nuclear translocation machinery.
Common regulatory networks in leaf and fruit patterning revealed by mutations in the<i>Arabidopsis ASYMMETRIC LEAVES1</i>gene (2007)

Carpels and leaves are evolutionarily related organs, as the former are thought to be modified leaves. Therefore, developmental pathways that play crucial roles in patterning both organs are presumably conserved. In leaf primordia of Arabidopsis thaliana, the ASYMMETRIC LEAVES1 (AS1) gene interacts with AS2 to repress the class I KNOTTED1-like homeobox (KNOX) genes BREVIPEDICELLUS (BP), KNAT2 and KNAT6, restricting the expression of these genes to the meristem. In this report, we describe how AS1, presumably in collaboration with AS2, patterns the Arabidopsis gynoecium by repressing BP, which is expressed in the replum and valve margin, interacts in the replum with REPLUMLESS (RPL), an essential gene for replum development, and positively regulates the expression of this gene. Misexpression of BP in the gynoecium causes an increase in replum size, while the valve width is slightly reduced, and enhances the effect of mutations in FRUITFULL (FUL), a gene with an important function in valve development. Altogether, these findings strongly suggest that BP plays a crucial role in replum development. We propose a model for pattern formation along the mediolateral axis of the ovary, whereby three domains (replum, valve margin and valve) are specified by the opposing gradients of two antagonistic factors, valve factors and replum factors, the class I KNOX genes working as the latter.
Regulation of Peripheral Cannabinoid Receptor CB2Phosphorylation by the Inverse Agonist SR 144528 (1999)

We recently demonstrated that the selective cannabinoid receptor antagonist SR 144528 acts as an inverse agonist that blocks constitutive mitogen-activated protein kinase activity coupled to the spontaneous autoactivated peripheral cannabinoid receptor (CB2) in the Chinese hamster ovary cell line stably transfected with human CB2. In the present report, we studied the effect of SR 144528 on CB2 phosphorylation. The CB2 phosphorylation status was monitored by immunodetection using an antibody specific to the COOH-terminal CB2 which can discriminate between phosphorylated and non-phosphorylated CB2 isoforms at serine 352. We first showed that CB2 is constitutively active, phosphorylated, and internalized at the basal level. By blocking autoactivated receptors, inverse agonist SR 144528 treatment completely inhibited this phosphorylation state, leading to an up-regulated CB2 receptor level at the cell surface, and enhanced cannabinoid agonist sensitivity for mitogen-activated protein kinase activation of Chinese hamster ovary-CB2 cells. After acute agonist treatment, serine 352 was extensively phosphorylated and maintained in this phosphorylated state for more than 8 h after agonist treatment. The cellular responses to CP-55,940 were concomitantly abolished. Surprisingly, CP-55,940-induced CB2 phosphorylation was reversed by SR 144528, paradoxically leading to a non-phosphorylated CB2 which could then be fully activated by CP-55,940. The process of CP-55,940-induced receptor phosphorylation followed by SR 144528-induced receptor dephosphorylation kept recurring many times on the same cells, indicating that the agonist switches the system off but the inverse agonist switches the system back on. Finally, we showed that autophosphorylation and CP-55, 940-induced serine 352 CB2 phosphorylation involve an acidotropic GRK kinase, which does not use Gibetagamma. In contrast, SR 144528-induced CB2 dephosphorylation was found to involve an okadaic acid and calyculin A-sensitive type 2A phosphatase.
Time-resolved second-harmonic study of femtosecond laser-induced disordering of GaAs surfaces (1991)

An abrupt (less than 100 fs) decrease in the second-harmonic intensity reflected from the surface of a GaAs (110) wafer has been observed experimentally. The linear reflectivity was found to increase on a time scale of ~1 ps. Thus the concept of fast atomic disorder induced by electronic excitation within a relatively cold lattice is given new experimental support.
Predicting and Designing for the Impact of Process Variations and Mismatch on the Trim Range and Yield of Bandgap References (2005)

Process tolerance and device mismatch produce significant random variations in bandgap voltage reference circuits. These variations lead to errors in the reference voltage and significantly impact manufacturing cost by increasing trimming requirements and decreasing yield. Current-mirror mismatch, followed by V/sub BE/ spread, package shift, and resistor mismatch are the dominant sources of random error in bandgap reference circuits. A folded-cascode topology, often used in low voltage applications, can be optimized to effectively alleviate the effects of a mismatch in the mirroring devices. By decreasing the ratio of the current in the cascode to that of the bandgap core circuit and ascertaining the best-matched devices for implementing current-mirrors and current sources, these mismatches can be significantly reduced.
Group mobility management in wireless ad hoc networks (2003)

