gebhart/patrepeval huggingface dataset:
The Transcriptional Basis of Steroid Physiology (1998)

The actions of steroids, the active metabolites of vitamins A and D and thyroid hormones, are mediated by intracellular nuclear receptors whose coordinate activitydefines the physiological response. During the past 80years, eight distinct classes of bioactive hormonal lipidshave been identified, whose comprise is generally viewedas a key part of the endocrine system. In the early part ofthis century, the endocrine glands were looked upon as anisolated group of structures, secreting substances which,in some mysterious fashion, were able to influence embryonic and postembryonic development, sexual maturation, biochemical pathways involving protein and sugarmetabolism, behavior, and reproductive physiology...
Sequence-specific Interaction between Mitochondrial Fe-S Scaffold Protein Isu and Hsp70 Ssq1 Is Essential for Their in Vivo Function (2004)

Isu, the scaffold for assembly of Fe-S clusters in the yeast mitochondrial matrix, is a substrate protein for the Hsp70 Ssq1 and the J-protein Jac1 in vitro. As expected for an Hsp70-substrate interaction, the formation of a stable complex between Isu and Ssq1 requires Jac1 in the presence of ATP. Here we report that a conserved tripeptide, PVK, of Isu is critical for interaction with Ssq1 because amino acid substitutions in this tripeptide inhibit both the formation of the Isu-Ssq1 complex and the ability of Isu to stimulate the ATPase activity of Ssq1. These biochemical defects correlate well with the growth defects of cells expressing mutant Isu proteins. We conclude that the Ssq1-Isu substrate interaction is critical for Fe-S cluster biogenesis in vivo. The ability of Jac1 and mutant Isu proteins to cooperatively stimulate the ATPase activity of Ssq1 was also measured. Increasing the concentration of Jac1 and mutant Isu together but not individually partially overcame the effect of the reduced affinity of the Isu mutant proteins for Ssq1. These results, along with the observation that overexpression of Jac1 was able to suppress the growth defect of an ISU mutant, support the hypothesis that Isu is "targeted" to Ssq1 by Jac1, with a preformed Jac1-Isu complex interacting with Ssq1.
Extracting Reverberant Sound Using a Linearly Constrained Minimum Variance Spatial Filter (2014)

Microphone arrays are typically used to extract the direct sound of sound sources while suppressing noise and reverberation. Applications such as immersive spatial sound reproduction commonly also require an estimate of the reverberant sound. A linearly constrained minimum variance filter, of which one of the constraints is related to the spatial coherence of the assumed reverberant sound field, is proposed to obtain an estimate of the sound pressure of the reverberant field. The proposed spatial filter provides an almost omnidirectional directivity pattern with spatial nulls for the directions-of-arrival of the direct sound. The filter is computationally efficient and outperforms existing methods.
Protein adsorption on biomedical polymers with a phosphorylcholine moiety adsorbed with phospholipid (1992)

The effects of phospholipid adsorption onto the polymer surface during adsorption of plasma proteins were investigated. When a polymer with the phosphorylcholine moiety, 2-methacryloyloxyethyl phosphorylcholine (MPC) co-polymer, was treated with dipalmitoylphosphatidylcholine (DPPC) liposome solution, an organized adsorption layer of DPPC was formed on the MPC co-polymer surface, which was confirmed by differential scanning calorimetric analysis and X-ray photoelectron spectroscopy. On the other hand, an organized layer of DPPC on poly(n-butyl methacrylate) and poly(2-hydroxyethyl methacrylate) could not be found. The amount of albumin adsorbed on the polymer surfaces was decreased by pretreatment of the surface with DPPC liposome solution in every polymer case. The smallest amount of adsorbed proteins was found on the MPC co-polymer. Protein adsorption on the surface of MPC co-polymers from the plasma was also small. The difference in protein adsorption on the polymers probably reflects the difference in the orientation of the phospholipid molecules which cover the polymer surface.
CCR1 Antagonists: What Have We Learned From Clinical Trials (2010)

