gebhart/patrepeval huggingface dataset:
Allosteric Interactions between the Myristate- and ATP-Site of the Abl Kinase (2011)

Abl kinase inhibitors targeting the ATP binding pocket are currently employed as potent anti-leukemogenic agents but drug resistance has become a significant clinical limitation. Recently, a compound that binds to the myristate pocket of Abl (GNF-5) was shown to act cooperatively with nilotinib, an ATP-competitive inhibitor to target the recalcitrant "T315I" gatekeeper mutant of Bcr-Abl. To uncover an explanation for how drug binding at a distance from the kinase active site could lead to inhibition and how inhibitors could combine their effects, hydrogen exchange mass spectrometry (HX MS) was employed to monitor conformational effects in the presence of both dasatinib, a clinically approved ATP-site inhibitor, and GNF-5. While dasatinib binding to wild type Abl clearly influenced Abl conformation, no binding was detected between dasatinib and T315I. GNF-5, however, elicited the same conformational changes in both wild type and T315I, including changes to dynamics within the ATP site located approximately 25 Å from the site of GNF-5 interaction. Simultaneous binding of dasatinib and GNF-5 to T315I caused conformational and/or dynamics changes in Abl such that effects of dasatinib on T315I were the same as when it bound to wild type Abl. These results provide strong biophysical evidence that allosteric interactions play a role in Abl kinase downregulation and that targeting sites outside the ATP binding site can provide an important pharmacological tool to overcome mutations that cause resistance to ATP-competitive inhibitors.
DETERMINANTS OF PARTICIPATION BEHAVIOR OF LIMITED RESOURCE FARMERS IN CONSERVATION RESERVE PROGRAM IN ALABAMA (2003)

This study investigated factors that affect participation behavior of limited resource farmers (LRF) in Conservation Reserve Program (CRP) in Alabama. A binary logit model was employed to analyze data obtained from 611 respondents. Results indicated that males, part-time occupation, total acres, participation in non-conservation related programs, direct method of receiving CRP information, and respondents' interest in receiving CRP information, were strong predictors of participation in the CRP. Key words: Limited resource, CRP, minorities, participation behavior
SFigure S3 from Age and Gender Associations of Virus Positivity in Merkel Cell Carcinoma Characterized Using a Novel RNA <i>In Situ</i> Hybridization Assay (2023)

&lt;p&gt;(A) Percentage of positive cells in MCPyV-positive tumors by RNA-ISH (n=42). (B) Photomicrograph of MCC/25 (Patient 12) with positive MCPyV RNA-ISH. The tumor (lymph node metastasis) was composed of a focal area of tumor cells surrounded by lymphocytes (green arrow). Tumor cells stain positively (red arrows) with punctate brown staining (400X magnification). (C) Comparison of percentage of positive cells by RNA-ISH and LTAg copy number by qPCR.&lt;/p&gt;
ChemInform Abstract: CORRELATION OF THE DITERPENOIDS SIDERITOL AND JATIVATRIOL (1975)

Abstract Die Beziehung zwischen den Titelverbindungen (Ia) und (IV) wird durch ihre Umwandlung in das Noratisendion (III) begründet.
The interaction of bovine factor IX, its activation intermediate, factor IX α, and its activation products, factor IXaα and factor IXaβ, with acidic phospholipid vesicles of various compositions (1986)

The interactions of bovine factor IX, its activation intermediate, Factor IX alpha, and its activation products, Factor IXa alpha and Factor IXa beta, with phospholipid vesicles, of mean radius of approx. 30 nm, containing various amounts of phosphatidylserine (PS) and phosphatidylcholine (PC), have been examined. For Factor IX, Factor IX alpha, Factor IXa alpha and Factor IXa beta, the dissociation constants, at saturating levels of Ca2+, are independent of the PS concentration in the vesicle after levels of 20-30% (w/w) have been reached, and attain minimum values of approx. 1.7, 1.7, 0.7 and 1.0 microM, respectively, with vesicles containing 50% PS. The amount of protein bound per vesicle particle is independent of the PS content, above 20% PS, for Factor IX and Factor IXa beta, with values of approx. 995-1197 and 1128-1566 molecules/vesicle, respectively. With Factor IX alpha, a dependence on the amount of protein bound with the content of PS is seen, which ranges from 338 to 619 molecules/vesicle with membranes containing 30-50% PS. For Factor IXa alpha, no regularity is noted and a range of 583-1083 molecules of protein/vesicle is observed with the systems employed. Examination of the radii of the proteins on the vesicle demonstrates that Factors IX alpha and IXa alpha occupy considerably more of the surface than do Factors IX and IXa beta, suggesting that a reason for the decreased number of binding sites for the former two proteins on the vesicle may be related to their greater surface spatial requirements.
Cutaneous Connective Tissue Diseases: Epidemiology, Diagnosis, and Treatment (2009)

