gebhart/patrepeval huggingface dataset:
2C1512 High-precision Torsional Motion Analysis of Group II Chaperonin using Diffracted X-ray Tracking(Protein: Function 1,The 48th Annual Meeting of the Biophysical Society of Japan) (2011)

TheBiophysicalSociety of Japan General IncorporatedAssociation significantly slow.There is also a criticul hydration ]cycl below which proteins do not function.Those facts indicatc that the dynamics of water play an impertant rote for proteins to function.However its underlyillg molecular mechanism has not been clarified yet.To understand it, it is vital to understand the role ofwater molecule for protcins to change their conformations, since the function of the proteins can be understood as the consecutive collfoirnation changes ofthe proteins triggered by the external stimuli.In order to understand the mechanism, we do molecu]ar dynamics simu]ation ofa peptide.Met-Enkephalin, -'hich consists of 5 am{no acids, in explicit -,ater solvent.The conformation changes of the peptide can be classificd into thc foTlewing two cases.One is water assisting.that is, the surrounding water performs ma.ior mechanical work for the peptide to change its conformation.The other is water hindering, that is, the water prevents peptide from changing its conformation, The di fference between the two can be understood in tenns or thc cooperative behavior of the vL'ater.We extract the cooperative bchafoior from density, moinentum and encrgy density of the water by us{ng ouT coarse-grained mcthod, GAIO extended to non-stationary dynamical system due to Froyland.
Clinical, genomic, and metagenomic characterization of oral tongue squamous cell carcinoma in patients who do not smoke (2014)

The young age of nonsmoking patients with oral tongue cancer and fewer TP53 mutations suggest a viral role in this disease. Our efforts to identify such a virus were unsuccessful. Further studies are warranted to elucidate the drivers of carcinogenesis in these patients.
ChemInform Abstract: Metal Cluster‐Induced Electrophilicity of Arenes. (1989)

Abstract Hydride or carbanion attack on the cluster (I) with the μ3‐η2:η2:η2 arene bonding mode proceeds highly regio‐ and stereo‐selectively at the face‐capping arene ligand.
KAL'TsIY I VITAMIN D V VEDENIIOSTEOPOROZA (2007)

Для достижения консенсуса по ряду вопросов, касающихся использования добавок кальция и витамина Д для профилактики и лечения остеопороза, между экспертами был организован круглый стол. Это собрание было инициировано the Group for the Respect of Ethics and Excellence in Science (GREES) и the European Society for Clinical and Economic Aspects of Osteoporosis and Osteoarthritis (ESCEO). На круглом столе были рассмотрены пять специфических вопросов по теме использования добавок кальция и витамина Д у женщин в постменопаузе, что стало актуальным в свете недавних публикаций, которые посеяли сомнения о пользе их применения. Выводы были основаны на рассмотрении доступных доказательств и представлены ниже.
Processing-Structure-Properties Relations in Titanium-Boron-Carbon Ceramic-Ceramic Composites Produced by Transient Plastic Phase Processing (2008)

Transient Plastic Phase Processing (TPPP) is a new technique capable of in-situ manufacturing complex shaped, fully dense, ultra-refractory ceramic-ceramic composites at temperatures that are significantly lower than their melting points (T < 0.65 Tm). In TPPP two phases in particulate form are mixed, of which one is a transient plastic phase (TPP) and the other is a reactant phase (RP). In essence, TPPP includes: (i) plastic forming at a relatively low temperature in a soft condition resulting in densification of the powder mix with no change in the composition of the constituents, followed by (ii) reaction synthesis at a higher temperature in which the RP reacts with the TPP and shifts its stoichiometry to a harder, more refractory composition. The feasibility of this technique has been demonstrated on the Ti-B-C system. Experimental observations of the effect of the starting compositions on the final microstructures, porosity, and the mechanical properties of produced composites are discussed.
Derivation and Expansion of PAX7-Positive Muscle Progenitors from Human and Mouse Embryonic Stem Cells (2014)

