gebhart/patrepeval huggingface dataset:
Cutting Edge: Identification of a Pre-Ligand Assembly Domain (PLAD) and Ligand Binding Site in the IL-17 Receptor (2007)

IL-17 is the hallmark cytokine of the newly described "Th17" lymphocyte population. The composition, subunit dynamics, and ligand contacts of the IL-17 receptor are poorly defined. We previously demonstrated that the IL-17RA subunit oligomerizes in the membrane without a ligand. In this study, computational modeling identified two fibronectin-III-like (FN) domains in IL-17RA connected by a nonstructured linker, which we predicted to mediate homotypic interactions. In yeast two-hybrid, the membrane-proximal FN domain (FN2), but not the membrane-distal domain (FN1), formed homomeric interactions. The ability of FN2 to drive ligand-independent multimerization was verified by coimmunoprecipitation and fluorescence resonance energy transfer microscopy. Thus, FN2 constitutes a "pre-ligand assembly domain" (PLAD). Further studies indicated that the FN2 linker domain contains the IL-17 binding site, which was never mapped. However, the FN1 domain is also required for high affinity interactions with IL-17. Therefore, although the PLAD is located entirely within FN2, effective ligand binding also involves contributions from the linker and FN1.
ChemInform Abstract: Recent Progress in the Synthetic Methodologies of Peptide Thioesters (2011)

Abstract Review: ca. 60 refs.
Performance and fuel cell applications of reacted ball-milled MgH<sub>2</sub>/5.3 wt% TiH<sub>2</sub> nanocomposite powders (2018)

The present study aimed to enhance the kinetics behavior and destabilize the thermal stability of MgH<sub>2</sub> powder by high-energy milling of Mg powder under 50 bar of H<sub>2</sub> for several hours using Ti-balls as the milling media. The results showed a monotonical increase in Ti content worn off the milling media and introduced into the milled powders. This gradual doping led to homogeneous distribution of fine Ti particles into the Mg/MgH<sub>2</sub> powder matrix without agglomeration or compositional fluctuations at the micro-level. During the activation stage of the powders, achieved at 350 °C/35 bar H<sub>2</sub> prior to hydrogenation kinetics measurements, elemental Ti reacted with H<sub>2</sub> to form fine TiH<sub>2</sub> particles. Our proposed <i>in situ</i> mechanically induced catalyzation approach was found to be mutually beneficial for decreasing the apparent activation energy of decomposition. In addition, introducing 5.3 wt% of TiH<sub>2</sub> to the MgH<sub>2</sub> powder obtained after 50 h led to the achievement of superior enhancement of gas uptake/release kinetics at relatively low temperatures. The nanocomposite MgH<sub>2</sub>/5.3 TiH<sub>2</sub> powder possessed fast hydrogenation/dehydrogenation kinetics behaviors and revealed long cycle lifetimes. This system was successfully employed as a solid-state hydrogen source to charge the battery of a cell-phone device using an integrated Ti-tank/commercial proton exchange membrane-fuel cell system.
Defining regions of the Y‐chromosome responsible for male infertility and identification of a fourth AZF region (AZFd) by Y‐chromosome microdeletion detection (1999)

