gebhart/patrepeval huggingface dataset:
Two-and-a-half-year clinical experience with the world's first magnetic resonance image guided radiation therapy system (2017)

MR-IGRT has been successfully implemented in a high-volume radiation clinic and provides unique advantages in the treatment of a variety of malignancies. Additional clinical trials are in development to formally evaluate MR-IGRT in the treatment of multiple disease sites with techniques such as SBRT and ART.
Some Characteristics of Corticosterone Uptake by the Dorsal Hippocampus and the Adenohypophysis in the Rat (1974)

In addition to confirming the reports by McEwen and co-workers of a selective uptake of corticosterone by the dorsal hippocampus in adrenalectomized rats, our findings have brought to light an inverse relationship between corticosterone retention by the hippocampus and its binding by plasma transcortin, 4 days after adrenalectomy, which raises the possibility of a competition between extracellular and intracellular binding sites for corticosterone.A subsequent study of the uptake characteristics of the 30 000 × g pellet and supernatant of the dorsal hippocampus, the cerebral cortex, and the adenohypophysis, under conditions of dynamic equilibrium between corticosterone and its binding sites achieved by perfusing at a constant rate graded concentrations of the steroid, has yielded evidence for the selective uptake of corticosterone by both the particulate (chiefly nuclei and mitochondria) and the soluble (cytosol) fractions of the dorsal hippocampus and of the adenohypophysis, the hippocampus showing a greater uptake capacity than the hypophysis. The observed saturation of the sites of the dorsal hippocampus and of the adenohypophysis at physiological concentrations of plasma corticosterone is consistent with the involvement of these two structures in the feedback control of adrenocorticotropin secretion by circulating corticosteroids.
Cathepsin D deficiency underlies congenital human neuronal ceroid-lipofuscinosis (2006)

Congenital neuronal ceroid-lipofuscinosis (NCL) is a devastating inherited neurodegenerative disorder of unknown metabolic basis. Eight patients with this rare disorder, all with similar clinical and neuropathological findings, have been reported, and here we describe two further patients. Previously, we showed that a mutation in the cathepsin D gene causes congenital NCL in sheep. On the basis of the neuropathological and ultrastructural similarities between the sheep and patients affected with congenital NCL, we screened the cathepsin D gene for mutations in a patient of Pakistani origin. We identified a nucleotide duplication, c.764dupA, in the cathepsin D gene in homozygous form in the patient, and in heterozygous form in his father. This duplication is likely to be disease-causing, as it creates a premature stop codon, predicting a truncation of the protein. When transiently expressed in cell cultures, the mutant protein was enzymatically inactive, but stable. In paraffin-embedded brain tissue samples of two affected siblings of the Pakistani patient, cathepsin D was absent, suggesting rapid degradation of the c.764dupA mutant cathepsin D at mRNA or protein level in vivo. Further, we were able to confirm lack of cathepsin D in the brain tissue of yet another, unrelated, patient of English origin with congenital NCL. On the basis of the present data, and the nearly identical clinical and/or pathological phenotype of the other reported cases of congenital NCL, it is reasonable to suggest that cathepsin D deficiency caused by mutations in the corresponding gene may underlie all cases of congenital NCL. The present observations also suggest that cathepsin D deficiency should be considered as a possible diagnosis in microcephalic neonates, who present with seizures at or before birth.
Optimized liquid and gas phase fractionation increase HLA-peptidome coverage for primary cell and tissue samples (2021)

Abstract Mass spectrometry is the most effective method to directly identify peptides presented on HLA molecules. However, current standard approaches often require many millions of cells for input material to achieve high coverage of the immunopeptidome and are therefore not compatible with the often limited amounts of tissue available from clinical tumor samples. Here, we evaluated microscaled basic reversed-phase fractionation to separate HLA peptide samples off-line followed by ion mobility coupled to LC-MS/MS for analysis. The combination of these two separation methods enabled identification of 20% to 50% more peptides compared to samples analyzed without either prior fractionation or use of ion mobility alone. We demonstrate coverage of HLA immunopeptidomes with up to 8,107 distinct peptides starting with as few as 100 million cells or 150 milligrams of wet weight tumor tissue. This increased sensitivity can improve HLA binding prediction algorithms and enable detection of clinically relevant epitopes such as neoantigens.
Plenary address (2015)

