gebhart/patrepeval huggingface dataset:
Practical guide on chemometrics/informatics in x-ray photoelectron spectroscopy (XPS). II. Example applications of multiple methods to the degradation of cellulose and tartaric acid (2022)

Chemometrics/informatics, and data analysis in general, are increasingly important in x-ray photoelectron spectroscopy (XPS) because of the large amount of information (spectra/data) that is often collected in degradation, depth profiling, operando, and imaging studies. In this guide, we present chemometrics/informatics analyses of XPS data using a summary statistic (pattern recognition entropy), principal component analysis, multivariate curve resolution (MCR), and cluster analysis. These analyses were performed on C 1s, O 1s, and concatenated (combined) C 1s and O 1s narrow scans obtained by repeatedly analyzing samples of cellulose and tartaric acid, which led to their degradation. We discuss the following steps, principles, and methods in these analyses: gathering/using all of the information about samples, performing an initial evaluation of the raw data, including plotting it, knowing which chemometrics/informatics analyses to choose, data preprocessing, knowing where to start the chemometrics/informatics analysis, including the initial identification of outliers and unexpected features in data sets, returning to the original data after an informatics analysis to confirm findings, determining the number of abstract factors to keep in a model, MCR, including peak fitting MCR factors, more complicated MCR factors, and the presence of intermediates revealed through MCR, and cluster analysis. Some of the findings of this work are as follows. The various chemometrics/informatics methods showed a break/abrupt change in the cellulose data set (and in some cases an outlier). For the first time, MCR components were peak fit. Peak fitting of MCR components revealed the presence of intermediates in the decomposition of tartaric acid. Cluster analysis grouped the data in the order in which they were collected, leading to a series of average spectra that represent the changes in the spectra. This paper is a companion to a guide that focuses on the more theoretical aspects of the themes touched on here.
Reply: The classification of p53 immunohistochemical staining results and patient outcome in ovarian cancer (2007)

Reply: The classification of p53 immunohistochemical staining results and patient outcome in ovarian cancer
Specific Gene Repression by CRISPRi System Transferred through Bacterial Conjugation (2014)

In microbial communities, bacterial populations are commonly controlled using indiscriminate, broad range antibiotics. There are few ways to target specific strains effectively without disrupting the entire microbiome and local environment. Here, we use conjugation, a natural DNA horizontal transfer process among bacterial species, to deliver an engineered CRISPR interference (CRISPRi) system for targeting specific genes in recipient Escherichia coli cells. We show that delivery of the CRISPRi system is successful and can specifically repress a reporter gene in recipient cells, thereby establishing a new tool for gene regulation across bacterial cells and potentially for bacterial population control.
Theory for spiralling ions for 2D FT-ICR and comparison with precessing magnetization vectors in 2D NMR (2016)

Two-dimensional (2D) Fourier transform ion cyclotron resonance (FT-ICR) offers an approach to mass spectrometry (MS) that pursuits similar objectives as MS/MS experiments. While the latter must focus on one ion species at a time, 2D FT ICR can examine all possible correlations due to ion fragmentation in a single experiment: correlations between precursors, charged and neutral fragments. We revisited the original 2D FT-ICR experiment that has hitherto fallen short of stimulating significant analytical applications, probably because it is technically demanding. These shortcomings can now be overcome by improved FT-ICR instrumentation and computer hard- and software. We seek to achieve a better understanding of the intricacies of the behavior of ions during a basic two-dimensional ICR sequence comprising three simple monochromatic pulses. Through simulations based on Lorentzian equations, we have mapped the ion trajectories for different pulse durations and phases.
Effect of Nutritional Stress on the Expression of Sirtuin Gene Family (2020)

