Miracle-dz/UniFAR-FTUs huggingface dataset:
β‐Adrenergic agonists regulate cell membrane fluctuations of human erythrocytes

1 Mechanical fluctuations of the cell membrane (CMFs) in human erythrocytes reflect the bending deformability of the membrane‐skeleton complex. These fluctuations were monitored by time‐dependent light scattering from a small area (≈0.25 μm2) of the cell surface by a method based on point dark field microscopy. 2 Exposure of red blood cells (RBCs) to adrenaline (epinephrine) and isoproterenol (isoprenaline) resulted in up to a 45 % increase in the maximal fluctuation amplitude and up to a 35 % increase in the half‐width of the amplitude distribution. The power spectra of membrane fluctuations of control and treated cells revealed that adrenaline stimulated only the low frequency component (0.3‐3 Hz). Analysis of the dose‐response curves of β‐adrenergic agonists yielded an EC50 of 5 × 10−9 and 1 × 10−11 M for adrenaline and isoproterenol, respectively. Propranolol had an inhibitory effect on the stimulatory effect of isoproterenol. These findings show a potency order of propranolol > isoproterenol > adrenaline. 3 The stimulatory effect of adrenaline was a temporal one, reaching its maximal level after 20‐30 min but being abolished after 60 min. However, in the presence of 3‐isobutyl‐1‐methylxanthine, a partial stimulatory effect was maintained even after 60 min. Pentoxifylline and 8‐bromo‐cAMP elevated CMFs. However, exposure of ATP‐depleted erythrocytes to adrenaline or 8‐bromo‐cAMP did not yield any elevation in CMFs. These findings suggest that the β‐agonist effect on CMFs is transduced via a cAMP‐dependent pathway. 4 Deoxygenation decreased CMFs and filterability of erythrocytes by ≈30 %. The stimulatory effect of isoproterenol on CMFs was 2.2‐fold higher in deoxygenated RBCs than in oxygenated cells. 5 Exposure of RBCs to adrenaline resulted in a concentration‐dependent increase in RBC filterability, demonstrating a linear relationship between CMFs and filterability, under the same exposure conditions to adrenaline. These findings suggest that β‐adrenergic agonists may improve passage of erythrocytes through microvasculature, enhancing oxygen delivery to tissues, especially under situations of reduced oxygen tension for periods longer than 20 min.
Minimum mean square error quantizers with uncorrelated input and quantization noise

Scalar quantizers with the minimum mean square error are designed in the case where the input signal and the quantization noise are uncorrelated. The probability density function (pdf) of the stochastic signal is assumed to be known. This design is then generalized to vector quantizers in the case where the expected value of the inner product between the input and quantization noise vector are equal to zero. The results show that the representation levels of the proposed quantizers are scaled versions of the representation levels of the well-known pdf optimized quantizers. The proposed quantizers are useful in subband coding applications.
Mining super-secondary structure motifs from 3d protein structures: a sequence order independent approach.

Super-Secondary structure elements (super-SSEs) are the structurally conserved ensembles of secondary structure elements (SSEs) within a protein. They are of great biological interest. In this work, we present a method to formally represent and mine the sequence order independent super-SSE motifs that occur repeatedly in large data sets of protein structures. We represent a protein structure as a graph, and mine the common cliques from a set of protein graphs in order to find the motifs. We mine two categories of super-SSE motifs: the generic motifs that occur frequently across the entire database of protein structures, and the fold-preferential motifs that are concentrated in particular protein fold types. From the experimental data set of 600 proteins belonging to 15 large SCOP Folds, we have discovered 21 generic motifs and 75 fold-preferential motifs that are both statistically significant and biologically relevant. A number of the discovered motifs (both generic and fold-preferential) resemble the well-known super-SSE motifs in the literature such as beta hairpins, Greek keys, zinc fingers, etc. Some of the discovered motifs are of novel shapes that have not been documented yet. Our method is time-efficient where it can discover all the motifs across the 600 proteins in less than 14 minutes on a standalone PC. The discovered motifs are reported in our project webpage: http://www1.i2r. a-star.edu. sg/~azeyar/SuperSSE/
Compact dual segment cylindrical dielectric resonator antenna for X-band applications

