gebhart/patrepeval huggingface dataset:
Small, Membrane-bound, Alternatively Spliced Forms of Ankyrin 1 Associated with the Sarcoplasmic Reticulum of Mammalian Skeletal Muscle (1997)

We have recently found that the erythroid ankyrin gene, Ank1, expresses isoforms in mouse skeletal muscle, several of which share COOH-terminal sequence with previously known Ank1 isoforms but have a novel, highly hydrophobic 72-amino acid segment at their NH2 termini. Here, through the use of domain-specific peptide antibodies, we report the presence of the small ankyrins in rat and rabbit skeletal muscle and demonstrate their selective association with the sarcoplasmic reticulum. In frozen sections of rat skeletal muscle, antibodies to the spectrin-binding domain (anti-p65) react only with a 210-kD Ank1 and label the sarcolemma and nuclei, while antibodies to the COOH terminus of the small ankyrin (anti-p6) react with peptides of 20 to 26 kD on immunoblots and decorate the myoplasm in a reticular pattern. Mice homozygous for the normoblastosis mutation (gene symbol nb) are deficient in the 210-kD ankyrin but contain normal levels of the small ankyrins in the myoplasm. In nb/nb skeletal muscle, anti-p65 label is absent from the sarcolemma, whereas anti-p6 label shows the same distribution as in control skeletal muscle. In normal skeletal muscle of the rat, anti-p6 decorates Z lines, as defined by antidesmin distribution, and is also present at M lines where it surrounds the thick myosin filaments. Immunoblots of the proteins isolated with rabbit sarcoplasmic reticulum indicate that the small ankyrins are highly enriched in this fraction. When expressed in transfected HEK 293 cells, the small ankyrins are distributed in a reticular pattern resembling the ER if the NH2-terminal hydrophobic domain is present, but they are uniformly distributed in the cytosol if this domain is absent. These results suggest that the small ankyrins are integral membrane proteins of the sarcoplasmic reticulum. We propose that, unlike the 210-kD form of Ank1, previously localized to the sarcolemma and believed to be a part of the supporting cytoskeleton, the small Ank1 isoforms may stabilize the sarcoplasmic reticulum by linking it to the contractile apparatus.
A recurrent idiotype on monoclonal anti-human Ia antibodies. (1982)

We report a recurrent idiotype on a remarkably high fraction (4/19) of murine monoclonal antibodies specific for human Ia monomorphic determinants and elicited by separate immunizations. For three of them, the shared idiotype is associated with the antigen-combining site. These results indicate that the spectrum of mouse antibody responses to human Ia antigens may be based on recurrent idiotypes, suggesting a limited potential repertoire of murine monoclonal antibodies to human Ia antigens. Anti-idiotypic reagents might be helpful in dissecting this repertoire and to generate a mirror image of a human Ia antigenic map. Furthermore, antisera to the idiotype of antibodies specific for human Ia monomorphic determinants might help in elucidating the interactions between Ia molecules and receptors on immune cells.
Myocardial Electrode Implantation by the Subxiphoid Approach Using a Heart Stabilizer (2005)

During implantation of a pacemaker into a 15-year-old male (height: 155 cm, weight: 65 kg) suffering from complete atrioventricular block, it was difficult to exteriorize the myocardium by approaching from below the xiphoid process so an operative field was obtained by using a heart stabilizer. A myocardial electrode was fixed after confirming stable circulatory dynamics with no arrhythmia and good R wave amplitude and pacing thresholds. As the heart stabilizer is now a vital device for off-pump coronary artery bypass (OPCAB), we consider that it will also become a useful device for procedures other than OPCAB in the field of cardiac surgery.
Removal of Selenocyanate in Water by Precipitation:  Characterization of Copper−Selenium Precipitate by X-ray Diffraction, Infrared, and X-ray Absorption Spectroscopy (1997)

