gebhart/patrepeval huggingface dataset:
B-trees, Shadowing, and Clones. (2007)

B-trees are used by many file-systems to represent files and directories. They provide guarantied logarithmic time key-search, insert, and remove. File systems like WAFL and ZFS use shadowing, or copy-on-write, to implement snapshots, crash-recovery, write-batching and RAID. Serious difficulties arise when trying to use b-trees and shadowing in a single system. This paper is about a set of b-tree algorithms that respects shadowing, achieves good concurrency, and implements cloning (writeable-snapshots). Our cloning algorithm is efficient and allows the creation of a large number of clones. We believe that using our b-trees would allow shadowing file-systems to scale their on-disk data structures better.
Translational control of 5-aminolevulinate synthase mRNA by iron-responsive elements in erythroid cells. (1993)

Hemoglobin synthesis in red cells is the major iron utilization pathway in the human body and accounts for > 80% of systemic iron turnover. The first step in erythroid heme biosynthesis is catalyzed by a tissue-specific isoform of 5-aminolevulinate synthase (ALAS). The previous identification of iron-responsive elements in the 5'-untranslated region of human and murine erythroid ALAS mRNA raised the intriguing possibility that eALAS expression might be under iron-dependent translational control. As a consequence, a single post-transcriptional regulatory system could coordinate cellular iron acquisition via the transferrin receptor, storage via ferritin, and utilization via eALAS. We directly demonstrate iron-dependent translational regulation of eALAS mRNA in murine erythroleukemia (MEL) cells. The iron-responsive element motif contained in eALAS mRNA is shown to be sufficient to confer translational control to a reporter mRNA both in transfected MEL cells and in vitro.
Non-Contacting Electro-Optical Contouring of Helicopter Rotor Blades. (1978)

Abstract : Non-contact contour measurements of helicopter rotor blades to accuracies of 0.001 inch are possible via rangefinding by triangulation employing electro-optical techniques. A prototype of a portion of such a system has been built and tested. The result of these tests indicate that the construction of the full prototype system is feasible and desirable. (Author)
Altered vascular remodeling in fibulin-5-deficient mice reveals a role of fibulin-5 in smooth muscle cell proliferation and migration (2005)

Fibulin (fbln)-5 is an elastin-binding protein required for assembly and organization of elastic fibers. To examine the potential role of fbln-5 in vascular remodeling and neointima formation, we induced vascular injury by carotid artery ligation in fbln-5(-/-) mice. Mutant mice displayed an exaggerated vascular remodeling response that was accompanied by severe neointima formation with thickened adventitia. These abnormalities were not observed in elastin(+/-) mice that exhibited a comparable reduction of vessel extensibility to fbln-5(-/-) mice. Thus, the severe remodeling response could not be attributed to altered extensibility of the vessel wall alone. Vascular smooth muscle cells cultured from fbln-5(-/-) mice displayed enhanced proliferative and migratory responses to mitogenic stimulation relative to wild-type cells, and these responses were inhibited by overexpression of fbln-5. These findings demonstrate the importance of the elastic laminae in vascular injury, and reveal an unexpected role of fbln-5 as an inhibitor of vascular smooth muscle cell proliferation and migration.
Emotional and neurocognitive deficits in fragile X (1994)

We have studied the neurocognitive deficit in premutation and full mutation women as compared to control women and to explore the relationship between those deficits and the incidence of emotional problems. Four groups of women were examined: two fragile X (fra(X)) negative control groups, one of which grew up in fra(X) families and one not; and two DNA positive groups, one with a premutation (CGG repeats < 200) and one with an expanded mutation (CGG repeats > 200). All women were assessed using the MMPI-2, the SADS-L, and a battery of neuropsychological tests. Full mutation women had lower scores on composite measures of executive function and nonverbal function. There was no difference between the groups in terms of the lifetime incidence of depressive and anxiety disorders on the SADS-L. Full mutation women displayed Lie scales higher than the other groups on the MMPI-2. Neurocognitive measures were not related to SADS-L diagnoses but were related to the Lie scale on the MMPI-2. Finally, number of CGG repeats was related to the neuropsychological variables and the Lie scale.
Chemically-defined induction of a primitive endoderm and epiblast-like niche supports post-implantation progression from blastoids (2019)

