gebhart/patrepeval huggingface dataset:
Data from Genomic Profiling of Pediatric Acute Myeloid Leukemia Reveals a Changing Mutational Landscape from Disease Diagnosis to Relapse (2023)

&lt;div&gt;Abstract&lt;p&gt;The genomic and clinical information used to develop and implement therapeutic approaches for acute myelogenous leukemia (AML) originated primarily from adult patients and has been generalized to patients with pediatric AML. However, age-specific molecular alterations are becoming more evident and may signify the need to age-stratify treatment regimens. The NCI/COG TARGET-AML initiative used whole exome capture sequencing (WXS) to interrogate the genomic landscape of matched trios representing specimens collected upon diagnosis, remission, and relapse from 20 cases of &lt;i&gt;de novo&lt;/i&gt; childhood AML. One hundred forty-five somatic variants at diagnosis (median 6 mutations/patient) and 149 variants at relapse (median 6.5 mutations) were identified and verified by orthogonal methodologies. Recurrent somatic variants [in (greater than or equal to) 2 patients] were identified for 10 genes (&lt;i&gt;FLT3, NRAS, PTPN11, WT1, TET2, DHX15, DHX30, KIT, ETV6, KRAS&lt;/i&gt;), with variable persistence at relapse. The variant allele fraction (VAF), used to measure the prevalence of somatic mutations, varied widely at diagnosis. Mutations that persisted from diagnosis to relapse had a significantly higher diagnostic VAF compared with those that resolved at relapse (median VAF 0.43 vs. 0.24, &lt;i&gt;P&lt;/i&gt; &lt; 0.001). Further analysis revealed that 90% of the diagnostic variants with VAF &gt;0.4 persisted to relapse compared with 28% with VAF &lt;0.2 (&lt;i&gt;P&lt;/i&gt; &lt; 0.001). This study demonstrates significant variability in the mutational profile and clonal evolution of pediatric AML from diagnosis to relapse. Furthermore, mutations with high VAF at diagnosis, representing variants shared across a leukemic clonal structure, may constrain the genomic landscape at relapse and help to define key pathways for therapeutic targeting. &lt;i&gt;Cancer Res; 76(8); 2197–205. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Levosimendan pretreatment improves survival of septic rats after partial hepatectomy and suppresses iNOS induction in cytokine-stimulated hepatocytes (2019)

We evaluated the survival effects and biochemical profiles of levosimendan in septic rats after partial hepatectomy and investigated its effects in cultured hepatocytes. Thirty-two rats underwent 70% hepatectomy and were randomised equally into four groups, followed by lipopolysaccharide (LPS) injection (250 µg/kg, i.v.) after 48 h. Levosimendan was given (i.p.) 1 h before LPS injection [group (A) levosimendan 2 mg/kg; (B) 1; (C) 0.5; (D) vehicle]. Survival at 7 days was increased significantly in group A compared with that in group D [A: 63%; B: 38%; C: 13%; D: 0%]. In serum, levosimendan decreased the level of tumour necrosis factor-α, interleukin (IL)-1β, IL-6 and nitric oxide (NO). In remnant livers, levosimendan inhibited inducible nitric oxide synthase (iNOS) gene expression. In primary cultured rat hepatocytes stimulated by IL-1β, levosimendan suppressed NO production by inhibiting iNOS promoter activity and stability of its mRNA.
Identification of a Mg2+-dependent protease in human placenta which cleaves hydrophobic folate-binding proteins to hydrophilic forms (1989)

