gebhart/patrepeval huggingface dataset:
Developments in dynamic MR elastography for in vitro biomechanical assessment of hyaline cartilage under high‐frequency cyclical shear (2007)

The design, construction, and evaluation of a customized dynamic magnetic resonance elastography (MRE) technique for biomechanical assessment of hyaline cartilage in vitro are described. For quantification of the dynamic shear properties of hyaline cartilage by dynamic MRE, mechanical excitation and motion sensitization were performed at frequencies in the kilohertz range. A custom electromechanical actuator and a z-axis gradient coil were used to generate and image shear waves throughout cartilage at 1000-10,000 Hz. A radiofrequency (RF) coil was also constructed for high-resolution imaging. The technique was validated at 4000 and 6000 Hz by quantifying differences in shear stiffness between soft ( approximately 200 kPa) and stiff ( approximately 300 kPa) layers of 5-mm-thick bilayered phantoms. The technique was then used to quantify the dynamic shear properties of bovine and shark hyaline cartilage samples at frequencies up to 9000 Hz. The results demonstrate that one can obtain high-resolution shear stiffness measurements of hyaline cartilage and small, stiff, multilayered phantoms at high frequencies by generating robust mechanical excitations and using large magnetic field gradients. Dynamic MRE can potentially be used to directly quantify the dynamic shear properties of hyaline and articular cartilage, as well as other cartilaginous materials and engineered constructs.
SmartScope2: Simultaneous Imaging and Reconstruction of Neuronal Morphology (2017)

Quantitative analysis of neuronal morphology is critical in cell type classification and for deciphering how structure gives rise to function in the brain. Most current approaches to imaging and tracing neuronal 3D morphology are data intensive. We introduce SmartScope2, the first open source, automated neuron reconstruction machine integrating online image analysis with automated multiphoton imaging. SmartScope2 takes advantage of a neuron's sparse morphology to improve imaging speed and reduce image data stored, transferred and analyzed. We show that SmartScope2 is able to produce the complex 3D morphology of human and mouse cortical neurons with six-fold reduction in image data requirements and three times the imaging speed compared to conventional methods.
Electron transport in edge-disordered graphene nanoribbons (2011)

We report an electron transport study of lithographically fabricated graphene nanoribbons (GNRs) of various widths and lengths. At the charge neutrality point, a length-independent transport gap forms whose size is inversely proportional to the GNR width. In this gap, electrons are localized, and charge transport exhibits a transition between thermally activated behavior at higher temperatures and variable range hopping at lower temperatures. By varying the geometric capacitance, we find that charging effects constitute a significant portion of the activation energy.
Glucose and fructose to platform chemicals: understanding the thermodynamic landscapes of acid-catalysed reactions using high-level ab initio methods (2012)

Molecular level understanding of acid-catalysed conversion of sugar molecules to platform chemicals such as hydroxy-methyl furfural (HMF), furfuryl alcohol (FAL), and levulinic acid (LA) is essential for efficient biomass conversion. In this paper, the high-level G4MP2 method along with the SMD solvation model is employed to understand detailed reaction energetics of the acid-catalysed decomposition of glucose and fructose to HMF. Based on protonation free energies of various hydroxyl groups of the sugar molecule, the relative reactivity of gluco-pyranose, fructo-pyranose and fructo-furanose are predicted. Calculations suggest that, in addition to the protonated intermediates, a solvent assisted dehydration of one of the fructo-furanosyl intermediates is a competing mechanism, indicating the possibility of multiple reaction pathways for fructose to HMF conversion in aqueous acidic medium. Two reaction pathways were explored to understand the thermodynamics of glucose to HMF; the first one is initiated by the protonation of a C2-OH group and the second one through an enolate intermediate involving acyclic intermediates. Additionally, a pathway is proposed for the formation of furfuryl alcohol from glucose initiated by the protonation of a C2-OH position, which includes a C-C bond cleavage, and the formation of formic acid. The detailed free energy landscapes predicted in this study can be used as benchmarks for further exploring the sugar decomposition reactions, prediction of possible intermediates, and finally designing improved catalysts for biomass conversion chemistry in the future.
Prediction with local patterns using cross-entropy (1999)

Sets of local patterns in the forms of rules and co-occurrence counts are produced by many data mining methods such as association rule algorithms.
Mycobacterial Carbohydrate Antigens for Serological Testing of Patients with Leprosy (1987)