Abstract The early mammalian conceptus (blastocyst) contains two supporting extraembryonic tissues - the trophectoderm and the primitive endoderm (PrE) - that encase and guide the epiblast (Epi) to eventually form the all body. Modifications of the conceptus exposed key genes regulating these tissues co-development. However, the combinations of signalling pathways underlying the interplay of PrE and Epi remains elusive. Stem cell-based models including embryoid bodies and blastoids can be generated in large numbers and subjected to high-content screens. Here, we use combinatorial screens of proteins, GPCR ligands and small molecules to rapidly (72 hours) and efficiently (80%) guide embryoid bodies to form a three-dimensional PrE-/Epiblast-like niche in chemically-defined conditions (gel-free, serum-free). This bipotent niche spontaneously progresses, without growth factors, to form a pro-amniotic cavity surrounded by a polarized Epi covered with parietal and visceral endoderm-like cells. In blastoids, these molecules enhance the ratio and number of Gata6+/Nanog+ cells and promote the survival, expansion and morphogenesis of a post-implantation-like Epi in vitro . Altogether, modelling early development in chemically-defined conditions delineates the pathways sufficient to form a functional PrE/Epiblast niche that fuels post-implantation development.
Cyclophilin40 isomerase activity is regulated by a temperature-dependent allosteric interaction with Hsp90 (2015)

Cyclophilin 40 (Cyp40) comprises an N-terminal cyclophilin domain with peptidyl-prolyl isomerase (PPIase) activity and a C-terminal tetratricopeptide repeat (TPR) domain that binds to the C-terminal-EEVD sequence common to both heat shock protein 70 (Hsp70) and Hsp90. We show in the present study that binding of peptides containing the MEEVD motif reduces the PPIase activity by ∼30%. CD and fluorescence assays show that the TPR domain is less stable than the cyclophilin domain and is stabilized by peptide binding. Isothermal titration calorimetry (ITC) shows that the affinity for the-MEEVD peptide is temperature sensitive in the physiological temperature range. Results from these biophysical studies fit with the MD simulations of the apo and holo (peptide-bound) structures which show a significant reduction in root mean square (RMS) fluctuation in both TPR and cyclophilin domains when-MEEVD is bound. The MD simulations of the apo-protein also highlight strong anti-correlated motions between residues around the PPIase-active site and a band of residues running across four of the seven helices in the TPR domain. Peptide binding leads to a distortion in the shape of the active site and a significant reduction in these strongly anti-correlated motions, providing an explanation for the allosteric effect of ligand binding and loss of PPIase activity. Together the experimental and MD results suggest that on heat shock, dissociation of Cyp40 from complexes mediated by the TPR domain leads to an increased pool of free Cyp40 capable of acting as an isomerase/chaperone in conditions of cellular stress.
TR assay validation—Lineweaver-Burk plots for known inhibitors. (2015)

&lt;p&gt;The K&lt;sub&gt;&lt;b&gt;i&lt;/b&gt;&lt;/sub&gt; values were determined by three independent experiments. &lt;b&gt;Mepacrine:&lt;/b&gt; measured Ki 20.71 ± 5.47 μM, competitive binding mode; &lt;b&gt;BG237:&lt;/b&gt; measured Ki 42.13 ± 4.38 μM, noncompetitive binding mode, partial. The factor beta reflects the modification of the rate of product formation by the enzyme that is caused by the inhibitor. &lt;b&gt;Chlorhexidine:&lt;/b&gt; measured Ki 6.13 ± 1.65 μM, competitive binding mode. Graphs are created using the SigmaPlot Enzyme Kinetics Module routine based on the relevant binding models and the calculated parameter values.&lt;/p&gt;
Accuracy of the Microsoft Kinect sensor for measuring movement in people with Parkinson's disease (2014)

