Miracle-dz/UniFAR-FTUs huggingface dataset:
Japanese medaka (Oryzias latipes): developmental model for the study of alcohol teratology.

BACKGROUND Animal models are necessary to investigate the mechanism of alcohol-induced birth defects. We have used Japanese medaka (Oryzias latipes) as a non-mammalian model to elucidate the molecular mechanism(s) of ethanol teratogenesis. METHODS Medaka eggs, within 1 hr post-fertilization (hpf) were exposed to waterborne ethanol (0-1000 mM) in hatching solution for 48 hr. Embryo development was observed daily until 10 days post-fertilization (dpf). The concentration of embryonic ethanol was determined enzymatically. Cartilage and bones were stained by Alcian blue and calcein, respectively and skeletal and cardiovascular defects were assessed microscopically. Genetic gender of the embryos was determined by PCR. Levels of two isoenzymes of alcohol dehydrogenase (Adh) mRNAs were determined by semi-quantitative and real-time RT-PCR. RESULTS The concentration of ethanol required to cause 50% mortality (LC50) in 10 dpf embryos was 568 mM, however, the embryo absorbed only 15-20% of the waterborne ethanol at all ethanol concentrations. The length of the lower jaw and calcification in tail fin cartilaginous structures were reduced by ethanol exposure. Active blood circulation was exhibited at 50+ hpf in embryos treated with 0-100 mM ethanol; active circulation was delayed and blood clots developed in embryos treated with 200-400 mM ethanol. The deleterious effects of ethanol were not gender-specific. Moreover, ethanol treatment was unable to alter the constitutive expression of either Adh5 or Adh8 mRNA in the medaka embryo. CONCLUSIONS Preliminary results suggested that embryogenesis in medaka was significantly affected by ethanol exposure. Phenotypic features normally associated with ethanol exposure were similar to that observed in mammalian models of fetal alcohol syndrome. The results further indicated that medaka embryogenesis might be used as an alternative non-mammalian model for investigating specific alterations in gene expression as a means to understand the molecular mechanism(s) of ethanol-induced birth defects.
Backscatter Coefficient Measurements Using a Reference Phantom to Extract Depth-Dependent Instrumentation Factors

In previous work, we demonstrated that accurate backscatter coefficient measurements are obtained with a data reduction method that explicitly accounts for experimental factors involved in recording echo data. An alternative, relative processing method for determining the backscatter coefficient and the attenuation coefficient is presented here. This method involves comparison of echo data from a sample with data recorded from a reference phantom whose backscatter and attenuation coefficients are known. A time domain processing technique is used to extract depth and frequency dependent signal ratios for the sample and the reference phantom. The attenuation coefficient and backscatter coefficient of the sample are found from these ratios. The method is tested using tissue-mimicking phantoms with known scattering and attenuation properties.
Constituting origami models from sketches

This paper proposes an approach to constituting crease patterns, the unfolded origami models, by using skeletons obtained from 2-D images such as handwriting sketches. Firstly, we describe a method for constructing a data structure which represents all the parts of an origami model and their relationships based on an extracted skeleton, and then give an algorithm for constituting a crease pattern using this data structure. To show the validity of proposed method and algorithm, we finally demonstrate how a crease pattern is generated and how a origami model is actually realized using some real illustrations taken from a origami drill book.
Low energy body design and nonlinear control of balance in a one legged robot

Postural control of a two degree of freedom hopping robot with a novel balancing mechanism is revisited. The balancing mechanism is a concave downward-swinging body whose center of gravity lies below the hip joint. It is shown that at a specific body curvature, the linearized system is transformed from non-minimum to minimum phase, the conditions for feedback linearization of the nonlinear model satisfied and minimal mechanical power required for stability during stance observed. Control of the nonlinear postural dynamics is then attempted using feedback linearization and its performance in achieving our control objective is compared against that of a linear quadratic regulator.
Agroecology to Promote Just Sustainability Transitions: Analysis of a Civil Society Network in the Rwenzori Region, Western Uganda

Agroecology is gaining ground within the debate on how to address systemic social and environmental problems in agriculture. However, it remains marginalized in agricultural research and development plans around the world. This paper analyzes agroecology as a socio-technical niche in Uganda, where its emergence in part can be seen as an unintended consequence of neoliberalist development. The case studied is a civil society network that links farmer groups and non-governmental organizations across different levels. Through the analytical lens of regime dimensions, we find that agroecology is practiced as a smallholder-centric approach that champions collective action, locally appropriate technologies, participatory methods in research and extension, and calls for more active state guidance of agricultural change along specific principles. However, two major concerns are raised; the niche converges with the dominant discourse around commercialization, and policy advocacy is hampered by the apolitical history of NGOs and an increasingly tense political climate. These two areas are critical for agroecology to contribute to just sustainability transitions, and civil society organizations with strong links to smallholder farmers need to be included in the growing scholarly debate both to inform it and to receive guidance from it. Transition frameworks can help facilitate the development of viable institutional designs and explicitly transformative strategies, but we also point towards the need for engagement with theories on civil society collective action and political mobilization.
Engineering the acceptor specificity of trehalose phosphorylase for the production of trehalose analogs

