gebhart/patrepeval huggingface dataset:
Mantle Cell Lymphoma International Prognostic Index but Not Pretransplantation Induction Regimen Predicts Survival for Patients With Mantle-Cell Lymphoma Receiving High-Dose Therapy and Autologous Stem-Cell Transplantation (2011)

An intensive induction regimen before HDT and ASCT was not associated with improved survival after adjusting for differences in MIPI scores at diagnosis.
1-Octyl-3-(3-(1-methylpyrrolidiniumyl)propyl)imidazolium Bis(trifluoromethane)sulfonimide (2019)

The title compound 1-octyl-3-(3-(1-methylpyrrolidiniumyl)propyl)imidazolium bis(trifluoromethane)sulfonimide was prepared in three steps. This asymmetrical dicationic ionic liquid (ADIL) is composed of two different positively charged head groups (1-octylimidazolium and methylpyrrolidinium cations), which are linked through a propyl alkyl chain and by two bis(trifluoromethane)sulfonimide anions. The final ADIL was obtained by a simple metathesis reaction of the corresponding dibromide ionic liquid, in turn prepared by alkylation of 3-(3-bromopropyl)-1-propylimidazolium bromide. The ADIL structure and those of its precursors were confirmed through NMR and infrared spectroscopy, and the thermal properties of all compounds were evaluated by thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). Density, solubility, and viscosity were measured for the prepared compounds.
1862 – The Effects Of Eeg-neurofeedback On Adhd Symptoms And Eeg Parameters (2013)

Introduction EEG-neurofeedback is used as a component of therapy in patients diagnosed with ADHD. The efficacy of NF on inattentive symptoms has been previously suggested. Objective The aim of the study was to assess the efficacy of 20 sessions training of eeg-neurofeedback (NF) in patients suffered from ADHD. Methods The studied group consisted of 44 patients (34 boys and 7 girls).To determine the efficacy of EEG-B on symptoms intensity, The Symptoms of ADHD Questionnaire was used: before the treatment and after 20 sessions of NF. NF trainings took place once or twice a week. The trainings were conduct based on two protocols: theta/beta and theta/SMR for left hemisphere and for right hemisphere, respectively. The changes in theta/beta and theta/SMR ratios were estimated to assess the influence of NF on eeg parameters. Results The significant reduction in symptoms intensity was found after 20 sessions of NF. Theta/beta and theta/SMR ratios median values have been significantly decreased. Conclusions The results of the study indicate the 20 sessions NF training being efficacious in reduction of the intensity of ADHD symptoms. The improvement of eeg parameters responsible for attention functions was also observed.
Overexpression, characterization, and purification of a recombinant mouse immunophilin FKBP-52 and identification of an associated phosphoprotein. (1993)

To gain insight into the structure and function of the immunophilin FKBP-52, a mouse FKBP-52 was overexpressed in Spodoptera frugiperda insect cells (Sf9 cells) with the baculovirus expression system. The purification and characterization of the recombinant FKBP-52 (rFKBP-52) was facilitated by incorporating a histidine 6-mer domain at its N terminus. The rFKBP-52 was highly purified on a N(i)2+ affinity resin with an estimated recovery of 10 mg of pure protein from 1 liter of Sf9 cell culture. Subcellular fractionation revealed that the rFKBP-52 is expressed predominantly in the nuclei of infected Sf9 cells maximally at 48 hr after infection, consistent with the nuclear localization of FKBP-52 in mammalian cells. The rFKBP-52 can be assembled in vitro with the glucocorticoid receptor complex, establishing its functionality and confirming that it is a component of the unactivated glucocorticoid receptor complex. The rFKBP-52 possesses an ATP/GTP binding activity that is stimulated by divalent cations. Furthermore, incubation of purified rFKBP-52 with [gamma-32P]ATP and MgCl2 resulted in the phosphorylation of a 59-kDa nuclear protein. Amino acid sequence analysis of this protein revealed that it is a phosphoprotein or kinase that is associated with the rFKBP-52.
Differential RNA Expression Profile of Skeletal Muscle Induced by Experimental Autoimmune Myasthenia Gravis in Rats (2016)

