gebhart/patrepeval huggingface dataset:
Transactive Control of Commercial Building HVAC Systems (2016)

This document details the development and testing of market-based transactive controls for building heating, ventilating and air conditioning (HVAC) systems. These controls are intended to serve the purposes of reducing electricity use through conservation, reducing peak building electric demand, and providing demand flexibility to assist with power system operations. This report is the summary of the first year of work conducted under Phase 1 of the Clean Energy and Transactive Campus Project. The methods and techniques described here were first investigated in simulation, and then subsequently deployed to a physical testbed on the Pacific Northwest National Laboratory (PNNL) campus for validation. In this report, we describe the models and control algorithms we have developed, testing of the control algorithms in simulation, and deployment to a physical testbed. Results from physical experiments support previous simulation findings, and provide insights for further improvement.
Asymmetric transfer hydrogenation of imines and iminiums catalyzed by a water-soluble catalyst in water (2006)

The first asymmetric transfer hydrogenation of cyclic imines and iminiums in water was successfully performed in high yields and enantioselectivities with sodium formate as the hydrogen source and CTAB as an additive catalyzed by a water-soluble and recyclable ruthenium(II) complex of the ligand (R,R)-2.
Organosilicon uptake by biological membranes (2021)

Organosilicon compounds are ubiquitous in everyday use. Application of some of these compounds in food, cosmetics and pharmaceuticals is widespread on the assumption that these materials are not systemically absorbed. Here the interactions of various organosilicon compounds (simeticone, hexamethyldisilazane and polydimethylsiloxane) with cell membranes and models thereof were characterized with a range of analytical techniques, demonstrating that these compounds were retained in or on the cell membrane. The increasing application of organosilicon compounds as replacement of other plastics calls for a better awareness and understanding of these interactions. Moreover, with many developments in biotechnology relying on organosilicon materials, it becomes important to scrutinize the potential effect that silicone leaching may have on biological systems.
Relationship between phase shift and energy dissipation in tapping-mode scanning force microscopy (1998)

Force curves taken during a load–unload cycle show the presence of a hysteresis loop. The area enclosed by the loop is used to measure the energy dissipated by the tip-sample interaction in tapping-mode scanning force microscopy. The values of the energy loss obtained from force curves are compared with the results derived from a model based on phase shift measurements. The agreement obtained between both methods demonstrates that for the same operating conditions, the higher the phase shift the larger the amount of energy dissipated by the tip-sample interaction. It also confirms the prediction that phase-contrast images can only arise if there are tip-sample inelastic interactions.
Dissociating Hippocampal versus Basal Ganglia Contributions to Learning and Transfer (2003)

Based on prior animal and computational models, we propose a double dissociation between the associative learning deficits observed in patients with medial temporal (hippocampal) damage versus patients with Parkinson's disease (basal ganglia dysfunction). Specifically, we expect that basal ganglia dysfunction may result in slowed learning, while individuals with hippocampal damage may learn at normal speed. However, when challenged with a transfer task where previously learned information is presented in novel recombinations, we expect that hippocampal damage will impair generalization but basal ganglia dysfunction will not. We tested this prediction in a group of healthy elderly with mild-to-moderate hippocampal atrophy, a group of patients with mild Parkinson's disease, and healthy controls, using an "acquired equivalence" associative learning task. As predicted, Parkinson's patients were slower on the initial learning but then transferred well, while the hippocampal atrophy group showed the opposite pattern: good initial learning with impaired transfer. To our knowledge, this is the first time that a single task has been used to demonstrate a double dissociation between the associative learning impairments caused by hippocampal versus basal ganglia damage/dysfunction. This finding has implications for understanding the distinct contributions of the medial temporal lobe and basal ganglia to learning and memory.
Selection based on the folding properties of proteins with ribosome display (2003)

