gebhart/patrepeval huggingface dataset:
Injury to skeletal muscle fibers of mice following lengthening contractions (1985)

We tested the hypothesis that lengthening contractions result in greater injury to skeletal muscle fibers than isometric or shortening contractions. Mice were anesthetized with pentobarbital sodium and secured to a platform maintained at 37 degrees C. The distal tendon of the extensor digitorum longus muscle was attached to a servomotor. A protocol consisting of isometric, shortening, or lengthening contractions was performed. After the contraction protocol the distal tendon was reattached, incisions were closed, and the mice were allowed to recover. The muscles were removed after 1-30 days, and maximum isometric force (Po) was measured in vitro at 37 degrees C. Three days after isometric and shortening contractions and sham operations, histological appearance was not different from control and Po was 80% of the control value. Three days after lengthening contractions, histological sections showed that 37 +/- 4% of muscle fibers degenerated and Po was 22 +/- 3% of the control value. Muscle regeneration, first seen at 4 days, was nearly complete by 30 days, when Po was 84 +/- 3% of the control value. We conclude that, with the protocol used, lengthening, but not isometric or shortening contractions, caused significant injury to muscle fibers.
Role of Light Scatterng in Whole Blood Oximetry (1986)

We investigated the role of light scattering in whole blood oximetry by transmission spectrophotometry. To delineate the role of scattering and absorbance in the measurement of oxyhemoglobin saturation, we applied Twersky's theory of radiation scattering and measured the apparent optical density of whole blood and hemoglobin solutions. The optical density versus hematocrit relationship predicted by Twersky's theory was found to give a good fit to the data obtained at 660, 813, 880, and 940 nm. A semi-empirical variation of Twersky's equation and photon diffusion equations were also compared to the data, and Twersky's original equation was found to give the best fit. Therefore, Twersky's equation was employed throughout the rest of the data analysis. Total scattering effects were shown to be wavelength and oxygenation dependent. Moreover, the relationship between total scattering effects and percent O2 saturation was approximately linear, and it had a greater slope (at 660 nm) than absorbance versus O2 saturation. Thus, scattering effects in the red-infrared range do not detract from the linearity of whole blood oximeters. By contrast, scattering effects increase the sensitivity of oximeters by contributing linearly to the total O. D. change that occurs with altered oxygenation.
Toward a Fully Automated Stock Exchange, Part I (1971)

(1971). Toward a Fully Automated Stock Exchange, Part I. Financial Analysts Journal: Vol. 27, No. 4, pp. 28-35, 44.
Growth hormone induces age-dependent alteration in the expression of hippocampal growth hormone receptor and N -methyl- d -aspartate receptor subunits gene transcripts in male rats (2002)

Studies were conducted to evaluate the effects of s.c. injected recombinant human growth hormone (GH) on the expression of the gene transcript of N-methyl-D-aspartate receptor subunits type 1 (NR1), type 2A (NR2A), and type 2B (NR2B) in the male rat hippocampus. The GH-induced effects on the expression of hippocampal gene transcripts of GH receptor (GHR) and GH-binding protein were also examined. Male Sprague-Dawley rats, kept in four groups of two different ages, was treated with the hormone or saline during 10 days before decapitation and tissue dissection. Brain tissues collected were analyzed for mRNA content by using the Northern blot technique. The results indicated that in adult young rats (11 weeks of age) the hormone elicited a decrease in the mRNA expression of NR1 but an increase in that of the NR2B subunit. In elderly adult rats (57-67 weeks of age) GH induced an increase in the expression of the hippocampal message for NR1 and NR2A. Meanwhile, the hormone induced a significant up-regulation of the GHR transcript in hippocampus of adult young rats but not in elderly adult rats. It was further found that a significant positive correlation exists between the level of GHR mRNA and the expression of the NR2B subunit transcript in adult young rats. The GH-induced increase in the expression of hippocampal mRNA for the NR2B subunit is compatible with a previously observed memory promoting effect seen for the hormone, because overexpression of this N-methyl-D-aspartate receptor subunit is shown to enhance cognitive capabilities.
Molecular and biochemical mechanisms associated with dormancy and drought tolerance in the desert legume Retama raetam (2002)