The Kinect can accurately measure timing and gross spatial characteristics of clinically relevant movements but not with the same spatial accuracy for smaller movements, such as hand clasping.
Composition of Grape Skin Proanthocyanidins at Different Stages of Berry Development (2001)

The composition of grape (Vitis vinifera L. cv. Shiraz) skin proanthocyanidins has been determined at different stages of berry development. Beginning approximately 3 weeks after fruit set and concluding at commercial ripeness, the composition of isolated skin proanthocyanidins was determined using the following analytical techniques: elemental analysis, UV-Vis absorption spectroscopy, reversed-phase HPLC after acid-catalysis in the presence of excess phloroglucinol, gel permeation chromatography, electrospray ionization mass spectrometry (ESI-MS), and (13)C NMR. On the basis of these analyses, berry development was correlated with an increase in proanthocyanidin mean degree of polymerization, an increase in the proportion of (-)-epigallocatechin extension subunits, and increases in the level of anthocyanins associated with the proanthocyanidin fraction. Additionally, data acquired from ESI-MS of the isolates following acid-catalysis in the presence of excess phloroglucinol is consistent with pectin-bound proanthocyanidins.
Adding capability checks enhances error detection and isolation in object-based systems (2002)

Error detection and error isolation are becoming stringent requirements for many computational problems requiring high reliability in addition to high performance. This paper presents CAPACETI, a technique for utilizing capabilities at the application level in order to achieve dependable operations. The proposed technique is further augmented with executable assertions and other software error detection techniques. The effectiveness of the techniques to detect errors, their contribution to the overall coverage, and their performance overhead were experimentally obtained using fault/error injection. Results obtained from these experiments show that high coverage with a low performance overhead can be achieved by selectively combining different error detection techniques.
Activity of Empty, Headlike Particles for Packaging of DNA of Bacteriophage λ In Vitro (1974)

A precursor head of phage lambda is synthesized after induction of cells lysogenic for λ D - F - and λ A - (head-defective) mutants. This precursor head can be assayed by complementation in vitro and can be purified by CsCl gradient centrifugation and sucrose gradient sedimentation. The precursor head contains no DNA and has the same dimensions as the petit λ particle. It can be packed with λ DNA in an extract from induced Escherichia coli lysogenic for a λ E - mutant.
Dye-enhanced multimodal confocal microscopy for noninvasive detection of skin cancers in mouse models (2010)

Skin cancer is the most common form of human cancer. Its early diagnosis and timely treatment is of paramount importance for dermatology and surgical oncology. In this study, we evaluate the use of reflectance and fluorescence confocal microscopy for detecting skin cancers in an in-vivo trial with B16F10 melanoma and SCCVII squamous cell carcinoma in mice. For the experiments, the mice are anesthetized, then the tumors are infiltrated with aqueous solution of methylene blue and imaged. Reflectance images are acquired at 658 nm. Fluorescence is excited at 658 nm and registered in the range between 690 and 710 nm. After imaging, the mice are sacrificed. The tumors are excised and processed for hematoxylin and eosin histopathology, which is compared to the optical images. The results of the study indicate that in-vivo reflectance images provide valuable information on vascularization of the tumor, whereas the fluorescence images mimic the structural features seen in histopathology. Simultaneous dye-enhanced reflectance and fluorescence confocal microscopy shows promise for the detection, demarcation, and noninvasive monitoring of skin cancer development.
Graft modification of cellulose nanocrystals via nitroxide-mediated polymerisation (2016)

Cellulose nanocrystals were graft modfied with PMA and PMMA <italic>via</italic> nitroxide mediated polymerisation.
Spectromicroscopy of tantalum oxide memristors (2011)

