gebhart/patrepeval huggingface dataset:
Role of Stimuli-Sensitive Polymers in Protein Refolding:  α-Amylase and CcdB (Controller of Cell Division or Death B) as Model Proteins (2006)

Alginate, a calcium-sensitive polymer, could carry out simultaneous purification and refolding of 8 M urea/100 mM dithiothreitol (DTT) denatured and thermally denatured alpha-amylase present in a commercial preparation. Activity recoveries of 80 and 70% in the former and the latter cases, respectively, were obtained. The fluorescence spectra showed refolding, and PAGE showed the absence of any aggregates in the refolded preparation. As another example, Eudragit S-100, a pH-sensitive poly(methyl methacrylate), was used to refold CcdB (controller of cell division or death B) protein. Initial experiments with wild-type (WT) CcdB showed that Eudragit bound and precipitated (upon lowering the pH to 4.0) CcdB quantitatively from the latter's aqueous solution. The bioconjugate showed DNA gyrase inhibition activity of CcdB and could be recycled. The inclusion bodies of CcdB mutant CcdB-17P were solubilized in 8 M urea/100 mM dithiothreitol. This preparation could be refolded by precipitation with Eudragit. The fluorescence and CD spectra showed that protein refolding has occurred.
Stavreva et al., 2019, Mol. Cell (2019)

Representative datasets associated with article "Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility."
Globally exponentially stable Kalman filtering for SLAM with AHRS (2016)

The Simultaneous Localization And Mapping (SLAM) estimation problem using range or bearing angle sensors is an inherently nonlinear problem due to the nonlinear relationship between the measurements and the positions of the landmarks and the pose of the vehicle. Assuming an Attitude and Heading Reference System (AHRS) and that velocity is measured, it is shown that the nonlinear kinematic models in the inertial coordinate frame and the nonlinear measurement models can be re-formulated globally as a linear time-varying system. This allows a globally exponentially stable Kalman filter to be used for real-time recursive estimation, under natural assumptions on the trajectory of the vehicle relative to the landmarks. This ensures theoretical guarantees of robustness of the estimate of the vehicle and landmark positions to inaccuracies and arbitrary estimator initialization. Simulations are used to illustrate the results.
Orthopedic Considerations During Pregnancy (2003)

Department of Orthopedic Surgery, Saint Louis University, Des Peres, Missouri Correspondence: Joseph R. Ritchie, MD, Department of Orthopedic Surgery, Saint Louis University, 2325 Dougherty Ferry Road, Ste. 200, Des Peres, MO 63122. E-mail:[email protected]
Pre‐ and Postoperative Force Plate Analysis of Dogs with Experimentally Transected Cranial Cruciate Ligaments Treated Using Tibial Plateau Leveling Osteotomy (2004)

TPLO induces lameness that returns to near normal at 18 weeks. The severity and duration of lameness was similar to that reported for other experimental models of stifle instability repaired by different techniques.
Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS (2015)

RNA-binding protein with multiple splicing (designated RBPMS) is a higher vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM). RBPMS has been shown to be involved in mRNA transport, localization and stability, with key roles in axon guidance, smooth muscle plasticity, as well as regulation of cancer cell proliferation and migration. We report on structure-function studies of the RRM domain of RBPMS bound to a CAC-containing single-stranded RNA. These results provide insights into potential topologies of complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites as detected by photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation. These studies establish that the RRM domain of RBPMS forms a symmetrical dimer in the free state, with each monomer binding sequence-specifically to all three nucleotides of a CAC segment in the RNA bound state. Structure-guided mutations within the dimerization and RNA-binding interfaces of RBPMS RRM on RNA complex formation resulted in both disruption of dimerization and a decrease in RNA-binding affinity as observed by size exclusion chromatography and isothermal titration calorimetry. As anticipated from biochemical binding studies, over-expression of dimerization or RNA-binding mutants of Flag-HA-tagged RBPMS were no longer able to track with stress granules in HEK293 cells, thereby documenting the deleterious effects of such mutations in vivo.
Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in drought tolerance (2018)