Main Text(Stem Cell Reports 3, 516–529, September 9, 2014)In the Supplemental Experimental Procedures of this article as originally published, the concentration of monothioglycerol was stated at 39 λ/mL instead of the correct concentration of 0.45 mM. The Supplemental Information document has been corrected and replaced online. Main Text(Stem Cell Reports 3, 516–529, September 9, 2014)In the Supplemental Experimental Procedures of this article as originally published, the concentration of monothioglycerol was stated at 39 λ/mL instead of the correct concentration of 0.45 mM. The Supplemental Information document has been corrected and replaced online. (Stem Cell Reports 3, 516–529, September 9, 2014) In the Supplemental Experimental Procedures of this article as originally published, the concentration of monothioglycerol was stated at 39 λ/mL instead of the correct concentration of 0.45 mM. The Supplemental Information document has been corrected and replaced online. Derivation and Expansion of PAX7-Positive Muscle Progenitors from Human and Mouse Embryonic Stem CellsShelton et al.Stem Cell ReportsAugust 7, 2014In BriefIn this article, Skerjanc and colleagues show a monolayer-based protocol for the in vitro differentiation of human embryonic stem cells (ESCs) into the skeletal muscle lineage. Ninety-one percent ± 6% of hESCs stain positive for T following CHIR99021-based mesoderm induction. After 50 days of culture, 47% ± 3% of cells are MYH+ve myocytes/myotubes surrounded by a 43% ± 4% population of PAX7+ve muscle progenitor cells (MPCs). Full-Text PDF Open Access
Supplementary Table 2 from Mechanistic Contribution of Ubiquitous 15-Lipoxygenase-1 Expression Loss in Cancer Cells to Terminal Cell Differentiation Evasion (2023)

&lt;p&gt;PDF file - 50KB&lt;/p&gt;
Sampling High Throughput Data for Anomaly Detection of Data-Base\n Activity (2017)

Data leakage and theft from databases is a dangerous threat to organizations.\nData Security and Data Privacy protection systems (DSDP) monitor data access\nand usage to identify leakage or suspicious activities that should be\ninvestigated. Because of the high velocity nature of database systems, such\nsystems audit only a portion of the vast number of transactions that take\nplace. Anomalies are investigated by a Security Officer (SO) in order to choose\nthe proper response. In this paper we investigate the effect of sampling\nmethods based on the risk the transaction poses and propose a new method for\n"combined sampling" for capturing a more varied sample.\n
Interleukin-22 regulates B3GNT7 expression to induce fucosylation of glycoproteins in intestinal epithelial cells (2021)

Interleukin (IL)-22 is a cytokine that plays a critical role in intestinal epithelial homeostasis. Its downstream functions are mediated through interaction with the heterodimeric IL-22 receptor and subsequent activation of signal transducer and activator of transcription 3 (STAT3). IL-22 signaling can induce transcription of genes necessary for intestinal epithelial cell proliferation, tissue regeneration, tight junction fortification, and antimicrobial production. Recent studies have also implicated IL-22 signaling in the regulation of intestinal epithelial fucosylation in mice. However, whether IL-22 regulates intestinal fucosylation in human intestinal epithelial cells and the molecular mechanisms that govern this process are unknown. Here, in experiments performed in human cell lines and human-derived enteroids, we show that IL-22 signaling regulates expression of the B3GNT7 transcript, which encodes a β1-3-N-acetylglucosaminyltransferase that can participate in the synthesis of poly-N-acetyllactosamine (polyLacNAc) chains. Additionally, we find that IL-22 signaling regulates levels of the α1-3-fucosylated Lewis X (Le<sup>x</sup>) blood group antigen, and that this glycan epitope is primarily displayed on O-glycosylated intestinal epithelial glycoproteins. Moreover, we show that increased expression of B3GNT7 alone is sufficient to promote increased display of Le<sup>x</sup>-decorated carbohydrate glycan structures primarily on O-glycosylated intestinal epithelial glycoproteins. Together, these data identify B3GNT7 as an intermediary in IL-22-dependent induction of fucosylation of glycoproteins and uncover a novel role for B3GNT7 in intestinal glycosylation.
Alternative antimicrobial compounds to control potential Lactobacillus contamination in bioethanol fermentations. (2011)

Antibiotics are commonly used to control microbial contaminants in yeast-based bioethanol fermentation. Given the increase in antibiotic-resistant bacteria, alternative natural antimicrobials were evaluated against the potential contaminant, Lactobacillus. The effects of nisin, ϵ-polylysine, chitosan (CS) and lysozyme were screened against 5 Lactobacillus strains. A standard broth- microdilution method was used in 96-well plates to assess the minimal inhibitory concentration (MIC). L. delbrueckii subsp lactis ATCC479 exhibited maximal MICs with CS, ϵ-polylysine and nisin (1.87, 0.3125 and 0.05 mg/mL, respectively). Nisin reduced most Lactobacillus strains by 6 log CFU/mL after 48 hours with the exception of L. casei. Synergism occurred when ethylenediaminetetraacetic acid (EDTA) was added with nisin. An MIC of 0.4 mg/mL of nisin combined with the EDTA at an MIC of 1 mg/ml markedly suppressed L .casei by 6 log CFU/mL. In conclusion, alternative antimicrobials proved to be a potential candidate for controlling bacterial contamination in the fermentation process. Synergistic effect of nisin with EDTA successfully inhibited the nisin-resistant contaminant, L. casei.
A Comparison of the Physiological Effects of RSU1069 and RB6145 in the SCCVII Murine Tumour (1996)

