gebhart/patrepeval huggingface dataset:
Improved Basis-Set Incompleteness Potentials for Accurate Density-Functional Theory Calculations in Large Systems (2020)

The accurate calculation of chemical properties using density-functional theory (DFT) requires the use of a nearly complete basis set. In chemical systems involving hundreds to thousands of atoms, the cost of the calculations place practical limitations on the number of basis functions that can be used. Therefore, in most practical applications of DFT to large systems, there exists a basis-set incompleteness error (BSIE). In this article, we present the next iteration of the basis-set incompleteness potentials (BSIPs), one-electron potentials designed to correct for basis-set incompleteness error. The ultimate goal associated with the development of BSIPs is to allow the calculation of molecular properties using DFT with near-complete-basis-set results at a computational cost that is similar to a small basis set calculation. In this work, we develop BSIPs for 10 atoms in the first and second rows (H, B-F, Si-Cl) and 15 common basis sets of the Pople, Dunning, Karlsruhe, and Huzinaga types. Our new BSIPs are constructed to minimize BSIE in the calculation of reaction energies, barrier heights, noncovalent binding energies, and intermolecular distances. The BSIPs were obtained using a training set of 15 944 data points. The fitting approach employed a regularized linear least-squares method with variable selection (the LASSO method), which results in a much better fit to the training data than our previous BSIPs while, at the same time, reducing the computational cost of BSIP development. The proposed BSIPs are tested on various benchmark sets and demonstrate excellent performance in practice. Our new BSIPs are also transferable; i.e., they can be used to correct BSIE in calculations that employ density functionals other than the one used in the BSIP development (B3LYP). Finally, BSIPs can be used in any quantum chemistry program that have implemented effective-core potentials without changes to the software.
Development of a Surrogate for SASOL IPK and Its Validation in Ignition Quality Tester (2017)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;SASOL IPK is a low cetane number synthetic fuel formed from coal by the Fischer-Tropsch process which can be used as an extender to JP8, currently used in military ground vehicles. This paper presents two surrogates developed considering the following criteria: (a) availability of kinetic combustion models for each component, (b) smallest number of components to reduce computation time and cost, (c) matching the following properties of target fuel DCN, distillation curve, density, LHV, MW and H/C ratio. The autoignition and combustion characteristics of the surrogates were validated in IQT according to ASTM D6890-10a. Surrogate formulation strategy involves an equation to calculate DCN of the surrogate mixture from the DCN of each component. The linear equation commonly used for such calculations was modified to include a multiplier, based on regression analysis, for each component to produces DCN values that agree well with the measured DCN in the IQT.&lt;/div&gt;&lt;/div&gt;
Quantitative metric for assessment of pancreatic ductal adenocarcinoma treatment response in T1-weighted gadolinium-enhanced magnetic resonance imaging (2020)

<i>T1C</i> significantly increases in all phases of CE-MRI in responders to treatment, but does not change in non-responders. <i>T1C</i> correlates with treatment response, can be computed from clinical MRI exams, and may be useful as an additional metric to stratify patients undergoing treatment.
Transport and scattering of a wavepacket in a GaAs stadium disc (2004)

The inter- and intra-subband relaxation of electrons emitting an LO-phonon in GaAs/AlGaAs mesoscopic discs were investigated by femtosecond reflectance spectroscopy. It was found that the relaxation time depends on the size as well as on the shape of the disc. The relaxation time in a stadium disc is shorter than that found in circular discs. A possible origin of the enhancement of the LO-phonon emission rate in a stadium disc is discussed in terms of the electron–electron scattering rate modified in the mesoscopic discs.
Frog PNKT-4B cells express specific extracellular matrix-degrading enzymes and cytokines correlated with an invasive phenotype (1997)