During refining of sour crude oils produced from reservoirs containing seleniferous marine shales, selenium is concentrated into process waters and wastewaters. Selenium, present in the waters as selenocyanate, must be removed to meet regulatory discharge limits. Treatment of wastewaters with copper(II) salts effectively precipitates selenium. An objective of the present study was to determine whether selenium was precipitated as elemental Se or immobilized in the form of cyanate complexes or any other form that remains to be identified. The precipitate had a Se/(Se+S) mole ratio of 0.09. The incorporation of selenium in the copper thiocyanate lattice was proven by X-ray diffraction. The presence of native selenium was disallowed by Se K-edge X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectroscopy. Selenium was shown by EXAFS to be present as selenide and surrounded by one nearest C atom and three next-nearest Cu atoms. This local environment is typical of the copper thiocyanate structure, which proves that Se substitutes for S on the atomic scale. Based on results of chemical analyses and structural methods, it is concluded that the sludge consists primarily of an α-Cu(S0.91Se0.09)CN solid solution. Some copper is not reduced and is liganded to O, OH, or H2O. These results indicate that, when added to process water, cupric ions are reduced by sodium thiosulfate and sulfites initially present in the solution to yield primarily cuprous thiocyanate/selenocyanate.
PTRF/Cavin-1 decreases prostate cancer angiogenesis and lymphangiogenesis (2013)

Caveolae are specialized plasma membrane subdomains implicated in cellular functions such as migration, signalling and trafficking. Caveolin-1 and polymerase I and transcript release factor (PTRF)/cavin-1 are essential for caveola formation. Caveolin-1 is overexpressed and secreted in prostate tumors and promotes aggressiveness and angiogenesis. In contrast, a lack of PTRF expression is reported in prostate cancer, and ectopic PTRF expression in prostate cancer cells inhibits tumor growth and metastasis. We experimentally manipulated PTRF expression in three prostate cancer cell lines, namely the caveolin-1 positive cells PC3 and DU145 and the caveolin-1-negative LNCaP cells, to evaluate angiogenesis- and lymphangiogenesis-regulating functions of PTRF. We show that the conditioned medium of PTRF-expressing prostate cancer cells decreases ECs proliferation, migration and differentiation in vitro and ex vivo. This can occur independently from caveolin-1 expression and secretion or caveola formation, since the anti-angiogenic effects of PTRF were detected in caveolin-1-negative LNCaP cells. Additionally, PTRF expression in PC3 cells significantly decreased blood and lymphatic vessel densities in orthotopic tumors in mice. Our results suggest that the absence of PTRF in prostate cancer cells contributes significantly to tumour progression and metastasis by promoting the angiogenesis and lymphangiogenesis potential of the cancer cells, and this could be exploited for therapy.
Strategy for Discovering Chemical Inhibitors of Human Cyclophilin A:  Focused Library Design, Virtual Screening, Chemical Synthesis and Bioassay (2006)

The discovery of cyclophilin A (CypA) inhibitor is now of special interest in the treatment of immunological disorders. In this work, using a strategy integrating focused combinatorial library design, virtual screening, chemical synthesis, and bioassay, a series of novel small molecular CypA inhibitors have been discovered. First, using the fragments taken from our previously discovered CypA inhibitors (Bioorg. Med. Chem. 2006, 14, 2209-2224) as building blocks, we designed a focused combinatorial library containing 255 molecules employing the LD1.0 program (J. Comb. Chem. 2005, 7, 398-406) developed by us. Sixteen compounds (1a-e, 2a-b, 3a-b, and 4a-g) were selected by using virtual screening against the X-ray crystal structure of CypA as well as druglike analysis for further synthesis and bioassay. All these sixteen molecules are CypA binders with binding affinities (K(D) values) ranging from 0.076 to 41.0 microM, and five of them (4a, 4c, and 4e-g) are potent CypA inhibitors with PPIase inhibitory activities (IC(50) values) of 0.25-6.43 microM. The hit rates for binders and inhibitors are as high as 100% and 31.25%, respectively. Remarkably, both the binding affinity and inhibitory activity of the most potent compound increase approximately 10 times than that of the most active compound discovered previously. The high hit rate and the high potency of the new CypA inhibitors demonstrated the efficiency of the strategy for focused library design and screening. In addition, the novel chemical entities reported in this study could be leads for discovering new therapies against the CypA pathway.
A High Efficiency 3.6-4.0 GHz Envelope-Tracking Power Amplifier Using GaN Soft-Switching Buck-Converter (2018)