Connective tissue diseases (CTDs) are a group of clinical disorders that have an underlying autoimmune pathogenesis. These include a diverse set of diseases such as relapsing polychondritis, rheumatoid arthritis, and eosinophilic fasciitis, along with more common entities like Sjogren's syndrome, dermatomyositis, scleroderma, and lupus erythematosus. The latter three will be the focus of this review, as they constitute the most significant and common CTD with cutaneous manifestations. The cutaneous signs often represent the preliminary stages of disease and the presenting clinical symptoms. Therefore, comprehensive knowledge of CTD manifestations is essential for accurate diagnosis, better assessment of prognosis, and effective management. Although the precise etiologies of CTDs remain obscure, recent advances have allowed for further understanding of their pathogenesis and improved disease classifications. In addition, there have been developments in therapeutic options for CTDs. This review provides an overview of the epidemiology, clinical presentations, and current treatment options of cutaneous lupus erythematous, dermatomyositis and scleroderma.
Optical Proximity Correction Feature Extraction Method Using Reticle Scanning Electron Microscope Images (2003)

Optical proximity correction (OPC) features are frequently used in photolithography. It is necessary to measure the shape characteristics such as height, width, area, position of center of gravity, and corner-rounding with nm-order accuracy. For this purpose, critical-dimension scanning electron microscope (CD-SEM) images are utilized. However, it is difficult to extract the shape characteristics mentioned above from a corrected pattern with conventional CD-SEM measurement. The authors developed a method to extract the shape characteristics automatically from a corrected reticle pattern with high accuracy, with combination of discriminant analysis and nonlinear regression.
<title>Three-dimensional computed tomography using a double-axis fluorescence microscope</title> (1996)

We developed a double-axis fluorescence microscope as a new type of 3D microscope, in which two conventional microscopes are placed perpendicularly to one another. This optical microscope provides a solution to extend the spatial frequency band in the depth direction, which is greatly limited for conventional single-axis microscopes. In addition, this equipment has a capability of implementing a fast image acquisition system by simultaneously taking images through both microscopes. We evaluated the 3D imaging properties of our system using 3D observation images of a micro-fluorescent sphere. In order to reconstruct 3D images of micro-objects, we applied a CT-based method we proposed to the 3D microscopic imaging system. Our experiments using a biological micro-specimen verified usefulness and effectiveness of our system.
1-((S)-2-Aminopropyl)-1H-indazol-6-ol:  A Potent Peripherally Acting 5-HT2Receptor Agonist with Ocular Hypotensive Activity (2005)

Serotonin 5-HT(2) receptor agonists have been identified as a potential new class of agents for the treatment of ocular hypertension and glaucoma. The initially reported tryptamine analogues displayed either poor solution stability, potent central nervous system activity, or both of these undesirable characteristics and were unacceptable for clinical evaluation. A series of 1-(2-aminopropyl)-1H-indazole analogues was synthesized and evaluated for their suitability for consideration as clinical candidates. 1-((S)-2-Aminopropyl)-1H-indazol-6-ol (9) was identified as a peripherally acting potent 5-HT(2) receptor agonist (EC(50) = 42.7 nM, E(max) = 89%) with high selectivity for the 5-HT(2) receptors relative to other serotonergic receptor subtypes and other families of receptors and has significantly greater solution stability than alpha-methyl-5-hydroxytryptamine. Additionally, 9 potently lowers intraocular pressure in conscious ocular hypertensive monkeys (-13 mmHg, 33%); this reduction appears to be through a local rather than a centrally mediated effect. Compound 9 appears to be an excellent 5-HT(2) receptor agonist for conducting further studies directed toward a clinical proof-of-concept study for this class of ocular hypotensive agents.
Improvements of background sound coding in linear predictive speech coders (2002)