The physiological and therapeutic effects of the bioreductive agent RSU1069 (80 mg/kg i.p.) and its prodrug RB6145 (240 mg/kg i.p.) were investigated in the SCCVII tumour. Using laser Doppler flowmetry it was found that RSU1069 produced a significant 30% reduction in tumour blood flow 30 min after administration, while RB6145 had no effect. Tumour oxygenation, measured with an Eppendorf oxygen electrode, was unchanged by either agent except for a reduction in values less than 2.5 mmHg at 30 min after injection. Neither agent significantly altered tumour energy metabolism, assessed by 31P magnetic resonance spectroscopy. Both agents significantly increased tumour glucose content by a factor of 1.6-1.7 at 30 min after injection, but had no effect on glucose-6-phosphate or lactate levels. Tumour growth was significantly delayed by heating (42.5 degrees C, 60 min), and although neither RSU1069 nor RB6145 alone had any effect on tumour growth they produced a similar enhancement of the tumour response to heat. The therapeutic effects are consistent with the known conversion in vivo of one third of the pro-drug RB6145 to its active product RSU1069, however the physiological effects of the two agents in the SCCVII tumour are not identical.
Rechargeable Lithium‐Ion Cells Using Graphitized Mesophase‐Pitch‐Based Carbon Fiber Anodes (1995)

The electrochemistry of lithium intercalation into a graphitized mesophase‐pitch‐based carbon fiber with a radial‐like texture used as the anode material in rechargeable lithium‐ion cells was characterized. The radial‐like texture in the cross section of the carbon fiber contributed to the rapid diffusion of lithium ions, resulting in the high rate capability. The anode performance of the graphitized carbon fiber was superior to that of the graphite. Experimental flat‐plate lithium‐ion cells using the graphitized carbon fiber anode exhibited a high mid‐discharge voltage of 3.7 V, a high rate capability, and a long cycle life of more than 400 cycles at 2 mA/cm2 during charge‐discharge cycling between 4.2 and 2.7 V. The long cycle life obtained for the cell was due to no significant change in resistance associated with the passivating films on the graphitized carbon fiber with extended cycles. It was also demonstrated that A size cells using the graphitized carbon fiber anode have excellent rate performance at discharge currents between 0.25 and 3 A, a large discharge capacity of 0.95 Ah, and a high energy density of 310 Wh/dm33 and 120 Wh/kg.
Structure and Functional Characterization of a Novel Human Low‐Voltage Activated Calcium Channel (1999)

We have isolated and characterized overlapping cDNAs encoding a novel, voltage-gated Ca2+ channel alpha1 subunit, alpha1H, from a human medullary thyroid carcinoma cell line. The alpha1H subunit is structurally similar to previously described alpha1 subunits. Northern blot analysis indicates that alpha1H mRNA is expressed throughout the brain, primarily in the amygdala, caudate nucleus, and putamen, as well as in several nonneuronal tissues, with relatively high levels in the liver, kidney, and heart. Ba2+ currents recorded from human embryonic kidney 293 cells transiently expressing alpha1H activated at relatively hyperpolarized potentials (-50 mV), rapidly inactivated (tau = 17 ms), and slowly deactivated. Similar results were observed in Xenopus oocytes expressing alpha1H. Single-channel measurements in human embryonic kidney 293 cells revealed a single-channel conductance of approximately 9 pS. These channels are blocked by Ni2+ (IC50 = 6.6 microM) and the T-type channel antagonists mibefradil (approximately 50% block at 1 microM) and amiloride (IC50 = 167 microM). Thus, alpha1H-containing channels exhibit biophysical and pharmacological properties characteristic of low voltage-activated, or T-type, Ca2+ channels.
Internal Cardioversion of Atrial Fibrillation (1997)

