gebhart/patrepeval huggingface dataset:
The Effect of Calcium Citrate on Bone Density in the Early and Mid-postmenopausal Period (1999)

This placebo-controlled randomized trial was conducted to ascertain the value of calcium citrate supplementation in averting bone loss in 63 postmenopausal women, 57 of whom were early postmenopausal (five years after menopause) and six of whom were mid-postmenopausal (five to ten years after menopause). Bone density data were available for 25 women who took 800 mg of calcium citrate daily and 31 women who received placebo for one to two years. The two groups were similar in baseline age, years postmenopause (3.3 in the calcium citrate group vs 2.7 in the placebo group), height, weight, calcium intake, and L2-L4 bone density. L2-L4 bone density did not change during calcium citrate treatment (+ 1.03% after two years), whereas it declined significantly by -2.38% after two years on placebo (P < .001). Femoral neck bone density did not change in either group. Radial shaft bone density did not change in the calcium citrate group (-0.02% after two years), but it declined significantly in the placebo group (-1.79% after one year and -3.03% after two years, P < .01). The difference in bone density of the L2-L4 vertebrae and radial shaft after two years of treatment was significant between the two groups. An analysis of covariance disclosed no significant effect of calcium citrate on L2-L4 bone density during the first three years after menopause, but a protective effect after three years. Although serum PTH did not change, serum and urinary calcium increased and serum calcitriol and urinary phosphorus decreased in the calcium citrate group, indicative of parathyroid suppression. Serum bone-specific alkaline phosphatase and osteocalcin, and urinary hydroxyproline and N-telopeptide decreased during some calcium citrate treatment periods, indicative of a reduction in bone turnover. Thus, calcium citrate supplementation (400 mg of calcium twice daily) averted bone loss and stabilized bone density in the spine, femoral neck, and radial shaft in women relatively soon after menopause. This bone-sparing action was probably due to the inhibition of bone resorption from parathyroid suppression.
Hierarchical Multi‐Step Folding of Polymer Bilayers (2012)

Abstract A highly complex multi‐step folding of isotropic stimuli‐responsive polymer bilayers resulting in a variety of 2D and 3D structures is reported. Experimental observations allow determination of empirical rules, which can be used to direct the folding of polymer films in a predictable manner. In particular, it is demonstrated that these rules can be used for the design of a 3D pyramid. The understanding and know‐how attained in this study allow the very simple design of highly complex, self‐folding 3D objects and open new horizons for 3D patterning, important for the design of microfluidic devices, biomaterials, and soft electronics.
Clinical supervision and practice nursing (1996)

In the second article in her series, Rosemary Cook looks at the practicalities of clinical supervision.
I/o paravirtualization at the device file boundary (2014)

Paravirtualization is an important I/O virtualization technology since it uniquely provides all of the following benefits: the ability to share the device between multiple VMs, support for legacy devices without virtualization hardware, and high performance. However, existing paravirtualization solutions have one main limitation: they only support one I/O device class, and would require significant engineering effort to support new device classes and features. In this paper, we present Paradice, a solution that vastly simplifies I/O paravirtualization by using a common paravirtualization boundary for various I/O device classes: Unix device files. Using this boundary, the paravirtual drivers simply act as a class-agnostic indirection layer between the application and the actual device driver.
Gadolinium-Based Contrast Exposure, Nephrogenic Systemic Fibrosis, and Gadolinium Detection in Tissue (2008)

An association with GBCAs in the development of NSF is suggested in the setting of renal insufficiency, but other factors seem to play a role. Dialysis did not prevent the development of NSF. Gadolinium was detected in skin samples from NSF patients.
Fortran 77 : Principles of programming (1980)

The complete guide to computer programming with FORTRAN 77, the cost effective workhorse among programming languages for scientific and engineering work. FORTRAN 77 retains the efficiency of FORTRAN IV while being a more elegant language. The text is written for the beginner without previous computer experience.
DESIGN OF DUAL-FEED DUAL-POLARIZED MICROSTRIP ANTENNA WITH HIGH ISOLATION AND LOW CROSS POLARIZATION (2013)