Ribosome display is a powerful tool for selecting and evolving protein functions through ligand-binding. Here, this in vitro system was used to perform selection based on the folding properties of proteins, independent of specific ligand-binding. The selection is based on two properties of misfolded proteins: (1) increased sensitivity to proteolysis and (2) greater exposure of hydrophobic area. By targeting these properties, we show that compactly folded and soluble proteins can be enriched over insoluble and random coil proteins. This approach may be especially useful for selection and evolution of folded proteins from random sequence libraries.
Scheme for a 60-nm laser based on photopumping of a high level of Mo^6+ by a spectral line of Mo^11+ (1989)

A near coincidence between lines of two molybdenum ions at 13.650 nm creates conditions that satisfy requirements for producing a short-wavelength photopumped laser in a plasma containing ions of Mo6+. The scheme is based on the use of radiation from the 4s24p P23/2∘-4s25s S21/2 transition of galliumlike Mo11+ to pump the 4s24p6 1S0–4s24p56s 1/2[1/2]1 transition of kryptonlike Mo6+. The Mo6+ ion would then lase through several possible 4s24p55p–4s24p56s transitions near 60 nm.
Increased Energy Expenditure, Lipolysis and Hyperinsulinemia Confer Resistance to Central Obesity and Type 2 Diabetes in Mice Lacking Alpha2α-Adrenoceptors (2018)

The alpha2A-adrenoceptors (α2A-ARs) are Gi-coupled receptors, which prejunctionally inhibit the release of norepinephrine (NE) and epinephrine (Epi), and postjunctionally inhibit insulin secretion and lipolysis. We have earlier shown that α2A-/- mice display sympathetic hyperactivity, hyperinsulinemia and improved glucose tolerance. Here we employed α2A-/- mice and placed the mice on a high-fat diet (HFD) to test the hypothesis that lack of α2A-ARs protects from diet-induced obesity and type 2 diabetes (T2D). In addition, a high-caloric diet was combined with running wheel exercise to test the interaction of diet and exercise. HFD was obesogenic in both genotypes, but α2A-/- mice accumulated less visceral fat than the wild-type controls, were protected from T2D, and their insulin secretion was unaltered by the diet. Lack of α2A-ARs is associated with an increased sympatho-adrenal tone, which resulted in increased energy expenditure and fat oxidation rate potentiated by HFD. Fittingly, α2A-/- mice displayed enhanced lipolytic responses to Epi, and increased faecal lipids suggesting altered fat mobilization and absorption. Subcutaneous white fat appeared to be thermogenically more active (measured as Ucp1 mRNA expression) in α2A-/- mice, and brown fat showed an increased response to NE. Exercise was effective in reducing total body adiposity and increasing lean mass in both genotypes, but there was a significant diet-genotype interaction, as even modestly increased physical activity combined with lack of α2A-AR signalling promoted weight loss more efficiently than exercise with normal α2A-AR function. These results suggest that blockade of α2A-ARs may be exploited to reduce visceral fat and to improve insulin secretion.
Peroxisomal Alanine: Glyoxylate Aminotransferase AGT1 Is Indispensable for Appressorium Function of the Rice Blast Pathogen, Magnaporthe oryzae (2012)

The role of β-oxidation and the glyoxylate cycle in fungal pathogenesis is well documented. However, an ambiguity still remains over their interaction in peroxisomes to facilitate fungal pathogenicity and virulence. In this report, we characterize a gene encoding an alanine, glyoxylate aminotransferase 1 (AGT1) in Magnaporthe oryzae, the causative agent of rice blast disease, and demonstrate that AGT1 is required for pathogenicity of M. oryzae. Targeted deletion of AGT1 resulted in the failure of penetration via appressoria; therefore, mutants lacking the gene were unable to induce blast symptoms on the hosts rice and barley. This penetration failure may be associated with a disruption in lipid mobilization during conidial germination as turgor generation in the appressorium requires mobilization of lipid reserves from the conidium. Analysis of enhanced green fluorescent protein expression using the transcriptional and translational fusion with the AGT1 promoter and open reading frame, respectively, revealed that AGT1 expressed constitutively in all in vitro grown cell types and during in planta colonization, and localized in peroxisomes. Peroxisomal localization was further confirmed by colocalization with red fluorescent protein fused with the peroxisomal targeting signal 1. Surprisingly, conidia produced by the Δagt1 mutant were unable to form appressoria on artificial inductive surfaces, even after prolonged incubation. When supplemented with nicotinamide adenine dinucleotide (NAD(+))+pyruvate, appressorium formation was restored on an artificial inductive surface. Taken together, our data indicate that AGT1-dependent pyruvate formation by transferring an amino group of alanine to glyoxylate, an intermediate of the glyoxylate cycle is required for lipid mobilization and utilization. This pyruvate can be converted to non-fermentable carbon sources, which may require reoxidation of NADH generated by the β-oxidation of fatty acids to NAD(+) in peroxisomes. Therefore, it may provide a means to maintain redox homeostasis in appressoria.
Cellulose Nanofibers Derived Surface Coating in Enhancing the Dye Removal with Cellulosic Ultrafiltration Membrane (2022)

