gebhart/patrepeval huggingface dataset:
Transcriptomic analysis of bone and fibrous tissue morphogenesis during digit tip regeneration in the adult mouse (2020)

Humans have limited regenerative potential of musculoskeletal tissues following limb or digit loss. The murine digit has been used to study mammalian regeneration, where stem/progenitor cells (the "blastema") completely regenerate the digit tip after distal, but not proximal, amputation. However, the molecular mechanisms responsible for this response remain to be determined. Here, we evaluated the spatiotemporal formation of bone and fibrous tissues after level-dependent amputation of the murine terminal phalanx and quantified the transcriptome of the repair tissue. Distal (regenerative) and proximal (non-regenerative) amputations showed significant differences in temporal gene expression and tissue regrowth over time. Genes that direct skeletal system development and limb morphogenesis are transiently upregulated during blastema formation and differentiation, including distal Hox genes. Overall, our results suggest that digit tip regeneration is controlled by a gene regulatory network that recapitulates aspects of limb development, and that failure to activate this developmental program results in fibrotic wound healing.
Design and synthesis of DYRK's family kinases inhibitors against neurodegenerative diseases (2017)

International audience
141 Local Disease Control for Spinal Metastases Following Separation Surgery and Adjuvant Hypofractionated or High-Dose Single-Fraction Stereotactic Radiation Therapy (2012)

INTRODUCTION: Decompression surgery followed by adjuvant radiotherapy is an effective therapy for preservation or recovery of neurologic function and achieving durable local disease control in patients suffering from metastatic epidural spinal cord compression. The authors examine the outcomes of postoperative image-guided intensity-modulated radiation therapy (IG-IMRT) delivered as single-fraction or hypofractionated stereotactic radiosurgery (SRS) for achieving long-term local tumor control. METHODS: A retrospective chart review identified 186 patients with epidural spinal cord compression from spinal metastases who were treated with surgical decompression, instrumentation, and postoperative radiation delivered as either single-fraction SRS (24 Gy) in 40 patients (22%), high-dose hypofractionated SRS (24-30 Gy in 3 fractions) in 37 patients (20%), or low-dose hypofractionated SRS (18-36 Gy in 5 or 6 fractions) in 109 patients (58%). The relationships between postoperative adjuvant SRS dosing and fractionation, patient characteristics, tumor histology-specific radiosensitivity, grade of epidural spinal cord compression, extent of surgical decompression, response to preoperative radiotherapy, and local tumor control were evaluated by competing risks analysis. RESULTS: The total cumulative incidence of local progression was 16.4% one year after SRS. Multivariate Gray's competing risks analysis revealed a significant improvement in local control with high-dose hypofractionated SRS (4.1% cumulative incidence of local progression at 1 year; hazard ratio = 0.12, P = 0.04) as compared to low-dose hypofractionated SRS (22.6% local progression at 1 year; HR = 1). No other variable significantly correlated with progression-free survival, including radiation sensitivity of tumor histology, preoperative radiotherapy, grade of epidural spinal cord compression, extent of surgical decompression, or gender in multivariate analysis. CONCLUSION: Postoperative adjuvant SRS following epidural spinal cord decompression and instrumentation is a safe and effective strategy for establishing durable local tumor control regardless of tumor histology-specific radiosensitivity. Patients who received high-dose hypofractionated SRS demonstrated one-year local progression rates less than 5% (95% CI: 0-12.2%), which were superior to the results of low-dose hypofractionated SRS. The local progression rate after single-fraction SRS was less than 10% (95% CI: 0-19.0%).
Physicochemical Properties of Glucomannan-Alginate as Vitamin C Excipient (2018)

This work investigated the physicochemical properties of glucomannan-alginate combination as an excipient of vitamin C encapsulation. The effects of glucomannan-alginate ratio, concentration of vitamin C and preparation method on the encapsulation physicochemical properties were studied. Swelling and solubility of the vitamin C encapsulation were determined in 2 pH conditions which mimic the environment pH of the stomach and the lower gastrointestinal tract. The ratio of glucomannan-alginate on swelling at both pHs had a similar impact on the solubility. Higher values of swelling and solubility were observed at pH 6.8 than those at pH 1.2. The second method preparation of 1:1 (w/w) ratio of glucomannan-alginate showed the most soluble excipient in pH 6.8. The highest viscosity was observed at encapsulation of 3% vitamin C prepared using the second method of 3:1 (w/w) of glucomannan-alginate.
Cover Picture: Macromol. Biosci. 3/2015 (2015)

