gebhart/patrepeval huggingface dataset:
Measurements of carbon sequestration by long‐term eddy covariance: methods and a critical evaluation of accuracy (1996)

Abstract The turbulent exchanges of CO 2 and water vapour between an aggrading deciduous forest in the north‐eastern United States (Harvard Forest) and the atmosphere were measured from 1990 to 1994 using the eddy covariance technique. We present a detailed description of the methods used and a rigorous evaluation of the precision and accuracy of these measurements. We partition the sources of error into three categories: (1) uniform systematic errors are constant and independent of measurement conditions (2) selective systematic errors result when the accuracy of the exchange measurement varies as a function of the physical environment, and (3) sampling uncertainty results when summing an incomplete data set to calculate long‐term exchange. Analysis of the surface energy budget indicates a uniform systematic error in the turbulent exchange measurements of ‐20 to 0%. A comparison of nocturnal eddy flux with chamber measurements indicates a selective systematic underestimation during calm (friction velocity &lt; 0.17 m s −1 ) nocturnal periods. We describe an approach to correct for this error. The integrated carbon sequestration in 1994 was 2.1 t C ha −1 y −1 with a 90% confidence interval due to sampling uncertainty of ±0.3 t C ha −1 y −1 determined by Monte Carlo simulation. Sampling uncertainty may be reduced by estimating the flux as a function of the physical environment during periods when direct observations are unavailable, and by minimizing the length of intervals without flux data. These analyses lead us to place an overall uncertainty on the annual carbon sequestration in 1994 of ‐0.3 to +0.8 t C ha −1 y −1 .
Translating PI3K-Delta Inhibitors to the Clinic in Chronic Lymphocytic Leukemia: The Story of CAL-101 (GS1101) (2012)

Targeted therapy with imatinib has transformed the treatment of chronic myeloid leukemia (CML). Unlike CML, chronic lymphocytic leukemia (CLL) lacks a common genetic aberration but does demonstrate constitutive activation of PI3-kinase (PI3K) as compared to normal B cells. This constitutively active PI3K in CLL likely relates to tonic B-cell receptor signaling that is present across a wide variety of B-cell malignancies. Although PI3K is quite proximal and represents an ideal target to pharmacologically modulate, the complexity of this pathway on which many normal functions are dependent had for many years been problematic. The p110 delta isoform of PI3K is relatively specific to hematopoietic cells, and elegant mouse studies where p110 delta was genetically inactivated demonstrated only a selective B-cell defect. Subsequent development of a potent, selective p110 delta inhibitor prompted translation into the clinic for the treatment of CLL and low-grade non-Hodgkin lymphoma (NHL). From the first patient treated where a dramatic early nodal response was noted, considerable excitement has developed for this class of drugs in CLL and NHL. We will summarize the development process of CAL-101 (now GS1101) in the treatment of chronic lymphoid malignancies such as CLL.
Macromolecular Interactions and Ion Transport in Cystic Fibrosis (2004)

Cystic fibrosis (CF) is a genetic disease caused by autosomal recessive mutations of the CF transmembrane regulator, CFTR. CFTR functions in the plasma membrane of epithelial cells lining the lung, pancreas, liver, intestines, sweat duct, and the epididymis. The primary problem in CF is that mutations in CFTR affect its ability to be made, processed, and trafficked to the plasma membrane and/or its function as a Cl(-) channel and conductance regulator. Many proteins and processes normally interact with normal CFTR throughout its life cycle and mutant CFTR during the disease process. Understanding the function of these proteins and processes is expected to provide a clearer understanding of how normal CFTR is involved in salt movement and how mutant CFTR is handled by the cell and leads to the pathophysiology of CF. Recently, efforts to find therapies that correct defective CFTR have been intensifying. To facilitate our understanding of normal and mutant CFTR and the identification of new drug targets for developing novel therapies, a panel of experts was convened by the National Heart, Lung, and Blood Institute to explore the critical questions, challenges, and current opportunities to highlight new areas of research that would facilitate a integrated understanding of the processes and proteins that impact CFTR. The meeting highlighted the multiple pathways and interacting proteins involved in CFTR folding and biosynthesis, processing, and trafficking. A number of critical areas for future study were identified. Although these therapies are promising, a big question remains as to whether simply correcting defective CFTR will lead to significant improvement in patient health or whether the symptoms manifested in CF will require therapies in addition to those that target defective CFTR specifically.
Esaliency (Extended Saliency): Meaningful Attention Using Stochastic Image Modeling (2009)