Commercially available ultrafiltration membranes were coated with cellulose nanofibers (CNFs) produced from softwood pulp by a two-step process: a non-derivatizing DES treatment and a simple mechanical treatment (high-speed homogenization and sonification). The CNFs coating aimed at enhancement of the removal of methylene blue (MB) from water and was investigated at different concentrations of the coating, quantified in grams of CNFs per square meter of the membrane (1.3, 6.5, 13, and 19.5 g/m<sup>2</sup>). The pure water permeability (PWP) was unaffected up to the concentration of 6.5 g/m<sup>2</sup> but the dye retention increased approximately 2.5-fold. Even higher improvement of MB removal, about 4-fold, was observed when 19.5 g/m<sup>2</sup> were used, however, the pure water permeability also decreased by about 30%. In addition, it was proved that the coating can be removed and created again several times which shows that the concept could be used to improve the retention of organic compounds when high permeability membranes are used.
ChemInform Abstract: Heterogeneous Catalysis in Organic Chemistry. Part 7. Stereochemistry of the Hydrogenation of 1,3,5‐Trimethylcyclohexene. (1987)

Abstract The hydrogenation of the cyclohexenes (I) with different catalysts is investigated.
Meiosis-Induced Double-Strand Break Sites Determined by Yeast Chromatin Structure (1994)

Double-strand DNA breaks (DSBs) occur at recombination hotspots during Saccharomyces cerevisiae meiosis and are thought to initiate exchange at these loci. Analysis of DSB sites in three regions of the yeast genome indicated that breaks occur at or near many potential transcription promoters and that DSBs initiate most, if not all, meiotic recombination. DSB sites displayed deoxyribonuclease I hypersensitivity in chromatin from mitotic and meiotic cells, and changes in chromatin structure produced parallel changes in the occurrence of DSBs. Thus, features of chromatin structure that are established before meiosis play a role in determining where meiotic recombination events initiate.
Experimental antegrade enema: effects on water, electrolyte and acid-base balances with different solutions (2007)

All solutions used in this study caused minor alterations on water, electrolyte or acid-base balances. The most intense ones were caused by hypertonic sodium phosphate solution (SPS) and isotonic saline solution (ISS) and the least by polyethyleneglycol electrolyte solution (PEG) and glycerin solution 12% (GS).
Oxidative microelectrode voltammetry of tetraphenylporphyrin and copper tetraphenylporphyrin in toluene solvent (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxidative microelectrode voltammetry of tetraphenylporphyrin and copper tetraphenylporphyrin in toluene solventL. Geng and Royce W. MurrayCite this: Inorg. Chem. 1986, 25, 18, 3115–3120Publication Date (Print):August 1, 1986Publication History Published online1 May 2002Published inissue 1 August 1986https://doi.org/10.1021/ic00238a003RIGHTS & PERMISSIONSArticle Views312Altmetric-Citations41LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (715 KB) Get e-Alerts Get e-Alerts
The ultrastructure of the moss Tortula ruralis on recovery from desiccation (1975)