The differential susceptibility of skeletal muscle by myasthenia gravis (MG) is not well understood. We utilized RNA expression profiling of extraocular muscle (EOM), diaphragm (DIA), and extensor digitorum (EDL) of rats with experimental autoimmune MG (EAMG) to evaluate the hypothesis that muscles respond differentially to injury produced by EAMG. EAMG was induced in female Lewis rats by immunization with acetylcholine receptor purified from the electric organ of the <i>Torpedo</i>. Six weeks later after rats had developed weakness and serum antibodies directed against the AChR, animals underwent euthanasia and RNA profiling performed on DIA, EDL, and EOM. Profiling results were validated by qPCR. Across the three muscles between the experiment and control groups, 359 probes (1.16%) with greater than 2-fold changes in expression in 7 of 9 series pairwise comparisons from 31,090 probes were identified with approximately two-thirds being increased. The three muscles shared 16 genes with increased expression and 6 reduced expression. Functional annotation demonstrated that these common expression changes fell predominantly into categories of metabolism, stress response, and signaling. Evaluation of specific gene function indicated that EAMG led to a change to oxidative metabolism. Genes related to muscle regeneration and suppression of immune response were activated. Evidence of a differential immune response among muscles was not evident. Each muscle had a distinct RNA profile but with commonality in gene categories expressed that are focused on muscle repair, moderation of inflammation, and oxidative metabolism.
A comparison of software cost, duration, and quality for waterfall vs. iterative and incremental development: A systematic review (2009)

The objective of this study is to present a body of evidence that will assist software project managers to make informed choices about software development approaches for their projects. In particular, two broadly defined competing approaches, the traditional ldquowaterfallrdquo approach and iterative and incremental development (IID), are compared with regards to development cost and duration, and resulting product quality. The method used for this comparison is a systematic literature review. The small set of studies we located did not demonstrate any identifiable cost, duration, or quality trends, although there was some evidence suggesting the superiority of IID (in particular XP). The results of this review indicate that further empirical studies, both quantitative and qualitative, on this topic need to be undertaken. In order to effectively compare study results, the research community needs to reach a consensus on a set of comparable parameters that best assess cost, duration, and quality.
Learning from imperfect data in theory and practice (1996)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1996.
Towards high spatially resolved microproteomics using expansion microscopy (2021)

Abstract Expansion microscopy is an emerging approach for morphological examination of biological specimens at nanoscale resolution using conventional optical microscopy. To achieve physical separation of cell structures, tissues are embedded in a swellable polymer and expanded several folds in an isotropic manner. This work shows the development and optimization of physical tissue expansion as a new method for spatially resolved large scale proteomics. Herein, we established a novel method to enlarge the tissue section to be compatible with manual microdissection on regions of interest and to carry out MS-based proteomic analysis. A major issue in the Expansion microscopy is the loss of proteins information during the mechanical homogenization phase due to the use of Proteinase K. For isotropic expansion, different homogenization agents are investigated, both to maximize protein identification and to minimize protein diffusion. Better results are obtained with SDS. From a tissue section enlarge more than 3-fold, we have been able to manually cut out regions of 1mm in size, equivalent to 300µm in their real size. We identified up to 655 proteins from a region corresponding to an average of 940 cells. This approach can be performed easily without any expensive sampling instrument. We demonstrated the compatibility of sample preparation for expansion microscopy and proteomic study in a spatial context. Abstract graphic
Increased bone mineral content but not bone mineral density in the hip in surgically treated knee and hip osteoarthritis. (2005)

Hip BMD of women treated surgically for hip or knee OA was not different from that of healthy controls when measured twice with a 5-year interval. However, at 5-year followup, OA can be accompanied by an increase in bone size or changes in shape, and faster loss of BMD.
Excitation‐contraction coupling in skeletal muscle fibers injected with the InsP3blocker, heparin (1988)