Abstract The sirtuin (SIRT) proteins are a highly conserved family of NAD+-dependent deacetylases that regulate histones as well as non-histone proteins. Seven sirtuin genes have been identified (SIRT1 to SIRT7) in mammals. SIRT1, SIRT6, and SIRT7 are primarily localized in the nucleus. SIRT2 is localized mainly in the cytoplasm. SIRT3, SIRT4, and SIRT5 are often located in the mitochondria. Therefore, the sirtuin family proteins exert their diverse functions at various cellular locations and regulate metabolism, stress responses, growth and aging processes. The sirtuin proteins are often considered as nutrient sensors. This study assessed the expression of sirtuin genes in C2C12 muscle cells under glucose stress conditions at different time points. Expression of all seven sirtuins was confirmed by Real-Time PCR analysis. SIRT1 (24 h) and SIRT3 (6 h and 15 h) are highly expressed under low glucose (2.7 mM) and high glucose (25 mM) conditions, whereas SIRT2 and SIRT4, SIRT5, SIRT6 and SIRT7 expressions were either relatively lower or there was no significant change under glucose stress conditions. Our results indicate that SIRT1 and SIRT3 demonstrated the greatest fluctuation in response to glucose stress, whether high or low glucose. These findings will help elucidate the role of sirtuins in the regulation of cellular processes, including metabolism. It will also help to enhance our understanding of the roles of sirtuin genes in regulation of blood sugar fluctuation in normal persons and diabetic patients, as well as in elderly individuals, many of whom are insulin resistant and “prediabetic” or diabetic.
Electrically controlled phase shifter using semiconductor laser in optical single sideband system (2009)

This investigation experimentally explores a microwave phase shifter using a semiconductor laser in an optical single sideband system. The operational bandwidth from 12 to 20 GHz is achieved by adjusting the bias current.
Continuous-wave 532 nm pumped MgO:PPLN optical parametric oscillator with external power regulation and spatial mode filtering (2008)

We report a continuous-wave (CW) optical parametric oscillator (OPO) based on a MgO-doped periodically poled LiNbO(3) (MgO:PPLN) crystal. The 532 nm pump generates coherent radiation that is tunable from 800 to 920 nm for the signal and from 1250 to 1580 nm for the idler, respectively. The OPO output power exhibits a slowly varying instability that we attribute to a thermal effect induced by the pump. This instability is truncated by means of a low-pass servo that includes a single-mode fiber that filters the beam into a single spatial mode. The resulting output characteristics are promising for radiometric applications in the near infrared including most fiber-optic communication bands.
FAST-Phase1: Flexible Adaptive and Synergistic Training (Pre-Registration) (2015)

The primary objective of the Flexible Adaptive and Synergistic Training (FAST) effort is to develop and validate interventions designed to enhance reasoning and problem solving skills. The interventions of interest include cognitive training, focusing on core processes associated with executive function (EF), and low-current transcranial electrical stimulation (tES) to enhance the activity of the cortical substrate that is recruited by the EF training tasks. The FAST effort aims to validate these interventions in the context of a study involving 440 individuals. This research is supported by the Intelligence Advanced Research Projects Agency (IARPA) via contract# 2014-13121700007 isssued to Honeywell International. Members of the SHARP team include researchers representing Honeywell Labs, Harvard Medical School, Northeastern University, Oxford University, and SimCoach Games. The points noted here reflect the position of the research team and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of IARPA, the Office of the Director of National Intelligence, or the U.S. Government.
Set estimation via ellipsoidal approximations (1997)

We present ellipsoid algorithms for convexly constrained estimation and design problems. The proposed polynomial time algorithms yield both an estimate of the complete set of feasible solutions and a point estimate in the interior. Optimal cutting hyperplanes are derived, and a computationally efficient sequential cut algorithm is proposed and shown to achieve the best existing polynomial time performance bound.
Covalent linkage of a protein to a defined nucleotide sequence at the 5'-terminus of virion and replicative intermediate RNAs of poliovirus. (1977)