The papillose cells of T. ruralis are composed of cytoplasm containing a nucleus, four or five chloroplasts, mitochondria, endoplasmic reticulum, golgi bodies, electron-dense cytoplasmic bodies, and many small vesicles. Their adaxial and abaxial cell walls are composed of two fibrous layers and a cuticle, from which filamentous threads arise. These cells are interconnected by membrane-lined plasmodesmata.Dehydration causes condensation of the protoplasm at the distal and proximal cell ends, rounding and compacting of the chloroplasts, and vesicle disappearance. Immediately upon rehydration the chloroplasts and mitochondria swell and their internal membrane structures are rearranged. However, during a 24-h rehydrating period the cell structure returns to that of the normal hydrated state.
A Rare Case of Infectious Colitis with Ulcers in the Cecum Caused by Mycobacterium Gordonae (2011)

A 69-year-old female complained of persistent abdominal pain, and annular ulcers and ulcer scars were detected endoscopically in the cecum. Pathological findings included caseous granulomas with some Langhans giant cells, and Ziehl-Neelsen staining was negative. Mycobacterium gordonae (M. gordonae) was identified by the DNA-DNA hybridization method and culture (Ogawa medium) of biopsy samples from ulcerous cecal lesions. After 6 months of antibiotic therapy, ulcerous cecal lesions were healed, and no acid-fast bacteria were detected by culture of biopsy samples from scar tissue. We believe this is the first report of M. gordonae infection in the alimentary tract.
Comparison of 3D Quantitative Osteoarthritis Imaging Biomarkers from Paired CT and MR Images: data from the IMI-APPROACH study (2022)

Abstract Introduction: MRI bone surface area and femoral bone shape (B-score) measures have been employed as quantitative endpoints in DMOAD clinical trials. Computerized Tomography (CT) imaging is more commonly used for 3D visualization of bony anatomy due to its high bone-soft tissue contrast. We aimed to compare CT and MRI assessments of 3D imaging biomarkers. Methods: We used baseline and 24-month image data from the IMI-APPROACH 2-year prospective cohort study. Femur and tibia were automatically segmented using active appearance models to measure 3D bone shape, area and 3D joint space width (3DJSW). Linear regression was used to test for correlation between measures. Limits of agreement and bias were tested using Bland-Altman analysis. Results: CT-MR pairs of the same knee were available from 434 participants (78% female). B-scores from CT and MR were strongly correlated (R 2 = 0.938) with minimal bias of 0.1. Area measures were also correlated but showed a consistent bias (MR smaller). 3DJSW showed different bias (MR larger) in lateral and medial sides. Discussion: The strong correlation and small B-score bias suggests that B-score may be measured reliably using either modality. It is likely that the bone surface identified using MR and CT will be at slightly different positions within the bone/cartilage boundary. The negative bone area bias suggests the MR bone boundary is inside the CT boundary producing smaller areas for MR, consistent with the positive 3DJSW bias. The lateral-medial 3DJSW difference is possibly due to a difference in knee pose during acquisition (fully extended for CT, flexed for MR). Trial registration number: NCT03883568
Rapamycin extends life span of Rb1+/− mice by inhibiting neuroendocrine tumors (2013)

Chronic treatment of mice with an enterically released formulation of rapamycin (eRapa) extends median and maximum life span, partly by attenuating cancer. The mechanistic basis of this response is not known. To gain a better understanding of thesein vivo effects, we used a defined preclinical model of neuroendocrine cancer, Rb1+/- mice. Previous results showed that diet restriction (DR) had minimal or no effect on the lifespan of Rb1+/- mice, suggesting that the beneficial response to DR is dependent on pRb1. Since long-term eRapa treatment may at least partially mimic chronic DR in lifespan extension, we predicted that it would have a minimal effect in Rb1+/- mice. Beginning at 9 weeks of age until death, we fed Rb1+/- mice a diet without or with eRapa at 14 mg/kg food, which results in an approximate dose of 2.24 mg/kg body weight per day, and yielded rapamycin blood levels of about 4 ng/ml. Surprisingly, we found that eRapa dramatically extended life span of both female and male Rb1+/- mice, and slowed the appearance and growth of pituitary and decreased the incidence of thyroid tumors commonly observed in these mice. In this model, eRapa appears to act differently than DR, suggesting diverse mechanisms of action on survival and anti-tumor effects. In particular the beneficial effects of rapamycin did not depend on the dose of Rb1.
BMP2 and BMP7 play antagonistic roles in feather induction (2008)