Trehalose (α‐D‐glucopyranosyl‐(1,1)‐α‐D‐glucopyranoside) is widely used in the food industry, thanks to its protective effect against freezing and dehydration. Analogs of trehalose have the additional benefit that they are not digested and thus do not contribute to our caloric intake. Such trehalose analogs can be produced with the enzyme trehalose phosphorylase, when it is applied in the reverse, synthetic mode. Despite the enzyme's broad acceptor specificity, its catalytic efficiency for alternative monosaccharides is much lower than for glucose. For galactose, this difference is shown here to be caused by a lower Km whereas the kcat for both substrates is equal. Consequently, increasing the affinity was attempted by enzyme engineering of the trehalose phosphorylase from Thermoanaerobacter brockii, using both semirational and random mutagenesis. While a semirational approach proved unsuccessful, high‐throughput screening of an error‐prone PCR library resulted in the discovery of three beneficial mutations that lowered Km two‐ to three‐fold. In addition, it was found that mutation of these positions also leads to an improved catalytic efficiency for mannose and fructose, suggesting their involvement in acceptor promiscuity. Combining the beneficial mutations did not further improve the affinity, and even resulted in a decreased catalytic activity and thermostability. Therefore, enzyme variant R448S is proposed as new biocatalyst for the industrial production of lactotrehalose (α‐D‐glucopyranosyl‐(1,1)‐α‐D‐galactopyranoside). © 2012 American Institute of Chemical Engineers Biotechnol. Prog. , 2012
Revisiting self-regulatory techniques to promote physical activity in older adults: null-findings from a randomised controlled trial

Objective. A randomised controlled trial (RCT) was conducted to evaluate a three-hour face-to-face physical activity (PA) intervention in community-dwelling older German adults with four groups: The intervention group (IG) received behaviour change techniques (BCTs) based on the health action process approach plus a views-on-ageing component to increase PA. The second intervention group ‘planning’ (IGpl) contained the same BCTs, only substituted the views-on-ageing component against an additional planning task. An active control group received the same BCTs, however, targeting volunteering instead of PA. A passive control group (PCG) received no intervention. Design. The RCT comprised 5 time-points over 14 months in N = 310 participants aged 64+. Main outcome measures. Self-reported as well as accelerometer-assessed PA. Results. Neither PA measure increased in the IG as compared to the other groups at any point in time. Bayes analyses supported these null-effects. Conclusion. A possible explanation for this null-finding in line with a recent meta-analysis is that some self-regulatory BCTs may be ineffective or even negatively associated with PA in interventions for older adults as they are assumed to be less acceptable for older adults. This interpretation was supported by observed reluctance to participate in self-regulatory BCTs in the current study.
Skeletal Muscle

It is generally accepted that eccentric exercise, when performed by a muscle that is unaccustomed to that type of contraction, results in a delayed onset of muscle soreness (DOMS). A prolonged exposure to eccentric exercise leads to the disappearance of the signs and symptoms associated with DOMS, which has been referred to as the repeated bout effect (RBE). Although the mechanisms underlying the RBE remain unclear, several mechanisms have been proposed, including the serial sarcomere number addition following exercise induced muscle damage. In the traditional DOMS and RBE protocols, muscle injury has been treated as a global parameter, with muscle force and strain assumed to be uniform throughout the muscle. To assess the effects of muscle-tendon unit strain, fiber strain, torque and injury on serial sarcomere number adaptations, three groups of New Zealand White (NZW) rabbits were subjected to chronic repetitive eccentric exercise bouts of the ankle dorsiflexors for 6 weeks. These eccentric exercise protocols consisted of identical muscle tendon unit (MTU) strain, but other mechanical factors were systematically altered. Following chronic eccentric exercise, serial sarcomere number adaptations were not identical between the three eccentric exercise protocols, and serial sarcomere number adaptations were not uniform across all regions of the muscle. Peak torque and relaxation fiber strain were the best predictors of serial sarcomere number across all three protocols. Therefore, MTU strain does not appear to be the primary cause for sarcomerogenesis, and differential adaptations within the muscle may be explained by the nonuniform architecture of the muscle, resulting in differential local fiber strains.
Breast cancer knowledge and screening behaviour among women with a positive family history: a cross sectional study.