Computer vision attention processes assign variable-hypothesized importance to different parts of the visual input and direct the allocation of computational resources. This nonuniform allocation might help accelerate the image analysis process. This paper proposes a new bottom-up attention mechanism. Rather than taking the traditional approach, which tries to model human attention, we propose a validated stochastic model to estimate the probability that an image part is of interest. We refer to this probability as saliency and thus specify saliency in a mathematically well-defined sense. The model quantifies several intuitive observations, such as the greater likelihood of correspondence between visually similar image regions and the likelihood that only a few of interesting objects will be present in the scene. The latter observation, which implies that such objects are (relaxed) global exceptions, replaces the traditional preference for local contrast. The algorithm starts with a rough preattentive segmentation and then uses a graphical model approximation to efficiently reveal which segments are more likely to be of interest. Experiments on natural scenes containing a variety of objects demonstrate the proposed method and show its advantages over previous approaches.
In Situ Studies of Protein Conformation in Supercritical Fluids: Trypsin in Carbon Dioxide (1992)

The conformation of the monomeric enzyme trypsin has been studied in supercritical carbon dioxide. Steady-state fluorescence spectroscopy is used to follow the conformation of trypsin in situ as a function of CO2 density. Our results show for the first time that protein denaturation can occur during the fluid compression step and that the native trypsin is only slightly more stable (1.2 kcal/mol) than the unfolded form. These results demonstrate the power of fluorescence spectroscopy as a tool for studying protein conformation and dynamics in supercritical fluids.
Clinical Use of Aromatase Inhibitors in Adult Males (2014)

With the better understanding of the T/E<sub>2</sub> ratio in adult males, the lack of scientific data to show that bone health is adversely affected by AI usage in adult males, the positive effects of AIs on the treatment of conditions like late-onset hypogonadism and male subfertility encourages conducting large-scale, multicenter, randomized controlled trials for the clinical use of AIs in adult males. Tan RBW, Guay AT, and Hellstrom WJG. Clinical use of aromatase inhibitors in adult males. Sex Med Rev 2014;2:79-90.
Comorbidity Clusters in Autism Spectrum Disorders: An Electronic Health Record Time-Series Analysis (2013)

Three distinct patterns of medical trajectories were identified by unsupervised clustering of electronic health record diagnoses. These may point to distinct etiologies with different genetic and environmental contributions. Additional clinical and molecular characterizations will be required to further delineate these subgroups.
Rates of electron transfer from osmium(II) to iron(III) complex ions containing 2,2'-bipyridine or its derivatives as ligands. Effects of electrolytes at low concentrations and reactant-separation distance (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRates of electron transfer from osmium(II) to iron(III) complex ions containing 2,2'-bipyridine or its derivatives as ligands. Effects of electrolytes at low concentrations and reactant-separation distanceT. G. Braga and Arthur C. WahlCite this: J. Phys. Chem. 1985, 89, 26, 5822–5828Publication Date (Print):December 1, 1985Publication History Published online1 May 2002Published inissue 1 December 1985https://doi.org/10.1021/j100272a049RIGHTS & PERMISSIONSArticle Views167Altmetric-Citations19LEARN 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 (929 KB) Get e-Alerts
Simplification of Aggregate Culture of Human Mesenchymal Stem Cells as a Chondrogenic Screening Assay (2007)

Aggregate culture provides a three-dimensional (3-D) environment for differentiating or differentiated cells; it is particularly useful to study in vitro chondrogenesis and cartilage biology. We have recently ported this method from a conical tube-based format to a 96-well plate format for the study of mesenchymal stem cell (MSC) chondrogenesis. The microplate format has greatly reduced the workload and materials cost, while maintaining reproducible chondrogenic differentiation. A long-term goal is to fully automate aggregate culture--this requires critically identifying all the indispensable steps of the protocol. Robotic laboratory equipment for manipulating microplate assays are commercially available; however centrifugation steps are difficult to implement automatically. We, therefore, tested whether the centrifugation step can be eliminated, thus significantly streamlining the assay workflow. By comparing aggregates prepared from human bone marrow-derived MSCs (hMSCs) that were formed either through centrifugation or through free sedimentation, we found that both methods produce aggregates with similar formation kinetics, and that there was no perceptible difference in the timing of the appearance of markers of chondrogenesis. Thus, it appears safe to eliminate the centrifugation step from the aggregate culture protocol. This results in significant time and effort savings and paves the way for future full automation of the aggregate assay.
Nanoparticles in SiH4-Ar plasma: Modelling and comparison with experimental data (2011)

Experimental and theoretical investigations for growth of silicon nanoparticles (4 to 14 nm) in radio frequency discharge were carried out. Growth processes were performed with gas mixtures of SiH4 and Ar in a plasma chemical reactor at low pressure. A distinctive feature of presented kinetic model of generation and growth of nanoparticles (compared to our earlier model) is its ability to investigate small “critical” dimensions of clusters, determining the rate of particle production and taking into account the influence of SiH2 and Si2Hm dimer radicals. The experiments in the present study were extended to high pressure (≥20 Pa) and discharge power (≥40 W). Model calculations were compared to experimental measurements, investigating the dimension of silicon nanoparticles as a function of time, discharge power, gas mixture, total pressure, and gas flow.
The miR-144/451 locus is required for erythroid homeostasis (2010)