The simulation and experimental studies of a compact dual segment cylindrical dielectric resonator antenna (DRA) for X-band applications are presented in this paper. The antenna consists of Teflon (εr = 2.1) as lower segment and ceramic material (Sr La2 Mg2 W2 O12) of dielectric constant εr = 22 and loss tangent tan δ = 0.0021 as upper segment. The simulation study of the antenna is carried out using Ansoft's HFSS software. Parametric study of the antenna has been carried out by varying the Teflon and probe heights. The simulated and measured bandwidths of the proposed antenna are 1.11 GHz and 1.69 GHz respectively whereas corresponding values of average gain are 6.39 dB and 6.43 dB. The broadside radiation patterns are obtained (in both E-and H-planes) in the applicable frequency range with fairly low cross-polarization levels in E-plane. The experimental results are in good agreement with simulated results.
Effect of water vapor pressure on the thermal decomposition of 2-chloroethylphosphonic Acid.

Decomposition of 2-chloroethylphosphonic acid (Ethephon) was studied in dried films at various water vapor pressures (0.6 to 86.9 millimeters Hg, 3.2 to 93.9% relative humidity) and temperatures (20, 30, 40, and 50 C) at pH 6.3 and 7.0. The rate of decomposition could be determined equally well by [(14)C]Ethephon or ethylene measurements. The rate increases at increasing water vapor pressures at a constant temperature and pH, up to an optimum. The optimum vapor pressure for decomposition approximately doubles for each 10 C increase. The activation energy for the decomposition reaction in water vapor pressures of 3.2 to 12 millimeters Hg is 8.7 and 14.3 kilocalories per mole at pH 6.3 and 7.0, respectively.Decomposition of Ethephon is inhibited above an optimum vapor pressure. The inhibition is stronger at lower temperatures and at pH 6.3 than at pH 7.0. The rate of decomposition and the inhibition observed at a low temperature (20 C) was found to be similar on various surfaces, including olive leaves.Failure to induce olive (Olea europaea L.) fruit abscission under certain environmental conditions can be readily attributed to rapid breakdown of Ethephon at elevated temperatures and low relative humidities.
ePlace: Electrostatics-Based Placement Using Fast Fourier Transform and Nesterov's Method

We develop a flat, analytic, and nonlinear placement algorithm, ePlace, which is more effective, generalized, simpler, and faster than previous works. Based on the analogy between placement instance and electrostatic system, we develop a novel placement density function eDensity, which models every object as positive charge and the density cost as the potential energy of the electrostatic system. The electric potential and field distribution are coupled with density using a well-defined Poisson's equation, which is numerically solved by spectral methods based on fast Fourier transform (FFT). Instead of using the conjugate gradient (CG) nonlinear solver in previous placers, we propose to use Nesterov's method which achieves faster convergence. The efficiency bottleneck on line search is resolved by predicting the steplength using a closed-form equation of Lipschitz constant. The placement performance is validated through experiments on the ISPD 2005 and ISPD 2006 benchmark suites, where ePlace outperforms all state-of-the-art placers (Capo10.5, FastPlace3.0, RQL, MAPLE, ComPLx, BonnPlace, POLAR, APlace3, NTUPlace3, mPL6) with much shorter wirelength and shorter or comparable runtime. On average, of all the ISPD 2005 benchmarks, ePlace outperforms the leading placer BonnPlace with 2.83% shorter wirelength and runs 3.05× faster; and on average, of all the ISPD 2006 benchmarks, ePlace outperforms the leading placer MAPLE with 4.59% shorter wirelength and runs 2.84× faster.
Predicting academic achievement in the medical school with high school grades.