Hydrophobic folate-binding proteins (FBPs), which are only 5-10 kDa larger than 40-kDa hydrophilic FBPs, bind significant quantities of Triton X-100 micelles and elute as apparent 160-kDa species on Sephacryl S-200 gel filtration in Triton X-100. Detergent-solubilized placental membranes release a major (greater than 95%) 40-kDa hydrophilic FBP species as well as a minor apparent 160-kDa folate binding species when similarly analyzed. We tested the hypothesis that this recovery of predominantly hydrophilic FBPs was mediated by a putative hydrophobic FBP-specific placental protease. When placenta was solubilized in the presence of increasing concentrations of EDTA, there was a progressive increase in apparent 160-kDa folate binding moieties concomitant with a decrease in 40-kDa FBPs. At 20 mM EDTA, a single apparent 160-kDa folate binding species was recovered and the 40-kDa FBPs could not be detected by radioligand binding or specific radioimmunoassay. The apparent 160-kDa species specifically bound radiolabeled folates and were specifically immunoprecipitated by rabbit anti-40-kDa FBP antiserum. On 15% sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by transfer to nitrocellulose and probing with anti-40-kDa FBP antiserum, the apparent 160-kDa FBPs electrophoresed as 45-kDa species. Detergent binding studies indicated that apparent 160-kDa FBPs were hydrophobic, thus accounting for the molecular weight discrepancy in gel filtration in Triton X-100 versus sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The EDTA-mediated inhibition of conversion of hydrophobic FBPs to hydrophilic FBPs by protease was reversed in a dose-dependent manner by Mg2+. If this protease is physiologically relevant, it could play an important regulatory role in folate transport by influencing the net number of hydrophobic FBPs on the cell surface.
Production d'anticorps monoclonaux in vitro, mise au point d'un milieu de culture synthetique et selection d'un procede (1989)

Les nouvelles applications des anticorps monoclonaux (acm) remettent en cause le schema classique de production des acm. Le developpement de la production in vitro, a grande echelle est necessaire. Les milieux de culture classiques de cellules animales ne sont pas adaptes car ils contiennent du serum animal. Ils sont donc tres onereux et sont une source importante de contaminants d'origine animale. Le developpement du milieu synthetique sf6 a ete realise par le remplacement successif des composes d'origine animale et ceux juges trop couteux. Sf6 permet un gain de productivite de 47% et une baisse du prix du milieu d'un facteur 10 par rapport a un milieu contenant 10% de serum de veau ftal. Les procedes de culture en masse principalement utilises jusqu'alors ne sont pas adaptes a la production d'acm a visee therapeutique. Nous avons donc etudie de nouveaux procedes et particulierement la culture continue en fermenteur et sur un systeme de fibres creuses (acusyst jr). Ce dernier nous semble le plus adapte a la production d'acm a usage therapeutique, pour deux raisons principales: la concentration d'acm dans le surnageant (en moyenne 5 g/l) et la modularite du systeme
Anonieme bitten en verborgen signalen (2003)

gefascineerd door deze magische formule.
Crystal structure of dilithiumsulfíde, Li2S (1999)

Li2S, cubic, Fiiβm (No. 225), a = 5.7158(1) A, V= 186.7 A3, Z = 4, REi(F) = 0.009, Rv.(F) = 0.009, T= 293 K.
Rapid parameter estimation for selective inversion recovery myelin imaging using an open-source Julia toolkit (2021)

Abstract Background Magnetic resonance imaging (MRI) is used extensively to quantify myelin content, however computational bottlenecks remain challenging for advanced imaging techniques in clinical settings. We present a fast, open-source toolkit for processing quantitative magnetization transfer derived from selective inversion recovery (SIR) acquisitions that allows parameter map estimation, including the myelin-sensitive macromolecular pool size ratio ( PSR ). Significant progress has been made in reducing SIR acquisition times to improve clinically feasibility. However, parameter map estimation from the resulting data remains computationally expensive. To overcome this computational limitation, we developed a computationally efficient, open-source toolkit implemented in the Julia language. Methods To test the accuracy of this toolkit, we simulated SIR images with varying PSR and spin-lattice relaxation time of the free water pool ( R 1f ) over a physiologically meaningful scale from 5 to 20% and 0.5 to 1.5 s -1 , respectively. Rician noise was then added, and the parameter maps were estimated using our Julia toolkit. Probability density histogram plots and Lin’s concordance correlation coefficients (LCCC) were used to assess accuracy and precision of the fits to our known simulation data. To further mimic biological tissue, we generated five cross-linked bovine serum albumin (BSA) phantoms with concentrations that ranged from 1.25 to 20%. The phantoms were imaged at 3T using SIR, and data were fit to estimate PSR and R 1f . Similarly, a healthy volunteer was imaged at 3T, and SIR parameter maps were estimated to demonstrate the reduced computational time for a real-world clinical example. Results Estimated SIR parameter maps from our Julia toolkit agreed with simulated values (LCCC&gt; 0.98). This toolkit was further validated using BSA phantoms and a whole brain scan at 3T. In both cases, SIR parameter estimates were consistent with published values using MATLAB. However, compared to earlier work using MATLAB, our Julia toolkit provided an approximate 20-fold reduction in computational time. Conclusions Presented here, we developed a fast, open-source, toolkit for rapid and accurate SIR MRI using Julia. The reduction in computational cost should allow SIR parameters to be accessible in clinical settings.
An evaluation of fibrous structure and physical characteristics of Cutia nut (Couepia edulis Prance) shell (2009)