A proper coding of background sounds has proven to be important in digital cellular telephone systems. It is therefore of considerable interest to find methods that improve also background sound coding, in particular in medium and low bitrate speech coders. In many coders operating around 8 kbps, one significant effect has been a swirling distortion when coding for example smooth car noise. The paper discusses the origin of this problem, and presents an algorithm that reduces swirling, giving a significant overall perceptual improvement, as shown by field tests in commercial D-AMPS systems in the US. A related new algorithm for error concealment is also presented. This method makes it possible to perceptually remove the effect of fading dips persisting for a few seconds, during nonspeech periods.
HIGH-IMPACT, ENERGY-ABSORBING VEHICLE BARRIER SYSTEM: U.S. Patent No. US 6,926,461 B1 (2005)

A high-impact, energy-absorbing vehicle barrier system generally includes a substantially rigid outer containment wall coupled via cable restraint assemblies with an energy-absorbing inner impact wall, and energy-absorbing cartridges strategically positioned between the impact wall and containment-wall: The impact wall is constructed of a number of rectangular tubes coupled with one another to presents a substantially smooth, uniform surface to passing vehicles. The energy-absorbing cartridges generally consist of a number of foam sheets which compress and crush between the containment wall and impact wall to absorb energy from an errant vehicle striking the face of the impact wall, while the deflection and deformation of the impact wall tubes dissipates additional energy to reduce peak decelerations and mitigate the severity of high-energy vehicular impacts. The splice units and quick-disconnect cable restraint system provide for relatively easy and quick replacement of damaged impact wall sections and energy-absorbing cartridges.
Apelin targets gut contraction to control glucose metabolism via the brain (2015)

Here, we identify a novel mode of communication between the intestine and the hypothalamus that controls glucose utilisation. Moreover, our data identified oral apelin administration as a novel potential target to treat metabolic disorders.
MR imaging volumetry of subcortical structures and cerebellar hemispheres in temporal lobe epilepsy. (2007)

Unilateral amygdalar and bilateral thalamic volume loss, in the absence of caudate head atrophy, is likely to reflect seizure-induced injury due to TLE. Correlations of VRs affecting the amygdala, caudate, and cerebellum with GTCS frequency may also reflect injury or a prediposition for secondary generalization. Potential effects of complex partial seizures, febrile seizures, or antiepileptic medications on subcortical structures need to be evaluated in future studies.
Effective Technology of Preventive Measures against Piping Damage on Steam Lines in Nuclear Power Plants (2011)

Nuclear power plants are required to have especially high reliability and increasingly longer service life. As a contribution to the solution of these issues, an analysis was conducted on steam field-related troubles and their causes based on a data from an online database that tracks troubles at nuclear power plants and the authors' experience. As a result, the reality of piping damage attributed to the two-phase flow of steam and condensate characteristic of nuclear power plants was elucidated. This note introduces preventive measures against piping damage to steam and condensate lines that has been proven effective through actual use in various industries under the following topics: 1) technology for the separation of steam/condensate in steam piping, 2) technology for the discharge of condensate from steam piping, and 3) technology for the measurement, inspection or monitoring of steam and condensate lines.
Impaired neurogenesis and activated caspase 3‐dependent apoptosis pathway in the rostral ventrolateral medulla cause hypertension in stroke‐prone spontaneously hypertensive rats (2008)