To determine whether quantitation of antibodies to mycobacterial carbohydrate determinants would be valuable in serodiagnosis and monitoring of leprosy, we tested serum IgM antibody to Mycobacterium leprae phenolic glycolipid I and IgM and IgG antibodies to Mycobacterium tuberculosis and M. leprae lipoarabinomannan (LAM) by enzyme-linked immunosorbent assay. Seventy-one percent of patients with paucibacillary disease and 85.5% of patients with multibacillary disease were positive for at least one of the three antibodies. The 15% of antibody-negative patients with multibacillary disease were mostly long-term-treated patients, with inactive disease by biopsy. There was excellent agreement between M. tuberculosis LAM and M. leprae LAM in detection of antibodies. Bacillary index and levels of both IgG and IgM antibodies to LAM were positively correlated when all patients were analyzed. When patients with a history of erythema nodosum leprosum (ENL) were analyzed separately, there was no correlation between IgM or IgG antibody to LAM and bacillary index, a result suggesting a possible role for LAM in the pathogenesis of ENL.
A “Learned” Approach to Quicken and Compress Rank/Select Dictionaries (2021)

We address the well-known problem of designing, implementing and experimenting compressed data structures for supporting rank and select queries over a dictionary of integers. This problem has been studied far and wide since the end of the ‘80s with tons of important theoretical and practical results. Following a recent line of research on the so-called learned data structures, we first show that this problem has a surprising connection with the geometry of a set of points in the Cartesian plane suitably derived from the input integers. We then build upon some classical results in computational geometry to introduce the first “learned” scheme for implementing a compressed rank/select dictionary. We prove theoretical bounds on its time and space performance both in the worst case and in the case of input distributions with finite mean and variance. We corroborate these theoretical results with a large set of experiments over datasets originating from a variety of sources and applications (Web, DNA sequencing, information retrieval and natural language processing), and we show that a carefully engineered version of our approach provides new interesting space-time trade-offs with respect to several well-established implementations of Elias-Fano, RRR-vector, and random-access vectors of Elias γ/δ-coded gaps.
Symptoms and Quality of Life (QOL) in a Cohort of Patients with Mesenteric Panniculitis (2010)

Purpose: To measure symptom (severity and frequency) and their impact on QOL in patients with MP. Methods: The International Mesenteric Panniculitis Society is a Yahoo User group with 60 active members. Members were invited to complete an online survey using Survey Monkey (SurveyMonkey.com) from 10/26/09 to 11/13/09. All survey responses were anonymous. No additional medical history was obtained. The survey consisted of two parts; the Mesenteric Panniculitis Symptom Assessment Scale (MPSAS), and the Functional Assessment of Non-Life Threatening Conditions (FANLTC) QOL scale. The MPSAS measures frequency and severity of common symptoms of MP. The FANLTC includes physical (PWB), emotional (EWB), functional (FWB), social (SWB) and family (FWB) well-being, with higher scores indicating better QOL. Pearson's correlation was used to compare MPSAS and FANLTC scores. Results: Thirty nine (65%) questionnaires were completed. The most common symptoms reported were abdominal pain (80%), fatigue (79%), bloating (55%) and nausea (45%). Abdominal pain and/or fatigue occurred daily in 60% of patients. Mean FANTLC scores were below average when compared to other chronic conditions. FANTLC scores were negatively correlated with MPSAS for PWB (R=-0.705, p<0.05), EWB (R =-0.470, p<0.05) and FWB (R=-0.460, P<0.05). Conclusion: Frequent and severe symptoms are characteristic in community patients with MP. These impact negatively on QOL. The Internet provides new opportunities to study rare diseases.
Characterization of the Thermal Time Constants of HAMR Media (2022)

Here we describe experimental spin stand measurements as well as simulations of the time constants associated with thermal transients in heat-assisted magnetic recording (HAMR) media. The thermal transients associated with both increasing and decreasing steps in laser power contain at least two time constants each, one on the order of 1 ns and another on the order of 10 ns. These time constants are associated with the central thermal peak in the media and the diffuse thermal background, respectively. In addition, the measured thermal fall time is longer than the thermal rise time due to the disk’s motion relative to the head. Whereas in conventional HAMR a constant laser power is applied during writes, a number of proposed advanced recording schemes use pulsed laser power to improve either recording performance or reliability. The thermal time constants reported here suggest care must be taken when implementing such schemes so that transition locations are not shifted to the detriment of areal density capability.
Efficient scheduling methods for partitioned systolic algorithms (2003)