Cytogenetic and molecular deletion analyses of azoospermic and oligozoospermic males have suggested the existence of AZoospermia Factor(s) (AZF) residing in deletion intervals 5 and 6 of the human Y-chromosome and coinciding with three functional regions associated with spermatogenic failure. Nonpolymorphic microdeletions in AZF are associated with a broad spectrum of testicular phenotypes. Unfortunately, Sequence Tagged Sites (STSs) employed in screening protocols range broadly in number and mapsite and may be polymorphic. To thoroughly analyze the AZF region(s) and any correlations that may be drawn between genotype and phenotype, we describe the design of nine multiplex PCR reactions derived from analysis of 136 loci. Each multiplex contains 4–8 STS primer pairs, amplifying a total of 48 Y-linked STSs. Each multiplex consists of one positive control: either SMCX or MIC2. We screened four populations of males with these STSs. Population I consisted of 278 patients diagnosed as having significant male factor infertility: either azoospermia, severe oligozoospermia associated with hypogonadism and spermatogenic arrest or normal sperm counts associated with abnormal sperm morphology. population II consisted of 200 unselected infertile patients. population III consisted of 36 patients who had previously been shown to have aneuploidy, cytological deletions or translocations involving the Y-chromosome or normal karyotypes associated with severe phenotype abnormalities. Population IV consisted of 920 fertile (control) males. The deletion rates in populations I, II and III were 20.5%, 7% and 58.3%, respectively. A total of 92 patients with deletions were detected. The deletion rate in population IV was 0.87% involving 8 fertile individuals and 4 STSs which were avoided in multiplex panel construction. The ability of the nine multiplexes to detect pathology associated microdeletions is equal to or greater than screening protocols used in other studies. Furthermore, the data suggest a fourth AZF region between AZFb and AZFc, which we have termed AZFd. Patients with microdeletions restricted to AZFd may present with mild oligozoospermia or even normal sperm counts associated with abnormal sperm morphology. Though a definitive genotype/phenotype correlation does not exist, large deletions spanning multiple AZF regions or microdeletions restricted to AZFa usually result in patients with Sertoli Cell Only (SCO) or severe oligozoospermia, whereas microdeletions restricted to AZFb or AZFc can result in patients with phenotypes which range from SCO to moderate oligozoospermia. The panel of nine multiplexed reactions, the Y-deletion Detection System (YDDS), provides a fast, efficient and accurate method of assessing the integrity of the Y-chromosome. To date, this study provides the most extensive screening of a proven fertile male population in tandem with 514 infertile males, derived from three different patient selection protocols. Mol. Reprod. Dev. 53:27–41, 1999. © 1999 Wiley-Liss, Inc.
Low Temperature Synthesis and Electrode Properties of Li4Mn5 O 12 (1998)

Stoichiometric spinel oxide has been synthesized by an oxidation of by lithium peroxide in the presence of excess lithium hydroxide followed by firing at T ⩽ 500°C. The sample has been characterized by X‐ray diffraction, elemental and oxidation state analyses and thermogravimetric analysis. X‐ray results indicate that begins to disproportionate at T > 500°C to give (x < 0.33) and . The samples fired at 400 and 500°C show in the voltage range 3.3–2.3 V, an initial capacity of 160 and 153 mAh/g, respectively, which is close to the theoretical value. The sample fired at 500°C shows excellent cyclability with <2% capacity decline over 40 cycles.
Generating summaries tailored to target characteristics (2019)

Recently, research efforts have gained pace to cater to varied user preferences while generating text summaries. While there have been attempts to incorporate a few handpicked characteristics such as length or entities, a holistic view around these preferences is missing and crucial insights on why certain characteristics should be incorporated in a specific manner are absent. With this objective, we provide a categorization around these characteristics relevant to the task of text summarization: one, focusing on what content needs to be generated and second, focusing on the stylistic aspects of the output summaries. We use our insights to provide guidelines on appropriate methods to incorporate various classes characteristics in sequence-to-sequence summarization framework. Our experiments with incorporating topics, readability and simplicity indicate the viability of the proposed prescriptions
Designable Biointerfaces Using Vapor-Based Reactive Polymers (2010)

Functionalized poly(p-xylylenes) constitute a versatile class of reactive polymers that can be prepared in a solventless process via chemical vapor deposition (CVD) polymerization. The resulting ultrathin coatings are typically pinhole-free and can be conformally deposited onto a wide range of substrates and materials. More importantly, appropriately selected functional groups can serve as anchoring sites for tailoring biointerface properties via the immobilization of biomolecules. In this article, controlled surface chemistries are outlined that use functionalized poly(p-xylylenes) as reactive coatings, including alkyne-functionalized coatings for Huisgen 1,3-dipolar cycloaddition reactions or aldehyde-functionalized coatings. The reactive coatings technology provides flexible access to a range of different surface chemistries, enabling a broad range of potential applications in microfluidics, medical device coatings, and biotechnology. In this feature article, we will highlight recent progress in vapor-based reactive coatings and will discuss potential benefits and current limitations.
Signal-to-Noise Analysis in Count Rate Dependent Adaptive Digital Pulse Processing for Gamma-Ray Spectroscopy (2017)