The process of erythropoiesis must be efficient and robust to supply the organism with red bloods cells both under condition of homeostasis and stress. The microRNA (miRNA) pathway was recently shown to regulate erythroid development. Here, we show that expression of the locus encoding miR-144 and miR-451 is strictly dependent on Argonaute 2 and is required for erythroid homeostasis. Mice deficient for the miR-144/451 cluster display a cell autonomous impairment of late erythroblast maturation, resulting in erythroid hyperplasia, splenomegaly, and a mild anemia. Analysis of gene expression profiles from wild-type and miR-144/451-deficient erythroblasts revealed that the miR-144/451 cluster acts as a "tuner" of gene expression, influencing the expression of many genes. MiR-451 imparts a greater impact on target gene expression than miR-144. Accordingly, mice deficient in miR-451 alone exhibited a phenotype indistinguishable from miR-144/451-deficient mice. Thus, the miR-144/451 cluster tunes gene expression to impart a robustness to erythropoiesis that is critical under conditions of stress.
Use of mass spectrometric molecular weight information to identify proteins in sequence databases (1993)

During the last decade new ionization techniques have made it possible to measure the molecular weight of many intact proteins by mass spectrometry, and they have made it much easier to obtain a mass spectrometric peptide map of a protein. At the same time advances in protein and DNA sequencing technology are resulting in an exponential increase in the number of sequences deposited in databases. Here we investigate the possibility to use mass spectrometric data to identify proteins in databases. Searching a database by total molecular weight is found to be an easy and sometimes sufficient approach. For more specificity and for error tolerance in both the mass spectrometric data and the database information we search by partial mass spectrometric peptide map of the protein. In general, just four to six proteolytic peptides measured with a mass accuracy between 0.1 and 0.01% allow a useful search of databases such as the Protein Identification Resource (PIR). As the size of DNA and protein sequence databases grows, protein identification by partial mass spectrometric peptide maps should become increasingly powerful and may become a general method to identify and characterize proteins.
Constructing reality and its alternatives: an inclusion/ exclusion model of assimilation and contrast effects in social judgment (1992)

Für die Untersuchung von sozialen Werturteilen und Einschätzungen wird mit dem Inklusion-Exklusion-Ansatz ein Instrument entwickelt, mit dessen Hilfe die Angleichungs- (assimilation) sowie Gegensatz-Variablen (contrast) bestimmt werden können. Insbesondere sind die Antworten auf Wertschätzungsfragen in starkem Maße abhängig von dem Informationskontext - also z.B. von den vorher gestellten Fragen - zu einem Sachverhalt. Das entwickelte Modell beschreibt diese Effekte als Kategorisierungsprozesse. (psz)
Dopamine receptor activation inhibits estrogen-stimulated transforming growth factor-alpha gene expression and growth in anterior pituitary, but not in uterus (1992)

Transforming growth factor-alpha (TGF alpha) has been localized to the anterior pituitary, specifically to the lactotroph and somatotroph cell populations, by our previous studies. Since pituitary lactotrophs are known to undergo growth in response to estrogens, we have used an estradiol-induced pituitary hyperplasia/adenoma model. Estradiol treatment resulted in induction of TGF alpha mRNA in anterior pituitary, evident by 48 h, preceding actual macroscopic growth, which attained a maximum greater than 500% by 12 weeks. This rapid effect of estradiol also enhanced PRL mRNA, but did not affect other species of mRNA encoding for proenkephalin, D2 receptor mRNA, or hexosaminidase-A. TGF alpha mRNA remained elevated for the duration of rapid pituitary growth. D2 receptor activation by its agonist bromocriptine resulted in marked attenuation of TGF alpha mRNA preceding regression of growth. Coadministration of bromocriptine with estradiol resulted in an involution of pituitary size, indicating the overriding influence of dopamine in spite of a continued estrogenic stimulus. Epidermal growth factor receptor mRNA was not affected by any of these manipulations, suggesting that the receptor was not coregulated in this tissue similarly to TGF alpha. Estradiol also induced uterine TGF alpha mRNA and marked growth of the organ, but TGF alpha in this location was not regulated by dopamine. These results indicate that TGF alpha in the anterior pituitary is rapidly induced by estrogen in a time course preceding the growth of the gland. Estrogen-induced TGF alpha is rapidly attenuated by D2 dopamine receptor activation and is accompanied by a regression of pituitary growth. Interaction between these opposing hormonal/transmitter responses will determine the growth potential of the anterior pituitary.
Effects of Reagent and Enzymatically Generated Hypochlorite on Physicochemical and Metabolic Properties of High Density Lipoproteins (1997)