Recent studies demonstrated that neural progenitor cells responsible for neurogenesis migrate to the sites of brain injury of epilepsy, stroke and neurodegenerative diseases. It is also well known that apoptosis is involved in regulating synaptic plasticity. It remains unknown the impact of balance between neurogenesis and apoptosis in the rostral ventrolateral medulla (RVLM) in the pathogenesis of hypertension. We examined neurogenesis and caspase 3‐dependent apoptosis initiated by mitochondrial translocation of Bax in the RVLM of stroke‐prone spontaneously hypertensive rats (SHRSP). We identified neuroblasts by staining for doublecortin (Dcx), cell proliferation by absorption of bromodeoxyuridine (BrdU), and apoptosis by staining for caspase‐3, Bax, PKC in membranous, cytosolic and mitochondorial fractions. In hypertensive states, SHRSP had significantly lower Dcx and BrdU expression than WKY (Dcx; −41±4%, BrdU; −33±5%, n=8 for each, P&lt;0.01). In pre‐hypertensive states, the expressions of Dcx and BrdU in the RVLM were significantly decreased compared with WKY. The expression of Bax in mitochondorial fraction and caspase‐3 in cytosolic fraction were significantly increased in SHRSP than in WKY, in either pre‐hypertensive or hypertensive states. In conclusion, the impaired neurogenesis and activated caspase 3‐dependent apoptosis pathway in the RVLM might be involved in hypertension in SHRSP.
Monocular passive ranging through a PQ:PMMA holographic wavelength division demultiplexer (2023)

Distance estimation is an important yet challenging part of any tracking system, as being able to quickly locate an object in 3D space allows for the automated targeting of communication, delivery, and interception systems, as well as providing important telemetry about fast moving objects. A monocular passive ranging system is defined as that which only requires one observation point through which it measures some outside signal to estimate range. The approach presented here simultaneously observes the intensity of light emitted by the target at three wavelength bands with ~10nm FWHM, centered at 750, 762, and 780 nm. The light is separated using a PQ:PMMA holographic optical element (HOE) configured as a wavelength division demultiplexer. Light at the two outer bands experiences negligible absorption in the atmosphere, while light at ~762 nm is strongly absorbed by O<sub>2</sub>. By comparing the intensity of the two unabsorbed bands, we may interpolate the expected intensity of the 762 nm band if there is no O<sub>2</sub> in the path. This is then used in conjunction with the 762 nm band measurement to approximate the total O<sub>2</sub> transmissivity. Finally, Beer’s law and the HITRAN database provide us with the tools to convert a transmissivity into a distance estimation. The use of an HOE is pivotal in the practicality of such a system, as it allows us to measure all three signals simultaneously, thus eliminating the effects of turbulence and reducing overall noise.
NUCLEUS TRACTUS SOLITARII: INTEGRATING STRUCTURES (1999)

Presently, many researchers have adopted a reductionistic approach to physiology. Specifically, this involves studies on acutely isolated or cultured cells. While this is essential for our understanding of important cellular and subcellular mechanisms, it should not be forgotten that physiology is about the function of an integrating body. One view point is that definitive interpretations can only be made by crossing boundaries of physiology from the molecular/ cellular to the systems/behavioural level. An aim of this lecture will stress the importance of a multidisciplinary approach to physiology, that is, 'putting the cell back into the system'. The lecture attempts to demonstrate why this is important for enhancing the functional significance and relevance of physiological data as well as for validating predictions.
A next generation CMOS-compatible GaN-on-Si transistors for high efficiency energy systems (2015)

CMOS-compatible 100 V / 650 V enhancement-mode high electron mobility transistors (E-HEMTs) and 650 V depletion-mode MISFET (D-MISFET) are fabricated on 6-inch GaN-on-Si wafers. These devices show excellent power converter switching performances. Both 100 V and 650 V E-HEMTs had passed industrial reliability qualifications. The importance of bulk leakage, interface quality and gate trapping in dynamic on-resistance is figured out. The device with optimized processes shows a significant reduction of the dynamic on-resistance degradation.
Synthesis and interaction with thymidylate synthase of 5'-dithiophosphate and 5'-fluorothiophosphate of thymidine. (1998)