Heparin, an inhibitor of inositol trisphosphate (InsP3)-induced Ca2+ release in smooth muscle and non-muscle cells, was injected into intact frog skeletal muscle fibres. Ca2+ release from the sarcoplasmic reticulum was elicited by the normal action potential mechanism and monitored by both fura-2 fluorescence and an intrinsic birefringence signal. Both optical signals, and hence Ca2+ release, were unaffected by high concentrations of heparin. This result argues against a major physiological role of InsP3 as a chemical messenger of excitation-contraction coupling in skeletal muscle.
Synthesis of an antimony rhodamine analog (2022)

We describe the synthesis, structure and characterization of an antimony-rhodamine derivative with a phenyl-antimony moiety installed at the 10' position of the central ring. This compound is a red fluorophore (λem = 655 nm) with a quantum yield of 12% in acetonitrile.
Ecological Consciousness as One of the Main Principles of Ecological Policy (2017)

The article presents the concept of ecological consciousness and analyzes main features of its development and implementation in the environmental policy in European practice on the example of Germany. The study of German experience is conditioned by the fact that among the other developed countries of the world Germany is the leading country in its active work carried out at all levels of the environmental policy. It is shown that actions aimed at the development of ecological culture and environmental education of the civil society in Germany are of the same priority as the use of renewable energy, development of green technologies, etc. The article provides an overview of the most important publications devoted to the phenomenon of ecological consciousness and highlights different approaches to this definition. Based on the German experience, it defines the prerequisites, main roots and sources of ecological consciousness creation and the ways in which it can be involved in the regional programs on sustainable development and ecological policy. It analyzes the main practical approaches to the implementation of the principles of ecological consciousness in Germany as well as the role of environmental organizations in the realization of environmentally oriented activities. Therefore, it presents the main results of socio-ecological surveys conducted in Germany and Russia and gives their comparative analysis. It indicates possible ways to transfer the German experience in the Russian context to improve the ecological awareness of the Russian society and to arise its ecological activity in addressing environmental issues.
Iterative Supervised Principal Component Analysis-Driven Ligand Design for Regioselective Ti-Catalyzed Pyrrole Synthesis (2020)

Herein, we describe the use of iterative supervised principal component analysis (ISPCA) in de novo catalyst design. The regioselective synthesis of 2,5-dimethyl-1,3,4-triphenyl-1H- pyrrole (C) via Ti- catalyzed formal [2+2+1] cycloaddition of phenyl propyne and azobenzene was targeted as a proof of principle. The initial reaction conditions led to an unselective mixture of all possible pyrrole regioisomers. ISPCA was conducted on a training set of catalysts, and their performance was regressed against the scores from the top three principal components. Component loadings from this PCA space along with k-means clustering were used to inform the design of new test catalysts. The selectivity of a prospective test set was predicted in silico using the ISPCA model, and only optimal candidates were synthesized and tested experimentally. This data-driven predictive-modeling workflow was iterated, and after only three generations the catalytic selectivity was improved from 0.5 (statistical mixture of products) to over 11 (> 90% C) by incorporating 2,6-dimethyl- 4-(pyrrolidin-1-yl)pyridine as a ligand. The successful development of a highly selective catalyst without resorting to long, stochastic screening processes demonstrates the inherent power of ISPCA in de novo catalyst design and should motivate the general use of ISPCA in reaction development.
Desiccant Enhanced Evaporative Air-Conditioning (DEVap): Evaluation of a New Concept in Ultra Efficient Air Conditioning (2011)

NREL has developed the novel concept of a desiccant enhanced evaporative air conditioner (DEVap) with the objective of combining the benefits of liquid desiccant and evaporative cooling technologies into an innovative 'cooling core.' Liquid desiccant technologies have extraordinary dehumidification potential, but require an efficient cooling sink. DEVap's thermodynamic potential overcomes manyshortcomings of standard refrigeration-based direct expansion cooling. DEVap decouples cooling and dehumidification performance, which results in independent temperature and humidity control. The energy input is largely switched away from electricity to low-grade thermal energy that can be sourced from fuels such as natural gas, waste heat, solar, or biofuels.
Efficient Processing of Uncertain Events in Rule-Based Systems (2010)