Many of the target genes, including transmembrane/transporter, vesicle related, auxin/hormone related, carbohydrate metabolic processes, and transcription factor genes, that are up-regulated by OsNACs act as the cellular components which would alter the root architectures of RCc3:OsNACs for drought tolerance.
Full CMOS video line-locked phase-locked loop system (1993)

A CMOS PLL (phase-locked loop) system for generation of a television line-locked clock in the frequency range 25 MHz to 40 MHz is described. The PLL system is designed for use as a generic building block with large-scale CMOS video signal processing integrated circuits. The development of a custom test chip version of the PLL system is reported. A test chip version of the PLL system has been fabricated in 0.8 mu m CMOS technology and tested to verify functionality and examine acquisition and racking behavior. The test chip version of the PLL includes a bidirectional test bus monitor system used to observe 28 signals and input five signals for the purpose of assessing circuit operation details. The open-loop measured noise bandwidth of the RC VCO (voltage-controlled oscillator) is -30 dB at 350 Hz. The short term stability within one second is approximately +or-150 Hz or 20 p.p.m., corresponding to 1.3 ns jitter in one horizontal line period of 63.5 mu s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Aspectos técnicos da cateterização do seio coronariano baseada no componente atrial do eletrograma intracavitário e anatomia radiológica durante o procedimento de implante de marcapasso biventricular (2006)

The implantation technique, using the atrial component morphology of the intracavitary electrogram and radiological anatomy showed to be workless, safe and effective for the cannulation of the coronary sinus ostium requesting reduced time of radioscopy.
Supplementary Table S1 from Lisaftoclax in Combination with Alrizomadlin Overcomes Venetoclax Resistance in Acute Myeloid Leukemia and Acute Lymphoblastic Leukemia: Preclinical Studies (2023)

&lt;p&gt;Supplementary Table 1. Clinical characteristics of patients with relapsed or refractory acute myeloid leukemia.&lt;/p&gt;
Current understanding of microbiota- and dietary-therapies for treating inflammatory bowel disease (2018)

Inflammatory bowel disease (IBD) is a result of chronic inflammation caused, in some part, by dysbiosis of intestinal microbiota, mainly commensal bacteria. Gut dysbiosis can be caused by multiple factors, including abnormal immune responses which might be related to genetic susceptibility, infection, western dietary habits, and administration of antibiotics. Consequently, the disease itself is characterized as having multiple causes, etiologies, and severities. Recent studies have identified >200 IBD risk loci in the host. It has been postulated that gut microbiota interact with these risk loci resulting in dysbiosis, and this subsequently leads to the development of IBD. Typical gut microbiota in IBD patients are characterized with decrease in species richness and many of the commensal, and beneficial, fecal bacteria such as Firmicutes and Bacteroidetes and an increase or bloom of Proteobacteria. However, at this time, cause and effect relationships have not been rigorously established. While treatments of IBD usually includes medications such as corticosteroids, 5-aminosalicylates, antibiotics, immunomodulators, and anti-TNF agents, restoration of gut dysbiosis seems to be a safer and more sustainable approach. Bacteriotherapies (now called microbiota therapies) and dietary interventions are effective way to modulate gut microbiota. In this review, we summarize factors involved in IBD and studies attempted to treat IBD with probiotics. We also discuss the potential use of microbiota therapies as one promising approach in treating IBD. As therapies based on the modulation of gut microbiota becomes more common, future studies should include individual gut microbiota differences to develop personalized therapy for IBD.
Explicit schemes for parabolic and hyperbolic equations (2013)

Standard explicit schemes for parabolic equations are not very convenient for computing practice due to the fact that they have strong restrictions on a time step. More promising explicit schemes are associated with explicit-implicit splitting of the problem operator (Saul'yev asymmetric schemes, explicit alternating direction (ADE) schemes, group explicit method). These schemes belong to the class of unconditionally stable schemes, but they demonstrate bad approximation properties. These explicit schemes are treated as schemes of the alternating triangle method and can be considered as factorized schemes where the problem operator is splitted into the sum of two operators that are adjoint to each other. Here we propose a multilevel modification of the alternating triangle method, which demonstrates better properties in terms of accuracy. We also consider explicit schemes of the alternating triangle method for the numerical solution of boundary value problems for hyperbolic equations of second order. The study is based on the general theory of stability (well-posedness) for operator-difference schemes.
Molecular mechanisms of Barrett's esophagus and adenocarcinoma (2011)