An optimum filter to achieve best signal to noise ratio is a primary prerequisite in high resolution gamma spectroscopy systems. Digital techniques for nuclear spectroscopy are increasingly implemented in modern radiation detection systems, which allow consideration of the attributes of the generated signal on a pulse-by-pulse basis. In this work, the limits of the count rate dependent signal-to-noise ratio (SNR) are established for time invariant (fixed) and time variant (adaptive) digital filters. The calculated results illustrate that the adaptive filter provides improved SNR for a given pulse throughput rate as compared to a fixed filter. Further analysis shows that the detector with a low input capacitance is a preferable choice to achieve better SNR and improved performance at high count rates. A 14-bit adaptor module with sampling rate of 250 MS/s is used for digitizing a high purity germanium (HPGe) detector's pre-amplifier pulses. Fixed and adaptive digital trapezoid shaping algorithms with timing filter, baseline restorer, and pile-up rejecter are implemented using field programmable gate array (FPGA) for real-time signal processing. The experimental results using the coaxial HPGe with fixed and adaptive shaping show reasonable agreement with the theoretical calculations. At input count rate of 400 kcps with 50% throughput rate after pile- up rejection, the improvement in measured SNR is 30% with adaptive trapezoid filter in comparison to the fixed filter.
Synthetic cyclin dependent kinase inhibitors. New generation of potent anti-cancer drugs. (1999)

The unsatisfactory results of current anti-cancer therapies require the active search for new drugs, new treatment strategies and a deeper understanding of the host-tumour relationship. From this point of view, the drugs with a capacity to substitute the functions of altered tumour suppressor genes are of prominent interest. Since one of the main functions of oncosuppressors is to mediate cell cycle arrest via modification of cyclin dependent kinases (CDKs) activity, the compounds with ability to substitute altered functions of these genes in neoplastic cells are of prominent interest. Synthetic inhibitors of cyclin dependent kinases (CDKIs) are typical representatives of such drugs. Olomoucine (OC), flavopiridol (FP), butyrolactone I (BL) and their derivatives selectively inhibit CDKs and thus constrain tumor cell proliferation under in vitro and/or in vivo conditions. We originally discovered OC and its inhibitory activity toward CDK1 family of CDKs, and recently reported the induction of apoptosis and tumor regression following OC application. Moreover, the OC family of synthetic CDKIs has the capacity of directly inhibit CDK7, the principal enzyme required for activating other CDKs, and thus these compounds are the first known CDK7 inhibitors. Its unique mechanism of action and potent anti-cancer activity under both in vitro and in vivo conditions provide a unique tool to inhibit tumour cell proliferation, and to selectively induce apoptosis in neoplastic tissues. The mechanisms of anti-cancer activities of FP, BL, OC and related synthetic CDKIs are compared and discussed in this paper.
Concentrator photovoltaic module architectures with capabilities for capture and conversion of full global solar radiation (2016)

Emerging classes of concentrator photovoltaic (CPV) modules reach efficiencies that are far greater than those of even the highest performance flat-plate PV technologies, with architectures that have the potential to provide the lowest cost of energy in locations with high direct normal irradiance (DNI). A disadvantage is their inability to effectively use diffuse sunlight, thereby constraining widespread geographic deployment and limiting performance even under the most favorable DNI conditions. This study introduces a module design that integrates capabilities in flat-plate PV directly with the most sophisticated CPV technologies, for capture of both direct and diffuse sunlight, thereby achieving efficiency in PV conversion of the global solar radiation. Specific examples of this scheme exploit commodity silicon (Si) cells integrated with two different CPV module designs, where they capture light that is not efficiently directed by the concentrator optics onto large-scale arrays of miniature multijunction (MJ) solar cells that use advanced III-V semiconductor technologies. In this CPV<sup>+</sup> scheme ("+" denotes the addition of diffuse collector), the Si and MJ cells operate independently on indirect and direct solar radiation, respectively. On-sun experimental studies of CPV<sup>+</sup> modules at latitudes of 35.9886° N (Durham, NC), 40.1125° N (Bondville, IL), and 38.9072° N (Washington, DC) show improvements in absolute module efficiencies of between 1.02% and 8.45% over values obtained using otherwise similar CPV modules, depending on weather conditions. These concepts have the potential to expand the geographic reach and improve the cost-effectiveness of the highest efficiency forms of PV power generation.
Abstract C135: Therapeutic targets for MYC-driven cancer. (2011)