We report a high efficiency sub-6GHz wideband Envelope-Tracking Power Amplifier (ET-PA) including a soft-switching buck-converter and a wideband RF-PA, used in conjunction with a digital front end (DFE) environment for signal generation and predistortion. Both buck-converter and RF-P A were fabricated using an 0.15um GaN HEMT process. The DFE can generate the input signals for both buck-converter and RF-P A, capture the output signal for feed-back and perform digital predistortion (DPD). The overall ET-P A achieves total efficiency of 39.5-46.7% and output power of 31.2-31.5dBm over 3.6-4.0GHz with 20MHz L TE signals. With DPD, ACLR was below -45dBc with total efficiency reaching 47% at 3.6GHz. This, to the best of the authors' knowledge, is the highest efficiency yet reported for an ET-PA at this carrier frequency.
Mobile Communication Network Planning Based on Big Data Analysis (2015)

According to explosive growth of network data and rapid development of big data technology, a method of mobile communication network planning based on big data analysis was presented. In the light of planning objective, user's value, perception, behavior and trajectory were multi-dimensionally excavated and analyzed by means of big data tools to fully describe user's demand on network. In addition, scientific and feasible solution oriented to market and user was drawn up. Finally, the application of the proposed method was presented with specific cases.
Occupancy Estimation in Smart Buildings using Audio-Processing Techniques (2016)

In the past few years, several case studies have illustrated that the use of occupancy information in buildings leads to energy-efficient and low-cost HVAC operation. The widely presented techniques for occupancy estimation include temperature, humidity, CO2 concentration, image camera, motion sensor and passive infrared (PIR) sensor. So far little studies have been reported in literature to utilize audio and speech processing as indoor occupancy prediction technique. With rapid advances of audio and speech processing technologies, nowadays it is more feasible and attractive to integrate audio-based signal processing component into smart buildings. In this work, we propose to utilize audio processing techniques (i.e., speaker recognition and background audio energy estimation) to estimate room occupancy (i.e., the number of people inside a room). Theoretical analysis and simulation results demonstrate the accuracy and effectiveness of this proposed occupancy estimation technique. Based on the occupancy estimation, smart buildings will adjust the thermostat setups and HVAC operations, thus, achieving greater quality of service and drastic cost savings.
Rule-Based Programming in the<i>Unix</i>® System (1988)

Rule-based tools are widely used for building expert systems, and rule-based programming is gaining acceptance as a general method. Our experience with building expert systems suggests that rule-based tools are most effectively used for developing expert systems when they are integrated with a general-purpose operating system such as the UNIX® system. This paper introduces the concepts of rule-based programming, discusses strengths and weaknesses of the method, and describes our current rule-based programming environment within the UNIX system.
pH effect on the aggregation of silver nanoparticles synthesized by chemical reduction (2014)

Silver colloidal nanoparticles were prepared according to the chemical reduction method in which the ascorbic acid was used as a reducing agent and sodium citrate as a stabilizing agent. The absorption spectra of all prepared samples obtained using the UV-Vis spectrophotometer showed a surface plasmon peak at a wavelength of about 420 nm. The size of the silver nanoparticles was controlled by changing the pH values of the reaction system. At high pH, smaller size silver nanoparticles were obtained compared to low pH values. This difference can be attributed to the difference in the reduction rate of the precursor. In addition to the inverse proportionality between the size and the pH value it is clear that increasing the pH value enables us to obtain spherical nanoparticles while at low pH, rods and triangular particle shapes were formed. Poor balance between nucleation and growth processes could be the cause of this result.
Detection of Biomarkers of Periodontal Disease in Human Saliva Using Stabilized, Vertical Flow Immunoassays (2017)

We report methods for stabilizing cellulose-based immunoassays and using this platform to analyze human saliva. Stabilization treatments of immunoassays for matrix metalloproteinases (MMP)-8 and -9, biomarkers of periodontal disease, were conducted and compared, revealing that anti-MMP-8 and -9 capture antibodies could be stabilized with the addition of a 5% trehalose solution to the test zones, followed by drying in a vacuum oven. After stabilization, the paper devices retained equivalent binding activity to that of freshly prepared tests for 14 days-a time frame that enables US-based clinical testing of this diagnostic assay. A saliva pretreatment method was developed to remove viscous elements without reducing the concentration or binding activity of dissolved proteins. Immunoassays were stored in ziplock bags containing desiccant, and used to detect nanomolar concentrations of MMP-9 in human saliva across the relevant clinical concentration range. These methods and findings facilitate rapid, affordable validation studies of this and other biomarkers that are found in saliva using vertical flow immunoassays.
Etnografinių tyrimų edukologijoje tarptautinės tendencijos ir raida (2017)

