gebhart/patrepeval huggingface dataset:
Abinitiodetermination of a structural phase transition temperature (1987)

The temperature of the structural phase transition in GeTe is calculated complete ab initio from a model lattice-dynamical Hamiltonian that is constructed from microscopic quantum-mechanical total-energy calculations. The phase transition in the model system is studied through a renormalization-group-theory approach, leading to the prediction of a fluctuation-driven first-order transition at 657\ifmmode\pm\else\textpm\fi{}100 K.
Liquid Chromatographic Determination of Serum Levels of d,l-4-Amino-N-( -methylbenzyl)-benzamide, a New Benzamide Anticonvulsant (1988)

A method for the high-performance liquid chromatographic (HPLC) determination of serum concentrations of d,l-4-amino-N-(alpha-methylbenzyl)-benzamide and its N-acetylated metabolite is described. The compounds are isolated from a 50-microL sample of serum using solid phase extraction. The compounds and internal standard are eluted from the extraction column with acetonitrile. Quantitation is performed via UV detection at 275 nm following isocratic reversed-phase (C18) separation using a ternary solvent system. The assay procedure is useful for the determination of concentrations of parent compound from 0.63 to 87.9 micrograms/mL from 50 microL of serum.
Chirality in halogen-bonded supramolecular architectures (2011)

advancing the field of homochiral MOFs. Biomolecules have emerged recently as particularly attractive building blocks for constructing MOFs. Following this direction, we turned our attention toward Cinchona alkaloids and our work aims to develop a novel attractive route to chiral bipyridine-type linkers based on N,N-ditopic metalloligands with the backbone of these readily accessible biomolecules.
Seabed property estimation from ambient-noise recordings: Part 2 — Scholte-wave spectral-ratio inversion (2007)

Abstract Having knowledge of the near-surface shear-velocity model is useful for various seismic processing methods such as shear-wave static estimation, wavefield separation, and geohazard prediction. I present a new method to derive a 2D near-surface shear-velocity model from ambient-noise recordings made at the seafloor. The method relies on inverting horizontal- and vertical-amplitude spectra of Scholte waves propagating in the seafloor. I compare the commonly used horizontal-over-vertical spectral ratio with three alternative spectral-ratio definitions through modeling. The modeling shows that the vertical-over-total spectral ratio has some favorable properties for inversion. I describe a nonlinear inversion method for the vertical-to-total spectral ratio of the Scholte waves and apply it to an ambient-noise data set recorded by an ocean-bottom-cable (OBC) system. A 1D near-surface shear-velocity model is derived through a joint inversion of the spectral-ratio and phase-velocity data. A 2D shear-velocity model is obtained through a local inversion of the spectral ratios averaged over small groups of receivers and shows evidence for lateral heterogeneity. The newly developed method for deriving near-surface shear-velocity distribution by inverting the Scholte-wave spectral ratio measured from seabed noise provides great opportunities for estimating the shallow-seabed shear velocity in deep water. Another benefit of the method is that, with the OBC system, no additional hardware is needed; only additional recording time is required. In this case, half an hour is sufficient.
Image Analysis in Patients with Cancer Studied with a Combined PET and CT Scanner (2000)

Combined PET-CT images appear more effective than PET images alone to localize precisely neoplastic lesions and to distinguish normal variants from juxtaposed neoplastic lesions.
The Use of LivingListeria Monocytogenesas an Active Immunotherapy for the Treatment of Cancer (2010)

This chapter contains sections titled: Introduction Listerial Disease Adaptive Immunity Nonclassical Immune Functions Recombinant L. Monocytogenes as a Vaccine Vector Cross-Presentation and Epitope Spreading Listeria LLO-AG Fusions and the Tumor Microenvironment Conclusions References
Is there value in the routine practice of discarding the incision scalpel from the surgical field to prevent deep wound contamination with Cutibacterium acnes? (2020)