A temperature-dependent metastatic phenotype reported for a frog cell line, PNKT-4B, provided a means for studying potential mediators of cell-matrix interaction involved in metastatic invasion. Zymography revealed that these cells secreted enzyme species with properties and characteristics of mammalian metalloproteinases: collagenase, stromelysin, gelatinase A, and gelatinase B. These enzymes were produced by PNKT-4B cultures maintained at both invasive-permissive (28 degrees C), and invasion-restrictive (20 degrees C) temperatures. However, under the invasive-permissive culture condition cells produced more of the putative gelatinase B and A enzymes. In addition, an activated form of gelatinase A was produced only in invasion-permissive cultures. DNA synthesis bioassays (Mv1Lu cell line and mouse thymocytes) to detect growth promoting and/or inhibitory cytokines, revealed that PNKT-4B cultures kept at 28 degrees C released significantly higher levels of stimulatory (interleukin-1-like) and latent inhibitory (transforming growth factor-beta-like) substances into the medium compared to 20 degrees C cultures. Pre-absorption of media samples with heparin-sepharose indicated a second stimulatory cytokine as well. A corneal fibroblast bioassay that tests for mediators of collagenase synthesis, detected a stimulatory substance whose activity was greatly reduced in the presence of interleukin-1 receptor antagonist protein. Collagenase stimulatory activity present in 28 degrees C culture medium was significantly higher than equal samples from 20 degrees C cultures. These studies provide a molecular correlation between release of cytokines with properties of the metastatic phenotype seen in vivo. They further provide some of the first characterizations of frog MMPs and cytokines, which are likely to be involved in other tissue remodeling events.
With Joint Forces - Establishing Situation Awareness for the Future Internet. (2009)

S.49-50
A Comparison of Low-Gravity Measurements On-Board Columbia During STS-40 (1993)

The first NASA Spacelab Life Sciences mission (SLS-1) flew 5 Jun. to 14 Jun. 1991 on the orbiter Columbia (STS-40). The purpose of the mission was to investigate the human body's adaptation to the low-gravity conditions of space flight and the body's readjustment after the mission to the 1 g environment of earth. In addition to the life sciences experiments manifested for the Spacelab module, a variety of experiments in other scientific disciplines flew in the Spacelab and in Get Away Special (GAS) Canisters on the GAS Bridge Assembly. Several principal investigators designed and flew specialized accelerometer systems to better assess the results of their experiments by means of a low-gravity environment characterization. This was also the first flight of the NASA Microgravity Science and Applications Division (MSAD) sponsored Space Acceleration Measurement System (SAMS) and the first flight of the NASA Orbiter Experiments Office (OEX) sponsored Orbital Acceleration Research Experiment accelerometer (OARE). A brief introduction to seven STS-40 accelerometer systems are presented and the resulting data are discussed and compared. During crew sleep periods, acceleration magnitudes in the 10(exp -6) to 10(exp -5) g range were recorded in the Spacelab module and on the GAS Bridge Assembly. Magnitudes increased to the 10(exp -4) g level during periods of nominal crew activity. Vernier thruster firings caused acceleration shifts on the order of 10(exp -4) g and primary thruster firings caused accelerations as great as 10(exp -2) g. Frequency domain analysis revealed typical excitation of Orbiter and Spacelab structural modes at 3.5, 4.7, 5.2, 6.2, 7, and 17 Hz.
Biomarkers for the Early Detection of Pancreatic Ductal Adenocarcinoma (2022)

Pancreatic ductal adenocarcinoma has one of the worst survival rates among adult cancers, with only 11% in the United States surviving five years after diagnosis. The majority of patients are diagnosed with late-stage disease, since early-stage pancreatic ductal adenocarcinoma is typically either asymptomatic or presents with non-specific symptoms. Pancreatic ductal adenocarcinoma thus remains a highly fatal disease. Today, surgical resection (removal of the pancreas) is the only potentially curative modality of treatment available. Detecting pancreatic cancer lesions early enough to perform surgery is, however, beset with difficulties. Nevertheless, the timeline of progression from low-grade precursor lesions to invasive cancer does offer a window of opportunity to detect the disease earlier than is currently possible. By providing physicians with actionable information early enough for the cancer to be removed surgically, the overall 5-year pancreatic ductal adenocarcinoma survival rate could increase from 11% to over 50%.&nbsp; In this chapter, we describe the development and clinical implementation of a proteomic, multi-biomarker blood test for the early detection of pancreatic ductal adenocarcinoma.
Prognostic value of heart rate variability in post-infarction patients (2014)