In wireless ad hoc networks, network partition, a large-scale topology change, would occur unexpectedly and disrupt the on-going routing paths as well as application connections. By observing the group mobility patterns that are aggregated from the movement of mobile nodes, the prospective network partitioning can be predicted and therefore we can reduce the amount of disruptions. In this paper, we proposed a group mobility model that uses mobility parameters, such as distance, velocity and acceleration for network partition prediction. We then demonstrate how to predict a network partition with these parameters, and illustrate how to apply the prediction to routing protocols. We also propose a group-id based clustering algorithm, which exactly determines the mobility groups as well as elects the clusterheads.
Analysis of Temperature-Promoted and Solvent-Assisted Cross-Linking in Sulfonated Poly(ether ether ketone) (SPEEK) Proton-Conducting Membranes (2009)

Sulfonated poly(ether ether ketone) (SPEEK) membranes were thermally treated at temperatures between 120 and 160 degrees C. Water uptake measured at different relative humidity values or by full immersion in water between 25 and 145 degrees C was found to depend very strongly on previous thermal treatment and casting solvent. Water-uptake coefficient values as low as 10-15 even upon immersion in water at 100 degrees C were obtained with membranes treated at 160 degrees C. This effect is related to cross-linking by SO2 bridges between macromolecular chains. An important role is also played by the casting solvent: among the investigated solvents, dimethylsulfoxide (DMSO) gave the best results. A chemical kinetics model is outlined that permits the estimation of the relevant kinetic parameters, especially the activation energy of the cross-linking reaction, which was found to be about 60 kJ/mol. These results are of significant importance for the improvement of proton-exchange membrane fuel cells.
Single cell protein analysis for systems biology (2018)

The cellular abundance of proteins can vary even between isogenic single cells. This variability between single-cell protein levels can have regulatory roles, such as controlling cell fate during apoptosis induction or the proliferation/quiescence decision. Here, we review examples connecting protein levels and their dynamics in single cells to cellular functions. Such findings were made possible by the introduction of antibodies, and subsequently fluorescent proteins, for tracking protein levels in single cells. However, in heterogeneous cell populations, such as tumors or differentiating stem cells, cellular decisions are controlled by hundreds, even thousands of proteins acting in concert. Characterizing such complex systems demands measurements of thousands of proteins across thousands of single cells. This demand has inspired the development of new methods for single-cell protein analysis, and we discuss their trade-offs, with an emphasis on their specificity and coverage. We finish by highlighting the potential of emerging mass-spec methods to enable systems-level measurement of single-cell proteomes with unprecedented coverage and specificity. Combining such methods with methods for quantitating the transcriptomes and metabolomes of single cells will provide essential data for advancing quantitative systems biology.
Making Clinical Policy Explicit:<i>Legislative Policy Making and Lessons for Developing Practice Guidelines</i> (1993)

Promulgation of practice guidelines in medicine has increased interest in the structure of clinical policy making. It is argued that with a generic definition of policy as "the rules governing the behavior of individuals or institutions," clinical policy making is analogous to legislative policy making. Practice guidelines emphasize the advantages of making clinical policy more explicit. The structure of legislative policy making has evolved over many years to meet the challenge of making both the policies and the process of policy making explicit. Processes to promulgate clinical policies may be able to exploit this experience to improve clinical policy making and thereby retain control of the process within medicine. Generic steps are outlined for making decisions with incomplete information; synthesis of facts, vested interests, and values; involvement of stakeholders; and implementation of policy. An illustration of the use of the generic steps to make and implement a clinical policy for cesarean birth follows, with evaluations of its impact on the behavior and satisfaction of clinical stakeholders.
Surfactant-Free RAFT Emulsion Polymerization Using Poly(<i><i>N,N</i></i>-dimethylacrylamide) Trithiocarbonate Macromolecular Chain Transfer Agents (2010)

Water-soluble poly(N,N-dimethylacrylamide)s (PDMAAm) with a reactive trithiocarbonate group exhibiting different structures were used as macromolecular RAFT (reversible addition−fragmentation chain transfer) agents in the surfactant-free emulsion polymerization of n-butyl acrylate and styrene, under ab initio, batch conditions. Independently of the structure of the RAFT group, the polymerizations were fast and controlled with molar masses that matched well the theoretical values and rather low polydispersity indexes. Monomer conversions close to 100% were reached and the polymerizations behaved as controlled systems, even when solids contents up to 40% were targeted. The system thus led to poly(N,N-dimethylacrylamide)-b-poly(n-butyl acrylate) and poly(N,N-dimethylacrylamide)-b-polystyrene amphiphilic diblock copolymers formed in situ and self-assembled upon chain extension. The stability of the aqueous dispersions, measured by the amount of coagulum formed, improved with increasing length of the stabilizing hydrophilic PDMAAm segments.
The third fibronectin type III repeat is required for L1 to serve as an optimal substratum for neurite extension (2000)