The presence of C acnes on the skin blade in 2 patients validates concerns that there is C acnes present in dermal tissue despite extensive attention to eradication of these microbes. There was a high rate of C acnes contamination on scalpel blades used for initial skin incisions and the authors conclude that there is value in discarding these blades from the surgical field.
Oleifolioside B-mediated autophagy promotes apoptosis in A549 human non-small cell lung cancer cells (2013)

The biochemical mechanisms of cell death by oleifolioside B (OB), a cycloartane-type triterpene glycoside isolated from Dendropanax morbifera Leveille, were investigated in A549 human lung carcinoma cells. Our data indicated that exposure to OB led to caspase activation and typical features of apoptosis; however, apoptotic cell death was not prevented by z-VAD-fmk, a pan-caspase inhibitor, demonstrating that OB-induced apoptosis was independent of caspase activation. Subsequently, we found that OB increased autophagy, as indicated by an increase in monodansylcadaverine fluorescent dye-labeled autophagosome formation and in the levels of the autophagic form of microtubule-associated protein 1 light chain 3 and Atg3, an autophagy-specific gene, which is associated with inhibiting phospho-nuclear factor erythroid 2-related factor 2 (Nrf2) expression. However, pretreatment with bafilomycin A1, an autophagy inhibitor, attenuated OB-induced apoptosis and dephosphorylation of Nrf2. The data suggest that OB-induced autophagy functions as a death mechanism in A549 cells and OB has potential as a novel anticancer agent capable of targeting apoptotic and autophagic cell death and the Nrf2 signaling pathway.
SAR in the human body by a wireless telemetry system for a retinal prosthesis (2007)

In this work, the 3D explicit FDTD method in a D-H formulation similar to (D. Sullivan, 2000) has been used to calculate the electromagnetic fields in the human head due to the operation of the wireless link at 10 MHz of the proposed retinal prosthesis system. The specific absorption rate (SAR) was obtained from the E-field values to compare with safety standards.
New High-Nuclearity Carbonyl and Carbonyl-Substituted Rhodium Clusters and Their Relationships with Polyicosahedral Carbonyl-Substituted Palladium- and Gold-Thiolates (2012)

A reinvestigation of the synthesis of [H(5-n)Rh(13)(CO)(24)](n-) (n = 2, 3) led to isolation of a series of Rh(19), Rh(26), and Rh(33) high-nuclearity carbonyl and carbonyl-substituted rhodium clusters. The [Rh(19)(CO)(31)](5-) (1) is electronically equivalent with [Pt(19)(CO)(22)](4-), but poor crystal diffraction data of all salts obtained to date have prevented its geometrical analysis. The structures of Rh(26)(CO)(29)(CH(3)CN)(11) (2) as 2·2CH(3)CN and [Rh(33)(CO)(47)](5-) (3) as [NEt(4)](5)[3]·Me(2)CO were determined from complete X-ray diffraction determinations. The latter two species adopt polyicosahedral metal frameworks, and notably, [Rh(33)(CO)(47)](5-) represents the molecular group 9 metal carbonyl cluster of highest nuclearity so far reported.
Supplementary Tables from LSD1-Mediated Epigenetic Reprogramming Drives CENPE Expression and Prostate Cancer Progression (2023)

&lt;p&gt;Table S1: Primers and siRNA sequences used in this study. Table S2-9: GO analysis of LSD1 and CENPE target genes in LNCaP and abl Cells.&lt;/p&gt;
Renewable surface fluorescence sandwich immunoassay biosensor for rapid sensitive botulinum toxin detection in an automated fluidic format (2009)