The 5'-terminus of poliovirus polyribosomal RNA is pUp. A candidate for the 5'-terminus of poliovirion RNA was recovered as a compound migrating toward the cathode when 32P-labeled virion RNA was completely digested with ribonucleases T1, T2 and A and analyzed by paper ionophoresis at pH 3.5. Treatment with proteinase K reversed its direction of migration, indicating the presence of protein. Treatment with venom phosphodiesterase liberated all of the radioactivity as pUp, suggesting that poliovirion RNA has a protein-pUp 5'-terminus. Treatment of virion RNA with T1 ribonuclease alone generated a proteinase K-sensitive oligoribonucleotide. Analysis of the oligoribonucleotide using ribonucleases A and U2 showed its structure to be protein-pU-U-A-A-A-A-C-A-G. Digests of replicative intermediate RNA contained sufficient protein-pUp to suggest that this structure is at the 5'-end of most nascent poliovirus RNA molecules. We suggest that a protein-nucleotide structure acts as a primer for initiating synthesis of poliovirus RNA.
Comparison of Low Complexity Coherent Receivers for UDWDM-PONs ($λ$-to-the-user) (2017)

It is predicted that demand in optical access networks will reach multi-Gb/s per user. However, the limited performance of the direct detection receiver technology currently used in the optical network units at the customers' premises restricts data rates/user. Therefore, the concept of coherent-enabled access networks has attracted attention in recent years, as this technology offers high receiver sensitivity, inherent frequency selectivity, and linear field detection enabling the full compensation of linear channel impairments. However, the complexity of conventional (dual-polarisation digital) coherent receivers has so far prevented their introduction into access networks. Thus, to exploit the benefits of coherent technology in the ONUs, low complexity coherent receivers, suitable for implementation in ONUs, are needed. In this paper, the recently proposed low complexity coherent (i.e., polarisation-independent Alamouti-coding heterodyne) receiver is, for the first time, compared in terms of its minimum receiver sensitivity with five previously reported receiver designs, including a detailed discussion on their advantages and limitations. It is shown that the Alamouti-coding based receiver approach allows the lowest number of photons per bit (PPB) transmitted (with a lower bound of 15.5 PPB in an ideal system simulations) whilst requiring the lowest optical receiver hardware complexity. It also exhibits comparable complexity to the currently deployed direct-detection receivers, which typically require &gt;1000 PPB. Finally, a comparison of experimentally achieved receiver sensitivities and transmission distances using these receivers is presented. The highest spectral efficiency and longest transmission distance at the highest bit rate reported using the Alamouti-coding receiver, which is also the only one, to date, to have been demonstrated in a full system bidirectional transmission.
Estimating the Effects of Microscopic Stress Concentrations on the Fatigue Endurance of Thin-walled High Strength Steel (2009)

The effects of microscopic surface stress concentrations on the fatigue endurance of thin-walled high strength steel were systematically estimated by numerical analysis and plane-bending fatigue tests with Schenck-type specimens, using the commercially available static implicit method FEA software I-DEAS ver. 11 for the stress distribution calculations. The microscopic stress concentration factor αi, from notch depth t=50 μm and notch root radius ρ=6 μm microscopic surface ridges, monotonously increased with increases in the roughness ridge direction, θ, from 1 to 7 in the bending mode. A fitted curve was developed for deriving the calculated stress concentration, αθ, from the superposition of the principal stresses. In the twisting mode, αi varied from about 4 to 7. The θ dependency of αi was smaller than that in bending mode. The empirical rule that the specimen collection direction has a lesser effect in twisting mode fatigue was supported by the αi value. It is reported that the fatigue notch factor β increased linearly with increases in the macroscopic stress concentration factor αa of up to 3. On the other hand, β slowly increased with increases in αi until it exceeded about 2. This marked difference might be due to differences between their respective stress gradients, which was well described by Nisitani and Endo by using a parameter ρ. A plane-bending fatigue test was performed with an artificial surface micro-groove of θ=0, 90° using 590 MPa class strength circumferentially flattened electric resistance welded tube. The θ=0° micro-groove had little effect on the fatigue endurance in bending. On the other hand, the fatigue cracks of all the θ=90° specimens initiated at the basilar part of the micro-groove without any nonpropagating cracks. The fatigue notch factor β seems to be determined by only αi independent of ρ in the microscopic stress concentration field.
OpenMP-based Parallel Algorithms for Solving Kronecker Descriptors (2010)