Front Cover: Heparin-based ECM nanofilms formed on living cells by layer-by-layer assembly induce cell-cell crosslinking through bio-molecular recognition between highly-sulfated polymers and membrane proteins. Cell aggregates display network structures of cells and the cell-cell crosslinking process leads to in vitro 3D-tissue construction with rich glycosaminoglycan. The cellular assembly technique presented by M. Akashi and co-workers on page 312 has potential for tissue engineering and intercellular signalling assay.
Effects of EGR Constituents and Fuel Composition on DISI Engine Knock: An Experimental and Modeling Study (2018)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;The use of exhaust gas recirculation (EGR) in spark ignition engines has been shown to have a number of beneficial effects under specific operating conditions. These include reducing pumping work under part load conditions, reducing NO&lt;sub&gt;x&lt;/sub&gt; emissions and heat losses by lowering peak combustion temperatures, and by reducing the tendency for engine knock (caused by end-gas autoignition) under certain operating regimes. In this study, the effects of EGR addition on knocking combustion are investigated through a combined experimental and modeling approach. The problem is investigated by considering the effects of individual EGR constituents, such as CO&lt;sub&gt;2&lt;/sub&gt;, N&lt;sub&gt;2&lt;/sub&gt;, and H&lt;sub&gt;2&lt;/sub&gt;O, on knock, both individually and combined, and with and without traces species, such as unburned hydrocarbons and NO&lt;sub&gt;x&lt;/sub&gt;. The effects of engine compression ratio and fuel composition on the effectiveness of knock suppression with EGR addition were also investigated.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;A parametric, experimental matrix of diluents, compression ratio, and fuels was tested to measure knock-limited combustion phasing of each combination. The resulting knock limits were evaluated in the context of thermodynamic effects on the closed cycle, chemical interactions between the EGR constituents and the fuel-oxidizer mixture, and the effect of altered pressure-temperature trajectories on fuel-autoignition behavior. This paper provides an overview of the experimental results, and uses chemical-kinetic modeling to investigate the behavior of a particular fuel - diluent combination which had a strong sensitivity to compression ratio variation. The numerical results shed light on the complex interactions between fuel chemistry, the engine’s thermodynamic cycle, and the effect of residence times on the autoignition chemistry which leads to knock. An important and fuel-dependent role of thermal stratification in the end-gas is also suggested by the chemical-kinetics modeling of the experimentally observed knock limits.&lt;/div&gt;&lt;/div&gt;
Mindfulness Training Enhances Endurance Performance and Executive Functions in Athletes: An Event-Related Potential Study (2020)

Mindfulness interventions have been linked to improved sport performance and executive functions; however, few studies have explored the effects of mindfulness on sport performance and executive functions simultaneously. This study sought to examine whether a mindfulness training program would affect both the endurance performance and executive functions of athletes. In addition, event-related potentials (ERPs) associated with the Stroop task were assessed to investigate the potential electrophysiological activation associated with the mindfulness training. Applying a quasiexperimental design, forty-six university athletes were recruited and assigned into a five-week mindfulness training program or a waiting list control group. For each participant, the mindfulness level, endurance performance assessed by a graded exercise test, executive functions assessed via Stroop task, and N2 component of ERPs were measured prior to and following the 5-week intervention. After adjusting for the preintervention scores as a covariate, it was found that the postintervention mindfulness level, exhaustion time, and Stroop task accuracy scores, regardless of task condition, of the mindfulness group were higher than those of the control group. The mindfulness group also exhibited a smaller N2 amplitude than the control group. These results suggest that the five-week mindfulness program can enhance the mindfulness level, endurance performance, and multiple cognitive functions, including executive functions, of university athletes. Mindfulness training may also reduce conflict monitoring in neural processes.
Effect of alkylpyridinium chlorides on aggregation stability of aqueous dispersions of detonation nanodiamonds (2017)