The Cutia-nut (Couepia edulis Prance), a species originally from the Amazon region, has a kernel with reasonable nutritional value and a hard and thick woody shell that constitute most of the fruit. After the kernel removal, the shells are regarded as waste. The possibility of using such shells, as raw material for burning or charcoal production, as well as milled residue for structural reinforcement materials is quite feasible, considering environmental and economical aspects. There is, however, a complete lack of characterization of the Cutia-nut shell and other similar species which can aggregate desirable qualities for application as engineering material. In this study some analyses are presented aiming at providing information for potential uses of these residues. In general, the shells follow a regular shape with certain dimensional proportionality to the kernel. The shell is a fibrous material with high lignin content, present low water absorption and high resistance to natural degradation.
The evaluation of forms of assessment using n-dimensional filtering (2004)

This article describes the use of the CoFIND (Collaborative Filter in N Dimensions) system to evaluate two assessment styles. CoFIND is a resource database which organizes itself around its users’ needs. Learners enter resources, categorize then rate them using aspects of resources which learners find worthwhile, the n dimensions of CoFIND. CoFIND’s users create the categories and qualities, so the system sculpts itself to a group’s expressed needs.Two uses of CoFIND contrast where students added and rated their own Web-based assignments. The first of these provided useful material to help the students with further learning goals, while the second let them use skills they had acquired in a concrete setting. The use of qualities in each instance was very different, reflecting the students’ different needs in each case. Based on these results, we can suggest how virtual ecologies of self-organising groups of learners might be encouraged to thrive and grow.
Efficiency Improvement of Solution Processed Blue Phosphorescent Devices Using High Triplet Energy Electron Transport Layer (2010)

High efficiency solution processed blue phosphorescent organic light emitting diodes (PHOLEDs) were developed using a high triplet energy exciton blocking layer. A spirobifluorene-based phosphine oxide compound was used as the exciton blocking layer for poly(-vinylcarbazole) (PVK):iridium(III) bis[4,6-(difluorophenyl)-pyridinato-] picolinate (FIrpic) emitting layer. A high quantum efficiency of 12.6% and a high current efficiency of 22.9 cd/A were obtained from the PVK:FIrpic PHOLED due to efficient exciton blocking and electron injection.
Ursolic Acid Inhibits STAT3 Activation Pathway Leading to Suppression of Proliferation and Chemosensitization of Human Multiple Myeloma Cells (2007)

The activation of signal transducers and activators of transcription 3 (STAT3) has been linked with the proliferation of a variety of human cancer cells, including multiple myeloma. Agents that can suppress STAT3 activation have potential for prevention and treatment of cancer. In the present report, we tested an agent, ursolic acid, found in basil, apples, prunes, and cranberries, for its ability to suppress STAT3 activation. We found that ursolic acid, a pentacyclic triterpenoid, inhibited both constitutive and interleukin-6-inducible STAT3 activation in a dose- and time-dependent manner in multiple myeloma cells. The suppression was mediated through the inhibition of activation of upstream kinases c-Src, Janus-activated kinase 1, Janus-activated kinase 2, and extracellular signal-regulated kinase 1/2. Vanadate treatment reversed the ursolic acid-induced down-regulation of STAT3, suggesting the involvement of a tyrosine phosphatase. Indeed, we found that ursolic acid induced the expression of tyrosine phosphatase SHP-1 protein and mRNA. Moreover, knockdown of SHP-1 by small interfering RNA suppressed the induction of SHP-1 and reversed the inhibition of STAT3 activation, thereby indicating the critical role of SHP-1 in the action of this triterpene. Ursolic acid down-regulated the expression of STAT3-regulated gene products such as cyclin D1, Bcl-2, Bcl-xL, survivin, Mcl-1, and vascular endothelial growth factor. Finally, ursolic acid inhibited proliferation and induced apoptosis and the accumulation of cells in G1-G0 phase of cell cycle. This triterpenoid also significantly potentiated the apoptotic effects of thalidomide and bortezomib in multiple myeloma cells. Overall, these results suggest that ursolic acid is a novel blocker of STAT3 activation that may have a potential in prevention and treatment of multiple myeloma and other cancers.
Importance of hydration in exoelectron emission from ceramic BeO (1976)