Provides an abstract of the plenary presentation and a brief professional biography of the presenter. The complete presentation was not made available for publication as part of the conference proceedings.
Non-Quasi-Static Carrier Dynamics of MOSFETs under Low-Voltage Operation (2009)

We analyze the carrier dynamics in MOSFETs under low-voltage operation. For this purpose the displacement (charging/discharging) current, induced during switching operations is studied experimentally and theoretically for a 90nm CMOS technology. It is found that the experimental transient characteristics can only be well reproduced in the circuit simulation of low voltage applications by considering the carrier-transit delay in the compact MOSFET model. Long carrier transit delay under the low voltage switching-on operation results in long duration of the displacement current flow. On the other hand, the switching-off characteristics are independent of the bias condition.
Filter Selection for Multispectral Imaging Optimizing Spectral, Colorimetric and Image Quality (2017)

This paper will demonstrate the filter selection methods for wide band multispectral capturing system considering spectral and colorimetric reproduction as well as noise propagation. Spectral sensitivity of seven channel bandpass filter set was modeled and optimized first. Schott filters can be glued together to have bandpass shapes, which can be used to build the spectral camera. The glued Schott filters were selected based on the optimal modeling spectral sensitivity considering optical throughputs and infrared sensitivity. The second method to select the glued Schott filters is to divide the spectrum of interest evenly and select the combinations of filters whose peak wavelength were located in the range of spectrum subsets manually. An alternative option is to use single Schott filter set to build the spectral camera. However, although its spectral and colorimetric reproduction is accurate, single Schott filter set generates high propagated noise. Therefore, the glued Schott filters are preferred. The research provides insights for filter selection in multi-spectral camera design.
Linear minimum mean-square error estimation based on high-dimensional data with missing values (2014)

In linear minimum mean-square error (LMMSE) estimation problems, the observation data may have missing entries. Processing such data vectors may have high complexity if the observation data vector has high-dimensionality and the LMMSE estimator must be re-derived whenever there are missing values. In this context, a means of reducing the computational complexity is introduced when the number of missing entries is relatively small. All first- and second-order data statistics are assumed known, and the positions of the missing values are also known. The proposed method works by first applying the LMMSE estimator on the data vector with missing values replaced by zeros, and then applying a low-complexity update that depends on the positions of the missing. The method achieves exact LMMSE based on only observed data with lower complexity compared to the direct implementation of a time-varying LMMSE filter based on the incomplete data. We also show that if LMMSE imputation is used to fill the missing entires first based on the non-missing entries, and then a complete-data LMMSE filter is applied to the completed data vector, then the same linear MMSE is also achieved, but with higher complexity.
StriSynth: synthesis for live programming (2015)

Motivated by applications in automating repetitive file manipulations, we present a tool called StriSynth, which allows end-users to perform transformations over data using examples. Based on provided examples, our tool automaticallygenerates scripts for non-trivial file manipulations. Although the current focus of StriSynth are file manipulations, it implements a more general string transformation framework. This framework builds on and further extends the functionality of Flash Fill -- a Microsoft Excel extension for string transformations. An accompanying video to this paper is available at the following website http://youtu.be/kkDZphqIdFM.
The right touch: design of artificial antigen-presenting cells to stimulate the immune system (2014)