Internal atrial defibrillation thresholds can be markedly reduced with two sequential biphasic shocks delivered over two current pathways compared with the standard single shock delivered over a single current pathway or with sequential shocks delivered over a single current pathway.
DSP-based simple and efficient synchronizer for three-phase grid-connected renewable energy systems (2013)

The generated power's frequency, rotating sequence, and phase angle must be conditioned corresponding to both of power grid specifications, and energy system needs. This paper proposes a novel DSP-based simple and efficient synchronizer for three-phase grid-connected renewable energy systems. “Efficient” refers to its low-cost, fast response, and immunity to distorted voltage of the power grid. The proposed synchronizer contains two parts: 1. Peripheral hardware part, which employs a conventional simple photocoupler-based zero-crossing detector. 2. Embedded software part, which processes the only single signal-generated by the zero-crossing detector-to safely extract power grid information, and to efficiently synchronize the turning on/off of the power switches. A simulation model is developed in MATLAB Simulink and is implemented using a fixed-point digital signal processor (DSP) TMS320F2812. Moreover, a breadboard circuit is built-up for experimental investigations in a three-phase grid-connected PV system. Both of simulation and experimental results show that proposed synchronizer attains a good performance.
huASH1 protein, a putative transcription factor encoded by a human homologue of the Drosophila ash1 gene, localizes to both nuclei and cell–cell tight junctions (2000)

During animal development, regions of the embryo become committed to position-specific identities, which are determined by spatially restricted expression of Hox/homeotic genes. This expression pattern is initially established by the activity of the segmentation genes and is subsequently maintained during the proliferative stage through the action of transcription factors encoded by the trithorax (trx) and Polycomb (Pc) groups of genes. trithorax (trx)and ash1 (absent, small, or homeotic 1) are members of the Drosophila trx group. Their products are associated with chromosomes and are believed to activate transcription of target genes through chromatin remodeling. Recently, we reported molecular studies indicating that TRX and ASH1 proteins act in concert to bind simultaneously to response elements located at close proximity within the same set of target genes. Extension of these and other studies to mammalian systems required identification and cloning of the mammalian homologue of ash1 (the mammalian homologue of trx, ALL-1, was previously cloned). We have identified a human expressed sequence tag (EST) clone with similarity to the SET domain of Drosophila ASH1, and used it to clone the human gene. huASH1 resides at chromosomal band 1q21. The gene is expressed in multiple tissues as an approximately 10.5-kb transcript and encodes a protein of 2962 residues. The protein contains a SET domain, a PHD finger, four AT hooks, and a region with homology to the bromodomain. The last region is not present in Drosophila ASH1, and as such might confer to the human protein a unique additional function. Using several anti-huASH1 Ab for immunostaining of cultured cells, we found that the protein is distributed in intranuclear speckles, and unexpectedly also in intercellular junctions. Double-immunofluorescence labeling of huASH1 and several junctional proteins localized the huASH1 protein into tight junctions. The significance of huASH1 dual location is discussed. In particular, we consider the possibility that translocation of the protein between the junctional membrane and the nucleus may be involved in adhesion-mediated signaling.
Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma (2015)

Follicular lymphoma is an incurable B cell malignancy characterized by the t(14;18) translocation and mutations affecting the epigenome. Although frequent gene mutations in key signaling pathways, including JAK-STAT, NOTCH and NF-κB, have also been defined, the spectrum of these mutations typically overlaps with that in the closely related diffuse large B cell lymphoma (DLBCL). Using a combination of discovery exome and extended targeted sequencing, we identified recurrent somatic mutations in RRAGC uniquely enriched in patients with follicular lymphoma (17%). More than half of the mutations preferentially co-occurred with mutations in ATP6V1B2 and ATP6AP1, which encode components of the vacuolar H+-ATP ATPase (V-ATPase) known to be necessary for amino acid−induced activation of mTORC1. The RagC variants increased raptor binding while rendering mTORC1 signaling resistant to amino acid deprivation. The activating nature of the RRAGC mutations, their existence in the dominant clone and their stability during disease progression support their potential as an excellent candidate for therapeutic targeting.
Development of Nd-Doped CaWO4 Single Crystalline Scintillators Emitting Near-Infrared Light (2022)