The following on molecular mechanisms of Barrett's esophagus and adenocarcinoma contains commentaries on the mechanism of bile and gastric acid induced damage; the roles of BMP-4 and CDX-2 in the development of intestinal metaplasia; the transcription factors driving intestinalization in Barrett's esophagus; the contribution of bone marrow to metaplasia and adenocarcinoma; activation and inactivation of transcription factors; and a novel study design targeting molecular pathways in Barrett's esophagus.
Effect of Divergent Selection for Intramuscular Fat Content on Muscle Lipid Metabolism in Chickens (2019)

Intramuscular fat (IMF)-an important factor affecting meat quality-can be appropriately increased by genetic selection. Chicken lines divergently selected for IMF content were used in this study to investigate the mechanisms behind differential IMF deposition. Sixty 15th generation chickens were genotyped using the IASCHICK 55K single nucleotide polymorphism (SNP) chip. After quality control, 59 chickens and 36,893 SNPs were available for subsequent analysis. Population structure assessment indicated that the lines were genetically differentiated. Based on the top 1% paired fixation index values, three pathways were significantly (<i>p</i> < 0.05) enriched, and nine genes were considered candidate genes for differential IMF deposition. Differences between the lines in the expressions of representative genes involved in the above pathways were detected in 16th generation chickens. This study suggests that genetic selection for increased IMF in the pectoralis major muscle may enhance fatty acid synthesis, transport, and esterification, and reduce triglyceride hydrolysis. The peroxisome proliferator-activated receptor (PPAR) signaling pathway, glycerolipid metabolism, and fatty acid degradation pathway may have contributed to the differences in IMF deposition between the lines. These results contribute to the understanding of the genetic mechanisms behind IMF deposition, and the improvement of chicken meat quality.
The Use of UV Radiation to Control the Architecture of Salvia splendens Plants. I. Effects on Plant Growth, Water Relations and Gas Exchange (1996)

Abstract In experiments with Salvia splendens plants grown in the greenhouse we evaluated the possible use of irradiation with unfiltered UV (UVA + UVB + UVC) lamps for the control of plant growth. The effect of UV Irradiation on the growth of S. splendens plants in the grcenhouse was closely dependent on the growing season and the level of available photosynthetically active radiation. In summer UV treatments were ineffective, but in the low light conditions of winter UV irradiation inhibited the growth via both photomorphogenic and photosynthetic effects. The reduction of stomatal conductance and expansion growth, which in turn depressed photosynthesis and dry matter accumulation, were not a consequence of an impairment of plant water status but appeared to be a direct UV effect on stomata and cell wall rheological propertles. Our findings suggest that the use of unfiltered UV irradiation could become an effective tool for the regulation of growth in greenhouse crops, particularly during the poor light conditions of the winter season.
Ethanol-induced structural transitions of DNA on mica (1999)

The effect of ethanol on the structure of DNA confined to mica in the presence of Mg 2+ was examined by varying the ethanol concentration and imaging the DNA by atomic force microscopy. Contour length measurements of the DNA show a transition from all-B-form at 0% ethanol to all-A-form at >25% ethanol. At intermediate ethanol concentrations, contour lengths suggest that individual molecules of air-dried DNA are trapped with mixed compositions of A-form and B-form. The relative composition depends on the ethanol concentration. Fitting the length distributions at intermediate ethanol concentrations to a simple binomial model results in an upper bound estimate for the A-form and B-form domains of 54 bp in the individual molecules. In addition to length changes, the apparent persistence length of DNA decreases with increasing ethanol concentration. At high concentrations of ethanol (>20%), DNA formed several higher order structures, including flower shaped condensates and toroids.
TEXT COMPRESSION OPTIMIZATION. (1967)