OBJECTIVE The present study investigated whether high school grades can predict medical school grades after controlling for the effects of demographics and entrance examination scores. MATERIAL AND METHOD The authors used hierarchical multiple regression analyses to predict medical school grades of 223 medical students in the 1997 entering class of the Faculty of Medicine Siriraj Hospital, Thailand, using age, gender, entrance examination scores, and high school grades as predictors. RESULTS After controlling for demographics and entrance examination scores, high school grades provided significant prediction only for premedical grades. The type of entrance examination that students took and the type of high school curriculum that the students studied were significant predictors of medical school grades in every level. CONCLUSION Measures of cognitive abilities in academic content were good in predicting short-term academic achievement. Long-term academic achievement in the medical school could be better predicted from academic orientation, commitment to the medical study, and demographic traits.
DISEASES AND DEVELOPMENT: A Theory of Infection Dynamics and Economic Behavior

We propose an economic theory of infectious disease transmission and rational behavior. Diseases are costly due to mortality (infected individuals can die prematurely) and morbidity (lower productivity and quality of life). Our model offers three main insights. First, a greater prevalence of diseases implies a lower savings-investment propensity because of mortality and morbidity. The extent to which preventive health investment can counter this depends on the prevalence rate and, specifically, on the strength of the disease externality. Second, infectious diseases can generate low-growth traps in which income alone can not push the economy out of underdevelopment. This is distinctly different from the development traps found by previous literature. Third, income per se does not cause health when prevalence is high. Successful interventions should therefore be health specific and when possible channeled via the public health delivery system.
Interaction of pyrogallol red with peroxyl radicals. A basis for a simple methodology for the evaluation of antioxidant capabilities

A competitive method to evaluate the reactivity of highly reactive antioxidants is reported. Pyrogallol red (PGR) and AAPH (2,2′-azo-bis-(2-amidinopropane) dihydrochloride) were employed as target-molecule and peroxyl radical source, respectively. In the zero-order kinetic limit in PGR, the dependence of the ratio R°/R (where R° is the rate of the process in the absence of additive and R is the rate of the process in the presence of additive) upon the additive concentration (Stern-Volmer like plots) was studied. Various polyphenols (n=10) and ascorbic acid (AA) were tested as additives. In PGR protection by AA, was observed a neat induction time, associated to the total protection of the target molecule. On the other hand, the experiments that were carried out in presence of phenolic compounds allowed a relative evaluation of their reactivity towards peroxyl radicals. This reactivity follows the order quercetin>gallic acid>Trolox > kaempferol. Data obtained employing quercetin and Trolox are compatible with a competitive protection by these antioxidants. Due to the high reactivity of PGR towards peroxyl radicals and its high extinction coefficient at long wavelengths, it is a very suitable molecule to be employed as target in the evaluation of the free radical scavenging capability of very reactive phenolic compounds.
A note on the population genetic consequences of delayed larval development in insects

Observations by Dobzhansky’s group in the 1940s suggesting that the presence of recessive genotypes could account for lower larval developmental rates in Drosophila melanogaster were not confirmed at the time and all subsequent investigations on this subject focused on the analysis of ecological models based on competition among pre-adult individuals. However, a paper published in this journal in 1991 eventually confirmed the finding made by Dobzhansky and his co-workers. In this report, we provide a theoretical analysis of the population genetic effects of a delay in the rate of larval development produced by such a genetic mechanism.
Establishing Caenorhabditis elegans as a model for Mycobacterium avium subspecies hominissuis infection and intestinal colonization

ABSTRACT The nematode Caenorhabditis elegans has become a model system for studying the disease interaction between pathogens and the host. To determine whether the transparent nematode could serve as a useful model for Mycobacterium avium subspecies hominissuis (MAH) infection of the intestinal tract, worms were fed MAH and assayed for the effects of the bacterial infection on the worm. It was observed during feeding that viable MAH increases in the intestinal lumen in a time dependent manner. Ingestion of MAH was deemed non-toxic to worms as MAH-fed populations have similar survival curves to those fed E. coli strain OP50. Pulse-chase analysis using E. coli strain OP50 revealed that MAH colonize the intestinal tract, as viable MAH remain within the intestine after the assay. Visualization of intestinal MAH using histology and transmission electron microscopy demonstrates that MAH localizes to the intestinal lumen, as well as establishes direct contact with intestinal epithelium. Bacterial colonization appears to have a detrimental effect on the microvilli of the intestinal epithelial cells. The MAH ΔGPL/4B2 strain with a mutation in glycopeptidolipid production is deficient in binding to human epithelial cells (HEp-2), as well as deficient in its ability to bind to and colonize the intestinal tract of C. elegans as efficiently as wild-type MAH. These data indicate the C. elegans may serve as a useful model system for MAH pathogenesis and in determining the mechanisms used by MAH during infection and colonization of the intestinal epithelium.
Obstructive sleep apnoea syndrome does not negatively affect oral and dental health