Various methods for mapping signal processing algorithms into systolic arrays have been developed in the past few years. In this paper, efficient scheduling techniques are developed for the partitioning problem, i.e. problems with size that do not match the array size. In particular, scheduling for the locally parallel-globally sequential (LPGS) technique and the locally sequential-globally parallel (LSGP) technique are developed. The scheduling procedure developed exploits the fact that after LPGS and LSGP partitioning, the locality constraints become modified allowing for more flexibility. The new structure allows the authors to develop a flexible scheduling order for LPGS that is useful in evaluating a trade-off between execution time and size of partitioning buffers. The benefits of the scheduling techniques are illustrated with the help of matrix multiplication and least-squares examples.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Direct Palladium-Catalyzed C-2 and C-3 Arylation of Indoles:  A Mechanistic Rationale for Regioselectivity [J. Am. Chem. Soc. 2005, 127, 8050−8057]. (2007)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionDirect Palladium-Catalyzed C-2 and C-3 Arylation of Indoles: A Mechanistic Rationale for Regioselectivity [J. Am. Chem. Soc. 2005, 127, 8050−8057].Benjamin S. Lane, Meghann A. Brown, and Dalibor SamesCite this: J. Am. Chem. Soc. 2007, 129, 1, 241Publication Date (Web):January 3, 2007Publication History Published online3 January 2007Published inissue 1 January 2007https://pubs.acs.org/doi/10.1021/ja0699790https://doi.org/10.1021/ja0699790correctionACS PublicationsCopyright © 2007 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views2665Altmetric-Citations5LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (10 KB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Temporary Corrosion Protection and Bond of Prestressing Steel (2008)

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Adaptive virtual model control of a bipedal walking robot (2002)

The robustness of bipedal walking robots can be enhanced by the use of adaptive control techniques. We extend a previous control approach, virtual model control (VMC) (Pratt et al., 1997), to create adaptive virtual model control (AVMC). The adaptation compensates for external disturbances and unmodelled dynamics, enhancing robustness in the control of height, pitch, and forward speed. The state machine used to modulate the virtual model components and to select the appropriate virtual to physical transformations (as in traditional VMC) is also used to inform the adaptation about the robot's changing configuration. The design procedure for AVMC is described in this paper and simulation results are presented for a planar walking biped.
Intrinsic subtype characterization of local recurrences and new contralateral primary tumors in patients with low risk breast cancer. Influence of age and primary surgery (2017)

We have recently demonstrated that the local failure rate among early-stage node-negative breast cancer patients receiving no adjuvant systemic treatment was high among young patients (≤45 years) r...
Immunolabeling of the Na+/C1− dependent “orphan” transporter Rxt1 in the rat central nervous system (1995)

Previous studies have shown that the mRNA encoding the Na+/Cl(-)-dependent "orphan" transporter Rxt1 is expressed exclusively in the central nervous system (CNS). In the present study, specific antibodies were raised in rabbits for the detailed mapping of this transporter in the rat. The C-terminal part of Rxt1 was fused with glutathione-S-transferase (Rxt1ct-GST) and the resulting fusion protein was used as antigen. The specificity of the antiserum toward Rxt1 was confirmed by immunofluorescent, Western blot, and immunoautoradiographic experiments. In cerebral cortex membranes, Rxt1-like material recognized by the antiserum is a glycosylated protein of 97-116 kDa. This protein was the most abundant in the caudate-putamen, followed, in decreasing order, by the cerebral cortex approximately hippocampus > cerebellum > brainstem > spinal cord. In contrast, no immunoreactive material could be detected in peripheral tissues (tongue, thymus, heart, lung, spleen, kidney, adrenals, liver, skeletal muscle, intestine, testis). Immunoautoradiographic labeling with affinity-purified anti-Rxt1ct-GST antibodies showed high levels of Rxt1-like material in the olfactory bulb, cerebral cortex, striatal complex, hippocampal formation, superior layer of the anterior colliculus, cortex, and deep nuclei in the cerebellum. The regional distribution of Rxt1-like material generally matched that of GABAergic and glutamatergic projections in agreement with previous in situ hybridization data.
Vascularized Osteomyocutaneous Allografts Are Permissive to Tolerance by Induction-Based Immunomodulatory Therapy (2013)

Vascularized composite allografts (VCAs) are unique among transplanted organs in that they are composed of multiple tissues with disparate antigenic and immunologic properties. As the predominant indications for VCAs are non-life-threatening conditions, there is an immediate need to develop tolerance induction strategies and to elucidate the mechanisms of VCA rejection and tolerance using VCA-specific animal models. In this study, we explore the effects of in vitro induced donor antigen-specific CD4(-) CD8(-) double negative (DN) Treg-based therapy, in a fully MHC mismatched mouse VCA such as a vascularized osteomyocutaneous as compared to a non-VCA such as a full thickness skin (FTS) transplantation model to elucidate the unique features of VCA rejection and tolerance. We demonstrate that combined therapy with antigen-induced CD4 derived DN Tregs and a short course of anti-lymphocyte serum, rapamycin and IL-2/Fc fusion protein results in donor-specific tolerance to VCA, but not FTS allografts. Macrochimerism was detected in VCA but not FTS allograft recipients up to >60 days after transplantation. Moreover, a significant increase of CD4(+) Foxp3(+) Tregs was found in the peripheral blood of tolerant VCA recipients. These data suggest that VCA are permissive to tolerance induced by DN Treg-based induction therapy.
Effect of Reinforcement on Infantsʼ Performance in a Preferential Looking Acuity Task (1988)