A broadband dual-feed dual-polarized microstrip antenna with low cross polarization and high isolation is presented. The dual- orthogonal linearly polarized mode is excited by two difierent feed mechanisms from a single circular radiating patch. One of the two modes is excited by a pair of L-shaped probes with a 180 - phase difierences, and the other is excited by an H-shaped aperture. The proposed design has a very simple antenna structure with a wide input impedance bandwidth (23.25% for Port 1 and 35% for Port 2) and also its two input port isolation is found to be as low as i40dB. Measured results of the fabricated antenna prototypes are also carried out to verify the simulation analysis.
Self-Organized Clustering Architecture for Vehicular Ad Hoc Networks (2015)

Vehicular Ad Hoc NETworks (VANETs) are likely to be deployed in the near future. Then, they will become the platform for much of the relayed information in the Internet of Things. This paper proposes a new system based on 1-hop clustering to reduce the number of VANET communications in dense road traffic scenarios while maintaining the security of communications by combining public-key with secret-key cryptography. The proposed distributed clustering architecture creates a dynamic virtual backbone in the network, formed by Cluster-Heads and cluster-gateways, so that these nodes are responsible for the efficient message propagation in the network. The main aim of the described architecture is to balance both stability of backbone connections and cost/efficiency trade-off. Full definitions of all the architecture procedures are provided, including a cluster-head selection algorithm based on a version of the independent set problem and a secret-key agreement scheme that uses the generalized Diffie-Hellman protocol. Simulations show that the proposal improves network performance and security.
The importance of REM sleep for brain maturation (1993)

A number of studies, some done by us, are reviewed concerning the function of foetal/neonatal REM sleep. The hypothesis is put forward that REM sleep in early life serves as an indicator for: (1) the degree of brain maturation, and (2) the promotion of further brain development. This hypothesis, although not exclusive, differs from: the original theory of Roffwarg et al. (1966) that REM sleep serves as "wakefulness" during the period in which wakefulness is limited; and also from the theory of Crick and Mitchson (1983-the "unlearning" hypothesis of REM sleep). As the functions of sleep in general, and REM sleep in particular, are still unclear, we hope this review will suggest new possibilities for future research.
Cortical Transcriptomic Alterations in Association With Appetitive Neuropeptides and Body Mass Index in Posttraumatic Stress Disorder (2020)

PTSD-associated cortical transcriptomic modules contain transcripts of appetitive genes, and BMI further interacts with PTSD to impact expression. DEGs and inferred upstream regulators of these modules could represent targets for future pharmacotherapies for obesity in PTSD.
Glycogen depletion contributes to ischemic preconditioning in the rat heart in vivo (1996)

Ischemic preconditioning depletes the myocardium of glycogen, thus blunting lactic acidosis during subsequent episodes of ischemia. Preconditioning also protects against reperfusion arrhythmias and infarction. To test whether glycogen depletion is necessary for this ischemic tolerance, we preconditioned two groups of intact rats with a series of 3-min coronary artery occlusions. In one group, preconditioning lowered the glycogen concentration of the ischemic region by approximately 50% (24.9 +/- 2.5 to 12.5 +/- 1.8 mumol/g; P < 0.01). In the other, the heart was first loaded with glycogen via glucose-insulin infusion so that preconditioning merely reduced its glycogen concentration back to normal physiological levels. Compared with nonpreconditioned control rats, preconditioned rats with both normal and subnormal glycogen concentrations were protected from reperfusion arrhythmias after a 6-min coronary occlusion (incidence: control rats, 100%; normal glycogen rats, 11%; reduced glycogen rats, 11%). In contrast, only rats with subnormal glycogen concentration after preconditioning exhibited reduced lactate formation and infarct size after a 45-min coronary occlusion [infarct size (percentage of risk area): control rats, 53 +/- 10%; normal glycogen rats, 50 +/- 16%, P = not significant; subnormal glycogen rats, 18 +/- 10%, P < 0.01]. Thus, in the intact rat, myocardial glycogen depletion appears to be necessary for the infarct-limiting, but not for the antiarrhythmic, effects of ischemic preconditioning.
Stable domain propagation in the Gunn effect (1966)