Myeloperoxidase (MPO), a protein secreted by activated phagocytes, may be a potential candidate for the generation of modified/oxidized lipoproteins in vivo via intermediate formation of HOCl, a powerful oxidant. During the present study, the effects of reagent NaOCl and OCl- generated by the MPO/H2O2/Cl- system on physicochemical and metabolic properties of high density lipoprotein (HDL) subclass 3 (HDL3) were investigated. Up to a molar oxidant:lipoprotein ratio of approximately 30:1, apolipoprotein A-I (apoA-I), the major HDL3 apolipoprotein component, represented the preferential target for OCl- attack (consuming 35-76% of the oxidant), thereby protecting HDL3 fatty acids (consuming between 17 and 30% of the oxidant) against OCl--mediated modification. At molar oxidant:HDL3 ratios >/= 60:1, we have observed pronounced consumption of HDL3 unsaturated fatty acids with concomitant formation of fatty acid chlorohydrins. Modification of HDL3 in the presence of the MPO/H2O2/Cl- system resulted in amino acid oxidation in a manner comparable with that found with reagent NaOCl only. Treatment of HDL3 with reagent NaOCl as well as modification by the MPO/H2O2/Cl- system resulted in significantly enhanced turnover rates of HDL3 by mouse peritoneal macrophages, an effect that was not a result of HDL3 aggregation as judged by dynamic and static light-scattering experiments. In comparison with native HDL3, the degradation by macrophages was enhanced by 4- and 15-fold when HDL3 was modified with reagent NaOCl or the MPO/H2O2/Cl- system. Finally, the ability of HDL3 to promote cellular cholesterol efflux from macrophages was significantly diminished after modification with reagent NaOCl. Collectively, these results demonstrate that the modification of HDL3 by hypochlorite (added as reagent or generated by the MPO/H2O2/Cl- system) transformed an antiatherogenic lipoprotein particle into a modified lipoprotein with characteristics similar to lipoproteins commonly thought to initiate foam cell formation in vivo.
Deep Learning for Computer Vision: A Brief Review (2018)

Over the last years deep learning methods have been shown to outperform previous state-of-the-art machine learning techniques in several fields, with computer vision being one of the most prominent cases. This review paper provides a brief overview of some of the most significant deep learning schemes used in computer vision problems, that is, Convolutional Neural Networks, Deep Boltzmann Machines and Deep Belief Networks, and Stacked Denoising Autoencoders. A brief account of their history, structure, advantages, and limitations is given, followed by a description of their applications in various computer vision tasks, such as object detection, face recognition, action and activity recognition, and human pose estimation. Finally, a brief overview is given of future directions in designing deep learning schemes for computer vision problems and the challenges involved therein.
Rapid hydrolysis of atrazine to hydroxyatrazine by soil bacteria (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleRapid hydrolysis of atrazine to hydroxyatrazine by soil bacteriaRaphi T. Mandelbaum, Lawrence P. Wackett, and Deborah L. AllanCite this: Environ. Sci. Technol. 1993, 27, 9, 1943–1946Publication Date (Print):September 1, 1993Publication History Published online1 May 2002Published inissue 1 September 1993https://pubs.acs.org/doi/10.1021/es00046a028https://doi.org/10.1021/es00046a028research-articleACS PublicationsRequest reuse permissionsArticle Views605Altmetric-Citations122LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
UKPDS 20: Plasma Leptin, Obesity, and Plasma Insulin in Type 2 Diabetic Subjects (1997)

We measured plasma leptin and insulin concentrations across a spectrum of obesity in 829 white Caucasian, 154 Afro-Caribbean, and 204 Asian type 2 diabetic subjects. Although the leptin concentrations covered a large range, there were no subgroups of diabetic subjects with very high or low leptin levels that would suggest mutations in the leptin gene or leptin receptor gene comparable to the obese diabetic ob/ob and db/db mice models respectively. In all three ethnic groups, leptin concentrations correlated with body mass index (BMI) in a similar manner to nondiabetic patients and were higher in females than males after adjustment for BMI, with no difference between ethnic groups. In a multivariate regression analysis, plasma leptin was associated with gender and BMI, (both P < 1 × 10−17) and with fasting plasma insulin concentrations (P = 5 × 10−9). Subjects treated with insulin had both raised insulin and leptin concentrations. When matched for different therapies, gender, and BMI, diabetic subjects with high leptin levels also had high insulin levels (P < 0.0009). High leptin concentrations may in part be influenced by hyperinsulinemia or impaired insulin sensitivity.