A renewable surface biosensor for rapid detection of botulinum neurotoxin serotype A is described based on fluidic automation of a fluorescence sandwich immunoassay, using a recombinant protein fragment of the toxin heavy chain ( approximately 50 kDa) as a structurally valid simulant. Monoclonal antibodies AR4 and RAZ1 bind to separate non-overlapping epitopes of the full botulinum holotoxin ( approximately 150 kDa). Both of the targeted epitopes are located on the recombinant fragment. The AR4 antibody was covalently bound to Sepharose beads and used as the capture antibody. A rotating rod flow cell was used to capture these beads delivered as a suspension by a sequential injection flow system, creating a 3.6 microL column. After perfusing the bead column with sample and washing away the matrix, the column was perfused with Alexa 647 dye-labeled RAZ1 antibody as the reporter. Optical fibers coupled to the rotating rod flow cell at a 90 degrees angle to one another delivered excitation light from a HeNe laser (633 nm) using one fiber and collected fluorescent emission light for detection with the other. After each measurement, the used Sepharose beads are released and replaced with fresh beads. In a rapid screening approach to sample analysis, the toxin simulant was detected to concentrations of 10 pM in less than 20 minutes using this system.
Extended Lapped Transforms: Properties, Applications, and Fast Algorithms (1992)

The family of lapped orthogonal transforms is extended to include basis functions of arbitrary length. Within this new family, the extended lapped transform (ELT) is introduced, as a generalization of the previously reported modulated lapped transform (MLT). Design techniques and fast algorithms for the ELT are presented, as well as examples that demonstrate the good performance of the ELT in signal coding applications. Therefore, the ELT is a promising substitute for traditional block transforms in transform coding systems, and also a good substitute for less efficient filter banks in subband coding systems.
An Online Repository for Pre-Clinical Imaging Protocols (PIPs) (2023)

Providing method descriptions that are more detailed than currently available in typical peer reviewed journals has been identified as an actionable area for improvement. In the biochemical and cell biology space, this need has been met through the creation of new journals focused on detailed protocols and materials sourcing. However, this format is not well suited for capturing instrument validation, detailed imaging protocols, and extensive statistical analysis. Furthermore, the need for additional information must be counterbalanced by the additional time burden placed upon researchers who may be already overtasked. To address these competing issues, this white paper describes protocol templates for positron emission tomography (PET), X-ray computed tomography (CT), and magnetic resonance imaging (MRI) that can be leveraged by the broad community of quantitative imaging experts to write and self-publish protocols in protocols.io. Similar to the Structured Transparent Accessible Reproducible (STAR) or Journal of Visualized Experiments (JoVE) articles, authors are encouraged to publish peer reviewed papers and then to submit more detailed experimental protocols using this template to the online resource. Such protocols should be easy to use, readily accessible, readily searchable, considered open access, enable community feedback, editable, and citable by the author.
Robot-aided rehabilitation task design for inner shoulder muscles (2012)

In this paper, we propose a simultaneous design method of motion and external force trajectories for shoulder inner muscles in the robot-aided rehabilitation system, based on a biomechanical analysis of patient's body. The rehabilitation efficiency evaluation function was maximized by Genetic Algorithm (GA), where the structure of spline curves parameters are pre-defined, and the structural parameters are explored to design smooth rehabilitation motion and external force trajectories.
Epidemic Graph Convolutional Network (2020)

A growing trend recently is to harness the structure of today's big data, where much of the data can be represented as graphs. Simultaneously, graph convolutional networks (GCNs) have been proposed and since seen rapid development. More recently, due to the scalability issues that arise when attempting to utilize these powerful models on real-world data, methodologies have sought the use of sampling techniques. More specifically, minibatches of nodes are formed and then sets of nodes are sampled to aggregate from in one or more layers. Among these methods, the two prominent ways are based on sampling nodes from either a local or global perspective. In this work, we first observe the similarities in the two sampling strategies to that of epidemic and diffusion network models. Then we harness this understanding to fuse together the benefits of sampling from both a local and global perspective while alleviating some of the inherent issues found in both through the use of a low-dimensional approximation for the path-based Katz similarity measure. Our proposed framework, Epidemic Graph Convolutional Network (EGCN), is thus able to achieve improved performance over sampling from just one of the two perspectives alone. Empirical experiments are performed on several public benchmark datasets to verify the effectiveness over existing methodologies for the node classification task and we furthermore present some empirical parameter analysis of EGCN.
Deep learning assisted CSI estimation for joint URLLC and eMBB resource allocation (2020)