Abstract Objective: Obstructive sleep apnoea syndrome can lead to unhealthy open-mouth breathing. We investigated the possible relationship between obstructive sleep apnoea syndrome and dental health. We also evaluated other clinical factors that may affect oral health. Methods: We measured sleep using polysomnography and determined the apnoea–hypopnoea index for a total of 291 patients. We also recorded the demographic data, duration of snoring complaints, educational status and income levels for our patient cohort; finally, we calculated the decayed, missing and filled teeth index. Results: Forty-one patients presented with primary snoring (control group) and 250 patients (study group) presented with mild, moderate and severe obstructive sleep apnoea syndrome. We found no correlation between obstructive sleep apnoea syndrome severity and the decayed, missing and filled teeth index (p = 0.057). We also found no correlation between the apnoea–hypopnoea and decayed, missing and filled teeth indexes. Age and the duration of snoring complaints were positively correlated with the decayed, missing and filled teeth index while educational status and income levels were negatively correlated (p < 0.001). Conclusion: Obstructive sleep apnoea syndrome does not negatively affect oral and dental health.
A High Frequency of Activating Extracellular Domain ERBB2 (HER2) Mutation in Micropapillary Urothelial Carcinoma

Purpose: Micropapillary urothelial carcinoma (MPUC) is a rare and aggressive form of bladder cancer. We conducted genomic analyses [next-generation sequencing (NGS)] of MPUC and non-micropapillary urothelial bladder carcinomas (non-MPUC) to characterize the genomic landscape and identify targeted treatment options. Experimental Design: DNA was extracted from 40 μm of formalin-fixed paraffin-embedded sections from 15 MPUC and 64 non-MPUC tumors. Sequencing (NGS) was performed on hybridization-captured, adaptor ligation–based libraries to high coverage for 3,230 exons of 182 cancer-related genes plus 37 introns from 14 genes frequently rearranged in cancer. The results were evaluated for all classes of genomic alteration. Results: Mutations in the extracellular domain of ERBB2 were identified in 6 of 15 (40%) of MPUC: S310F (four cases), S310Y (one case), and R157W (one case). All six cases of MPUC with ERBB2 mutation were negative for ERBB2 amplification and Erbb2 overexpression. In contrast, 6 of 64 (9.4%) non-MPUC harbored an ERBB2 alteration, including base substitution (three cases), amplification (two cases), and gene fusion (one case), which is higher than the 2 of 159 (1.3%) protein-changing ERBB2 mutations reported for urinary tract cancer in COSMIC. The enrichment of ERBB2 alterations in MPUC compared with non-MPUC is significant both between this series (P < 0.0084) and for all types of urinary tract cancer in COSMIC (P < 0.001). Conclusions: NGS of MPUC revealed a high incidence of mutation in the extracellular domain of ERBB2, a gene for which there are five approved targeted therapies. NGS can identify genomic alteration, which inform treatment options for the majority of MPUC patients. Clin Cancer Res; 20(1); 68–75. ©2013 AACR.
DNA extraction from formalin-fixed laryngeal biopsies: Comparison of techniques

Abstract Conclusion: PCR-quality DNA could be extracted from formalin-fixed paraffin-embedded (FFPE) samples with amplicons of at least 390 bp. Paraffin removal was not a necessary step. Proteinase K digestion was as efficient as the commercial kit for DNA extraction with a lower cost. Objectives: To compare different DNA extraction protocols for FFPE samples and to describe the suitability of the extracted DNA for PCR reactions. Methods: For deparaffinization the following techniques were compared: alkaline heat, xylene, and no removal. For DNA extraction, proteinase K digestion and organic extraction were compared. A commercial extraction kit was included as standard. DNA quality was assessed by PCR amplification of the HFE gene, for amplicons of 208 and 390 bp. Results: Extraction with the commercial kit and proteinase K digestion were more efficient than other techniques, with no statistical difference between them for both amplicons. The proteinase K digestion buffer had a cost of U$ 0.2 per sample and the commercial kit of U$7 per sample.
A Comparative Analysis of Extracted Grammars