The identification of chemokines and their receptors as potent mediators of leukocyte infiltration raised interest in the potential role of these proteins on disease pathogenesis. This is exemplified by the chemokine receptor, CCR1, which has been shown to be up-regulated in a number of human diseases, the implications of which have been suggested by animal models where inhibition of CCR1 or its ligands have shown beneficial effects. These data support the possibility that a CCR1 antagonist will provide therapeutic benefit to patients with inflammatory diseases. Over the last several years, several of these antagonists entered clinical trials, including CP-481,715 (Pfizer) and MLN3897 (Millennium) for rheumatoid arthritis, BX471 (Berlex / Scherring AG) for multiple sclerosis, and AZD-4818 (Astra-Zeneca) for COPD. This review will describe the evidence that supported the role of CCR1 in these diseases, the results from clinical trials, and provide perspectives on what has been learned from these trials for potential application / consideration to other studies with chemokine receptor antagonists.
X chromosome inactivation in the normal female genital tract: implications for identification of neoplasia. (1995)

Monoclonal proliferative lesions may be identified by X chromosome inactivation skewing relative to normal polyclonal tissues. We have quantitatively analyzed X-inactivation patterns throughout polyclonal uterine tissues to develop interpretive criteria for recognition of monoclonal neoplasms. Six fresh tissue samples (two samples each of cervix, endometrium, and myometrium) were collected from hysterectomy specimens, and the percentage of androgen receptor (HUMARA) marker allele present on inactive X chromosomes was calculated from a PCR assay. Exact balancing yields 50% of the marker on the inactive X, whereas complete skewing shows either 0 or 100%. X inactivation was similar throughout the tissues of each uterus but was significantly different among the 11 women studied. Comparison of differences in X inactivation between pairs of polyclonal tissue samples within each uterus (Xi spread) permitted delineation of cumulative experimental and biological variation of this parameter. Polyclonal-polyclonal Xi spread averaged 10.7 and was independent of the tissue type, sampling site, or the individual studied. Severe baseline skewing of reference polyclonal tissues or contamination of monoclonal tissue by polyclonal cells may reduce the polyclonal-monoclonal Xi spread. The extent of X-inactivation skewing necessary to infer a monoclonal process should exceed the 20 or 27 point spread seen, respectively, between 85 and 95% of polyclonal samples.
Stability Analysis of a High Speed Automotive Turbocharger (2006)

Automotive turbochargers are known to have operation into the linear unstable region. The operation in the nonlinear limit cycle has been tolerated on most applications to date. The need for quieter, smoother operation and reduced emissions has prompted new evaluations of the rotor bearing design for these systems. In this research a commercial rotordynamics computer program is used to evaluate the stability and transient response of a high speed automotive turbocharger. Various models with varying bearing designs and properties have been solved to obtain the linear stability threshold speeds and also the non- linear transient response. The predicted whirl speed map shows two modes of instability and is very similar to the limited test results in the literature. The calculation process is discussed in detail and the results of the current research will be compared to the literature. An experimental research project is currently in progress at Virginia Tech and those results will be documented in a future publication.
Establishment of the human reflex tear two‐dimensional polyacrylamide gel electrophoresis reference map: New proteins of potential diagnostic value (1997)

To understand the changes in protein expression associated with various physiological states as well as the development of pathological eye disease, we have begun to map the protein components of normal human reflex tears. An analytical reference map of normal human reflex tears was created using two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) with pH 3.5-10 immobilized pH gradients (IPGs). Micropreparatively loaded gels were transferred to polyvinylidene difluoride (PVDF) and analysed by a combination of N-terminal sequence tagging and amino acid compositional analysis. Thirty spots were sequence tagged, resulting in identification of six different proteins (lipocalin, lysozyme, lactotransferrin, zinc-alpha-2 glycoprotein, cystatin S, cystatin SN) that matched to entries in the SWISS-PROT database. A group of N-terminally blocked proteins was clearly identified from SWISS-PROT by amino acid analysis, isoelectric point (pI) and molecular weight (Mr). A number of highly expressed protein components remain unidentified despite being subjected to amino acid analysis and Edman sequencing. A majority of the abundant proteins showed varying degrees of charge heterogeneity attributed to post-translational processing such as glycosylation and N-terminal truncation. We have identified a previously undescribed protein that we have named lacryglobin. This protein displays strong homology with mammaglobin, a protein overexpressed in breast cancer. The discovery of this homologue in tears offers the potential for disease diagnosis by screening tear fluid proteins.
Probing molecular interaction in ionic liquids by low frequency spectroscopy: Coulomb energy, hydrogen bonding and dispersion forces (2014)