The influence of the state of hydration on the exoelectron emitting characteristics of BeO ceramic dosimeters for TSEE is very strong and very complex. For dosimetry the most unfavorable characteristics are a ruined TSEE peak shape and loss of intensity; this occurs if atmosphere moisture is allowed to condense onto, and evaporate from, the BeO surface. For unencapsulated dosimeters this occurs when the ambient temperature falls below the dew point. Immersion of irradiated detectors directly into liquid water for a few hours causes fading at a substantial rate, but surprisingly little change in the TSEE peak shape or intensity. The different behaviors with respect to immersion in liquid water and exposure to condensing atmospheric moisture present an enigma. Ceramic BeO TSEE dosimeters can only be used with confidence in atmospheres where below dew point conditions are avoidable, such as inside air conditioned buildings or encapsulated, dry air containers.
Correcting Artifacts in Single Molecule Localization Microscopy Analysis Arising from Pixel Quantum Efficiency Differences in sCMOS Cameras (2019)

Optimal analysis of single molecule localization microscopy (SMLM) data acquired with a scientific Complementary Metal-Oxide-Semiconductor (sCMOS) camera relies on statistical compensation for its pixel-dependent gain, offset and readout noise. In this work we show that it is also necessary to compensate for differences in the relative quantum efficiency (RQE) of each pixel. We found differences in RQE on the order of 4% in our tested sCMOS sensors. These differences were large enough to have a noticeable effect on analysis algorithm results, as seen both in simulations and biological imaging data. We discuss how the RQE differences manifest themselves in the analysis results and present the modifications to the Poisson maximum likelihood estimation (MLE) sCMOS analysis algorithm that are needed to correct for the RQE differences.
Nonlinear BEM-surface impedance boundary condition formulation for unstructured meshes (2016)

Surface impedance boundary conditions are used to take into account electromagnetic phenomena in thin layers. By exploiting a dual geometrical discretisation of the surface of a conducting object, it can be used to formulate the skin effect as a circuit. The mesh can be either structured or unstructured as in case of triangular elements. The surface circuit can be coupled to a boundary element method for the region surrounding it giving rise to a hybrid solution. Field distribution along the depth of the conductor can account for nonlinearity if the analytical one dimensional solution is replaced by a numerical one. The hybrid technique is applied to the analysis of induction heating devices.
Eine vergleichende Studie des β‐Cholesteringehaltes und Apo‐B‐Gehaltes in Hyperlipoproteinämien (1977)

Abstract Die spezifische Bindungsstelle für Lipide wird in einigen Lipasen aus einer Sequenz von hydrophoben Aminosäuren in Nachbarschaft einer basischen Aminosäure gebildet. Ähnliche Charakteristika findet man auch in synthetischen kationischen Polymeren. Diese Produkte vermögen Lipoide fester zu binden als Albumin und die Hydrolyse von Estern langkettiger Fettsäuren in einem ähnlichen Ausmaß wie Enzyme zu katalysieren. Bei der Untersuchung der Wirkung von Polykationen auf isolierte natürliche Lipoproteine wurde ein unterschiedliches Verhalten beobachtet. Während VLDL‐ und HDL‐Lipoproteine an das Polymer gebunden wurden, konnte keine Reaktion zwischen dem Polykation und der LDL‐Lipoproteinfraktion festgestellt werden. Diese Beobachtung ermöglichte die Entwicklung eines Verfahrens zur direkten Bestimmung von β‐Lipoprotein Cholesterin nach selektiver Extraktion der VLDL und HDL mit Hilfe eines Polykations und eines Polykationen‐Austauschers. Die Selektivität der Reaktion wird auf eine Wechselwirkung zwischen dem Polykation und oberflächenständigen neutralen und sauren Lipiden in den VLDL‐und HDL‐Lipoproteinen zurückgeführt.
Effects Of Vitamin C Enriched Hydrolyzed Collagen On Explosive Performance (2020)