Multiple-input multiple-output (MIMO) is a key for the fifth generation (5G) and beyond wireless communication systems owing to higher spectrum efficiency, spatial gains, and energy efficiency. Reaping the benefits of MIMO transmission can be fully harnessed if the channel state information (CSI) is available at the transmitter side. However, the acquisition of transmitter side CSI entails many challenges. In this paper, we propose a deep learning assisted CSI estimation technique in highly mobile vehicular networks, based on the fact that the propagation environment (scatterers, reflectors) is almost identical thereby allowing a data driven deep neural network (DNN) to learn the non-linear CSI relations with negligible overhead. Moreover, we formulate and solve a dynamic network slicing based resource allocation problem for vehicular user equipments (VUEs) requesting enhanced mobile broadband (eMBB) and ultra-reliable low latency (URLLC) traffic slices. The formulation considers a threshold rate violation probability minimization for the eMBB slice while satisfying a probabilistic threshold rate criterion for the URLLC slice. Simulation result shows that an overhead reduction of 50% can be achieved with 12% increase in threshold violations compared to an ideal case with perfect CSI knowledge.
Purification, Pharmacological Modulation, and Biochemical Characterization of Interactors of Endogenous Human γ-Secretase (2009)

Gamma-secretase is a unique intramembrane-cleaving protease complex, which cleaves the Alzheimer's disease-associated beta-amyloid precursor protein (APP) and a number of other type I membrane proteins. Human gamma-secretase consists of the catalytic subunit presenilin (PS) (PS1 or PS2), the substrate receptor nicastrin, APH-1 (APH-1a or APH-1b), and PEN-2. To facilitate in-depth biochemical analysis of gamma-secretase, we developed a fast and convenient multistep purification procedure for the endogenous enzyme. The enzyme was purified from HEK293 cells in an active form and had a molecular mass of approximately 500 kDa. Purified gamma-secretase was capable of producing the major amyloid-beta peptide (Abeta) species, such as Abeta40 and Abeta42, from a recombinant APP substrate in physiological ratios. Abeta generation could be modulated by pharmacological gamma-secretase modulators. Moreover, the Abeta42/Abeta40 ratio was strongly increased by purified PS1 L166P, an aggressive familial Alzheimer's disease mutant. Tandem mass spectrometry analysis revealed the consistent coisolation of several proteins with the known gamma-secretase core subunits. Among these were the previously described gamma-secretase interactors CD147 and TMP21 as well as other known interactors of these. Interestingly, the Niemann-Pick type C1 protein, a cholesterol transporter previously implicated in gamma-secretase-mediated processing of APP, was identified as a major copurifying protein. Affinity capture experiments using a biotinylated transition-state analogue inhibitor of gamma-secretase showed that these proteins are absent from active gamma-secretase complexes. Taken together, we provide an effective procedure for isolating endogenous gamma-secretase in considerably high grade, thus aiding further characterization of this pivotal enzyme. In addition, we provide evidence that the copurifying proteins identified are unlikely to be part of the active gamma-secretase enzyme.
Handling Speech in the Wild (2012)

This is a broad overview of recent work related to processing speech embedded in noisy environments, delivered to Steve Colburn's group at Boston University.
Enhanced zero-valent metal permeable wall treatment of contaminated groundwater (1997)

On-going research at the University of Central Florida, supported by NASA, is investigating the use of sonicated zero-valent metal permeable treatment walls to remediate chlorinated solvent contaminated groundwater. Use of ultrasound within the treatment wall is proposed to enhance and/or restore the activity of the zero-valent metal. Batch studies designed to evaluate the destruction of chlorinated hydrocarbons using enhanced zero-valent metal reduction found a nearly three-fold increase in reaction rates after ultrasound treatment. Column studies substantiated these results. It is hypothesized that ultrasound serves to remove corrosion products from the iron surface and will prolong the reactive life and efficiency of the permeable treatment wall, thus decreasing long-term costs of wall construction and maintenance.
External validation of an electrocardiography artificial intelligence-generated algorithm to detect left ventricular systolic function in a general cardiac clinic in Uganda (2020)