Ionic liquids are defined as salts composed solely of ions with melting points below 100 °C. These remarkable liquids have unique and fascinating properties and offer new opportunities for science and technology. New combinations of ions provide changing physical properties and thus novel potential applications for this class of liquid materials. To a large extent, the structure and properties of ionic liquids are determined by the intermolecular interaction between anions and cations. In this perspective we show that far infrared and terahertz spectroscopy are suitable methods for studying the cation-anion interaction in these Coulomb fluids. The interpretation of the measured low frequency spectra is supported by density functional theory calculations and molecular dynamics simulations. We present results for selected aprotic and protic ionic liquids and their mixtures with molecular solvents. In particular, we focus on the strength and type of intermolecular interaction and how both parameters are influenced by the character of the ions and their combinations. We show that the total interaction between cations and anions is a result of a subtle balance between Coulomb forces, hydrogen bonds and dispersion forces. For protic ionic liquids we could measure distinct vibrational modes in the low frequency spectra indicating clearly the cation-anion interaction characterized by linear and medium to strong hydrogen bonds. Using isotopic substitution we have been able to dissect frequency shifts related to pure interaction strength between cations and anions and to different reduced masses only. In this context we also show how these different types of interaction may influence the physical properties of ionic liquids such as the melting point, viscosity or enthalpy of vaporization. Furthermore we demonstrate that low frequency spectroscopy can also be used for studying ion speciation. Low vibrational features can be assigned to contact ion pairs and solvent separated ion pairs. In conclusion we showed how detailed knowledge of the low frequency spectra can be used to understand the change in interaction strength and structure by variation of temperature, solvent polarity and solvent concentration in ionic liquids and their mixtures with molecular solvents. In principle the used combination of methods is suitable for studying intermolecular interaction in pure molecular liquids and their solutions including additive materials such as nanoparticles.
Upregulation of tumor necrosis factor alpha and interleukin-1 beta in Q fever endocarditis (1996)

The occurrence of Q fever endocarditis likely involves some alterations in the responses of monocytes, the in vivo targets of Coxiella burnetii. To test this hypothesis, the production of the inflammatory cytokines tumor necrosis factor alpha, interleukin-1 beta, and interleukin-6 was assessed in monocytes from patients with Q fever endocarditis. Spontaneous transcription and secretion of tumor necrosis factor and interleukin-1 were significantly higher in patient monocytes than in healthy controls. The interleukin-6 transcripts were also upregulated in patient cells. Moreover, in patients with recent endocarditis exhibiting high titers of immunoglobulin G directed to C. burnetii in phase I, monocytes released significantly higher levels of tumor necrosis factor and interleukin-1 than in patients with stabilized endocarditis. Immunoglobulin G titers and the overproduction of tumor necrosis factor and interleukin-1 were significantly correlated. Hence, the overproduction of inflammatory cytokines might be a marker of disease activity.
West Africa's River Basin Organizations (1991)

A conference entitled development from a regional perspective was held by the United States Agency for International Development (USAID) in 1969. It attempted to assess the possible advantages of a regional over a nation-by-nation approach to African development.1 Could a regional view permit a more effective use of the limited funds available by overcoming the need to single out particular recipients, especially where development potentialities overlapped international boundaries? Various models were considered, one of them being lake and river basins as a possible spatial and organizational framework for the planning and implementation of multi-purpose international projects. Support for this approach had come from the adoption in 1966 of the Helsinki rules on the uses of the waters of international rivers.
Functional Analysis of Lysosomes During Mouse Preimplantation Embryo Development (2012)