Adsorption of decyl-, dodecyl-, and hexadecylpyridinium chlorides (DePC, DoPC, and CPC, respectively) from aqueous solutions on the surface of detonation nanodiamonds (NDs) and its effect on the aggregation stability of ND hydrosols are studied. Hydrophobic interactions, which are enhanced with the length of hydrocarbon chains in surfactant molecules, are found to play the main role in surfactant adsorption on the ND surface. DePC is almost not adsorbed on NDs, and its addition has no effect on both the size and ζ potential of nanoparticles. Adsorption of DoPC decreases the ζ potential of ND particles, thus causing their coagulation. Superequivalent adsorption of CPC results in sign reversal of the ζ potential of ND particles, thereby leading to alternation of the zones of aggregation stability and coagulation of the hydrosols with a rise in the concentration of this surfactant.
THE DEVELOPMENT OF THE OPTIC NERVE IN RODENTS (1985)

In mammals, normal visual function depends upon both the retinotopic organization of visual nuclei and their interconnections. We have investigated in rodents some developmental mechanisms contributing to this organization. On embryonic day 14, in the rat, retinal ganglion cells first project axons through glial channels on the retinal surface before reaching the optic stalk. We suggest that the sequence in which axons enter the stalk (central before peripheral) and their prominent fasciculation impose some retinotopic order amongst the emerging optic nerve fibres. At birth (embryonic day 21) there are over 240 000 axons in the optic nerve, all non-myelinated. However, within one week, the number falls to the adult value (100 000) and myelination, complete in the adult, commences. Axons lost include some which misproject--to the opposite eye or to inappropriate parts of central visual regions. The number of surviving retinal ganglion cells depends on the amount of appropriate target tissue available. It is well established that removal of one eye early in development increases the survival of axons in the remaining optic nerve. However, in a group of adult mice with congenital unilateral anophthalmia, we counted only 21 000 optic axons in the remaining nerve compared with the 31 000 in normal mice of the same strain. Degenerating axons were observed, suggesting that the defect is not a simple developmental failure, but is associated with active degenerative processes throughout life.
Organization of the multifunctional enzyme type 1: interaction between N- and C-terminal domains is required for the hydratase-1/isomerase activity (2002)

Rat peroxisomal multifunctional enzyme type 1 (perMFE-1) is a monomeric protein of beta-oxidation. We have defined five functional domains (A, B, C, D and E) in the perMFE-1 based on comparison of the amino acid sequence with homologous proteins from databases and structural data of the hydratase-1/isomerases (H1/I) and (3 S )-hydroxyacyl-CoA dehydrogenases (HAD). Domain A (residues 1-190) comprises the H1/I fold and catalyses both 2-enoyl-CoA hydratase-1 and Delta(3)-Delta(2)-enoyl-CoA isomerase reactions. Domain B (residues 191-280) links domain A to the (3 S )-dehydrogenase region, which includes both domain C (residues 281-474) and domain D (residues 480-583). Domains C and D carry features of the dinucleotide-binding and the dimerization domains of monofunctional HADs respectively. Domain E (residues 584-722) has sequence similarity to domain D of the perMFE-1, which suggests that it has evolved via partial gene duplication. Experiments with engineered perMFE-1 variants demonstrate that the H1/I competence of domain A requires stabilizing interactions with domains D and E. The variant His-perMFE (residues 288-479)Delta, in which the domain C is deleted, is stable and has hydratase-1 activity. It is proposed that the extreme C-terminal domain E in perMFE-1 serves the following three functions: (i) participation in the folding of the N-terminus into a functionally competent H1/I fold, (ii) stabilization of the dehydrogenation domains by interaction with the domain D and (iii) the targeting of the perMFE-1 to peroxisomes via its C-terminal tripeptide.
Synthesis, anticancer, and computational studies of 1, 3, 4‐oxadiazole‐purine derivatives (2020)