Abstract Background Left ventricular systolic dysfunction (LVSD) is associated with increased morbidity and mortality. Although there are effective treatments for patients with LVSD to prevent mortality, heart failure and to improve symptoms, many patients remain undetected and untreated. We have recently derived a deep learning algorithm to detect LVSD using the electrocardiogram (ECG) which could have an important screening role, particularly in limited resources settings. We evaluated the accuracy of this algorithm for the first time in Africa in a sample of subjects attending a cardiology clinic. Methods We conducted a retrospective study in a general cardiac clinic in Uganda. Consecutive patients ≥18 years who had a digital ECG and echocardiogram done within two days of each other were included. We excluded patients with pacemakers or missing information regarding left ventricular ejection fraction (LVEF). Routine 10-second, twelve-lead surface rest ECG were performed using an Edan PC ECG Model SE-1515, Hamburg, Germany. The probability of LVSD was estimated with the Mayo Clinic artificial intelligence (AI) ECG algorithm. LVEF was calculated by the MMode (Teichholz method) using a Philips Ultrasound system, HD7XE, Bothel, Washington, USA. LVSD was defined as a LVEF≤35%. We assessed the overall diagnostic performance of the algorithm to identify LVSD in this population with the area under the receiver operating curve (AUC), and estimated sensitivity, specificity and accuracy using a pre-specified cut-off based on the probability for LVSD generated by the algorithm. We conducted secondary analyses using different LVEF cutoff values. Results We included 634 subjects, 32% (200) of whom had hypertension and 12% (77) clinical heart failure. Mean age was 57±18.8 years, 58% were women and the overall prevalence of LVSD was 4%. The AI-ECG had an AUC of 0.866 (see figure below), sensitivity 73.08%, specificity 91.10%, negative predictive value 98.75%, positive predictive value 26.03% and an accuracy of 90.96% using the original threshold. Using the optimal cutoff based on the AUCs, the sensitivity was 80.77% and specificity was 81.05% with a negative predictive value of 98.99%. The ROC for the detection of LVEF of 40% or below was 0.821. Conclusion The Mayo AI-ECG algorithm demonstrated good accuracy, sensitivity and specificity to detect LVSD in patients seen in a clinical setting in Uganda. This tool may facilitate the identification of people at a high risk for LVSD in settings with low resources. ROC Funding Acknowledgement Type of funding source: None
Surgical palliation for pancreatic carcinoma (1991)

A review of 122 patients treated for pancreatic adenocarcinoma from January 1978 through December 1984 was accomplished to determine patient survival and the effect of surgical palliation. One hundred patients underwent laparotomy, including biopsy only (n = 42), biliary bypass (n = 30), gastric bypass (n = 1), biliary and gastric bypass (n = 14), and curative resection (n = 13). Total patient median survival was 3.6 months and no patient lived 5 years. No significant difference in survival was found between the biliary bypass and combined biliary-gastric bypass groups. Only 1 of 30 patients (3.3%) undergoing biliary bypass alone without evidence of pre-operative gastric outlet obstruction developed late gastric outlet obstruction requiring gastrojejunostomy. Operative time and postoperative morbidity were greater in the biliary-gastric bypass group. These results do not support routine prophylactic use of gastrojejunostomy at the time of biliary bypass for patients with unresectable carcinoma of the pancreas.
Template-Directed Primer Extension Catalyzed by the Tetrahymena Ribozyme (1991)

The Tetrahymena ribozyme has been shown to catalyze an RNA polymerase-like reaction in which an RNA primer is extended by the sequential addition of pN nucleotides derived from GpN dinucleotides, where N = A, C, or U. Here, we show that this reaction is influenced by the presence of a template; bases that can form Watson-Crick base pairs with a template add as much as 25-fold more efficiently than mismatched bases. A mutant enzyme with an altered guanosine binding site can catalyze template-directed primer extension with all four bases when supplied with dinucleotides of the form 2-aminopurine-pN.