There is a growing need for systems that react automatically to events. While some events are generated externally and deliver data across distributed systems, others need to be derived by the system itself based on available information. Event derivation is hampered by uncertainty attributed to causes such as unreliable data sources or the inability to determine with certainty whether an event has actually occurred, given available information. Two main challenges exist when designing a solution for event derivation under uncertainty. First, event derivation should scale under heavy loads of incoming events. Second, the associated probabilities must be correctly captured and represented. We present a solution to both problems by introducing a novel generic and formal mechanism and framework for managing event derivation under uncertainty. We also provide empirical evidence demonstrating the scalability and accuracy of our approach.
Biochemical Characterization and Localization of a Non‐N‐Methyl‐D‐Aspartate Glutamate Receptor in Rat Brain (1992)

The structure and distribution of non-N-methyl-D-aspartate glutamate receptors in the rat brain were studied using subunit-specific antibodies that recognize the receptor subunit GluR1. The GluR1 protein, a 106-kDa glycoprotein, appears predominantly in synaptic plasma membranes, where it is highly enriched in the postsynaptic densities. When synaptic plasma membranes are solubilized with the detergent 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate, high-affinity alpha-amino-3-hydroxy-5-methylisoxazole-4-propionate (AMPA) binding and GluR1 immunoreactivity comigrate at a native Mr of 610,000. GluR1 is enriched in the hippocampus and cerebellar cortex but is present throughout the CNS. It is found on neuronal cell bodies and processes within most regions of the brain; within the cerebellum, however, it is localized to the Bergmann glia. These data suggest that the GluR1 protein is a subunit of multimeric AMPA-preferring glutamate receptors present on neurons and on specialized glia.
Impact de l’irradiation par électrons accélérés sur des biomatériaux injectables à base de polyméthacrylate / polyméthacrylamide pour l’embolisation (2010)

Ce travail porte sur l’etude des effets de l’irradiation sur des biomateriaux injectables par voie endovasculaire a base de copolymeres lineaire et reticule. Dans le cas du polymere lineaire, l’etude des masses molaires nous a permis de calculer les taux de scission et de reticulation et a reveler l’occurrence de degradation principalement par reaction scission au niveau des chaines macromoleculaires. L’etude du polymere reticule etait en revanche plus complexe et a necessite une approche plus structurale, portee sur l’evolution de la mobilite moleculaire du polymere avec l’irradiation. La relaxation beta () qui exprime le mouvement des groupes polaires lateraux ester et amide s’est montree comme un excellent indicateur des reactions de radiodegradation du polymere. Une perturbation dans les interactions par liaison hydrogene impliquant ces groupements apres irradiation a ete observe. Ce comportement a ete associe a la formation de produits de degradations polaires amorces par le depart des chaines laterales qui est a l’origine des mecanismes de radioscission du polymere.
Dual energy contrast enhanced X-ray CT characterization of malignancies from single acquisition data sets (2014)

Contrast agents in CT and MRI investigations have been used for obtaining better diagnosis, including whether a nodule in the breast is benign or malignant. Cone beam CT images of breast cancer nodules have been taken with iodine contrast enhancement using two CT data sets, before and after iodine contrast injection. After the CT reconstructions, by subtracting the pre-contrast HU values from those obtained with iodine contrast at the nodules, the contrast enhancement values of the suspicious nodules were obtained. This article describes a method of determining mean “quantitative imaging biomarker” values such as calibrated mean contrast concentrations of enhancement agents like iodine contrast agents in X-ray CT in segmented nodules identified using X-ray CT image data obtained in a single CT data set acquisitions instead of using two datasets (before and after contrast agent injection). This method can be applied to different organs and/or different contrast agents by using dual energy values optimized for the given cases by carefully calibrating the CT values for each energy pair.
Virtualizing performance asymmetric multi-core systems (2011)