Background/Aim. Depressed heart rate variability (HRV) indicating autonomic disequilibrium and propensity to ventricular ectopy can be useful for risk stratification in patients following acute myocardial infarction (AIM). The aim of the study was to assess heart rate variability as a predictor of allcause mortality in post-infarction patients. Methods. We analyzed the 24-hour electrocardiographic (ECG) recordings of 100 patients (80 males) during hospitalization for AIM. The mean age of patients was 56.99 + 11.03 years. Time domain heart rate variability analysis was obtained from 8 to 13 days after index infarction by mean of a 24- hour ECG recording, and the calculated parameters were: standard deviation of all normal to normal RR intervals (SDNN), RRmax-RRmin (difference between the longest RR interval and the shortest RR interval), mean RR interval. We also analyzed ventricular premature complexes from the ECG data. The patients underwent clinical evaluation, laboratory tests and echocardiography. Results. Within a oneyear follow-up period 11 patients experienced death, 10 of them because of cardiac reason and one because of stroke. There were significantly lower values of SDNN (60.55 ? 12.84 ms vs 98.38 ? 28.21 ms), RRmax-RRmin (454.36 ? 111.00 ms vs 600.99 ? 168.72 ms) and mean RR interval (695.82 ? 65.87 ms vs 840.07 ? 93.97 ms) in deceased patients than in the survivors, respectively (p &lt; 0.01). The deceased patients were of higher mean age, with lower left ventricular ejection fraction (0.46 ? 0.05 vs 0.56 ? 0.06 in survivors), and more frequent clinical signs of heart failure and ventricular ectopic activity (&gt; 10VPCs/h; p &lt; 0.01). Multivariate Cox analysis showed that SDNN was a significant, independent predictor of all-cause mortality in postinfarction patients. The other independent predictors were clinical signs of heart failure - Killip class II and III and ventricular ectopic activity. Conclusion. Depressed HRV is an independent predictor of mortality in post-infarction patients and may provide useful additional prognostic information in non-invasive risk stratification of these patients.
Aesthetic quality assessment of consumer photos with faces (2010)

Automatically assessing the subjective quality of a photo is a challenging area in visual computing. Previous works study the aesthetic quality assessment on a general set of photos regardless of the photo's content and mainly use features extracted from the entire image. In this work, we focus on a specific genre of photos: consumer photos with faces. This group of photos constitutes an important part of consumer photo collections. We first conduct an online study on Mechanical Turk to collect ground-truth and subjective opinions for a database of consumer photos with faces. We then extract technical features, perceptual features, and social relationship features to represent the aesthetic quality of a photo, by focusing on face-related regions. Experiments show that our features perform well for categorizing or predicting the aesthetic quality.
Structure of a bis(osmate ester) produced by addition of osmium tetroxide to diethyl 3,4-furandicarboxylate (1991)

[Os 2 (O) 4 (C 10 H 12 O 9 )(C 5 H 5 N) 4 ] cristallise dans C2/c avec a=18,593, b=13,240, c=16,639 A, β=122,10 o , Z=4; affinement jusqu'a R=0,0384. L'addition de deux parties OsO 4 /(pyridine) 2 au diethyl furane-3,4-dicarboxylate produit un bis (osmate ester), avec des atomes Os trans l'un par rapport a l'autre en fonction du cycle tetrahydrofurane. Ce dernier possede la conformation demi-chaise prevue
CAVITY-AWARE MOTIFS REDUCE FALSE POSITIVES IN PROTEIN FUNCTION PREDICTION (2006)