The properties of uniformly propagating stable domains are calculated using a constant diffusion coefficient of 178 cm2 sec-1 and an analytic approximation to a recently computed static velocity-field characteristic for gallium arsenide. The static characteristic has a steep slope in the negative resistivity range and then saturates at high fields. Consequently the peak domain field initially increases slowly as the domain velocity is reduced from its maximum value and then increases indefinitely as the domain velocity approaches the saturated drift velocity. Domain shapes are given for a resistivity ρ0 = 1 ω cm. The extreme degrees of depletion and accumulation, the widths of the depletion and accumulation layers and the domain potential are all plotted against the field outside the domain for ρ0 = 1, 5 and 10 ω cm. The domain has a rounded triangular shape which is asymmetric and shows large departures from neutrality at large domain voltages (except when ρ0 << 1 ω cm) but which becomes symmetrical and nearly neutral everywhere at low domain potentials, with a diffusion-limited width of 1·9 ρ01/2 μm. The domain potential increases slowly at first, with an initial slope of 4·53 ρ01/2 μm, as the outside field is reduced below threshold and then increases rapidly as the minimum outside field is approached. Consequently the length dependence of the domain potential for a fixed average field is less sensitive to resistivity variations than was found previously (using a schematic three-line static characteristic) and is in better agreement with the experimental data.
Facencounter: Bridging the Gap between Offline and Online Social Networks (2012)

Human beings are involved in a broad range of social relationships spanning from real life experiences to online media and social networks. This is leading people to act in a multilayered complex network whose relationships among different layers have still to be analyzed and understood in depth. In this paper, we focus on this problem by comparing and overlapping the online sociality (Facebook network) and the offline sociality (encounter network) of a group of students. First we describe the experiment we performed to trace the encounters, occurring with people both inside and outside the group of experimenters, and to gather information about their online friendships. On the basis of the obtained dataset, we obtain the relevant complex networks, whose separated analysis lead us to observe significant structural differences. Moreover, we study the correlations and overlap between the two interrelated networks, showing how users' centralities change in the two networks. Finally, the information transfer across layers of the unified complex network enables us to obtain results about the effects on paths and centrality.
svaseq: removing batch effects and other unwanted noise from sequencing data (2014)

It is now known that unwanted noise and unmodeled artifacts such as batch effects can dramatically reduce the accuracy of statistical inference in genomic experiments. These sources of noise must be modeled and removed to accurately measure biological variability and to obtain correct statistical inference when performing high-throughput genomic analysis. We introduced surrogate variable analysis (sva) for estimating these artifacts by (i) identifying the part of the genomic data only affected by artifacts and (ii) estimating the artifacts with principal components or singular vectors of the subset of the data matrix. The resulting estimates of artifacts can be used in subsequent analyses as adjustment factors to correct analyses. Here I describe a version of the sva approach specifically created for count data or FPKMs from sequencing experiments based on appropriate data transformation. I also describe the addition of supervised sva (ssva) for using control probes to identify the part of the genomic data only affected by artifacts. I present a comparison between these versions of sva and other methods for batch effect estimation on simulated data, real count-based data and FPKM-based data. These updates are available through the sva Bioconductor package and I have made fully reproducible analysis using these methods available from: https://github.com/jtleek/svaseq.
Mechanism of heterocyclic ring expansions. Part V. Base-catalysed rearrangement of 2-dichloromethyl-2,5-dimethyl-2H-pyrrole and related compounds (1969)

2-Dichloromethyl-2,5-dimethyl-2H-pyrrole gave 2-ethoxymethyl-5-methylpyridine with sodium ethoxide, 2,5-dimethylpyridine with sodium hydride, and, in a more extensive rearrangement, trans-1,2-di-5-methyl-2-pyridylethylene with potassium hydroxide.With sodium ethoxide 2-dichloromethyl-2,3,4,5-tetramethyl-2H-pyrrole gave 2-ethoxymethyl-3,4,5-trimethylpyridine and 4-ethoxymethyl-2,3,5-trimethylpyridine, 2-dichloromethyl-3,4-dimethyl-2,5-diphenyl-2H-pyrrole gave 4-ethoxymethyl-3-methyl-2,5-diphenylpyridine, and 4-dichloromethyl-3,4,5-trimethyl-4H-pyrazole gave 3-ethoxymethyl-4,6-dimethylpyridazine. Yields were generally in the order of 80%.A unifying mechanism viabicyclic[3,1,0] intermediates is proposed for this apparently general rearrangement of dichloromethyl-2H-pyrroles with active hydrogen atoms.
Oxygen evolution in a hypersaline crust: in situ photosynthesis quantification by microelectrode profiling and use of planar optode spots in incubation chambers (2009)