With the ever expanding possibilities to build supramolecular structures, chemists are challenged to mimic nature including the construction of artificial cells or functions thereof. Within the field of immunology, effective immunotherapy critically depends on efficient production of antigen-specific cytotoxic T-cells. Herein lies an opportunity for chemists to design and synthesize so-called artificial antigen presenting cells (aAPCs) that can promote T-cell activation and their subsequent expansion. In this review we discuss the current status of aAPC development, also focusing on developments in nanoscience which might improve future designs. As synthetic mimics of natural antigen-presenting cells, aAPCs encompass three basic signals required for T-cell activation: MHC–antigen complexes, costimulatory molecules and soluble immune modulating compounds. Both spatial and temporal organization of these signals during aAPC/T-cell contact is important for efficient T-cell activation. We discuss how signals have been incorporated in several aAPC designs, but also how physical properties such as size and shape are essential for targeting the aAPCs to T-cell rich areas in vivo.
Supplementary Table S2 from Sulforaphane Suppresses the Growth of Triple-negative Breast Cancer Stem-like Cells <i>In vitro</i> and <i>In vivo</i> (2023)

&lt;p&gt;NanoString nCounter® Stem Cell Gene Expression Codeset showing differentially expressed genes (p &lt; 0.05) between control and sulforaphane-treated groups during primary tumor growth&lt;/p&gt;
Removal of arsenate and 17α-ethinyl estradiol (EE2) by iron (hydr)oxide modified activated carbon fibers (2009)

Activated carbon fibers (ACF) were modified with iron (hydr)oxide and studied to determine their suitability to remove arsenate and 17alpha -ethinyl estradiol (EE2) from water. Two synthesis methods, one involving aqueous KMnO(4) pretreatment followed by Fe(II) treatment, and the other involving reaction with Fe(III) in an organic solvent followed by NaOH treatment, were used to produce modified ACF media containing 5.9% and 8.4% iron by dry weight, respectively. Scanning electron microscopy (SEM) and Electron dispersion X-ray (EDX) techniques indicated slightly higher iron content near the outer edges of the fibers. Pseudo-equilibrium batch test experimental data at pH = 7.0 +/- 0.1 in 5 mM NaHCO(3) buffered ultrapure water containing approximately 100 micro g(As)/L and approximately 500 micro gEE2/L were fitted with the Freundlich isotherm model (q = K x C(E)(1/n)). The adsorption capacity parameters (K) were approximately 2586 (micro gAs/gFe)(L/micro gAs)(1/n) and approximately 425 (micro gAs/gFe)(L/micro gAs)(1/n)), respectively, for the KMnO(4)/Fe(II) and Fe(III)/NaOH treated media. The KMnO(4)/Fe(II) media exhibited a lower adsorption capacity at 99% EE2 removal than did the Fe(III)/NaOH treated media (1.3 mgEE2/g -dry -media vs. 1.8 mgEE2/g -dry -media). The arsenate adsorption intensity parameters (1/n) for both modified ACF media were < 0.29, implying very favorable adsorption, which suggests that this type of media may be suitable for single point -of -use applications in which arsenic and organic co-contaminants require simultaneous removal and the depth of the packed bed is the key factor.
Fast and contrast-enhanced phase-sensitive magnetic resonance imaging (2009)