Determining the function of proteins is a problem with immense practical impact on the identification of inhibition targets and the causes of side effects. Unfortunately, experimental determination of protein function is expensive and time consuming. For this reason, algorithms for computational function prediction have been developed to focus and accelerate this effort. These algorithms are comparison techniques which identify matches of geometric and chemical similarity between motifs, representing known functional sites, and substructures of functionally uncharacterized proteins (targets). Matches of statistically significant geometric and chemical similarity can identify targets with active sites cognate to the matching motif. Unfortunately statistically significant matches can include false positive matches to functionally unrelated proteins. We target this problem by presenting Cavity Aware Match Augmentation (CAMA), a technique which uses C-spheres to represent active clefts which must remain vacant for ligand binding. CAMA rejects matches to targets without similar binding volumes. On 18 sample motifs, we observed that introducing C-spheres eliminated 80% of false positive matches and maintained 87% of true positive matches found with identical motifs lacking C-spheres. Analyzing a range of C-sphere positions and sizes, we observed that some high-impact C- spheres eliminate more false positive matches than others. High-impact C-spheres can be detected with a geometric analysis we call Cavity Scaling, permitting us to refine our initial cavity-aware motifs to contain only high-impact C-spheres. In the absence of expert knowledge, Cavity Scaling can guide the design of cavity-aware motifs to eliminate many false positive matches.
End‐Group‐Functionalized Poly(α‐olefinates) as Non‐Polar Building Blocks: Self‐Assembly of Sugar–Polyolefin Hybrid Conjugates (2016)

Abstract Living coordinative chain‐transfer polymerization of α‐olefins, followed by chemical functionalization of a Zn(polymeryl) 2 intermediate, provides entry to end‐group functionalized poly(α‐olefinates) (x‐PAOs) that can serve as a new class of non‐polar building block with tailorable occupied volumes. Application of these x‐PAOs for the synthesis and self‐assembly of sugar‐polyolefin hybrid conjugates demonstrate the ability to manipulate the morphology of the ultra‐thin film nanostructure through variation in occupied volume of the x‐PAO domain.
Abstract 359: Duke Activity Status Index is Sensitive to Non-Fatal Adverse Cardiac Events when Evaluating Patient Outcome at Late Follow-up (2015)

Objective: The Duke Activity Status Index (DASI) questionnaire has become an established measure of cardiac functional capacity and quality of life. However, the relationship between a low DASI score and presence of major adverse cardiac events has not yet been assessed. This study evaluates differences in patient function and occurrence of late cardiac events in patients undergoing coronary artery bypass (CAB). Methods: Patients undergoing CAB between 1994 and 2014 at the Valley Hospital were assessed and propensity matched for surgical approach. The resulting population of 1856 patients was followed for a mean time of 11.2 years ranging from 1 to 20 year. Survival, occurrence of MI, stroke, repeat revascularization and patient function using the DASI questionnaire were assessed. At the latest follow-up, 1363 patients were still alive, of which 776 had completed the DASI questionnaire. Patients who completed the questionnaire (Responders) were compared to those who did not complete the DASI (Non-Responders) on baseline demographic and clinical characteristics. Kaplan-Meier and Cox Proportional Hazards Regression were used to compare late non-fatal events that occurred in patients with a low (&lt;37, N=247), medium (37-52, N=209), or high (&gt;52, N=310) DASI score. Results: Responders had a higher rate of prior MI, increased hypertension, and were significantly older at baseline procedure compared to Non-Responders. Both groups had comparable surgical risk and left ventricle ejection fraction at baseline revascularization. Kaplan-Meier analysis of the Responders showed that patients with a low scoring DASI had significantly greater occurrence of all late events. Cox Regression analysis controlling for all baseline factors showed that patients with a low DASI score had a two-fold increase in late non-fatal events compared to medium and high DASI scoring patients (adjusted hazard ratio: 2.076, 95% C.I. 1.309-3.293, p=0.002) (Figure 1). Conclusions: This study demonstrates that in cardiac surgical patients, a low score on DASI is independently associated with a higher occurrence of late non-fatal cardiac events. This provides further evidence supporting the use of the DASI questionnaire in evaluating patient functioning after cardiac surgery.
Interfacial Tension of (Methane + Nitrogen) + Water and (Carbon Dioxide + Nitrogen) + Water Systems (2001)

Interfacial tension data of (CH4 + N2) + H2O and (CO2 + N2) + H2O systems were measured using a pendant-drop method. The temperature and pressure ranges were 298−373 K and 1−30 MPa, respectively. The effects of gas composition, temperature, and pressure on the interfacial tension of the systems studied have been investigated. The linear gradient theory (LGT) was used to calculate the interfacial tensions of these two systems. The results show good agreement between the calculated and experimental interfacial tension data for the (CH4 + N2) + H2O system. However, it was found that the LGT model with one adjustable parameter is inadequate to give accurate predictions for the CO2 + H2O system and thus is not suitable for the description of the (CO2 + N2) + H2O system.
TGF-β Inhibitor CILP as a Novel Biomarker for Cardiac Fibrosis (2020)