Dormancy is an important developmental program allowing plants to withstand extended periods of extreme environmental conditions, such as low temperature or drought. Seed dormancy, bud dormancy and desiccation tolerance have been extensively studied, but little is known about the mechanisms involved in the dormancy of drought-tolerant plants, key to the survival of many plant species in arid and semi-arid environments. Subtractive PCR cloning of cDNAs from Retama raetam, a C3 drought-tolerant legume, revealed that dormancy in this plant is accompanied by the accumulation of transcripts encoding a pathogenesis-related, PR-10-like protein; a low temperature-inducible dehydrin; and a WRKY transcription factor. In contrast, non-dormant plants subjected to stress conditions contained transcripts encoding a cytosolic small heat-shock protein, HSP18; an ethylene-response transcriptional co-activator; and an early light-inducible protein. Physiological and biochemical analysis of Rubisco activity and protein in dormant and non-dormant tissues suggested a novel post-translational mechanism of regulation that may be controlled by the redox status of cells. Ultrastructural analysis of dormant plants revealed that air spaces of photosynthetic tissues contained an extracellular matrix that may function to prevent water loss. The cytosol of dormant cells appeared to be in a glassy state, limiting metabolic activity. A combination of biochemical, molecular and structural mechanisms, in association with metabolic suppression, may be key to the extreme drought tolerance of R. raetam and its acclimation to the desert ecosystem. These may enable plants to withstand long periods of drought, as well as rapidly to exit dormancy upon rainfall.
Model of Photovoltaic Cell Circuits under Partial Shading (2006)

The PV-cell and natural energy production systems have been much attracted. Together with global warning and extensive applications of solar power electric generation, defects on PV-cell under the partial shading become interesting technical issue. This paper investigates the equivalent circuit model and its characteristics under the partial shading condition. And we have clarified the mechanism of PV-cell under the partial shading. As the extension of these considerations, we have proposed the new MPPT method (maximal power point tracking) for the sake of drastic energy generation improvement.
Montelukast in the Prophylaxis of Migraine: A Potential Role for Leukotriene Modifiers (2000)

We conclude, given the limitations of an open-label study design and the small sample size, that montelukast shows potential as an effective, well-tolerated prophylactic agent in migraine. Double-blinded, placebo-controlled studies are warranted. In addition, the leukotrienes, as suggested previously in the literature, may play a role in the pathogenesis of migraine.
Different Phototransduction Kinetics of Phytochrome A and Phytochrome B in Arabidopsis thaliana1 (1998)

The kinetics of phototransduction of phytochrome A (phyA) and phytochrome B (phyB) were compared in etiolated Arabidopsis thaliana seedlings. The responses of hypocotyl growth, cotyledon unfolding, and expression of a light-harvesting chlorophyll a/b-binding protein of the photosystem II gene promoter fused to the coding region of beta-glucuronidase (used as a reporter enzyme) were mediated by phyA under continuous far-red light (FR) and by phyB under continuous red light (R). The seedlings were exposed hourly either to n min of FR followed by 60 minus n min in darkness or to n min of R, 3 min of FR (to back-convert phyB to its inactive form), and 57 minus n min of darkness. For the three processes investigated here, the kinetics of phototransduction of phyB were faster than that of phyA. For instance, 15 min R h-1 (terminated with a FR pulse) were almost as effective as continuous R, whereas 15 min of FR h-1 caused less than 30% of the effect of continuous FR. This difference is interpreted in terms of divergence of signal transduction pathways downstream from phyA and phyB.
Reversed-phase high performance liquid chromatography of phosphatidylcholine: a simple method for determining relative hydrophobic interaction of various molecular species. (1981)