Lysosomes are acidic and highly dynamic organelles that are essential for macromolecule degradation and many other cellular functions. However, little is known about lysosomal function during early embryogenesis. Here, we found that the number of lysosomes increased after fertilization. Lysosomes were abundant during mouse preimplantation development until the morula stage, but their numbers decreased slightly in blastocysts. Consistently, the protein expression level of mature cathepsins B and D was high from the one-cell to morula stages but low in the blastocyst stage. One-cell embryos injected with siRNAs targeted to both lysosome-associated membrane protein 1 and 2 (LAMP1 and LAMP2) were developmentally arrested at the two-cell stage. Pharmacological inhibition of lysosomes also caused developmental retardation, resulting in accumulation of lipofuscin. Our findings highlight the functional changes in lysosomes in mouse preimplantation embryos.
A Novel Algorithm for Video Smoothness Evaluation (2008)

By making use of the temporal correlations of video sequences, a novel algorithm for video smoothness evaluation is proposed, which reflects the impact of frame loss on perceived visual quality. This metric particularly aims at measuring the perpetual quality degradation caused by video temporal fluctuations, based on the phenomenon that human visual system(HVS) pays more attention on difference among frames rather than a signal frame's sharpness. Then a visual smoothness degradation evaluation model is established, in which both source smoothness degradation and receiver smoothness degradation are measured to evaluate perceived video smoothness. Experimental results and subjective assessment results demonstrated the high performance of this algorithm on prediction of perceptual smoothness degradation.
Whey Protein Functional Properties and Applications in Food Formulation (2019)

Whey protein products have been widely used in infant formulae, dietetic foods and animal feeds. Polymerized whey protein (PWP) showed higher viscosity and has been widely used as a thickening agent. Emulsions are typically classified according to the spatial distribution of the oil and water phases relative to each other. Whey protein concentrate (WPC) has been employed quite effectively as a fat replacer. This chapter focuses on the interaction between the carotenoid nutraceuticals and elucidates the mechanism by which whey protein can be used as carotenoids carriers. Microencapsulation is a powerful technique commonly used for the protection of a wide range of biomolecules (small molecules and protein) and cells of bacterial, yeast and animal origin. Antimicrobial packaging is a form of active packaging that has the potential to extend the shelf-life of product and provide microbial safety for consumers.
ChemInform Abstract: Fast CO<sub>2</sub> Sequestration, Activation, and Catalytic Transformation Using N‐Heterocyclic Olefins. (2014)

Abstract This method uses a N‐heterocyclic olefin/carbon dioxide adduct as organocatalyst for the synthesis of dioxolane derivatives.
Triple-Stage-Actuator System of Head-Positioning Control in Hard Disk Drives (2013)

In this paper, we propose a triple-stage actuator system with a thermal actuator to increase a servo bandwidth of a head-positioning control system in hard disk drives. The thermal actuator is good for control in high frequency range because it has little negative impact caused by mechanical resonances. Therefore, the proposed system with a thermal actuator can control the head position beyond the major mechanical resonances caused by a voice coil motor (VCM) or piezoelectric (PZT) actuator. As a result, the servo bandwidth of the proposed triple-stage actuator system can be higher than that of the conventional dual-stage actuator system which consists of the VCM and the PZT actuators. Simulation results of sensitivity functions showed that the disturbance-compensation performance below 2 kHz will be improved by 6 dB with proposed control system.
Experimental study of the three-dimensional ac conductivity and dielectric constant of a conductor-insulator composite near the percolation threshold (1986)