Nd-doped CaWO4 single crystals with dopant concentrations of 0.1, 0.5, and 1% were synthesized by the floating zone method. The transmission, photoluminescence, and scintillation properties were evaluated from ultraviolet to near-infrared (NIR) ranges. An emission peak due to transitions of the host was observed at 400 nm, and several sharp peaks originating from Nd3+ 4f–4f transitions were confirmed at 900, 1060, and 1300 nm. The quantum yields of 0.1, 0.5, and 1% Nd-doped samples were 70.7, 79.5, and 61.2%, respectively, when monitored, and excited wavelengths were 750–1500 nm and 590 nm. Decay times consistent with typical Nd3+ transitions were obtained when NIR ranges were monitored. Additionally, the energy transfer between the host and Nd3+ occurred according to the decay measurement. The relationship between X-ray irradiated dose rate and intensity in the range of NIR was investigated by combining the crystals with an InGaAs-photodiode. The lowest detectable dose rate retaining the linearity of the present crystals was 0.3–0.06 Gy/h.
Mass Transfer in Amperometric Biosensors Based on Nanocomposite Thin Films of Redox Polymers and Oxidoreductases (2002)

Mass transfer in nanocomposite hydrogel thin films consisting of alternating layers of an organometallic redox polymer (RP) and oxidoreductase enzymes was investigated. Multilayer nanostructures were fabricated on gold surfaces by the deposition of an anionic self-assembled monolayer of 11-mercaptoundecanoic acid, followed by the electrostatic binding of a cationic redox polymer, poly[vinylpyridine Os(bis-bipyridine)2Clco-allylamine], and an anionic oxidoreductase. Surface plasmon resonance spectroscopy, Fourier transform infrared external reflection spectroscopy (FTIR-ERS), ellipsometry and electrochemistry were employed to characterize the assembly of these nanocomposite films. Simultaneous SPR/electrochemistry enabled real time observation of the assembly of sensing components, changes in film structure with electrode potential, and the immediate, in situ electrochemical verification of substrate-dependent current upon the addition of enzyme to the multilayer structure. SPR and FTIR-ERS studies also showed no desorption of polymer or enzyme from the nanocomposite structure when stored in aqueous environment occurred over the period of three weeks, suggesting that decreasing in substrate sensitivity were due to loss of enzymatic activity rather than loss of film compounds from the nanostructure.
Electrostatic Control of Isoform Selective Inhibitor Binding in Nitric Oxide Synthase (2016)

Development of potent and isoform selective nitric oxide synthase (NOS) inhibitors is challenging because of the structural similarity in the heme active sites. One amino acid difference between NOS isoforms, Asp597 in rat neuronal NOS (nNOS) versus Asn368 in bovine endothelial NOS (eNOS), has been identified as the structural basis for why some dipeptide amide inhibitors bind more tightly to nNOS than to eNOS. We now have found that the same amino acid variation is responsible for substantially different binding modes and affinity for a new class of aminopyridine-based inhibitors.
Complexity-effective verification of a multiprocessor cache coherence protocol (2004)

Verifying the correctness of a shared-memory multiprocessor cache coherence protocol, and its implementation in silicon, is an extraordinarily complex and time-consuming task. The detailed formal verification model developed for the Cray X1 cache coherence protocol, for instance, produces a search space with over 214 million reachable states. Exhaustively searching this space for errors in the protocol and its implementation is computationally prohibitive. To address this problem, we describe a novel method for extracting traces called “witness strings” from the formal verification process. These witness strings then are executed on a logic simulation of the hardware that implements the protocol. The witness strings approach combines both formal and informal verification methods to expose design errors in the cache coherence protocol and its implementation. To reduce the number of states that need to be explored to discover an error in a coherence protocol using this verification environment, we introduce and compare several search heuristics. We show that the min-max-predict search heuristic consistently outperforms both breadth-first search (BFS) and depth-first search (DFS) for 12 protocol errors manually embedded in the Cray X1 and Stanford DASH coherence protocols. In many cases, this heuristic was able to reduce the number of states that needed to be searched by a factor of 50–100.
Tandem Double Intramolecular [4+2]/[3+2] Cycloadditions of Nitroalkenes. The Fused/Bridged Mode (2003)

A new class of tandem [4+2]/[3+2] cycloadditions of nitroalkenes is described in which both pericyclic processes are intramolecular. Two subclasses of intra [4+2]/intra [3+2] cycloadditions have been explored in which the dipolarophile is tethered at either C(5) or C(6) of the nitronate. For both families of precursors, the cycloadditions occur in good yield and are found to be highly regio- and stereoselective. This method converts linear polyenes to functionalized polycyclic systems bearing up to six stereogenic centers.