Abstract Theophylline‐7‐acetic acid (acefylline) ( 3 ) and its derivatives are pharmacologically active compounds and generally recognized as bronchodilators for the treatment of respiratory diseases like acute asthma for over 70 years. In this article, synthesis of 2‐((5‐((1,3‐dimethyl‐2,6‐dioxo‐2,3‐dihydro‐1 H ‐purin‐7(6 H )‐yl)methyl)‐1,3,4‐oxadiazol‐2‐yl)thio)‐ N ‐arylacetamides ( 10a‐j ) has been reported. All the synthesized derivatives ( 10a‐j) were structurally verified by FT‐IR, 1 H NMR, 13 C NMR and evaluated for their anti‐cancer (using MTT assay), hemolytic and thrombolytic potential. N ‐(4‐Chlorophenyl)‐2‐(5‐((1,3‐dimethyl‐2,6‐dioxo‐2,3‐dihydro‐1 H ‐purin‐7(6 H )‐yl)methyl)‐1,3,4‐oxadiazol‐2‐ylthio)acetamide ( 10g ) was found to be the most active against human liver cancer cell lines (Huh7) having cell viability 53.58 ± 1.28 using 100 μg/mL concentration of compound which was further in‐silico modelled to describe the possible mechanistic insights for its anti‐proliferative activity. The results of hemolytic and thrombolytic activities indicated that these derivatives were less toxic and hold considerable potential as a drug candidate. 2‐(5‐((1,3‐Dimethyl‐2,6‐dioxo‐2,3‐dihydro‐1 H ‐purin‐7(6H)‐yl)methyl)‐1,3,4‐oxadiazol‐2‐ylthio)‐ N ‐(2‐fluorophenyl)acetamide ( 10c ) of the series was found to be least toxic with 0.1% hemolysis relative to ABTS (95.5%) as positive control. 2‐(5‐((1,3‐Dimethyl‐2,6‐dioxo‐2,3‐dihydro‐1 H ‐purin‐7(6 H )‐yl)methyl)‐1,3,4‐oxadiazol‐2‐ylthio)‐ N ‐(tetrahydro‐2 H ‐pyran‐4‐yl)acetamide ( 10j ) exhibited potent clot lysis activity (90%) as compared to negative control DMSO (0.57%).
Novel heterocyclic hybrids of pyrazole targeting dihydrofolate reductase: design, biological evaluation and in silico studies (2020)

A novel series of pyrazole analogues including hydrazones, pyrazolo[4,3-<i>c</i>]-pyridazines, pyrazolo[3,4-<i>e</i>][1,2,4]triazine and pyrazolo[3,4-<i>d</i>][1,2,3]triazoles was designed, synthesised and screened for their <i>in vitro</i> antimicrobial and DHFR inhibition activity. Compounds bearing benzenesulphonamide moiety incorporated with 3-methyl-5-oxo-1<i>H</i>-pyrazol-4(5<i>H</i>)-ylidene) hydrazine <b>3a</b> or 6-amino-7-cyano-3-methyl-5<i>H</i>-pyrazolo[4,3-<i>c</i>]pyridazine <b>6a</b> revealed excellent and broad spectrum antimicrobial activity comparable to ciprofloxacin and amphotericin B as positive antibiotic and antifungal controls, respectively. Furthermore, these derivatives proved to be the most active DHFR inhibitors with IC<sub>50</sub> values 0.11 ± 1.05 and 0.09 ± 0.91 µM, in comparison with methotrexate (IC<sub>50</sub> = 0.14 ± 1.25 µM). The <i>in silico</i> studies were done to calculate the drug-likeness and toxicity risk parameters of the newly synthesised derivatives. Additionally, the high potency of the pyrazole derivatives bearing sulphonamide against DHFR was confirmed with molecular docking and might be used as an optimum lead for further modification.
Circadian remodeling of the proteome by chaperone-mediated autophagy (2022)

The circadian clock drives daily cycles of physiology and behavioral outputs to keep organisms in tune with the environment. Cyclic oscillations in levels of the clock proteins maintain circadian rhythmicity. In our recent work, we have discovered the interdependence of the circadian clock and chaperone-mediated autophagy (CMA), a selective form of lysosomal protein degradation. Central and peripheral degradation of core clock proteins by CMA (selective chronophagy) modulates circadian rhythm. Loss of CMA in vivo disrupts physiological circadian cycling, resembling defects observed in aging, a condition with reduced CMA. Conversely, the circadian clock temporally regulates CMA activity in a tissue-specific manner, contributing to remodeling of a distinct subproteome at different circadian times. This timely remodeling cannot be sustained when CMA fails, despite rerouting of some CMA substrates to other degradation pathways.
Parallel 1/0 from the User's Perspective (1995)

Pamllel 1/0 systems are gaining popularity as a means for providing scalable high bandwidth I/O. In this paper we develop abstract models of parallel 1/0 systems and provide empirical results that show how 1/0 intensive applications interact with the elements of parallelI/O systems. The abstract models are useful for explaining parallel 1/0 performance to developers of applications requiring high performance 1/0 and the eqerimental results provide insight into the 1/0 performance of present genemtion parallel machines. We also identify optimizations for improving 1/0 performance, which should be useful for developers of applications and 1/0 libraries.
Mechanisms underlying the reduction of isometric force in skeletal muscle fatigue (1998)