Performance-asymmetric multi-cores consist of heterogeneous cores, which support the same ISA, but have different computing capabilities. To maximize the throughput of asymmetric multi-core systems, operating systems are responsible for scheduling threads to different types of cores. However, system virtualization poses a challenge for such asymmetric multi-cores, since virtualization hides the physical heterogeneity from guest operating systems. In this paper, we explore the design space of hypervisor schedulers for asymmetric multi-cores, which do not require asymmetry-awareness from guest operating systems. The proposed scheduler characterizes the efficiency of each virtual core, and map the virtual core to the most area-efficient physical core. In addition to the overall system throughput, we consider two important aspects of virtualizing asymmetric multi-cores: performance fairness among virtual machines and performance scalability for changing availability of fast and slow cores.
Unified representation of genetic variants (2015)

Supplementary data are available at Bioinformatics online.
Bringing 3D COTS DRAM Memory Cubes to Space (2019)

This paper details the architectural choices and implementation challenges faced in the building and validation of a space-qualified 3D DRAM memory system, in an effort to offer high memory capacity, increased bandwidth, fault tolerance and improved size-weight-and-power characteristics needed for harsh space mission environments. Our novel horizontal 3D stacking technology called “Loaf-Of-Bread” (LOB) is used to integrate multiple Commercial-Off-The-Shelf (COTS) DRAM memory dies into a cube structure (3D-M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ). A custom Radiation-Hardened-By-Design (RHBD) controller sitting underneath the cube supplements the 3D-M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> in addressing COTS radiation weaknesses by including advanced SEU and SEFI mitigation features such as error detection and correction, scrubbing, device data rebuilding and die management. We developed a custom DDR physical layer (PHY) for 14 independent dies to connect the 3D-M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> to its controller. Validation and functional evaluation of the ASIC controller will be conducted prior to tape-out on a custom FPGA-based emulator platform integrating the 3D-stack. The selected test methodology ensures high-quality RTL as well as allows to subject the cube structure to radiation testing. The proposed design concept allows for flexibility in the choice of the DRAM die in case of technology roadmap changes or unsatisfactory radiation results.
Morphological Inflection Generation Using Character Sequence to Sequence\n Learning (2015)

Morphological inflection generation is the task of generating the inflected\nform of a given lemma corresponding to a particular linguistic transformation.\nWe model the problem of inflection generation as a character sequence to\nsequence learning problem and present a variant of the neural encoder-decoder\nmodel for solving it. Our model is language independent and can be trained in\nboth supervised and semi-supervised settings. We evaluate our system on seven\ndatasets of morphologically rich languages and achieve either better or\ncomparable results to existing state-of-the-art models of inflection\ngeneration.\n
Faculty Opinions recommendation of Cell and fibronectin dynamics during branching morphogenesis. (2006)

Branching morphogenesis is a dynamic developmental process shared by many organs, but the mechanisms that reorganize cells during branching morphogenesis are not well understood. We hypothesized that extensive cell rearrangements are involved, and investigated cell migration using two-color confocal time-lapse microscopy to image cell and extracellular-matrix dynamics in developing salivary glands. We labeled submandibular salivary gland (SMG) epithelial cells with green fluorescent protein and matrix with fluorescent fibronectin. Surprisingly, we observed substantial, rapid and relatively random migration of individual epithelial cells during branching morphogenesis. We predicted that cell migration would decrease after formation of acini and, indeed, found that rapid cell movements do not occur in SMG from newborn mice. However, in embryonic SMG epithelial cells, we observed an absence of choreographed cell migration, indicating that patterned cell migration alone cannot explain the highly ordered process of branching morphogenesis. We therefore hypothesized a role for directional fibronection assembly in branching. Washout and pulse-chase experiments revealed that older fibronectin accumulates at the base of the clefts and translocates inwards as a wedge, with newer fibronectin assembling behind it. These findings identify a new mechanism for branching morphogenesis involving directional fibronectin translocation superimposed on individual cell dynamics. PMID: 16882689 Funding information This work was supported by: Intramural NIH HHS, United States