Phase-sensitive magnetic resonance (MR) imaging has a number of important clinical applications, such as phase-sensitive inversion recovery (PSIR) and Dixon water/fat imaging. PSIR and Dixon techniques are widely used in neurological and body imaging to improve tissue-contrast, the former by extending the dynamic range of image intensity and the later by suppressing unnecessary fat signals. Several important limitations, however, occur in these techniques: (1) Dixon techniques cannot decompose two signals if the resonance frequencies are close. For example, in MR mammography, it is difficult to separate silicone breast implants signals (4.0 ppm) from fat signals (3.5 ppm); (2) the signal dynamic range of images acquired using Dixon techniques is limited by the equilibrium magnetization; and (3) long image acquisition time. These limitations have hindered the applications of phase-sensitive Dixon imaging techniques on breast implant imaging or as a screening tool where fast acquisition is required. In this work, novel phase-sensitive MRI techniques were developed to enhance the capability, image-contrast, and scan-efficiency of Dixon imaging techniques. Specifically, we developed (1) a generalized chemical-shift imaging technique to separate spectrally overlapped signals both T1-contrast and chemical-shift; (2) a contrast-enhanced Dixon technique to extend the signal dynamic range of Dixon images; and (3) a single-echo acquisition (SEA) imaging technique integrated with phase-sensitive MR imaging to provide ultra-fast image acquisitions. Phantom studies, performed on 1.5 T and 4.7 T MR scanners, demonstrated the developed generalized chemical-shift imaging technique could clearly separate breast silicone implant signals (4.0 ppm) from fat (3.5 ppm). The contrast-enhanced Dixon technique, by extending the dynamic range of signal intensity from positive levels to positive/negative levels, could improve image-contrast by 1.6 times, compared with a conventional single-point Dixon technique. Phantom studies, using a 64-channel SEA imaging system, showed the integrated Dixon technique with SEA could acquire decomposed 2-D water-only and fat-only images with ultra-fast frame-rates up to 1/TR, while providing improved image-contrast (by 2.4 times in this experiment) compared with a conventional SEA imaging technique.
EMG study of hand muscle recruitment during hard hammer percussion manufacture of Oldowan tools (1998)

The activity of 17 hand muscles was monitored by electromyography (EMG) in three subjects during hard hammer percussion manufacture of Oldowan tools. Two of the subjects were archaeologists experienced in the replication of prehistoric stone tools. Simultaneous videotapes recorded grips associated with the muscle activities. The purpose of the study was to identify the muscles most likely to have been strongly and repeatedly recruited by early hominids during stone tool-making. This information is fundamental to the identification of skeletal features that may reliably predict tool-making capabilities in early hominids. The muscles most frequently recruited at high force levels for strong precision pinch grips required to control the hammerstone and core are the intrinsic muscles of the fifth finger and the thumb/index finger regions. A productive search for skeletal evidence of habitual Oldowan tool-making behavior will therefore be in the regions of the hand stressed by these intrinsic muscles and in the joint configurations affecting the relative lengths of their moment arms.
Direct Measurement of the Counterion Distribution within Swollen Polyelectrolyte Films (2005)

The depth profile of the counterion concentration within thin polyelectrolyte films was measured in situ using contrast variant specular neutron reflectivity to characterize the initial swelling stage of the film dissolution. We find substantial counterion depletion near the substrate and enrichment near the periphery of the film extending into the solution. These observations challenge our understanding of the charge distribution in polyelectrolyte films and are important for understanding film dissolution in medical and technological applications.
Dynamic Difficulty Adjustment for Maximized Engagement in Digital Games (2017)

Dynamic difficulty adjustment (DDA) is a technique for adaptively changing a game to make it easier or harder. A common paradigm to achieve DDA is through heuristic prediction and intervention, adjusting game difficulty once undesirable player states (e.g., boredom or frustration) are observed. Without quantitative objectives, it is impossible to optimize the strength of intervention and achieve the best effectiveness. In this paper, we propose a DDA framework with a global optimization objective of maximizing a player's engagement throughout the entire game. Using level-based games as our example, we model a player's progression as a probabilistic graph. Dynamic difficulty reduces to optimizing transition probabilities to maximize a player's stay time in the progression graph. We have successfully developed a system that applies this technique in multiple games by Electronic Arts, Inc., and have observed up to 9% improvement in player engagement with a neutral impact on monetization.
Ultrasonic Adaptive Sound Speed Estimation for the Diagnosis and Quantification of Hepatic Steatosis: A Pilot Study (2018)

SSE can be used to detect, quantify and grade liver steatosis and to calculate a US fat index.
Crystal structure of archaeal tRNA(m1G37)methyltransferase aTrm5 (2008)