Kaip teigiama Jeffrey, Walford, Delamont ir Atkinson Wiley tarptautinių edukologijos etnografinių tyrimų vadove (Beach, Bagley and Marques da Silva, 2018) keliuose publikuotuose skyriuose, Hammersley ir Atkinson Etnografija: principai praktikoje – viena iš dažniausiai cituojamų edukologijos etnografinių tyrimų publikacijų Šiaurės Europoje, ypač Jungtinėje Karalystėje. Pirmą kartą 1983 metais išleistoje knygoje etnografija aprašoma kaip tyrimo metodas, kuriuo siekiama giliau suprasti lokalias žinias ir kultūrą bei reprezentuoti šią kultūrą ją aprašant. Autoriai pažymi, kad „etnografija apima tiesioginį ir netiesioginį dalyvavimą žmonių gyvenime – stebint, kas vyksta, klausantis, kas sakoma, pateikiant esminius klausimus, renkant visus įmanomus duomenis, kurie padės atskleisti nagrinėjamą problemą – pagrindinį tyrimo objektą“ (1983, p. 1.). Panašių idėjų pateikia ir kiti autoriai. Pasak Trondman, Willis ir Lund (2018), šių idėjų ištakos – 1907 metais Paryžiuje pradėta diskusija apie etnografinius tyrimus, jų galimą vaidmenį ir vertę socialiniam teoretizavimui. Į šią diskusiją įsitraukė tokie socialinių mokslų atstovai, kaip antai Emile Durkheim ir René Worms. Pastarasis pradėjo diskusiją. Pasak jo, etnografija – metodas pavaizduoti „primityvias visuomenes“. Durkheim teigė, kad etnografinis tyrimas yra prasmingesnis ir gali suteikti patikimą pagrindą analizuojant kultūras, kultūros procesus ir jų istorinę raidą visose visuomenėse, ne tik vadinamosiose primityviose. Vėliau šiuo principu vadovavosi Čikagos sociologijos mokykla (angl. Chicago School of Sociology). Pastaraisiais dešimtmečiais Jungtinėse Amerikos Valstijose ir Jungtinėje Karalystėje šiuo principu remiantis nusakomi edukologijos etnografinių tyrimų parametrai. Edukologijos etnografiniai tyrimai pasklido ir kitose šalyse. Šiame straipsnyje apžvelgiama edukologijos etnografinio tyrimo istorinė raida ir šiuolaikiniai iššūkiai, ypač Europoje.
Reinforced magnetic cellulose fiber from ionic liquid solution (2012)

Composite fibers were prepared by homogeneous dispersion of nanomagnetite (NM) in the ionic liquid 1-ethyl-3-methylimidazolium acetate ([C 2 mim]OAc) using ultrasonication followed by dissolution of microcrystalline cellulose at 90°C and dry-jet wet spinning into a water coagulation bath. The processing method with specific successive steps regarding the addition of the components has a large influence on the quality of dispersion and thus the mechanical properties of the fibers. A nanomagnetite load of up to 0.75% (mass ratio expressed in percent of nanomagnetite to cellulose) in the cellulose matrix results in significantly improved mechanical properties of the fibers, while at loads higher than 1% NM, the ultimate stress and modulus of the fibers are lower because of the formation of large agglomerates that create defects within the fibers. Fibers with uniform diameter and better reproducibility of mechanical properties can be produced utilizing high-performance equipment for fiber processing.
Table 1. Fractional atomic coordinates and equivalent isotropic displacement parameters ( ~ 2) (1995)