Abstract Drugs directed toward oncoproteins have demonstrated efficacy while avoiding the systemic toxicity associated with standard chemotherapeutics. However, oncoproteins encoding for transcription factors, such as the MYC family, which are broadly implicated in many human cancers, are difficult to inhibit with small molecules or antibody based therapies. Thus, to target MYC-driven cancers, we have taken the approach of identifying druggable genes that exhibit a synthetic lethal relationship with aberrant MYC expression. Using an isogenic cell model system, we identified, via high throughput siRNA screening, more than 100 druggable genes that exhibit a synthetic lethal interaction with MYC (referred to as MYC-synthetic lethal genes, MYC-SL). Among the MYC-SL genes, we focused on casein kinase 1 epsilon (CSNK1e), whose relevance in MYC-driven human cancer was demonstrated by correlation between high levels of CSNK1e expression, MYCN amplification, and poor clinical prognosis in neuroblastoma cases. The requirement of CSNK1e for growth of neuroblastomas with MYCN amplification was validated in vivo by conditional knock-down and via a small molecule inhibitor of its activity. CSNK1e had previously been implicated in the regulation of WNT, however our data also suggest that in neuroblastoma the activity of CSNK1e is a key component of a positive autocrine circuit triggered by MYCN amplification that sustains both WNT and SHH pathways. In summary, our work elucidates a broad network of MYC synthetic lethal genes, perhaps a reflection of its widespread effects on gene expression, and demonstrates the power of high throughput siRNA screening as a rapid and unbiased approach to identify a network of synthetic lethal genes and potential new therapeutic targets functionally linked to a previously un-druggable oncogene. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr C135.
A novel smart fatigue damage sensor for structural health monitoring of critical components of structures (2016)

In this paper we present the details of a novel fatigue sensor designed to monitor health status of mission critical mechanical systems. The designed fatigue sensor is unique in the respect that it senses fatigue related degradation before the actual catastrophic failure happens and gives ample time for replacement of the fatigued part. The electronics of the sensor is wireless enabled and can be made to work without any power source so that it can be attached to critical structural members of the structure during manufacture and can be left in place until the part is replaced.
RubyACRs, non-algal anion channelrhodopsins with highly red-shifted absorption (2020)

Abstract Channelrhodopsins are light-gated ion channels widely used to control neuronal firing with light (optogenetics). We report two previously unknown families of anion channelrhodopsins (ACRs), one from the heterotrophic protists labyrinthulomycetes and the other from haptophyte algae. Four closely related labyrinthulomycete ACRs, named RubyACRs here, exhibit a unique retinal binding pocket that creates spectral sensitivities with maxima at 590-610 nm, the most red-shifted channelrhodopsins known, long-sought for optogenetics, and more broadly the most red-shifted microbial rhodopsins so far reported. We identified three spectral tuning residues critical for the red-shifted absorption. Photocurrents recorded from the RubyACR from Aurantiochytrium limacinum (designated Al ACR1) under single-turnover excitation exhibited biphasic decay, the rate of which was only weakly voltage-dependent, in contrast to that in previously characterized cryptophyte ACRs, indicating differences in channel gating mechanisms between the two ACR families. Moreover, in A. limacinum we identified three ACRs with absorption maxima at 485, 545, and 590 nm, indicating color-sensitive photosensing with blue, green and red spectral variation of ACRs within individual species of the labyrinthulomycete family. We also report energy transfer from a cytoplasmic fluorescent protein domain to the retinal chromophore bound within RubyACRs, not seen in similar constructs in other channelrhodopsins. Significance Statement Our identification and characterization of two ACR families, one from non-photosynthetic microorganisms, shows that light-gated anion conductance is more widely spread among eukaryotic lineages than previously thought. The uniquely far red-shifted absorption spectra of the subset we designate RubyACRs provide the long-sought inhibitory optogenetic tools producing large passive currents activated by long-wavelength light, enabling deep tissue penetration. Previously only low-efficiency ion-pumping rhodopsins were available for neural inhibition by the orange-red region of the spectrum. The unusual amino acid composition of the retinal-binding pocket in RubyACRs expands our understanding of color tuning in retinylidene proteins. Finally, energy transfer from the fluorescent protein used as a tag on RubyACRs opens a potential new dimension in molecular engineering of optogenetic tools.
Rotor system load monitoring using a neural network based approach (1997)