We report experiments to measure material changes in tantalum oxide-based memristive devices. The high endurance and low power demonstrated in this material system suggests a unique mechanism for the switching, which we investigated using x-ray based spectromicroscopy and nanospectroscopy. Our study nondestructively identified a localized (&amp;lt;150nm diameter) Ta-rich phase surrounded by nano- or polycrystalline Ta2O5.
Immunotherapy Targeting α-Synuclein, with Relevance for Future Treatment of Parkinson‘s Disease and Other Lewy Body Disorders (2014)

Immunotherapy targeting α-synuclein has evolved as a potential therapeutic strategy for neurodegenerative diseases, such as Parkinson's disease, and initial studies on cellular and animal models have shown promising results. α-synuclein vaccination of transgenic mice reduced the number of brain inclusions, whereas passive immunization studies demonstrated that antibodies against the C-terminus of α-synuclein can pass the blood-brain barrier and affect the pathology. In addition, preliminary evidence suggests that transgenic mice treated with an antibody directed against α-synuclein oligomers/protofibrils resulted in reduced levels of such species in the CNS. The underlying mechanisms of immunotherapy are not yet fully understood, but may include antibody-mediated clearance of pre-existing aggregates, prevention of protein propagation between cells and microglia-dependent protein clearance. Thus, immunotherapy targeting α-synuclein holds promise, but needs to be further developed as a future disease-modifying treatment in Parkinson's disease and other α-synucleinopathies.
On-Line Synthesis of Pseudopeptide Library Incorporating a Benzodiazepinone Turn Mimic:  Biological Evaluation on MC1 Receptors (2006)

Alpha melanocyte stimulating hormone (alpha-MSH) is a widely distributed hormone. This tridecapeptide exhibits various biological activities mediated through different receptors. alpha-MSH binds to the melanocortin-1 receptor (MC1-R), mainly expressed in keratinocytes and melanocytes, inducing melanogenesis and anti-inflammatory processes. The central His-Phe-Arg-Trp tetrapeptide sequence of alpha-MSH is known to form a turn in the bioactive conformation. To find new potent analogs of alpha-MSH, we decided to introduce non-peptide building blocks in the alpha-MSH sequence. Molecular modeling studies showed that two amino acids of the central core sequence could be replaced by the benzodiazepinone building block without loosing the beta-turn conformation. Benzodiazepines are well-known pharmacophores exhibiting a wide scope of biological activities and are described as constrained dipeptide mimics templates. Although numerous synthetic pathways leading to benzodiazepinones have been described in literature, no methodology has 1,4-benzodiazepine-2,5-diones building blocks bearing a free carboxylic acid function and a protected amino function suitable for incorporation into peptide sequences. In this study, we report the synthesis of peptides with a benzodiazepinone moiety obtained directly during the course of solid-phase peptide synthesis (SPPS). This "on-line" strategy leads to the generation of a 54-member pseudo-peptide library of alpha-MSH analogs. After LC/MS purification, binding assays were performed on the MC1 receptor leading to the discovery of several micromolar ligands.
Illuminating Shadows: The Power of Learning by Observing (2019)

"Shadowing" refers to the practice of a student following an instructor. Although the term implies less light, rather than more, shadowing as an instructional modality in medical education can illuminate, stimulate, and move students to emulate what they might otherwise never observe. In this Invited Commentary, the author reports on a teaching encounter in the office in which shadowing was the principal modality used. This modality is situated within the spectrum of approaches to learning-from experiential learning to passive learning. Based upon personal experience as both a teacher and learner, the author identifies the unique value of shadowing, including its value in influencing career choice.
Saliva Diagnosis as a Disease Predictor (2020)

It is concluded that measuring changes in essential gene products in saliva can predict onset of fatal diseases and open the door to effective protection measures, thus preventing premature death.
Evaluating a content based image retrieval system (2001)