Numerical analysis of Markovian models is relevant for performance evaluation and probabilistic analysis of systems' behavior from several fields such as Bioinformatics, Economics, and Engineering. These models can be represented in a compact fashion using Kronecker algebra. The Vector-Descriptor Product is the key operation to obtain stationary solutions of Kronecker-based descriptors. Due to its complexity, the numerical algorithms are usually CPU intensive, requiring alternatives such as data partitioning in order to produce results in less time. This paper proposes three OpenMP-based parallel implementations for solving descriptors to be deployed on shared-memory machines. We evaluated the implementations in a multi-core machine and obtained a speed-up near to eight when using eight cores with Intel Hyper-Threading technology.
Combined anti-tumor necrosis factor-α therapy and DMARD therapy in rheumatoid arthritis patients reduces inflammatory gene expression in whole blood compared to DMARD therapy alone (2012)

Periodic assessment of gene expression for diagnosis and monitoring in rheumatoid arthritis (RA) may provide a readily available and useful method to detect subclinical disease progression and follow responses to therapy with disease modifying anti-rheumatic agents (DMARDs) or anti-TNF-α therapy. We used quantitative real-time PCR to compare peripheral blood gene expression profiles in active ("unstable") RA patients on DMARDs, stable RA patients on DMARDs, and stable RA patients treated with a combination of a disease-modifying anti-rheumatoid drug (DMARD) and an anti-TNF-α agent (infliximab or etanercept) to healthy human controls. The expression of 48 inflammatory genes were compared between healthy controls (N = 122), unstable DMARD patients (N = 18), stable DMARD patients (N = 26), and stable patients on combination therapy (N = 20). Expression of 13 genes was very low or undetectable in all study groups. Compared to healthy controls, patients with unstable RA on DMARDs exhibited increased expression of 25 genes, stable DMARD patients exhibited increased expression of 14 genes and decreased expression of five genes, and combined therapy patients exhibited increased expression of six genes and decreased expression of 10 genes. These findings demonstrate that active RA is associated with increased expression of circulating inflammatory markers whereas increases in inflammatory gene expression are diminished in patients with stable disease on either DMARD or anti-TNF-α therapy. Furthermore, combination DMARD and anti-TNF-α therapy is associated with greater reductions in circulating inflammatory gene expression compared to DMARD therapy alone. These results suggest that assessment of peripheral blood gene expression may prove useful to monitor disease progression and response to therapy.
Selective Catalytic Oxidations: Opportunities and Challenges for the Selective Conversion of Renewable Resources (2022)

The goal of this DOE-funded project was to investigate the fundamental science related to selective catalytic oxidation reactions for converting renewable polyhydroxylated bio-feedstocks into new classes of value-added chemicals. The focus was on selective oxidation catalysis, specifically the mechanisms and origin of chemoselectivity for the selective Pd-catalyzed aerobic oxidations of biomass-derived polyols and carbohydrates.
X-ray Cherenkov-luminescence tomography reconstruction with a three-component deep learning algorithm: Swin transformer, convolutional neural network, and locality module (2023)

This study shows that the three-component deep learning algorithm provides an effective reconstruction method for x-ray Cherenkov-luminescence tomography.
Television Viewing Time And Mortality. The Ausdiab Study (2009)

Physical inactivity is a risk factor for premature mortality. However, the role of prolonged sedentary behavior (as distinct from lack of physical activity) in relation to mortality risk is less clear. Television (TV) viewing, which accounts for a high proportion of adults' discretionary sedentary time, has been associated with increased cardio-metabolic risk, but its relation with mortality is not known. PURPOSE: We examined TV time in relation to subsequent all-cause mortality and cardiovascular disease (CVD) mortality among 9,303 adults aged ≥ 25 years in the Australian Diabetes, Obesity and Lifestyle Study (AusDiab). METHODS: TV time was assessed at baseline in 1999-2000 using interviewer-administered questionnaires. Mortality follow-up was conducted through to November 2006 (median follow-up: 6.6 years). Cox proportional hazards regression models were adjusted for age, sex, smoking status, education, past history of self-reported CVD, diet and leisure-time physical activity and cardio-metabolic risk markers, including waist circumference. RESULTS: There were 368 deaths (124 due to CVD). Compared to those who watched TV for 0-1.9 hrs/day, the multivariate adjusted hazard ratios (HRs) (95% confidence interval) for all-cause mortality were 1.08 (0.85-1.36) for 2.0-3.9 hrs/day and 1.42 (1.06-1.92) for ≥ 4 hrs/day. For CVD, the corresponding HRs were 1.01 (0.67-1.52) and 1.68 (1.04-2.71) respectively. CONCLUSIONS: Independent of leisure-time physical activity, TV time was associated with a significantly increased risk of all-cause and CVD mortality among those watching more than 4 hours of TV per day. These results suggest that, in addition to the promotion of regular physical activity, preventative efforts could also be directed at reducing prolonged sitting; TV time may be an amenable target.
Isolation of Campylobacter concisus from feces of children with and without diarrhea (1996)