The development of wide-coverage grammars is at the core of robust NLP systems. This paper addresses the problem of grammar extraction from treebanks with respect to the issue of broad coverage along three dimensions: the grammar formalism (context-free grammar, dependency grammar, lexicalized tree adjoining grammar), the domain of the annotated corpus (press reports, civil law) and the language of the corpus (English, Korean, Chinese, Italian). We have extracted three grammars from an annotated corpus of Italian and we have comparatively analyzed the coverage of a test set; then, working on two different domain subcorpora we have compared the cross-domain coverage of the extracted grammars; finally, we have compared the grammars for four different languages. The results are that there are relevant differences in coverage among formalisms and domains; a more limited difference appears in the cross-linguistic comparison.
Efficient Java Communication Protocols on High-speed Cluster Interconnects

This paper presents communication strategies for achieving efficient parallel and distributed Java applications on clusters with high-speed interconnects. Communication performance is critical for the overall cluster performance. Previous efforts at obtaining efficient Java communications have a limited applicability on high-speed interconnects as they are focused on high level APIs like RMI, ignoring the particularities of these systems and their native high performance communication protocols. By relying on a custom Java socket implementation higher degrees of performance can be achieved exploiting high-speed interconnect facilities. Several protocol definitions are presented, looking for obtaining high performance Java communications. Moreover, the quality of the protocol implementations and their design decisions has been thoroughly evaluated on a scalable coherent interface (SCI) and gigabit Ethernet (GbE) testbed cluster. The results of this analysis have demonstrated that these Java protocols obtain similar results to native communications
Cold Shock Domain Protein 3 Regulates Freezing Tolerance in Arabidopsis thaliana*

In response to cold, Escherichia coli produces cold shock proteins (CSPs) that have essential roles in cold adaptation as RNA chaperones. Here, we demonstrate that Arabidopsis cold shock domain protein 3 (AtCSP3), which shares a cold shock domain with bacterial CSPs, is involved in the acquisition of freezing tolerance in plants. AtCSP3 complemented a cold-sensitive phenotype of the E. coli CSP quadruple mutant and displayed nucleic acid duplex melting activity, suggesting that AtCSP3 also functions as an RNA chaperone. Promoter-GUS transgenic plants revealed tissue-specific expression of AtCSP3 in shoot and root apical regions. When exposed to low temperature, GUS activity was extensively induced in a broader region of the roots. In transgenic plants expressing an AtCSP3-GFP fusion, GFP signals were detected in both the nucleus and cytoplasm. An AtCSP3 knock-out mutant (atcsp3-2) was sensitive to freezing compared with wild-type plants under non-acclimated and cold-acclimated conditions, whereas expression of C-repeat-binding factors and their downstream genes during cold acclimation was not altered in the atcsp3-2 mutant. Overexpression of AtCSP3 in transgenic plants conferred enhanced freezing tolerance over wild-type plants. Together, the data demonstrated an essential role of RNA chaperones for cold adaptation in higher plants.
Knowledge of Grammar, Knowledge of Usage: Syntactic Probabilities Affect Pronunciation Variation

Frequent words tend to shorten (see e.g. Schuchardt 1885, Hooper 1976), as do words that have a high probability of occurrence given a neighboring word (Jurafsky et al. 2001). This tendency has been cited in support of the claim that probabilities are an inherent part of grammar, and of syntax in particular. There is widespread consensus, however, that the syntax of natural languages cannot be captured in terms of item-to-item transitions (Chomsky 1957). Therefore, unless one considers probabilities of syntactic structures, rather than particular combinations of neighboring words, pronunciation variation cannot be said to reflect probabilistic effects in syntax. In this article, we report a case of pronunciation variation that reflects contextual probabilities of syntactic structures. The relevant probabilities are based on the probability of a given syntactic structure, given a particular verb. We showthat these probabilities affect American English /t,d/- deletion, as well as the durations of words and phrases. Our results are consistent with the notion that knowledge of grammar includes knowledge of probabilities of syntactic structures, and that this knowledge affects language production.