A convenient method for the separation of molecular species of phosphatidylcholine (PC) by reversed-phase high performance liquid chromatography (HPLC) is described. PC species from egg, bovine brain, and porcine liver were resolved into 11-13 separate peaks on a Nucleosil-5-C18 reversed-phase column with methanol-1 mM potassium phosphate buffer, pH 7.4, 9.5:0.5 (v/v) as the solvent. Detection was at 205 nm. PC species were primarily resolved due to specific hydrophobic interaction of their fatty acid side chains with the alkyl ligand of the stationary phase. The retention time and therefore the hydrophobic interaction of acyl chains of PC species increased logarithmically as the total number of carbon atoms in the chains increased in the homologous series. The retention times decreased nonlinearly as the number of double bonds in the fatty chains increased. Introduction of the first double bond in the side chain reduced the retention time to the greatest extent. From the chromatography data the reduction in the retention time was calculated to be equivalent to 1.8 carbon atoms compared to the fully saturated PC. Further introduction of 2, 3, 4, 5, and 6 double bonds in the same side chain reduced the retention time additionally, equivalent to 1.4, 1.2, 1.0, 1.0, and 1.0 less carbon atoms. Each molecular species of PC was assigned a "Hydrophobic Carbon Number" (HCN) based upon the total number of carbon atoms ad double bonds in the side chain. PC molecules with the same HCN had the same retention time. The average HCN was calculated for various PC preparations and found to be remarkably the same for all the three different naturally occurring sources considering a wide variety of different fatty acid compositions of each type. HCN provides a simple measure of relative hydrophobicity of each PC molecule.
Effects of transforming growth factor β and epidermal growth factor on cell proliferation and the formation of bone nodules in isolated fetal rat calvaria cells (1989)

When cells enzymatically isolated from fetal rat calvaria (RC cells) are cultured in vitro in the presence of ascorbic acid and Na beta-glycerophosphate, discrete three-dimensional nodules form with the histologic, immunohistochemical, and ultrastructural characteristics of bone (Bellows et al; Calcified Tissue International 38:143-154, 1986; Bhargava et al., Bone, 9:155-163, 1988). Quantitation of the number of bone nodules that forms provides a colony assay for osteoprogenitor cells present in the RC population (Bellows and Aubin, Develop. Biol., 133:8-13, 1989). Continuous culture with either epidermal growth factor (EGF) or transforming growth factor beta (TGF-beta) results in dose-dependent inhibition of bone nodule formation; however, the former causes increased proliferation and saturation density, while the latter reduces both parameters. Addition of EGF (48 h pulse, 2-200 ng/ml) to RC cells at day 1 after plating results in increased proliferation and population saturation density and an increased number of bone nodules formed. Similar pulses at confluence and in postconfluent multilayered cultures when nodules first begin forming (approx. day 11) inhibited bone nodule formation and resulted in a smaller stimulation of cell proliferation. Forty-eight hour pulses of TGF-beta (0.01-1 ng/ml) reduced bone nodule formation and proliferation at all times examined, with pulses on day 1 causing maximum inhibition. The effects of pulses with TGF-beta and EGF on inhibition of nodule formation are independent of the presence of serum in the culture medium during the pulse. The data suggest that whereas EGF can either stimulate or inhibit the formation of bone nodules depending upon the time and duration of exposure, TGF-B inhibits bone nodule formation under all conditions tested. Moreover, these effects on osteoprogenitor cell differentiation do not always correlate with the effects of the growth factors on RC cell proliferation.
AB ‐Bind: Antibody binding mutational database for computational affinity predictions (2015)