Feathers, like hairs, first appear as primordia consisting of an epidermal placode associated with a dermal condensation that is necessary for the continuation of their differentiation. Previously, the BMPs have been proposed to inhibit skin appendage formation. We show that the function of specific BMPs during feather development is more complex. BMP2 and BMP7, which are expressed in both the epidermis and the dermis, are involved in an antagonistic fashion in regulating the formation of dermal condensations, and thus are both necessary for subsequent feather morphogenesis. BMP7 is expressed earlier and functions as a chemoattractant that recruits cells into the condensation, whereas BMP2 is expressed later, and leads to an arrest of cell migration, likely via its modulation of the EIIIA fibronectin domain and alpha4 integrin expression. Based on the observed cell proliferation, chemotaxis and the timing of BMP2 and BMP7 expression, we propose a mathematical model, a reaction-diffusion system, which not only simulates feather patterning, but which also can account for the negative effects of excess BMP2 or BMP7 on feather formation.
<title>Adjuvant intraoperative photodynamic therapy (AIOPDT) after photosensitization with mTHPC in a CC531 colon carcinoma model in mice</title> (2001)

The effectiveness of PDT as an adjuvant alternative therapy method for diverse malignant tumors has been investigated in numerous studies. The therapeutic benefit and extent of side effects is mainly determined by the applied photoactive substance. The second generation photosensitizer (PS) mTHPC is capable of causing selective tumor cell death in colon carcinoma when combined with laser irradiation of a PS specific wavelength. Our study revealed PDT with mTHPC as an efficient adjuvant intraoperative modality after R1/R2 resection of a subcutaneously implanted colon tumor. There was a significant increase of postoperative recurrence-free survival time using PDT compared to a control group in a colon cancer model in nude mice. The accumulation of the PS determined by point spectrometry showed a high tumor-selectivity in the tumor, tumor bed, and overlying skin compared to muscle tissue as reference parameter.
Microbubble gas volume: A unifying dose parameter in blood-brain barrier opening by focused ultrasound (2016)

Focused ultrasound with microbubbles is being developed to transiently, locally and noninvasively open the blood-brain barrier (BBB) for improved pharmaceutical delivery. Prior work has demonstrated that, for a given concentration dose, microbubble size affects both the intravascular circulation persistence and extent of BBB opening. When matched to gas volume dose, however, the circulation half-life was found to be independent of microbubble size. In order to determine whether this holds true for BBB opening as well, we independently measured the effects of microbubble size (2 vs. 6 µm diameter) and concentration, covering a range of overlapping gas volume doses (1-40 µL/kg). We first demonstrated precise targeting and a linear dose-response of Evans Blue dye extravasation to the rat striatum for a set of constant microbubble and ultrasound parameters. We found that dye extravasation increased linearly with gas volume dose, with data points from both microbubble sizes collapsing to a single line. A linear trend was observed for both the initial sonication (R<sup>2</sup>=0.90) and a second sonication on the contralateral side (R<sup>2</sup>=0.68). Based on these results, we conclude that microbubble gas volume dose, not size, determines the extent of BBB opening by focused ultrasound (1 MHz, ~0.5 MPa at the focus). This result may simplify planning for focused ultrasound treatments by constraining the protocol to a single microbubble parameter - gas volume dose - which gives equivalent results for varying size distributions. Finally, using optimal parameters determined for Evan Blue, we demonstrated gene delivery and expression using a viral vector, dsAAV1-CMV-EGFP, one week after BBB disruption, which allowed us to qualitatively evaluate neuronal health.