A neural network model is developed to predict selected rotor system vibratory loads of an H-60 helicopter. The load model is based on input parameters which can be readily measured and recorded in the fuselage using a flight data recorder. The model has been developed using flight test data from a highly instrumented SH-60B aircraft which included a slipring assembly and strain gauges mounted in the rotating system. The strain gauge measurements provide a reference vibratory load for neural network model correlation. Load models are also assessed on flight test data from a second H-60 aircraft which was also instrumented with strain gauges in the rotating system. Two types of neural network algorithms are used in the analysis. A self organizing feature map algorithm is used for training data set selection and a modular neural network algorithm is used for load predictions. Predicted loads compare quite well with strain gauge measurements and results show that the load models provide good correlation on test data from the second H-60 aircraft.
Releasing Phosphorus from Calcium for Struvite Fertilizer Production from Anaerobically Digested Dairy Effluent (2009)

Being a non-renewable resource and a source of potential water pollution, phosphorus could be recovered from animal manure in the form of struvite (MgNH4PO4.6H2O) to be used as a slow-release fertilizer. It was found recently that the majority of phosphorus in anaerobically digested dairy effluent is tied up in a fine suspended calcium-phosphate solid, thus becoming unavailable for struvite formation. Acidification and use of a chelating agent were investigated for converting the calcium-associated phosphorus in the digested effluent to dissolved phosphate ions, so that struvite can be produced. The results demonstrated that the phosphorus in the effluent was released into the solution by lowering the pH. In addition, the phosphorus concentration in the solution increased significantly with increased ethylenediaminetetraacetic acid (EDTA) concentration, as EDTA has a high stability constant with calcium. Most of the phosphorus (91%) was released into the solution after adding EDTA. Further, the freed phosphorus ion precipitated out as struvite provided that sufficient magnesium ions (Mg2+) were present in the solution. Furthermore, the phase structure of the solid precipitate obtained from the EDTA treatment matched well with standard struvite, based on the data from X-ray diffraction analysis. These results provide methods for altering the forms of phosphorus for the design and application of phosphorus-removal technologies for dairy wastewater management.
A solution to the next best view problem for automated surface acquisition (1999)

A solution to the "next best view" (NBV) problem for automated surface acquisition is presented. The NBV problem is to determine which areas of a scanner's viewing volume need to be scanned to sample all of the visible surfaces of an a priori unknown object and where to position/control the scanner to sample them. A method for determining the unscanned areas of the viewing volume is presented. In addition, a novel representation, positional space, is presented which facilitates a solution to the NBV problem by representing what must be and what can be scanned in a single data structure. The number of costly computations needed to determine if an area of the viewing volume would be occluded from some scanning position is decoupled from the number of positions considered for the NBV, thus reducing the computational cost of choosing one. An automated surface acquisition systems designed to scan all visible surfaces of an a priori unknown object is demonstrated on real objects.
Toward Multiphase Flow Decomposition Based on Electrical Capacitance Tomography Sensors (2017)

We describe an approach, based on electrical capacitance tomography (ECT) sensors, to decompose and continuously monitor multiphase flow components (fractional areas or volumes) in mixtures containing conducting phases. The proposed approach exploits the Maxwell-Wagner-Sillars effect at distinct frequencies to reconstruct each phase of a multiphase flow and is also utilized to estimate the fractional volume of the various phases of the mixture. The approach is illustrated for a three-phase mixture composed of air, water, and oil. This approach utilizes the very same ECT measurement apparatus used for flow imaging and, as such, inherits its high speed of acquisition and suitability for real-time operation.