Content Based Image Retrieval (CBIR) presents special challenges in terms of how image data is indexed, accessed, and how end systems are evaluated. This paper discusses the design of a CBIR system that uses global colour as the primary indexing key, and a user centered evaluation of the systems visual search tools. The results indicate that users are able to make use of a range of visual search tools, and that different tools are used at different points in the search process. The results also show that the provision of a structured navigation and browsing tool can support image retrieval, particularly in situations in which the user does not have a target image in mind. The results are discussed in terms of their implications for the design of visual search tools, and their implications for the use of user-centered evaluation for CBIR systems.
A multiscale method for parameter estimation in reservoir simulation (2007)

Abstract We consider a multiscale approach to the problem of parameter estimation or history matching in reservoir simulation. To do this, we look at the problem upscaling as the most important component of the proposed method. For upscaling we suggest a global approach which seeks to minimize the misfit between fine scale and coarse scale simulations and then used the Simultaneous Perturbation Stochastic Approximation (SPSA) method to deal with the minimization process. The essential idea of multiscale history matching comsists of constructing a coarsening sequence of models, so that each one of them minimizes the misfit between preditctions and observations. Then, the cosarsest model is downscaled one step into the sequence and used as an initial guess for the next step of refinement. The process is repeated until no improvement is observed in the solution. Numerical experiment indicate that this approach produces consistent results. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
CNN-Aided Factor Graphs with Estimated Mutual Information Features for Seizure Detection (2022)

We propose a convolutional neural network (CNN) aided factor graphs assisted by mutual information features estimated by a neural network for seizure detection. Specifically, we use neural mutual information estimation to evaluate the correlation between different electroencephalogram (EEG) channels as features. We then use a 1D-CNN to extract extra features from the EEG signals and use both features to estimate the probability of a seizure event. Finally, learned factor graphs are employed to capture the temporal correlation in the signal. Both sets of features from the neural mutual estimation and the 1D-CNN are used to learn the factor nodes. We show that the proposed method achieves state-of-the-art performance using 6-fold leave-four-patients-out cross-validation.
Light hydrocarbon gas conversion using halogenated porphyrin catalysts (1994)

Enzymes such at the cytochromes P450 are known to catalyze the partial oxidation of unactivated alkanes to alcohols. Analysis of these natural systems indicates structural features needed to create a biomimetic catalyst which will mimic the enzyme`s high catalytic activity and selectivity. Metalloporphyrins have been reported to catalyze the oxidation of light alkanes to alcohols under mild conditions using molecular oxygen as the oxidant without the need for added co-reductant. The authors are attempting to develop more active catalysts for this process, toward the goal of obtaining a catalyst which is active enough to convert methane to methanol. They are using computer-aided molecular design (CAMD) in conjunction with activity testing to develop improved metalloporphyrin catalysts. The authors stepwise approach to catalyst development involves first using CAMD techniques to design potential porphyrin catalysts, followed by the synthesis and characterization of promising catalysts, and finally subjecting these catalysts to bench scale activity testing. Catalyst testing experiments give insights into important structure-activity relationships which are used to evaluate and refine their modeling tools so that better catalysts can be developed.
Real-time timbre analysis as a technique for live synthesis control (2004)

The possibility is explored of controlling synthesis using an instrumental or other sound source, not by trying to recreate the time-varying timbre of the musician’s sound exactly, but instead by making the output sound reflect changes in the input, in a way a musician can control in order to produce an interesting stream of synthetic sound. First the range of spectra available from the sound source, and also that available from the synthesis technique, are estimated. A very simple measure of timbre is used that maps any sound into a point in a ten-dimensional space. (As a byproduct, the ten-dimensional volume spanned by a sound source gives a rough measure of timbral variability.) Then synthesis parameters are chosen for the synthesis algorithm by searching a database of known output timbres.