The stiffness of a tendon is determined by the amount and cross-linking of collagen within the tissue. Acute exercise and possibly vitamin C-enriched collagen supplementation have been shown to increase collagen synthesis as well as the expression of the primary enzyme involved in collagen cross-linking (lysyl oxidase). The result may be a denser and stiffer tissue. Stiffness is directly related to force transfer. Whether this nutritional supplementation can further augment response to training, in particular rate of force development (RFD), and translate to improved explosive performance compared to training alone is unknown. PURPOSE: To determine if nutritional supplementation with vitamin C-enriched collagen improves RFD compared to placebo (PLA) with an explosive power-based training regime. METHODS: Healthy male collegiate football players (18-25 years) were enrolled in a 3-week double-blinded, parallel design study. Athletes were randomly assigned to the intervention group (COLL; 15g hydrolyzed collagen with 50mg vitamin C) or placebo group (PLA; 15g rice four). Supplements were ingested 60min prior to training 5 days per week and with breakfast on rest days. Athletes completed the same training program and progression. RFD was measured from the best of three maximal isometric squats, countermovement jumps and squat jumps (Kistler, Novi, MI) performed at the same time on each testing day (baseline and after 1,2 and 3 weeks of training). Two-way ANOVA (nutrition intervention and time) was used to compare RFD between groups. RESULTS: At time of analysis there were no significant difference for maximal RFD in the maximal isometric squat between the interventions. RFD data from CMJ and SJ are yet to be determined. CONCLUSION: Supplementation with vitamin C-enriched collagen prior to training throughout a 3-week explosive power-based training program does not improve maximal RFD compared to exercise alone. More comprehensive analysis of all RFD parameters is required to fully interpret results from this study and will be completed prior to abstract presentation.
Direct imaging of human Rad51 nucleoprotein dynamics on individual DNA molecules (2009)

Rad51 protein (Rad51) is central to recombinational repair of double-strand DNA breaks. It polymerizes onto DNA and promotes strand exchange between homologous chromosomes. We visualized the real-time assembly and disassembly of human Rad51 nucleoprotein filaments on double-stranded DNA by single-molecule fluorescence microscopy. Rad51 assembly extends the DNA by approximately 65%. Nucleoprotein filament formation occurs via rapid nucleation followed by growth from these nuclei. Growth does not continue indefinitely, however, and nucleoprotein filaments terminate when approximately 2 mum in length. The dependence of nascent filament formation on Rad51 concentration suggests that 2-3 Rad51 monomers are involved in nucleation. Rad51 nucleoprotein filaments are stable and remain extended when ATP hydrolysis is prevented; however, when permitted, filaments decrease in length as a result of conversion to ADP-bound nucleoprotein complexes and partial protein dissociation. Dissociation of Rad51 from dsDNA is slow and incomplete, thereby rationalizing the need for other proteins that facilitate disassembly.
Linking SCOR planning practices to supply chain performance (2004)

As supply chains continue to replace individual firms as the economic engine for creating value during the twenty‐first century, understanding the relationship between supply‐chain management practices and supply chain performance becomes increasingly important. The Supply‐Chain Operations Reference (SCOR) model developed by the Supply Chain Council provides a framework for characterizing supply‐chain management practices and processes that result in best‐in‐class performance. However, which of these practices have the most influence on supply chain performance? This exploratory study investigates the relationship between supply‐chain management planning practices and supply chain performance based on the four decision areas provided in SCOR Model Version 4.0 (PLAN, SOURCE, MAKE, DELIVER) and nine key supply‐chain management planning practices derived from supply‐chain management experts and practitioners. The results show that planning processes are important in all SCOR supply chain planning decision areas. Collaboration was found to be most important in the Plan, Source and Make planning decision areas, while teaming was most important in supporting the Plan and Source planning decision areas. Process measures, process credibility, process integration, and information technology were found to be most critical in supporting the Deliver planning decision area. Using these results, the study discusses the implications of the findings and suggests several avenues for future research.
Nonhuman primates’ tissue banks: resources for all model organism research (2021)

Biobanks containing tissue and other biological samples from many model organisms provide easy and faster access to ex vivo resources for a wide-range of research programmes. For all laboratory animals, collecting and preserving tissue at post-mortem is an effective way of maximising the benefits of individual animals and potentially reducing the numbers required for experimentation in the future. For primate tissues, biobanks represent the scarcest of these resources but quite possibly those most valuable for preclinical and translation studies.