[Figure: see text]
Mantis: A Fast, Small, And Exact Large-Scale Sequence-Search Index - Experiment List (2018)

This package contains three files describing the datasets used in all experiments done in Mantis paper. The experiment_cutoff file lists all the experiment accession numbers and the k-mer count cutoffs used to filter each experiment, which is based on the same conditions as in the SSBT paper (explained in detail in the paper). The url file contains all the urls to the parent directory of the fastq files for the paired-end or single-end reads indexed in the experiments. The valid experiments file lists all 2586 experiments out of the original 2652 that passed our "validity" criteria and were used in the experiments in the paper (further details explained in the paper).
Threshold damage of in vivo porcine skin at 2000-nm laser irradiation (2006)

A series of experiments were conducted <i>in vivo</i> on female Yucatan mini-pigs to determine the ED<sub>50</sub> damage thresholds for 2000 nm continuous wave laser irradiation. These results provide new information for refinement of Maximum Permissible Exposure (MPE). The study employed Gaussian laser beam exposures with spot diameters (1/e<sup>2</sup>) of 4.83 mm, 9.65 mm and 14.65 mm and exposure durations of 0.25 s, 0.5 s, 1.0 s and 2.5 seconds as a function of laser power. The effect of each irradiation was evaluated within one minute after irradiation and the final determination was made at 48 hours post exposure. Probit analysis was conducted to estimate the dose for 50% probability of laser-induced damage (ED<sub>50</sub>) defined as persistent redness at the site of irradiation for the mini-pig skin after 48 hours. Histopathologic procedures were used to determine the mechanisms of the laser effects in the skin and map the extent and severity of the lesions. The thresholds study shows that consideration for lowering the current Maximum Permissible Exposure (MPE) limits should be explored as the laser beam diameter becomes larger than 3.5 mm. Based on the limited experimental data, the duration and size dependences of the ED<sub>50</sub> damage thresholds could be described by an empirical equation: (Equation available in manuscript.)
ChemInform Abstract: Selective N3‐ and 5′‐O‐Alkylation of 2′,3′‐O‐Isopropylideneuridine with Methyl Iodide (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Autophagy protein microtubule-associated protein 1 light chain-3B (LC3B) activates extrinsic apoptosis during cigarette smoke-induced emphysema (2010)

Chronic obstructive pulmonary disease (COPD) is a debilitating disease caused by chronic exposure to cigarette smoke (CS), which involves airway obstruction and alveolar loss (i.e., emphysema). The mechanisms of COPD pathogenesis remain unclear. Our previous studies demonstrated elevated autophagy in human COPD lung, and as a cellular and tissue response to CS exposure in an experimental model of emphysema in vivo. We identified the autophagic protein microtubule-associated protein 1 light chain-3B (LC3B) as a positive regulator of CS-induced lung epithelial cell death. We now extend these initial observations to explore the mechanism by which LC3B mediates CS-induced apoptosis and emphysema development in vivo. Here, we observed that LC3B(-/-) mice had significantly decreased levels of apoptosis in the lungs after CS exposure, and displayed resistance to CS-induced airspace enlargement, relative to WT littermate mice. We found that LC3B associated with the extrinsic apoptotic factor Fas in lipid rafts in an interaction mediated by caveolin-1 (Cav-1). The siRNA-dependent knockdown of Cav-1 sensitized epithelial cells to CS-induced apoptosis, as evidenced by enhanced death-inducing signaling complex formation and caspase activation. Furthermore, Cav-1(-/-) mice exhibited higher levels of autophagy and apoptosis in the lung in response to chronic CS exposure in vivo. In conclusion, we demonstrate a pivotal role for the autophagic protein LC3B in CS-induced apoptosis and emphysema, suggestive of novel therapeutic targets for COPD treatment. This study also introduces a mechanism by which LC3B, through interactions with Cav-1 and Fas, can regulate apoptosis.