Two experiments examined the effect of reinforcement on infants' performance in a preferential looking acuity task. In experiment 1, performance of 3- and 5-month-old infants was assessed under three conditions. In one condition, reinforcement was contingent upon performance. In another, no reinforcement was provided. In the last condition, reinforcement was provided, but it was not contingent upon performance. Similar performance was observed in all three conditions. In experiment 2, 7-month-olds were tested in the first and second conditions. No differences in performance were observed between these two groups. Thus, the reinforcement used in preferential looking measurements does not appear to improve performance significantly for 3- to 7-month-old infants. Several interpretations of these results are presented. The most plausible is that performance under nonreinforced conditions is already nearly optimal, so the addition of reinforcement has little impact. General implications for estimates of infant visual sensitivity in the laboratory and clinic are discussed.
Catalytic conversion of cellulose to fuels and chemicals using boronic acids (2023)

Methods and catalyst compositions for formation of furans from carbohydrates. A carbohydrate substrate is heating in the presence of a 2-substituted phenylboronic acid (or salt or hydrate thereof) and optionally a magnesium or calcium halide salt. The reaction is carried out in a polar aprotic solvent other than an ionic liquid, an ionic liquid or a mixture thereof. Additional of a selected amount of water to the reaction can enhance the yield of furans.
Monkeys choose as if maximizing utility compatible with basic principles of revealed preference theory (2017)

Revealed preference theory provides axiomatic tools for assessing whether individuals make observable choices "as if" they are maximizing an underlying utility function. The theory evokes a tradeoff between goods whereby individuals improve themselves by trading one good for another good to obtain the best combination. Preferences revealed in these choices are modeled as curves of equal choice (indifference curves) and reflect an underlying process of optimization. These notions have far-reaching applications in consumer choice theory and impact the welfare of human and animal populations. However, they lack the empirical implementation in animals that would be required to establish a common biological basis. In a design using basic features of revealed preference theory, we measured in rhesus monkeys the frequency of repeated choices between bundles of two liquids. For various liquids, the animals' choices were compatible with the notion of giving up a quantity of one good to gain one unit of another good while maintaining choice indifference, thereby implementing the concept of marginal rate of substitution. The indifference maps consisted of nonoverlapping, linear, convex, and occasionally concave curves with typically negative, but also sometimes positive, slopes depending on bundle composition. Out-of-sample predictions using homothetic polynomials validated the indifference curves. The animals' preferences were internally consistent in satisfying transitivity. Change of option set size demonstrated choice optimality and satisfied the Weak Axiom of Revealed Preference (WARP). These data are consistent with a version of revealed preference theory in which preferences are stochastic; the monkeys behaved "as if" they had well-structured preferences and maximized utility.
Potent, Highly Selective, and Orally Bioavailable Gem -Difluorinated Monocationic Inhibitors of Neuronal Nitric Oxide Synthase (2010)

In our efforts to discover neuronal isoform selective nitric oxide synthase (NOS) inhibitors, we have developed a series of compounds containing a pyrrolidine ring with two stereogenic centers. The enantiomerically pure compounds, (S,S) versus (R,R), exhibited two different binding orientations, with (R,R) inhibitors showing much better potency and selectivity. To improve the bioavailability of these inhibitors, we have introduced a CF(2) moiety geminal to an amino group in the long tail of one of these inhibitors, which reduced its basicity, resulting in compounds with monocationic character under physiological pH conditions. Biological evaluations have led to a nNOS inhibitor with a K(i) of 36 nM and high selectivity for nNOS over eNOS (3800-fold) and iNOS (1400-fold). MM-PBSA calculations indicated that the low pK(a) NH is, at least, partially protonated when bound to the active site. A comparison of rat oral bioavailability of the difluorinated compound to the parent molecule shows 22% for the difluorinated compound versus essentially no oral bioavailability for the parent compound. This indicates that the goal of this research to make compounds with only one protonated nitrogen atom at physiological pH to allow for membrane permeability, but which can become protonated when bound to NOS, has been accomplished.
Sustained Progression-Free Survival Benefit of Rituximab Maintenance in Patients With Follicular Lymphoma: Long-Term Results of the PRIMA Study (2019)

Rituximab maintenance after induction immunochemotherapy provides a significant long-term PFS, but not OS, benefit over observation.
Adaptive mobile streaming over HTTP/2 with gradual quality transitions (2016)

In this paper, we study an adaptation method for mobile streaming over HTTP/2. Beside leveraging the server push feature of HTTP/2 to reduce request-related overheads, the proposed method can improve video quality by delivering gradual video bitrate transitions. Experimental results show that our method can provide smooth video quality while resulting in a low number of requests over a whole session.