Antibodies (Abs) are a crucial component of the immune system and are often used as diagnostic and therapeutic agents. The need for high-affinity and high-specificity antibodies in research and medicine is driving the development of computational tools for accelerating antibody design and discovery. We report a diverse set of antibody binding data with accompanying structures that can be used to evaluate methods for modeling antibody interactions. Our Antibody-Bind (AB-Bind) database includes 1101 mutants with experimentally determined changes in binding free energies (ΔΔG) across 32 complexes. Using the AB-Bind data set, we evaluated the performance of protein scoring potentials in their ability to predict changes in binding free energies upon mutagenesis. Numerical correlations between computed and observed ΔΔG values were low (r = 0.16-0.45), but the potentials exhibited predictive power for classifying variants as improved vs weakened binders. Performance was evaluated using the area under the curve (AUC) for receiver operator characteristic (ROC) curves; the highest AUC values for 527 mutants with |ΔΔG| > 1.0 kcal/mol were 0.81, 0.87, and 0.88 using STATIUM, FoldX, and Discovery Studio scoring potentials, respectively. Some methods could also enrich for variants with improved binding affinity; FoldX and Discovery Studio were able to correctly rank 42% and 30%, respectively, of the 80 most improved binders (those with ΔΔG < -1.0 kcal/mol) in the top 5% of the database. This modest predictive performance has value but demonstrates the continuing need to develop and improve protein energy functions for affinity prediction.
SCOPE (2008)

Companies providing cloud-scale services have an increasing need to store and analyze massive data sets such as search logs and click streams. For cost and performance reasons, processing is typically done on large clusters of shared-nothing commodity machines. It is imperative to develop a programming model that hides the complexity of the underlying system but provides flexibility by allowing users to extend functionality to meet a variety of requirements. In this paper, we present a new declarative and extensible scripting language, SCOPE (Structured Computations Optimized for Parallel Execution), targeted for this type of massive data analysis. The language is designed for ease of use with no explicit parallelism, while being amenable to efficient parallel execution on large clusters. SCOPE borrows several features from SQL. Data is modeled as sets of rows composed of typed columns. The select statement is retained with inner joins, outer joins, and aggregation allowed. Users can easily define their own functions and implement their own versions of operators: extractors (parsing and constructing rows from a file), processors (row-wise processing), reducers (group-wise processing), and combiners (combining rows from two inputs). SCOPE supports nesting of expressions but also allows a computation to be specified as a series of steps, in a manner often preferred by programmers. We also describe how scripts are compiled into efficient, parallel execution plans and executed on large clusters.
KCNQ channel openers reverse depressive symptoms via an active resilience mechanism (2016)

Less than half of patients suffering from major depressive disorder, a leading cause of disability worldwide, achieve remission with current antidepressants, making it imperative to develop more effective treatment. A new therapeutic direction is emerging from the increased understanding of natural resilience as an active stress-coping process. It is known that potassium (K(+)) channels in the ventral tegmental area (VTA) are an active mediator of resilience. However, no druggable targets have been identified to potentiate active resilience mechanisms. In the chronic social defeat stress model of depression, we report that KCNQ-type K(+) channel openers, including FDA-approved drug retigabine (ezogabine), show antidepressant efficacy. We demonstrate that overexpression of KCNQ channels in the VTA dopaminergic neurons and either local infusion or systemic administration of retigabine normalized neuronal hyperactivity and depressive behaviours. These findings identify KCNQ as a target for conceptually novel antidepressants that function through the potentiation of active resilience mechanisms.
Optical Spectroscopy of Nanometric Holes in Thin Gold Films (2004)

Elastic scattering measurements show that isolated nanometric holes in optically thin Au films exhibit a localized surface plasmon resonance in the red to near-infrared region. The hole plasmon red shifts with increasing hole diameter or increasing refractive index of the surrounding medium, analogous to a dipolar particle plasmon. A pronounced blue shift is observed when the distance between holes is decreased, indicating an enhanced coupling between holes mediated by surface plasmon polaritons of the intervening flat film surface.
A Survey of Accuracy Evaluation Metrics of Recommendation Tasks (2009)