As a means of defining functionally important regions of the L1 neuronal cell adhesion molecule, neurite outgrowth from cerebellar neurons was compared on monolayers of L1-negative B28 glioma cells, B28 cells transfected with wild-type human L1, and B28 cells transfected with variant forms of L1. Neurite outgrowth on L1-positive B28 cells is greatly enhanced over that seen on parental B28 cells. Neurite outgrowth on B28 cells expressing L1 variants that lack either the first or the fifth fibronectin type III repeat is comparable to that seen on monolayers expressing wild-type L1. In contrast, B28 cells expressing L1 without the third fibronectin type III repeat do not support neurite outgrowth above the background level seen on parental B28 cells. This suggests that the third fibronectin type III repeat plays a key role in the ability of L1 to promote neurite extension. This is consistent with reports that the third fibronectin type III repeat mediates L1 homomultimerization and integrin binding and that plasmin cleavage within this domain interferes with L1 function by abolishing these molecular interactions.
Reactive collisions in crossed molecular beams (1962)

The distribution of velocity vectors of reaction products is discussed with emphasis on the restrictions imposed by the conservation laws. The recoil velocity that carries the products away from the center of mass shows how the energy of reaction is divided between internal excitation and translation. Similarly, the angular distributions, as viewed from the center of mass, reflect the partitioning of the total angular momentum between angular momenta of individual molecules and orbital angular momentum associated with their relative motion. Crossed-beam studies of several reactions of the type M + RI yields R + MI are described, where M = K, Rb, Cs, and R = CH/sub 3/, C/sub 3/H/sub 5/, etc. The results show that most of the energy of reaction goes into internal excitation of the products and that the angular distribution is quite anisotropic, with most of the MI recoiling backward (and R forward) with respect to the incoming K beam. (auth)
A new  -1,2-N-acetylglucosaminyltransferase that may play a role in the biosynthesis of mammalian O-mannosyl glycans (2001)

Recent studies have shown that O-mannosyl glycans are present in several mammalian glycoproteins. Although knowledge on the functional roles of these glycans is accumulating, their biosynthetic pathways are poorly understood. Here we report the identification and initial characterization of a novel enzyme capable of forming GlcNAc beta 1-2Man linkage, namely UDP-N-acetylglucosamine: O-linked mannose beta-1,2-N-acetylglucosaminyltransferase in the microsome fraction of newborn rat brains. The enzyme transfers GlcNAc to beta-linked mannose residues, and the formed linkage was confirmed to be beta 1-2 on the basis of diplococcal beta-N-acetylhexosaminidase susceptibility and by high-pH anion-exchange chromatography. Its activity is linearly dependent on time, protein concentration, and substrate concentration and is enhanced in the presence of manganese ion. Its activity is not due to UDP-N-acetylglucosamine: alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I (GnT-I) or UDP-N-acetylglucosamine: alpha-6-D-mannoside beta-1,2-D-acetylglucosaminyltransferase II (GnT-II), which acts on the early steps of N-glycan biosynthesis, because GnT-I or GnT-II expressed in yeast cells did not show any GlcNAc transfer activity against a synthetic mannosyl peptide. Taken together, the results suggest that the GlcNAc transferase activity described here is relevant to the O-mannosyl glycan pathway in mammals.
Hessian and Concavity of Mutual Information, Differential Entropy, and Entropy Power in Linear Vector Gaussian Channels (2009)

Within the framework of linear vector Gaussian channels with arbitrary signaling, the Jacobian of the minimum mean square error and Fisher information matrices with respect to arbitrary parameters of the system are calculated in this paper. Capitalizing on prior research where the minimum mean square error and Fisher information matrices were linked to information-theoretic quantities through differentiation, the Hessian of the mutual information and the entropy are derived. These expressions are then used to assess the concavity properties of mutual information and entropy under different channel conditions and also to derive a multivariate version of an entropy power inequality due to Costa.
What Is The Real Story Behind Toys And Play (2001)

Some of us think play is what you do when you get done with the important stuff.But for children, play is the important stuff.In order to develop their understanding of the world, children need to try things.Children's experiments may not be done in a logical order, but each little discovery is being tucked away to form the basis of their understanding of the world.
Architecture and programming of a VLIW style programmable video signal processor (1991)

The architecture and programming aspects of a programmable video signal processor are discussed. The processor is an integrated circuit that has a modular architecture with a number of programmable, pipelined processing elements. Networks of these processors can be programmed conveniently with the aid of dedicated programming tools.
Participation: Some Basic Considerations on the Theme Of Academe (1973)

Considerations on