Net primary production and respiration were estimated in a hypersaline cyanobacterial mat colonizing a gypsum crust in the Eilat salterns, Israel. Two different approaches were used: in situ microprofiling with Clark-type O 2 sensors and application of optode sensor spots in incubation chambers. The net O 2 release rates of the mat phototrophs was high, with a maximum of 3.4 nmol O 2 cm -2 min -1 measured by microprofiling and 4.4 nmol O 2 cm -2 min -1 determined in the incubation chambers. The upper 2 layers of the mat as well as the overlying water quickly became O 2 saturated during the day. The respiration of the whole gypsum crust was also very intensive and corresponded to the O 2 produced by photosynthesis on a diurnal basis, which prevented most of the evolved O 2 from reaching the water. The results presented show that optode sensor spots are useful tools providing additional information about export and photosynthetic production rates of O 2 in hypersaline microbial mats.
Two types of potassium channels in murine T lymphocytes. (1987)

The properties of two types of K+ channels in murine T lymphocytes are described on the basis of whole-cell and isolated-patch recordings using the gigohm-seal technique. Type l (standing for "lpr gene locus" or "large") channels were characterized mainly in T cells from mutant MRL/MpJ-lpr/lpr mice, in which they are present in large numbers. Type n ("normal") K+ channels are abundant and therefore most readily studied in concanavalin A-activated T cells from four strains of mice, MRL-+/+, CBA/J, C57BL/6J, and BALB/c. Type l channels, compared with type n, are activated at potentials approximately 30 mV more positive, and close much more rapidly upon repolarization. Type l channels inactivate more slowly and less completely than type n during maintained depolarization, but recover from inactivation more rapidly, so that little inactivation accumulates during repetitive pulses. Type l channels have a higher unitary conductance (21 pS) than type n (12 pS) and are less sensitive to block by external Co++, but are 100-fold more sensitive to block by external tetraethylammonium (TEA), with half-block of type l channels at 50-100 microM TEA compared with 8-16 mM for type n. TEA blocks both types of channels by reducing the apparent single channel current amplitude, with a dose-response relation similar to that for blocking macroscopic currents. Murine type n K+ channels resemble K+ channels in human T cells.
General Purpose Compositional Model (1985)

Abstract A direct sequential method has been developed to simulate isothermal compositional systems. The solution technique is the same as that of the implicit pressure, explicit saturation (IMPES) method: one pressure is treated implicitly and (instead of the phase saturation) the component masses/moles are treated explicitly. A "volume balance" equation is used to obtain the pressure equation. A weighted sum of the conservation equations is used to eliminate the nonlinear saturation/concentration terms from the accumulation term of the pressure equation. The partial mass/mole volumes are used as "constants" to weight the mass/mole conservation equations. The method handles uniformly a range of cases from the simplified compositional (i.e., black-oil) models to the most complicated multiphase compositional models of incompressible and compressible fluid systems. The numerical solution is based on the integrated finite-difference method that allows one- (ID), two- (2D), and three-dimensional (3D) grids of regular or irregular volume elements to be handled with the same ease. The mathematical model makes it possible to develop modular versatile computer realizations; thus the model is highly suitable as a basis for general-purpose models.
Multi-scale Transformer Language Models (2020)

We investigate multi-scale transformer language models that learn representations of text at multiple scales, and present three different architectures that have an inductive bias to handle the hierarchical nature of language. Experiments on large-scale language modeling benchmarks empirically demonstrate favorable likelihood vs memory footprint trade-offs, e.g. we show that it is possible to train a hierarchical variant with 30 layers that has 23% smaller memory footprint and better perplexity, compared to a vanilla transformer with less than half the number of layers, on the Toronto BookCorpus. We analyze the advantages of learned representations at multiple scales in terms of memory footprint, compute time, and perplexity, which are particularly appealing given the quadratic scaling of transformers' run time and memory usage with respect to sequence length.
Comparison of the Bruker MALDI-TOF Mass Spectrometry System and Conventional Phenotypic Methods for Identification of Gram-Positive Rods (2014)