Recommender systems are now popular both commercially and in the research community, where many algorithms have been suggested for providing recommendations. These algorithms typically perform differently in various domains and tasks. Therefore, it is important from the research perspective, as well as from a practical view, to be able to decide on an algorithm that matches the domain and the task of interest. The standard way to make such decisions is by comparing a number of algorithms offline using some evaluation metric. Indeed, many evaluation metrics have been suggested for comparing recommendation algorithms. The decision on the proper evaluation metric is often critical, as each metric may favor a different algorithm. In this paper we review the proper construction of offline experiments for deciding on the most appropriate algorithm. We discuss three important tasks of recommender systems, and classify a set of appropriate well known evaluation metrics for each task. We demonstrate how using an improper evaluation metric can lead to the selection of an improper algorithm for the task of interest. We also discuss other important considerations when designing offline experiments.
Macrophage colony-stimulating factor induces substantial osteoclast generation and bone resorption in human bone marrow cultures (1996)

Macrophage colony-stimulating factor (M-CSF) is essential for murine osteoclast formation and its role in human hematopoiesis in vitro is not fully defined. Therefore, we have investigated the effect of M-CSF on the formation of human osteoclasts in vitro. M-CSF was found to induce substantial bone resorption and osteoclast formation in a dose-responsive and time-dependent manner above that induced by 1,25 dihydroxyvitamin D3 (1,25 vitamin D3) in cultures of human bone marrow (BM) stromal cells sedimented onto devitalized bone. By day 14 there was a mean of approximately 50% of the surfaces of the bone slices resorbed compared with only 6% in cultures treated with 1,25 vitamin D3 alone. Osteoclasts were identified as 23c6+ cells (an antibody that recognizes the vitronectin receptor), 87.5% of which coexpressed the calcitonin receptor. The number of 23c6+ cells correlated strongly with bone resorption spatially, and in a dose-responsive and time-dependent manner; the correlation coefficient in cultures treated with 1,25 vitamin D3 alone was 0.856 and those treated with both M-CSF and 1,25 vitamin D3 was 0.880. Granulocyte-macrophage colony-stimulating factor, IL-1 beta, IL-3, IL-6, tumor necrosis factor-alpha, transforming growth factor-beta, leukemia inhibitory factor, and IL-11 did not increase bone resorption above that in 1,25 vitamin D3-treated cultures. We also found that 1,25 vitamin D3 increased, to a minor but significant degree, both bone resorption and the concentration of M-CSF in the culture supernatants above that in vehicle-treated cultures, indicating that M-CSF is present in our BM cultures, but that there is insufficient to induce substantial osteoclast formation. These results define a critical role for M-CSF in the formation of human osteoclasts.
Consistent map-based 3D localization on mobile devices (2017)

In this paper, we seek to provide consistent, real-time 3D localization capabilities to mobile devices navigating within previously mapped areas. To this end, we introduce the Cholesky-Schmidt-Kalman filter (C-SKF), which explicitly considers the uncertainty of the prior map, by employing the sparse Cholesky factor of the map's Hessian, instead of its dense covariance-as is the case for the Schmidt-Kalman filter. By doing so, the C-SKF has memory requirements typically linear in the size of the map, as opposed to quadratic for storing the map's covariance. Moreover, and in order to bound the processing needs of the C-SKF (between linear and quadratic in the size of the map), we introduce two relaxations of the C-SKF algorithm: (i) The sC-SKF, which operates on the Cholesky factors of independent sub-maps resulting from dividing the map into overlapping segments. (ii) We formulate an efficient method for sparsifying the Cholesky factor by selecting and processing a subset of loop-closure measurements based on their temporal distribution. Lastly, we assess the processing and memory requirements of the proposed algorithms, and compare their positioning accuracy against other inconsistent map-based localization approaches that employ measurement-noise-covariance inflation to compensate for the map's uncertainty.
Linear time and frequency domain turbo equalization (2002)

For coded data transmission over channels introducing inter-symbol interference, one approach for joint equalization and decoding in the receiver is turbo equalization. We rederive existing linear equalization algorithms applicable to turbo equalization for 2/sup m/-ary signal alphabets and compare their computational complexity. Moreover by evaluating the algorithm performance properly, we select for each iteration the most suitable of the two algorithms with lowest computational complexity and achieve at low bit error rates a performance close to that of optimal approaches for equalization, ie, maximum a-posteriori probability symbol detection.