A prospective study compared fecal isolation rates of Campylobacter concisus for children with diarrhea and without diarrhea by a filter technique in which media were incubated for 4 days in a microaerobic atmosphere. No statistically significant difference in isolation rates was found (13.2% in patients with diarrhea and 9% in controls). Moreover, 35 of 37 children attending the same day care center harbored different C. concisus strains, as was demonstrated by arbitrary primer PCR DNA fingerprinting. These data suggest a lack of a pathogenic role for C. concisus in enteritis.
New injection moldable ESD compounds based on very low carbon black loadings (2002)

The electrical resistivity, mechanical properties, outgassing, ion contamination and particle-shedding characteristics of new electrostatic dissipative (ESD) injection moldable thermoplastic composites containing carbon black and glass fibers were studied. The results for polypropylene, polybutylene terephthalate and polycarbonate based compounds were compared to typical carbon black and carbon fiber filled materials. Injection moldable composites with desired resistivities in the static dissipative range (10/sup 6/-10/sup 9/ /spl Omega//sq) for conveying in production lines, storage, shipment and for cleanroom applications, having good and balanced mechanical properties can be prepared by combining a number of polymeric materials with glass fibers and less than 2 wt% carbon black.
Photographic Protocol for Image Acquisition in Craniofacial Microsomia (2019)

Abstract Craniofacial microsomia (CFM) is a congenital condition associated with orbital, mandibular, ear, nerve, and soft tissue anomalies. We present a standardized, two-dimensional, digital photographic protocol designed to capture the common craniofacial features associated with CFM.
Increasing the Performance of Portable Ion Mobility Analyzers: Development of the Periodic Focusing Differential Mobility Analyzer (PFDMA) (2014)

Ion mobility spectrometry (IMS) as a stand-alone technique has become increasingly important for applications in security, defense, and environmental monitoring, and also in biological applications such as molecular structure and -omic analysis when combined with mass spectrometry. Yet, the majority of these devices are drift cell based and limited by low duty cycles because of ion gating. Differential Mobility Analyzers (DMAs) are attractive alternatives due to their continuous ion transmission and success in analyzing aerosol particles in real time environmental tests. But, the resolution of a DMA is low due to difficulties in achieving laminar gas flow, low sample gas flow to sheath gas flow ratio, and high velocity sheath gas using small pumps, if portability is a concern. To overcome these challenges, we will introduce a new ion mobility spectrometer that increases the amount of work done on the ions during separation by introducing an electric field opposing the gas flow direction while simultaneously preserving laminar gas flow. The development of the Periodic Focusing Differential Mobility Analyzer (PFDMA) can lead to a portable device that exhibits both high resolution and sensitivity, to meet the needs of today’s expanding applications.
The Influence of Prayer Coping on Mental Health among Cardiac Surgery Patients (2007)

To address the inconsistent findings and based on Hegel's dialectic contradictive principle, this study tested a parallel mediation model that may underlie the association of using prayer for coping with cardiac surgery outcomes. Three sequential interviews were conducted with 310 patients who underwent open-heart surgery. A structural equation model demonstrated that optimism mediated the favorable effect of prayer coping. Prayer coping was also related to preoperative stress symptoms, which had a counterbalance effect on outcomes. Age was associated with better preoperative mental health, but age-related chronic conditions were associated with poor outcomes; both of these were mediated through the same mediators.