yz Ueq Te 0.04417 (4) 0.72426 (3) 0.48724 (4) 0.046 I -0.21613 (5) 0.82044 (4) 0.72481 (4) 0.065 N(1) 0.2476 (5) 0.6122 (4) 0.3297 (4) 0.046 C(I) 0.1798 (7) 0.5157 (5) 0.6112 (6) 0.047 C(2) 0.1465 (8) 0.4648 (6) 0.7562 (6) 0.056 C(3) 0.2469 (9) 0.3222 (6) 0.8218 (7) 0.065 C(4) 0.3799 (8) 0.2307 (6) 0.7459 (7) 0.061 C(5) 0.4152 (7) 0.2807 (6) 0.6017 (6) 0.056 C(6) 0.3163 (7) 0.4236 (5) 0.5326 (6) 0.048 C(7) 0.2531 (7) 0.6814 (5) 0.1793 (5) 0.047 C(8) 0.2228 (7) 0.8329 (6) 0.1351 (6) 0.054 C(9) 0.2251 (8) 0.9026 (6) -0.0069 (6) 0.056 C(10) 0.2511 (7) 0.8236 (6) -0.1078 (6) 0.055 C(ll) 0.2791 (8) 0.6714 (6) -0.0598 (6) 0.058 C(12) 0.2795 (7) 0.6003 (6) 0.0823 (6) 0.053 C(13) 0.2507 (9) 0.9000 (8) -0.2632 (7) 0.069 C(14) 0.3454 (7) 0.4793 (6) 0.3829 (6) 0.050
PSECMAC: A Novel Self-Organizing Multiresolution Associative Memory Architecture (2008)

The cerebellum constitutes a vital part of the human brain system that possesses the capability to model highly nonlinear physical dynamics. The cerebellar model articulation controller (CMAC) associative memory network is a computational model inspired by the neurophysiological properties of the cerebellum, and it has been widely used for control, optimization, and various pattern recognition tasks. However, the CMAC network's highly regularized computing structure often leads to the following: 1) a suboptimal modeling accuracy, 2) poor memory utilization, and 3) the generalization-accuracy dilemma. Previous attempts to address these shortcomings have limited success and the proposed solutions often introduce a high operational complexity to the CMAC network. This paper presents a novel neurophysiologically inspired associative memory architecture named pseudo-self-evolving CMAC (PSECMAC) that nonuniformly allocates its computing cells to overcome the architectural deficiencies encountered by the CMAC network. The nonuniform memory allocation scheme employed by the proposed PSECMAC network is inspired by the cerebellar experience-driven synaptic plasticity phenomenon observed in the cerebellum, where significantly higher densities of synaptic connections are located in the frequently accessed regions. In the PSECMAC network, this biological synaptic plasticity phenomenon is emulated by employing a data-driven adaptive memory quantization scheme that defines its computing structure. A neighborhood-based activation process is subsequently implemented to facilitate the learning and computation of the PSECMAC structure. The training stability of the PSECMAC network is theoretically assured by the proof of its learning convergence, which will be presented in this paper. The performance of the proposed network is subsequently benchmarked against the CMAC network and several representative CMAC variants on three real-life applications, namely, pricing of currency futures option, banking failure classification, and modeling of the glucose-insulin dynamics of the human glucose metabolic process. The experimental results have strongly demonstrated the effectiveness of the PSECMAC network in addressing the architectural deficiencies of the CMAC network by achieving significant improvements in the memory utilization, output accuracy as well as the generalization capability of the network.
Crystal Structure of Butyrate Kinase 2 from <i>Thermotoga maritima</i> , a Member of the ASKHA Superfamily of Phosphotransferases (2009)

The enzymatic transfer of phosphoryl groups is central to the control of many cellular processes. One of the phosphoryl transfer mechanisms, that of acetate kinase, is not completely understood. Besides better understanding of the mechanism of acetate kinase, knowledge of the structure of butyrate kinase 2 (Buk2) will aid in the interpretation of active-site structure and provide information on the structural basis of substrate specificity. The gene buk2 from Thermotoga maritima encodes a member of the ASKHA (acetate and sugar kinases/heat shock cognate/actin) superfamily of phosphotransferases. The encoded protein Buk2 catalyzes the phosphorylation of butyrate and isobutyrate. We have determined the 2.5-A crystal structure of Buk2 complexed with (beta,gamma-methylene) adenosine 5'-triphosphate. Buk2 folds like an open-shelled clam, with each of the two domains representing one of the two shells. In the open active-site cleft between the N- and C-terminal domains, the active-site residues consist of two histidines, two arginines, and a cluster of hydrophobic residues. The ATP binding region of Buk2 in the C-terminal domain consists of abundant glycines for nucleotide binding, and the ATP binding motif is similar to those of other members of the ASKHA superfamily. The enzyme exists as an octamer, in which four disulfide bonds form between intermolecular cysteines. Sequence alignment and structure superposition identify the simplicity of the monomeric Buk2 structure, a probable substrate binding site, the key residues in catalyzing phosphoryl transfer, and the substrate specificity differences among Buk2, acetate, and propionate kinases. The possible enzyme mechanisms are discussed.