Methylation of the N1 atom of guanosine at position 37 in tRNA, the position 3'-adjacent to the anticodon, generates the modified nucleoside m(1)G37. In archaea and eukaryotes, m(1)G37 synthesis is catalyzed by tRNA(m(1)G37)methyltransferase (archaeal or eukaryotic Trm5, a/eTrm5). Here we report the crystal structure of archaeal Trm5 (aTrm5) from Methanocaldococcus jannaschii (formerly known as Methanococcus jannaschii) in complex with the methyl donor analogue at 2.2 A resolution. The crystal structure revealed that the entire protein is composed of three structural domains, D1, D2, and D3. In the a/eTrm5 primary structures, D2 and D3 are highly conserved, while D1 is not conserved. The D3 structure is the Rossmann fold, which is the hallmark of the canonical class-I methyltransferases. The a/eTrm5-defining domain, D2, exhibits structural similarity to some class-I methyltransferases. In contrast, a DALI search with the D1 structure yielded no structural homologues. In the crystal structure, D3 contacts both D1 and D2. The residues involved in the D1:D3 interactions are not conserved, while those participating in the D2:D3 interactions are well conserved. D1 and D2 do not contact each other, and the linker between them is disordered. aTrm5 fragments corresponding to the D1 and D2-D3 regions were prepared in a soluble form. The NMR analysis of the D1 fragment revealed that D1 is well folded by itself, and it did not interact with either the D2-D3 fragment or the tRNA. The NMR analysis of the D2-D3 fragment revealed that it is well folded, independently of D1, and that it interacts with tRNA. Furthermore, the D2-D3 fragment was as active as the full-length enzyme for tRNA methylation. The positive charges on the surface of D2-D3 may be involved in tRNA binding. Therefore, these findings suggest that the interaction between D1 and D3 is not persistent, and that the D2-D3 region plays the major role in tRNA methylation.
Automatic and Manual Methodology for Three-Dimensional Measurements of Distal Femoral Gender Differences and Femoral Component Placement (2009)

Our study aimed to introduce an automatic three-dimensional method for measuring the distal femur and identifying potential gender differences and the effects on femoral component placement in total knee arthroplasty. Three hundred forty-two femora were scanned with computed tomography. Automatic and manual bone resection and component placement were compared using a virtual resection tool. For standard component use, 77.3% of the femora were male and 23.1% were female. For gender-specific component use, 91% were female and 7.3% were male. Surgeon errors in both component translation and rotation existed but were minimal. From these results, gender alone did not dictate component use in primary total knee arthroplasty. The restoration of femoral condylar profile in 3 dimensions can be obtained by accurately measuring patient distal femoral anatomy and the appropriate femoral component design selection. Additional bone cuts, soft-tissue maneuvers, and adverse outcomes in fitting the patient to the femoral component may be avoided.
Multiple metal-carbon bonds. 38. Preparation of trialkoxymolybdenum(VI) alkylidyne complexes, their reactions with acetylenes, and the x-ray structure of Mo[C3(CMe3)2][OCH(CF3)2](C5H5N)2 (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMultiple metal-carbon bonds. 38. Preparation of trialkoxymolybdenum(VI) alkylidyne complexes, their reactions with acetylenes, and the x-ray structure of Mo[C3(CMe3)2][OCH(CF3)2](C5H5N)2Laughlin G. McCullough, Richard R. Schrock, John C. Dewan, and John C. MurdzekCite this: J. Am. Chem. Soc. 1985, 107, 21, 5987–5998Publication Date (Print):October 1, 1985Publication History Published online1 May 2002Published inissue 1 October 1985https://pubs.acs.org/doi/10.1021/ja00307a025https://doi.org/10.1021/ja00307a025research-articleACS PublicationsRequest reuse permissionsArticle Views1724Altmetric-Citations163LEARN 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 Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts