gebhart/patrepeval huggingface dataset:
Accurate Nonempirical Range-Separated Hybrid van der Waals Density Functional for Complex Molecular Problems, Solids, and Surfaces (2022)

We introduce a new, general-purpose, range-separated hybrid van der Waals density functional termed vdW-DF2-ahbr within the nonempirical vdW-DF method [Hyldgaard, et al. J. Phys. Condens. Matter 32, 393001 (2020)]. It combines a correlation from vdW-DF2 with a screened Fock exchange that is fixed by a new model of exchange effects in the density-explicit vdW-DF-b86r or rev-vdW-DF2 functional [Hamada, Phys. Rev. B 89, 121103(R) ( The new vdW-DF2-ahbr prevents spurious exchange binding and has a small-density-gradient form set from many-body perturbation analysis. It is accurate for bulk as well as layered materials, and it systematically and significantly improves the performance of the present vdW-DFs for molecular problems. Importantly, vdW-DF2-ahbr also outperforms present-standard (dispersion-corrected) range-separated hybrids on a broad collection of noncovalent-interaction benchmark sets, while at the same time successfully mitigating the density-driven errors that often affect the description of molecular transition states and isomerization calculations. vdW-DF2-ahbr furthermore improves on state-of-the-art densityfunctional-theory approaches by succeeding at challenging problems. For example, it (1) correctly predicts both the substrate structure and the site preference for CO adsorption on Pt(111), (2) it outperforms existing nonempirical vdW-DFs for the description of CO 2 adsorption in both a functionalized and in a simple metalorganic framework, and (3) it is highly accurate for the set of base-pair interactions in a model of DNA assembly.
An experimental methodology to assess the impact of desaturation on gas diffusion in clay based materials (2023)

The transport of gas in clay-based materials is dominated by diffusion. SCK CEN has studied and recorded an extensive data set of diffusion coefficients of gases in various saturated clays (Boom Clay, Opalinus Clay, Callovo-Oxfordian claystone and bentonites) used in Europe as host formations or in engineered barrier systems in the context of deep geological disposal of high and intermediate level nuclear wastes. However, partially saturated conditions may exist during the life cycle of a radioactive waste repository. The current study aims at establishing an experimental method to measure the diffusion coefficients of various gases in partially saturated clay-based materials by means of double through diffusion tests (cross diffusion of gases across the porous sample, driven by concentration gradients) and to assess the impact of desaturation on gas diffusivity. Historically, gas diffusion measurements have been performed under dissolved conditions with continuous water and dissolved gas flow around the clay sample. However, since the saturation degree of the sample has to be constant, a novel setup has been designed and optimized to operate under a pure gas phase under controlled relative humidity (RH). The experimental concept consists of cross diffusion of gas mixtures from two reservoirs at a fixed relative humidity on either side of the sample cell, namely, the upstream and downstream reservoirs. The RH is controlled using the same saturated salt solutions in both reservoirs. During the experiment, gases will diffuse from the upstream to the downstream reservoir. By measuring the change in gas composition in the downstream reservoir with a gas analyzer equipped with a mass spectrometer (which expresses the gas composition in terms of partial pressure), the gas flux and hence the diffusion coefficient is estimated by applying steady state Fick’s first law. The experimental methodology has been validated by performing an experiment on a sandy-clay sample of known petrophysical properties, at full saturation.
Development of Positron-Emission Tomography/Single-Photon Emission Computed Tomography Imaging Probes for in Vivo Detection of .BETA.-Amyloid Plaques in Alzheimer's Brains (2009)

Currently, the development of radiotracers for in vivo imaging of beta-amyloid plaques in Alzheimer's disease (AD) brains is an important, active area of molecular imaging. Postmortem brains of AD patients reveal neuropathologic features: the presence of beta-amyloid plaques and neurofibrillary tangles, which contain beta-amyloid peptides and highly phosphorylated tau proteins. Increases in the concentration of beta-amyloid in the course of the disease lead to changes in AD brains. Thus, when used in combination with positron-emission tomography/single-photon emission computed tomography (PET/SPECT), beta-amyloid imaging agents could serve as surrogate markers for the early diagnosis and neuropathogenetic studies of AD. Furthermore, quantitative evaluation of beta-amyloid plaques in the brain could facilitate the evaluation of the efficacy of antiamyloid therapies that are currently being investigated. This paper reviews our research on the development of PET/SPECT imaging agents for in vivo detection of beta-amyloid plaques in Alzheimer's brains.
Position Paper: ASNR Scientific Issues Committee 1995 (1996)

The Scientific Issues Committee was formed in 1995. Participating were Mindy Aisen, M.D. (Chair), Michael Rosen, Ph.D., Steven Sparr, M.D., Barbara Giesser, M.D., Lau rie Laven, M.D., Laura Lennihan, M.D., and Thomas Wessel, M.D. As a newly formed committee, we explored means by which we could most effectively contribute to the ASNR. We determined that it is necessary to promote an awareness of the importance of scientific scholarship, enhance the communication of research ideas, and identify obstacles to neurorehabilitation research advancement. To meet these goals, we are pre pared to collaborate with the members of other ASNR committees to assist in prepar ing educational materials and assembling scientific programs. We are also considering conducting a survey of the ASNR membership to identify public policies that inhibit or promote scientific research in neurorehabilitation.Our major activity this year was the drafting of a Position Paper, which we hope reflects the specific vision of the ASNR membership. Our purpose was to identify pri orities for scientific study and articulate the unique contribution neurorehabilitation can make.
Mechanistic Studies of Zinc Electrodeposition from Deep Eutectic Electrolytes (2013)

Deep eutectic electrolytes have been suggested as alternatives to classical room temperature ionic liquids and been used for the electrodeposition of metals. We have investigated the electrodeposition of zinc from a Lewis-basic choline chloride/ethylene glycol deep eutectic solvent containing ZnCl2. Raman spectroscopy confirmed the presence of the [ZnCl4]2− ion in the electrolyte that was examined by cyclic voltammetry at static and rotating glassy carbon disk electrodes. The formation of a dissolved, intermediate reducible zinc species Z during the cathodic sweep is proposed to account for the unusual zinc electrodeposition behavior observed in the deep eutectic electrolyte in agreement with the effect of rotation rate, cathodic switching potential and potential sweep rate on the deposition current in RDE voltammetry. The zinc electrodeposition behavior with sodium ethoxide added to the deep eutectic solvent supports the suggestion that Z is a complex of Zn2+ and deprotonated components of the solvent. The absence of a current plateau in RDE experiments with ethoxide containing electrolyte is thought to be the result of a potential dependent blocking of the reduction of Z by a layer adsorbed on the electrode.
A Case of Abdominal Aortic Aneurysm with Horseshoe Kidney. (1993)

症例は65歳男性. 心筋梗塞の経過観察中に腹部拍動性腫瘤を指摘された. CT検査において腹部大動脈瘤とその腹側に馬蹄腎が認められた. 血管造影検査にて馬蹄腎峡部は明瞭に抽出され, 大動脈瘤は峡部の中央部から大動脈分岐部に及んでいた. 正常の左右腎動脈以外に瘤の直上からも一対の異常腎動脈が分岐していたが腎盂尿管には異常はなかった. 手術時異常腎動脈と馬蹄腎峡部を温存し腹部大動脈をY型人工血管にて置換したが, この際腎峡部にテープを通し牽引することにより手術操作は容易に行いえた. 本邦における手術例の報告は未だ少なく, 文献的考察を含め報告した.
Manual on the production and use of live food for aquaculture (1996)

Manual on the production and use of live food for aquaculture , Manual on the production and use of live food for aquaculture , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Navigational design of web information systems: Framework development and case study (2006)

As prior empirical and conceptual work indicates, success and usability of web information systems is subject to navigational design. Although web information systems are not a new phenomenon and were examined intensively in the past, holistic in-depth investigations of navigational issues seem to be arbitrary rather than theoretically and conceptually founded. In particular, we argue that we are lacking an appropriate description language serving as a shared conceptualization of our subject of research. We present a conceptual framework for describing and assessing web information systems and their navigational capabilities. Moreover, we provide some empirical evidence of its applicability by reporting on a case study that pays special regard to navigational design and usability improvement.
Healthcare Professionals and the Reciprocal Duty to Treat During a Pandemic Disaster (2008)

Malm and colleagues (2008) consider whether healthcare providers are duty-bound to expose themselves to a significant risk of illness and potential death in the service of patients during a pandemi...
Early diagnosis of mild cognitive impairment and Alzheimer's disease based on salivary lactoferrin (2017)

This biomarker may offer new insights in the early diagnostics for AD.
Abstract 154: Generation of Purified Cardiomyocytes from Pluripotent Stem Cells Using Molecular Beacons (2012)

Background: While various methods for generating cardiomyocytes (CMs) from pluripotent stem cells (PSCs) including both embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) have been reported, all available methods are only allowed to produce heterogeneous population of CM mixed with non-CM cells. Therefore, strategies to enrich pure CMs for scientific and clinical applications have been highly required. Hence, we developed a novel system in which CMs can be purified by cardiac specific molecular beacons (MBs). MBs are dual-labeled antisense nano-scale probes that emit a fluorescence signal when hybridized to target mRNAs. We hypothesized that MBs targeted to CM specific mRNAs can identify CMs and allow isolation of purified CMs by fluorescence-activated cell sorting (FACS). Methods and results: Five MBs targeting distinct sites on either cardiac troponin T (cTNT) or α/β myosin heavy chain (α/βMHC) were designed and characterized in various cell types. To find the optimal MB that can selectively identifying CMs, each MB was delivered into HL-1 CMs, an immortalized mouse CM cell line, smooth muscle cells, endothelial cells, mouse ESCs and fibroblasts and its specificity was determined by flow cytometry. As a result, two MBs identified MB+ cells up to 98% from HL-1 CMs but lower than 10% of the non-CM cells suggesting these MBs are CM specific. Subsequently, the selected MBs were delivered into both mouse and human PSCs derived CMs and 41 to 49% of the cells were identified as an MB+ population. Interestingly, the rate of MB+ cells was similar to CM quantification determined by cTNT intracellular flow cytometry. Finally, we determined whether cell sorting with cardiac-specific MBs can enrich CMs from the heterogeneous mouse and human PSC cultures and found that ∼97% of MB-based sorted CMs expressed cTNT. These enriched cells were further cultured and their CM identity was verified by immunocytochemistry and qRT-PCR analysis. Ca2+ transient analysis further confirmed that these purified CMs displayed functional CM characteristics Conclusion: Using cardiac specific MBs, we were able to obtain highly purified CMs. These purified CMs and the system can be highly useful for clinical applications as well as drug discovery.
Physical mechanisms for delaying condensation freezing on grooved and sintered wicking surfaces (2022)

Heat pipes are passive heat transfer devices crucial for systems on spacecraft; however, they can freeze when exposed to extreme cold temperatures. The research on freezing mechanisms on wicked surfaces, such as those found in heat pipes, is limited. Surface characteristics, including surface topography, have been found to impact freezing. This work investigates freezing mechanisms on wicks during condensation freezing. Experiments were conducted in an environmental chamber at 22 °C and 60% relative humidity on three types of surfaces (i.e., plain copper, sintered heat pipe wicks, and grooved heat pipe wicks). The plain copper surface tended to freeze via ice bridging—consistent with other literature—before the grooved and sintered wicks at an average freezing time of 4.6 min with an average droplet diameter of 141.9 ± 58.1 μm at freezing. The grooved surface also froze via ice bridging but required, on average, almost double the length of time the plain copper surface took to freeze, 8.3 min with an average droplet diameter of 60.5 ± 27.9 μm at freezing. Bridges could not form between grooves, so initial freezing for each groove was stochastic. The sintered wick's surface could not propagate solely by ice bridging due to its topography, but also employed stochastic freezing and cascade freezing, which prompted more varied freezing times and an average of 10.9 min with an average droplet diameter of 97.4 ± 32.9 μm at freezing. The topography of the wicked surfaces influenced the location of droplet nucleation and, therefore, the ability for the droplet-to-droplet interaction during the freezing process.
The Steel Scrap Age (2013)

Steel production accounts for 25% of industrial carbon emissions. Long-term forecasts of steel demand and scrap supply are needed to develop strategies for how the steel industry could respond to industrialization and urbanization in the developing world while simultaneously reducing its environmental impact, and in particular, its carbon footprint. We developed a dynamic stock model to estimate future final demand for steel and the available scrap for 10 world regions. Based on evidence from developed countries, we assumed that per capita in-use stocks will saturate eventually. We determined the response of the entire steel cycle to stock saturation, in particular the future split between primary and secondary steel production. During the 21st century, steel demand may peak in the developed world, China, the Middle East, Latin America, and India. As China completes its industrialization, global primary steel production may peak between 2020 and 2030 and decline thereafter. We developed a capacity model to show how extensive trade of finished steel could prolong the lifetime of the Chinese steelmaking assets. Secondary steel production will more than double by 2050, and it may surpass primary production between 2050 and 2060: the late 21st century can become the steel scrap age.
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures (2018)

Large amounts of data emerging from experiments in molecular medicine are leading to the identification of molecular signatures associated with disease subtypes. The contextualization of these patterns is important for obtaining mechanistic insight into the aberrant processes associated with a disease, and this typically involves the integration of multiple heterogeneous types of data. In this review, we discuss knowledge representations that can be useful to explore the biological context of molecular signatures, in particular three main approaches, namely, pathway mapping approaches, molecular network centric approaches and approaches that represent biological statements as knowledge graphs. We discuss the utility of each of these paradigms, illustrate how they can be leveraged with selected practical examples and identify ongoing challenges for this field of research.
Toward Quantifying Oil Contamination in Vegetated Areas Using Very High Spatial and Spectral Resolution Imagery (2019)

Recent remote sensing studies have suggested exploiting vegetation optical properties for assessing oil contamination, especially total petroleum hydrocarbons (TPH) in vegetated areas. Methods based on the tracking of alterations in leaf biochemistry have been proposed for detecting and quantifying TPH under controlled and field conditions. In this study, we expand their use to airborne imagery, in order to monitor oil contamination at a larger scale. Airborne hyperspectral images with very high spatial and spectral resolutions were acquired over an industrial site with oil-contamination (mud pits) and control sites both colonized by Rubus fruticosus L. The method of oil detection exploiting 14 vegetation indices succeeded in classifying the sites in the case of high TPH contamination (overall accuracy ≥ 91.8%). Two methods, based on either the PROSAIL (PROSPECT + SAIL) radiative transfer model or elastic net multiple regression, were also developed for quantifying TPH. Both methods were tested on reflectance measurements in the field, at leaf and canopy scales, and on the image, and achieved accurate predictions of TPH concentrations (RMSE ≤ 3.28 g/kg−1 and RPD ≥ 1.90). The methods were validated on additional sites and open up promising perspectives of operational application for oil and gas companies, with the emergence of new hyperspectral satellite sensors.
Risk factors for chronic pouchitis after ileal pouch–anal anastomosis: a prospective cohort study (2012)

Pancolitis and longer follow-up are directly related to the development of chronic pouchitis.
Effects of dasatinib on prostate cancer bone metastases and normal bone measured by 18F-fluoride PET: Preliminary results from ACRIN 6687 (2013)

A retrospective comparative chart audit was conducted to identify patient characteristics associated with falls in the acute care setting, to examine the extent to which the significant characteristics explained if falls occurred, and to test the ability of variables believed to be risk factors to predict falls. Patients aged 60 and older who fell during hospitalization (n = 331) were compared with a random sample of patients aged 60 and older who were hospitalized during the same time period but did not fall (n = 300). Two days of documentation were sampled: admission day and day preceding the fall for the fall group, and admission day and a random day of hospital stay for the no-fall group. Findings supported the idea that fall-prone patients can be identified and that significant differences between those who do and do not fall are evident at hospital admission. The findings also suggested an alteration in the constellation of characteristics nurses use to identify fall-prone patients. Of 11 variables representing standard risk factors, only 6 were significantly related to fall status; 5 entered the regression equation as significantly contributing to the 22% explained variance. When potential predictor variables were expanded to include additional patient characteristics, the explained variances for fall status were 31% from the admission day data and 34.5% from the fall/random day data.
Antiserum against Homologous Atrial Natriuretic Peptide Diminishes the Natriuretic Response during Mineralocorticoid Escape in Rats* (1991)

To elucidate the physiological role of atrial natriuretic peptide (ANP) in plasma during mineralocorticoid escape, we investigated the effects of passive immunization with ANP-specific antiserum on deoxycorticosterone (DOCA)-treated rats. Sodium was retained in excess of intake during the first day after treatment with DOCA, and sodium balance returned to control values by the second day, whereas the excretion of potassium exceeded the intake during all days after DOCA treatment. These changes in electrolyte balance were associated with a significant increase in plasma levels of ANP. Administration of ANP-specific antiserum significantly impaired the return to normal sodium balance as well as the augmented kaliuresis that were observed on the second day after injection of DOCA. No significant effect was observed on either sodium or potassium balance after the injection of normal rabbit serum. These results suggest that plasma ANP plays an important role in mineralocorticoid escape.
Prolyl 4-hydroxylase Isoenzymes I and II Have Different Expression Patterns in Several Human Tissues (2001)

Prolyl 4-hydroxylase plays a central role in the synthesis of all collagens. We have previously reported that the recently identified Type II isoenzyme is its main form in chondrocytes and possibly in capillary endothelial cells, while Type I is the main form in many other cell types. We report here that the Type II isoenzyme is clearly the main form in capillary endothelial cells and also in cultured umbilical vein endothelial cells, whereas no Type I isoenzyme could be detected in these cells by immunostaining or Western blotting. The Type II isoenzyme was also the main form in cells of the developing glomeruli in the fetal kidney and tubular structures of collecting duct caliber in both fetal and adult kidney, in occasional sinusoidal structures and epithelia of the bile ducts in the liver, and in some cells of the decidual membrane that probably represented invasive cytotrophoblasts in the placenta. Osteoblasts in a fetal calvaria, i.e., a bone developing by intramembranous ossification, stained strongly for both types of isoenzyme. The Type I isoenzyme was the main form in undifferentiated interstitial mesenchymal cells of the developing kidney, for example, and in fibroblasts and fibroblastic cells in many tissues. Skeletal myocytes and smooth muscle cells appeared to have the Type I isoenzyme as their only prolyl 4-hydroxylase form. Hepatocytes expressed small amounts of the Type I enzyme and very little if any Type II, the Type I expression being increased in malignant hepatocytes and cultured hepatoblastoma cells. The data suggest that the Type I isoenzyme is expressed especially by cells of mesenchymal origin and in developing and malignant tissues, whereas the Type II isoenzyme is expressed, in addition to chondrocytes and osteoblasts, by more differentiated cells, such as endothelial cells and cells of epithelial structures. (J Histochem Cytochem 49:1143-1153, 2001)
In vitro elution of moxifloxacin from cancellous bone allografts (2009)

The characteristics of cancellous bone allografts as carriers of moxifloxacin are described. Particles of cancellous bone were compressed into a wire-mesh cylinder and impregnated into a solution of moxifloxacin for different time periods. Five replicas were impregnated for 1 h; another five for 24 h; and another five for 48 h. Impregnated allografts were then transferred into vials containing 5 ml of Mueller-Hinton broth and incubated at 37 degrees C. Broth was replaced daily. Concentrations of moxifloxacin in broth were determined after analysis by an high performance liquid chromatography system. Moxifloxacin was eluted at very high concentrations within the first days. Concentrations remained above 100 microg/ml until day 8 and above 40 microg/ml until day 20. It is concluded that cancellous bone allografts may allow the adequate in vitro elution of moxifloxacin. The latter results support their application in experimental models of osteomyelitis.