Thymidine-5'-fluorothiophosphate, dTMP(S)-F, was synthesized by the oxathiaphospholane, and thymidine 5'-dithiophosphate, dTMPS2, by the dithiaphospholane, method. To estimate the role of 5'-phosphate group ionization in binding of pyrimidine nucleotides by thymidylate synthase, dTMP(S)-F was studied as an inhibitor of mouse tumour (L1210) enzyme, and its inhibitory properties were compared with those of dTMPS2, a close dTMP analogue. While dTMPS2 proved to be an inhibitor, competitive vs dUMP, with K(i)app = 94 microM, the 5'-fluorothiophosphate congener displayed no activity, indicating that the enzyme requires for binding the presence of a dianionic 5'-phosphate group in a nucleotide.
Laser-assisted writing of copper films through Nd:YAG laser radiation (2004)

The use of a laser-assisted process for direct writing of copper films and coatings has significant potential for several applications within the electronics industry. Experiments were conducted using a pulsed Nd:YAG (1064 nm) laser to irradiate a metallo-organic precursor film that had been predeposited onto glass and FR-4 substrates. Parameters that were investigated included irradiation wavelength, pulsing conditions, precursor thickness, and the use of inert and active shielding gas. Scanning electron microscopy, energy dispersive x-ray spectroscopy, and electrical resistivity measurements were used to characterize the processed specimens. Initial results of these experiments indicated that Nd:YAG irradiation resulted in decomposition of the precursor and deposition of copper; although, the crystalline deposits contained varying levels of oxide. It is believed that the decomposition mechanism is pyrolytic.
Wireless Fading Channels (2011)

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Enhancing the cycle stability of Li–O2 batteries via functionalized carbon nanotube-based electrodes (2020)

3,5-Bis(trifluoromethyl)phenylmaleimide functionalized CNT buckypapers are prepared as a binder-free oxygen electrode for Li–O<sub>2</sub> batteries with increased capacity and enhanced stability.
Robust transceiver design in full-duplex MIMO cognitive radios (2016)

We study a full duplex (FD) multiple-input multiple-output (MIMO) cognitive cellular network, in which a secondary base-station (BS) operating in FD mode serves multiple uplink (UL) and downlink (DL) secondary users (SUs) operating in half-duplex (HD) mode simultaneously. The spectrum is shared between secondary and primary networks, and thus uplink SUs and secondary BS generate interference on primary users (PUs). We assume that the channel state information (CSI) available at the transmitters is imperfect, and the errors of the CSI are assumed to be norm bounded. Under the impact of channel uncertainty, we address the robust minimization of the sum of mean-squared-errors (MSE) of all estimated symbols subject to power constraints at the uplink SUs and secondary BS, and interference constraints projected to each PU. We show that this problem can be cast as a Semidefinite programming (SDP), and joint design of transceiver matrices can be obtained through an iterative algorithm. Numerical results are presented to show the effectiveness and robustness of the proposed robust algorithm.
Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression (2019)

Characterization of Human Endogenous Retrovirus (HERV) expression within the transcriptomic landscape using RNA-seq is complicated by uncertainty in fragment assignment because of sequence similarity. We present Telescope, a computational software tool that provides accurate estimation of transposable element expression (retrotranscriptome) resolved to specific genomic locations. Telescope directly addresses uncertainty in fragment assignment by reassigning ambiguously mapped fragments to the most probable source transcript as determined within a Bayesian statistical model. We demonstrate the utility of our approach through single locus analysis of HERV expression in 13 ENCODE cell types. When examined at this resolution, we find that the magnitude and breadth of the retrotranscriptome can be vastly different among cell types. Furthermore, our approach is robust to differences in sequencing technology and demonstrates that the retrotranscriptome has potential to be used for cell type identification. We compared our tool with other approaches for quantifying transposable element (TE) expression, and found that Telescope has the greatest resolution, as it estimates expression at specific TE insertions rather than at the TE subfamily level. Telescope performs highly accurate quantification of the retrotranscriptomic landscape in RNA-seq experiments, revealing a differential complexity in the transposable element biology of complex systems not previously observed. Telescope is available at https://github.com/mlbendall/telescope.
ChemInform Abstract: Far‐IR Spectroscopy of Alkali‐Metal and Alkaline‐Earth Cations in Faujasite Zeolites (1989)

Abstract is used to study the factors influencing the frequencies of far‐IR cation translatory modes in faujasites, namely, the mass, charge, and size of the cation as well as its local environment.