Abstract : The report describes research performed on optimization techniques for the compression of text. The areas of concentration of effort were: (a) Evaluation of alternative text segmentation procedures on the basis of compression efficiency provided; (b) the problem of efficiency variability that occurs when codes designed to suit a particular sample of text are applied to other samples of text; (c) the automatic reduction of size of an encoding set, and the prediction of the effects of such size reductions; (d) the applicability of text compression techniques to document descriptor files. The pertinent conclusions are: (a) the text segmentation procedure adopted in the earlier research appears to be very close to optimal; (b) there is significant degradation of performance when encoding texts other than the ones used to obtain the code; (c) it is possible to predict quantitatively the effects of size reduction on compression efficiency, this being independent of the way the reduction is made; (d) document descriptor files are compressible using the techniques described. In addition, research was conducted on the statistics of language and on rate distortion theory. Motivated by the results obtained on the problem of efficiency variability, we developed generative models for the statistics of taxonomies, that are shown to be consistent with the available data. The aim of the research on rate distortion theory is roughly to predict how much is lost by overcompressing the text. The results presented pertain to the basic theory, that is just beginning to be developed.
The Immunobiology of SARS (2007)

Severe acute respiratory syndrome (SARS) presented as an atypical pneumonia that progressed to acute respiratory distress syndrome in approximately 20% of cases and was associated with a mortality of about 10%. The etiological agent was a novel coronavirus (CoV). Angiotensin-converting enzyme 2 is the functional receptor for SARS-CoV; DC-SIGN and CD209L (L-SIGN) can enhance viral entry. Although the virus infects the lungs, gastrointestinal tract, liver, and kidneys, the disease is limited to the lungs, where diffuse alveolar damage is accompanied by a disproportionately sparse inflammatory infiltrate. Pro-inflammatory cytokines and chemokines, particularly IP-10, IL-8, and MCP-1, are elevated in the lungs and peripheral blood, but there is an unusual lack of an antiviral interferon (IFN) response. The virus is susceptible to exogenous type I IFN but suppresses the induction of IFN. Innate immunity is important for viral clearance in the mouse model. Virus-specific neutralizing antibodies that develop during convalescence prevent reinfection in animal models.
Pirrarni nganimparnalu yanu...′– Yesterday we went...′: storytelling in Warlpiri and its implications for literacy (1995)

Article Pirrarni nganimparnalu yanu...′–Yesterday we went...′: storytelling in Warlpiri and its implications for literacy was published on January 1, 1995 in the journal International Journal of the Sociology of Language (volume 1995, issue 113).
Characterization of Chicken Feather Biocarbon for Use in Sustainable Biocomposites (2020)

With over 1 billion tonnes of food waste generated annually, there is potential for the waste to be re-purposed. The generation of products from food-industry waste not only reduces the environmental burden of the materials but gives a new value to waste. A common waste material from the food industry is chicken feathers (ChF), a by-product of the chicken meat processing industry. In this work, ChF were subject to slow pyrolysis at varying temperatures. A complete analysis was completed to determine the yield, ash, chemical composition and morphology of the samples. X-ray diffraction analysis indicated that lower temperature samples were more amorphous, whereas higher temperature samples exhibited more graphitic content. After characterization, the biocarbon was combined with poly(lactic acid) (PLA) to generate sustainable 100 % biobased composites. Both composites had moduli that were more than 115% greater than that of the neat polymer. The success of the composites demonstrated that ChF biocarbon can be used as a sustainable and cost effective filler. The use of this material gives new purpose to a waste product and contributes to the goal of sustainable product development.
Modulation of Macrophage Phenotype by Soluble Product(s) Released from Neutrophils (2005)