A decline of isometric force production is one characteristic of skeletal muscle fatigue. In fatigue produced by repeated short tetani, this force decline can be divided into two components: a reduction of the cross-bridges' ability to generate force, which comes early; and a reduction of the sarcoplasmic reticulum Ca2+ release, which develops late in fatigue. Acidification due to lactic acid accumulation has been considered as an important cause of the reduced cross-bridge force production. However, in mammalian muscle it has been shown that acidification has little effect on isometric force production at physiological temperatures. By exclusion, in mammalian muscle fatigue, the reduction of force due to impaired cross-bridge function would be caused by accumulation of inorganic phosphate ions, which results from phosphocreatine breakdown. The reduction of sarcoplasmic reticulum Ca2+ release in late fatigue correlates with a decline of ATP and we speculate that the reduced Ca2+ release is caused by a local increase of the ADP/ATP ratio in the triads.
Charting Democracy Across Parsers (2007)

Different parsers trained on the same corpus deliver different results, both in terms of overall performance and in terms of the individual analyses they provide. In particular, for any given sentence, one parser may provide a correct analysis, while another will produce an incorrect analysis; but when faced with a different sentence, the first parser may be in error while the second is correct. In this paper, we leverage this observation by exploring how the results of a number of different parsers may be combined to provide a better performance than any single parser. The method involves constructing a chart that contains edges contributed by a collection of parsers, with a simple voting mechanism to choose the most preferred constituents; this provides a significant improvement in performance over any individual parser. More sophisticated voting mechanisms are also discussed. 1
Low-Dose Aspirin for Primary Prevention of Cardiovascular Events in Japanese Patients 60 Years or Older With Atherosclerotic Risk Factors (2014)

clinicaltrials.gov Identifier: NCT00225849.
Microbubble Dissolution in a Multigas Environment (2010)

Microbubbles occur naturally in the oceans and are used in many industrial and biomedical applications. Here, a theoretical and experimental study was undertaken to determine the fate of a microbubble suddenly suspended in a medium with several gas species as in, for example, the injection of an ultrasound contrast agent into the bloodstream. The model expands on Epstein and Plesset's analysis to include any number of gases. An experimental system was developed which isolates the microbubble in a permeable hollow fiber submerged in a perfusion chamber, allowing rapid exchange of the external aqueous medium. Experimental verification of the model was performed with individual sulfur hexafluoride (SF(6)) microbubbles coated with the soluble surfactant, sodium dodecyl sulfate (SDS). SDS-coated microbubbles suddenly placed in an air-saturated medium initially grew with the influx of O(2) and N(2) and then dissolved under Laplace pressure. SF(6)-filled microbubbles coated with the highly insoluble lipid, dibehenoylphosphatidylcholine, were found to exhibit significantly different behavior owing to a dynamic surface tension. The initial growth phase was diminished, possibly owing to a shell "breakup" tension that exceeded the pure gas/liquid surface tension. Three dissolution regimes were observed: (1) an initial rapid dissolution to the initial diameter followed by (2) steady dissolution with monolayer collapse and finally (3) stabilization below 10 microm diameter. Results indicated that the lipid shell becomes increasingly rigid as the microbubble dissolves, which has important implications on microbubble size distribution, stability, and acoustic properties.
Novel fiber optic glucose biosensor based on fluorescence quenching (2002)

A new fiber optic glucose biosensor based on oxygen fluorescence quenching using lock-in technology has been presented. Ruthenium(II) complex, Ru(bpy)3Cl2, were used as the fluorescence indicator and cellulose acetate(CA) were used as the matrix membrane to immobilize the indicator and GOD, and the optimal conditions for the preparation of CA membrane has been studied. For the immobilization of GOD to CA membrane, albumin of bovine serum(BSA) and glutaraldehyde(GA) were used through covalence—cross bonding process. The relationship between the concentration of glucose and the phase delay??? has been studied, the results show that ??? has good relationship within the range of 50mg/dl—500mg/dl and the response time is less than 30 sec. Several factors to influence the sensor such as pH of the medium, the additional membrane layers, the properties of CA membrane have also been studied. The results indicate that its best pH range is between pH6.0 and 7.0, and the thickness of the additional membrane layers on the sensor head will influence the response time greatly, that is, the response time is controlled by the speed of dispersion of the dissolved oxygen into the fluorescence dye layer.