In recent years, MALDI-TOF Mass Spectrometry (MS) method has emerged as a promising and a reliable tool for bacteria identification. In this study we compared Bruker MALDI-TOF MS and conventional phenotypic methods to identify a collection of 333 Gram-positive clinical isolates comprising 22 genera and 60 species. 16S rRNA sequencing was the reference molecular technique, and rpoB gene sequecing was used as a secondary gene target when 16Sr RNA did not allow species identification of Corynebacterium spp. We also investigate if score cut-offs values of ≥ 1,5 and ≥ 1,7 were accurate for genus and species-level identification using the Bruker system. Identification at species level was obtained for 92,49% of Gram-positive rods by MALDI-TOF MS compared to 85,89% by phenotypic method. Our data validates the score ≥ 1,5 for genus level and ≥ 1,7 for species-level identification in a large and diverse collection of Gram-positive rods. The present study has proved the accuracy of MALDI-TOF MS as an identification method in Gram-positive rods compared to currently used methods in routine laboratories.
Problems in the prediction of protein values of diets (1961)

Platt & Miller (1958) have pointed out that the net protein utilization (N.P.u.) of whole diets depends not only on the amino-acid composition of the proteins they contain but also on a number of other factors, the more important of which are: (I) the protein-calorie ratio of the diet, (2) the adequacy of the calorie intake and (3) the level in the diet of some vitamins and minerals.
Inducible expression and pharmacology of the human excitatory amino acid transporter 2 subtype of L‐glutamate transporter (1999)

1. In this study we have examined the use of the ecdysone-inducible mammalian expression system (Invitrogen) for the regulation of expression of the predominant L-glutamate transporter EAAT2 (Excitatory Amino Acid Transporter) in HEK 293 cells. 2. HEK 293 cells which were stably transformed with the regulatory vector pVgRXR (EcR 293 cells) were used for transfection of the human EAAT2 cDNA using the inducible vector pIND and a clone designated HEK/EAAT2 was selected for further characterization. 3. Na+-dependent L-glutamate uptake activity (3.2 pmol min-1 mg-1) was observed in EcR 293 cells and this was increased approximately 2 fold in the uninduced HEK/EAAT2 cells, indicating a low level of basal EAAT2 activity in the absence of exogenous inducing agent. Exposure of HEK/EAAT2 cells to the ecdysone analogue Ponasterone A (10 microM for 24 h) resulted in a > or = 10 fold increase in the Na+-dependent activity. 4. L-glutamate uptake into induced HEK/EAAT2 cells followed first-order Michaelis-Menten kinetics and Eadie-Hofstee transformation of the saturable uptake data produced estimates of kinetic parameters as follows; Km 52.7+/-7.5 microM, Vmax 3.8+/-0.9 nmol min-1 mg-1 protein. 5. The pharmacological profile of the EAAT2 subtype was characterized using a series of L-glutamate transport inhibitors and the rank order of inhibitory potency was similar to that described previously for the rat homologue GLT-1 and in synaptosomal preparations from rat cortex. 6. Addition of the EAAT2 modulator arachidonic acid resulted in an enhancement (155+/-5% control in the presence of 30 microM) of the L-glutamate transport capacity in the induced HEK/EAAT2 cells. 7. This study demonstrates that the expression of EAAT2 can be regulated in a mammalian cell line using the ecdysone-inducible mammalian expression system.
Cysteine protease inhibition by azapeptide esters (1992)

Papain, a prototype cysteine protease, was inhibited in a time-dependent manner by azapeptide esters designed to deliver an azaglycine group to the active-site thiol. For example, the rate of inhibition was 18 M-1s-1 for Ac-L-PheAglyOiBu (2) and > 11,000 M-1s-1 for Ac-L-PheAglyOPh (7). The rate of inhibition was slowed in the presence of substrate, and there was no reactivation of the inhibited enzyme after dialysis and incubation in the assay buffer. The inhibited enzyme was completely reactivated after the addition of valine methyl ester. The inhibited form of the enzyme is presumed to be acylated on the active-site thiol. An azaalanine-based peptide inhibited papain much more slowly. Azapeptide alkyl esters are unreactive with serine proteases; therefore, these inhibitors are selective for cysteine proteases.