The regulation of macrophage phenotype by neutrophils was studied in the s.c. polyvinyl alcohol sponge wound model in mice made neutropenic by anti-Gr-1 Ab, as well as in cell culture. Wounds in neutropenic mice contained 100-fold fewer neutrophils than those in nonneutropenic controls 1 day after sponge implantation. Wound fluids from neutropenic mice contained 68% more TNF-alpha, 168% more IL-6, and 61% less TGF-beta1 than those from controls. Wound fluid IL-10 was not different between the two groups, and IL-4 was not detected. Intracellular TNF-alpha staining was greater in cells isolated from neutropenic wounds than in those from control wounds. The hypothesis that wound neutrophil products modulate macrophage phenotype was tested in Transwell cocultures of LPS-stimulated J774A.1 macrophages and day 1 wound cells (84% neutrophils/15% macrophages). Overnight cocultures accumulated 60% less TNF-alpha and IL-6 than cultures of J774A.1 alone. The suppression of cytokine release was mediated by a soluble factor(s), because culture supernatants from wound cells inhibited TNF-alpha and IL-6 release from LPS-stimulated J774A.1 cells. Culture supernatants from purified wound neutrophils equally suppressed TNF-alpha release from LPS-stimulated J774A.1 cells. Wound cell supernatants also suppressed TNF-alpha and superoxide release from murine peritoneal macrophages. The TNF-alpha inhibitory factor has a molecular mass <3000 Da and is neither PGE2 nor adenosine. The present findings confirm a role for neutrophils in the regulation of innate immune responses through modulation of macrophage phenotype.
16Mb ROM design using bank select architecture (1988)

Market nee& for high density and shorter turn around time (TAT) mask programmable ROM's I mask ROM's ) have increased rapidly due to the demand for storing the Kanji character fonts and dictionaries used in Japanese word processor and storing the software used in TV games.
P2P and P2MP TE-LSPs packing algorithms for MPLS networks (2005)

Two packing algorithms for traffic-engineered label-switched paths (TE-LSP) are proposed in order to efficiently accommodate point-to-point (P2P) and point-to-multipoint (P2MP) TE-LSPs in a multi-protocol label switching (MPLS) network. Computer simulation results show that these algorithms calculate more efficient routes and accommodate more LSPs than a traditional routing algorithm, namely the interior gateway protocol (IGP). The proposed algorithms are heuristic; they consider the residual bandwidth of each link in the network and the number of hops from the ingress node to the egress node(s). They are applicable to IP-VPN designs that require large numbers of P2P and P2MP TE- between pairs of provider edges (PEs).
Mass sensitive detection of solvent vapors with calix[n]arenes—conformational adaptation to the analyte (1993)

Calixarenes have a hig molecular flexibility, facilitating an optimized adaptation to the shape of a large variety of guest molecules. Large substituents result in conformationally rigid compounds (Figure) but other calixarenes are ideal for coatings exhibiting high chemical sensitivity. magnified image
Crud behaviors in high temperature water, (II) Characterization of corrosion layer on type 304 stainless steel and zircaloy-2. (1986)

Sample specimens of type 304 stainless steel and Zircaloy-2 were exposed to the OWL-1 loop water at 280°C for 23d. After the exposure, a number of crystallites are distributed either separately or sometimes in agglomerate on the surfaces. The X-ray diffraction analysis and XMA analysis of the type 304 stainless steel surface revealed that more than 95% of the crystallites have a M2O3-type of structure, and some are enriched in Cr. In the sub-sequent radiochemical analysis of the fractions detached by the various cleaning processes (ultrasonic, electrostripping and electropolishing), it is noticed that the 60Co/Co ratio decreases with the depth of the corrosion layer from the value close to that of insoluble crud in the water (crud-P) to that of soluble crud (crud-F).
Midregional proadrenomedullin reflects cardiac dysfunction in haemodialysis patients with cardiovascular disease (2007)

Plasma midregional proadrenomedullin levels increase in association with cardiac dysfunction, systemic inflammatory status and systemic blood volume in haemodialysis patients with concomitant cardiovascular disease.
Improved performance of AlGaN-based deep ultraviolet light-emitting diodes with nano-patterned AlN/sapphire substrates (2017)

We demonstrated AlGaN-based deep ultraviolet light-emitting diodes (DUV LEDs) with periodic air-voids-incorporated nanoscale patterns enabled by nanosphere lithography and epitaxial lateral overgrowth (ELO) on a 4-in. sapphire substrate. The nanoscale ELO improved the crystal quality of overgrown epitaxial layers at a relatively low growth temperature of 1050 °C and at small coalescence thickness less than 2 μm. The light output power of the DUV LED was enhanced significantly by 67% at an injection current of 20 mA. We attribute such a remarkable enhancement to the formation of embedded periodic air voids which cause simultaneous improvements in the crystal quality of epitaxial layers by ELO and light extraction efficiency enabled by breaking the predominant in-plane guided propagation of DUV photons.