We measured the ac conductivity and dielectric constant of a three-dimensional randomly mixed conductor-insulator system consisting of amorphous carbon and Teflon powder in the frequency range from 10 Hz to 13 MHz. Near the percolation threshold, these two quantities varied as a power of \ensuremath{\omega}, such as \ensuremath{\sigma}\ensuremath{\sim}${\ensuremath{\omega}}^{x}$, and \ensuremath{\epsilon}\ensuremath{\sim}${\ensuremath{\omega}}^{\mathrm{\ensuremath{-}}y}$. The values of x and y were found to be 0.86\ifmmode\pm\else\textpm\fi{}0.06 and 0.12\ifmmode\pm\else\textpm\fi{}0.04, respectively. These values are compared to the present percolation theories. We also measured the dc conductivity exponent t and dielectric constant exponent s to complete the study. Our data yielded t=1.85\ifmmode\pm\else\textpm\fi{}0.25 and s=0.68\ifmmode\pm\else\textpm\fi{}0.05.
ZORBAMYCIN AND RELATED ANTIBIOTICS (1971)

Zorbamycin and its related antibiotics, zorbonomycin B and zorbonomycin C, are three new antibiotics isolated from fermentations of Streptomyces bikiniensis var. zorbonensis. All three antibiotics are active against a variety of Gram-positive and Gram-negative bacteria and various fungi. Zorbamycin as well as zorbonomycins B and C appear to belong to the phleomycin and bleomycin families of antibiotics and to be most closely related to the phleomycins. The three antibiotics described in this paper show differences from the reported phleomycins and are likely new members of this group.
Leveraging Software-Defined Networking and Virtualization for a One-to-One Client-Server Model (2014)

Modern computer networks allow server resources to be shared. While this multiplexing is the unsung hero of scalability and performance, the fact that clients are sharing resources and each clientâ€™s network traffic is transmitted in a larger pool of the total network traffic, poses distinct challenges for security. By adopting multiplexing so broadly, the networking and systems communities have implicitly favored performance over security. When servers multiplexing clients are compromised, the attack is able to spread by exploiting unsuspecting clients sharing the resource. Drive-by-downloads are an example of an attack where a Web server is compromised and begins distributing malware to connecting clients. As a result of using todayâ€™s many-to-one client-server network model, current approaches are inadequate at protecting the network and its resources. We propose a redesign of the modern network infrastructure. Our approach involves moving from the current many-to-one client-server model to a one-to-one client-server model. In redesigning the network, we provide a means of better accountability for traffic between clients and servers. With accountability, we enable the ability to quickly determine which client is responsible for an attack. This allows us to quickly repair the affected entities. To accomplish this accountability, we separate each clientâ€™s communication into separate flows. A flow is identified by various network features, such as IP addresses and ports. Further, instead of allowing multiple clients to be multiplexed at the same server, we use a technique that allows each client to communicate with a server that is logically separate from all other clients. Accordingly, a server compromise only effects a single client. We create a one-to-one client-server model using virtualization techniques and OpenFlow, a software-defined network (SDN) protocol. We complete our model in three phases. In the first, we deploy a physical SDN using physical machines and a commodity network switch that supports OpenFlow to gain an initial understanding of SDNs. The next phase involves implementation of Choreographer, a DNS access control mechanism, in a virtualized SDN environment for better scalability over our physical configuration. Finally, we leverage Choreographer to dynamically instantiate a server for each client and create network flows that allow a client to reach the requested server.
Terahertz wavefront control by tunable metasurface made of graphene ribbons (2015)

We propose a tunable metasurface consisting of an array of graphene ribbons on a silver mirror with a SiO2 gap layer to control reflected wavefront at terahertz frequencies. The graphene ribbons exhibit localized plasmon resonances depending on their Fermi levels to introduce abrupt phase shifts along the metasurface. With interference of the Fabry-Perot resonances in the SiO2 layer, phase shift through the system is largely accumulated, covering the 0-to-2π range for full control of the wavefront. Numerical simulations prove that wide-angle beam steering up to 53° with a high reflection efficiency of 60% is achieved at 5 THz within a switching time shorter than 0.6 ps.