BACKGROUND Breast cancer is the commonest type of cancer among women, and in Malaysia 50-60% of the new cases are being detected at late stages. Do age, education level, income, ethnicity, relationship with breast cancer patients and knowledge of breast cancer risk factors influence breast screening practices? This study revealed interesting but significant differences. OBJECTIVES To assess the knowledge of breast cancer risk factors and early detection measures among women in a high risk group. MATERIALS AND METHODS A cross sectional survey of one hundred and thirty one women relatives of breast cancer patients was carried out. Participants were selected through purposive sampling, during hospital visits. A self-administered questionnaire was used for data collection. RESULTS The majority of the respondents (71%) had poor knowledge of the risk factors for breast cancer. Income, relationship with a patient and practise of breast cancer screening predicted performance of mammography, R2=0.467, F=12.568, p<0.0001. CONCLUSIONS The finding shows inadequate knowledge of breast cancer risk factors and poor cancer screening practise among women with family history of breast cancer. Poor knowledge and practise of breast screening are likely to lead to late stage presentation of breast cancer disease. Some important predictors of breast cancer screening behaviour among women with positive family history of breast cancer were identified. An understanding of the strengths and significance of the association between these factors and breast screening behaviour is vital for developing more targeted breast health promotion.
DIMENSIONAL STABILITY OF TWO POLYVINYL SILOXANE IMPRESSION MATERIALS IN DIFFERENT TIME INTERVALS

Abstract Statement of the Problem : Dental prosthesis is usually made indirectly; therefore dimensional stability of the impression material is very important. Every few years, new impression materials with different manufacturers’ claims regarding their better properties are introduced to the dental markets which require more research to evaluate their true dimensional changes. Objectives : The aim of this study was to evaluate dimensional stability of additional silicone impression material (Panasil® and Affinis®) in different time intervals. Materials and Methods : In this experimental study, using two additional silicones (Panasil® and Affinis®), we made sixty impressions of standard die in similar conditions of 23 °C and 59% relative humidity by a special tray. The die included three horizontal and two vertical lines that were parallel. The vertical line crossed the horizontal ones at a point that served as reference for measurement. All impressions were poured with high strength dental stone. The dimensions were measured by stereo-microscope by two examiners in three interval storage times (1, 24 and 168 hours). The data were statistically analyzed using t-test and ANOVA. Results : All of the stone casts were larger than the standard die. Dimensional changes of Panasil and Affinis were 0.07%, 0.24%, 0.27% and 0.02%, 0.07%, 0.16% after 1, 24 and 168 hours, respectively. Dimensional change for two impression materials wasn’t significant in the interval time, expect for Panasil after one week ( p = 0.004). Conclusions : According to the limitations of this study, Affinis impressions were dimensionally more stable than Panasil ones, but it was not significant. Dimensional change of Panasil impression showed a statistically significant difference after one week. Dimensional changes of both impression materials were based on ADA standard limitation in all time intervals (< 0.5%); therefore, dimensional stability of this impression was accepted at least until one week. Keywords : Polyvinyl Siloxane, Dimensional Stability, Stereomicroscope, Impressions
Effects of consonant aspiration on Mandarin tones

The influence of consonant aspiration on the F0 contours of tones in Mandarin Chinese was tested in continuous speech by reference to a minimal pair of syllables, /ta/ and /tha/, which differ only in terms of aspiration. It was found that, consonant aspiration affects the fundamental frequency (F0) of the following vowel. The onset F0 of a tone is higher following unaspirated consonants than following aspirated consonants, and the magnitude of the differences are related to the tone itself as well as the preceding tone. The underlying mechanisms of this effect, as well as its interaction with other effects on F0 contours, are discussed.
Simultaneous aluminum, silicon, and sodium coordination changes in 6 GPa sodium aluminosilicate glasses

Abstract We present the first direct observation of high-coordinated Si and Al occurring together in a series of high-pressure sodium aluminosilicate glasses, quenched from melts at 6 GPa. Using 29Si MAS NMR, we observe that a small amount of Al does not have a significant effect on the amount of VSi or VISi generated, but that larger Al concentrations lead to a gradual decrease in both these species. 27Al MAS NMR spectra show that samples with small amounts of Al have extremely high mean Al coordination values of up to 5.49, but that larger Al concentrations cause a gradual decrease in both VAl and VIAl. Although mean Al and Si coordination numbers both decrease with increasing Al contents, the weighted combined (Al+Si) coordination number increases. Silicon and Al resonances shift in frequency with increasing pressure or changing Al concentration, indicating additional structural changes, including compression of network bond angles. Increases in the 23Na isotropic chemical shifts indicate decreases in the mean Na-O bond lengths with increasing pressure, which are more dramatic at higher Al contents. Recovered glass densities are about 10 to 15% greater than those of similar ambient pressure samples. However, the density increases due to the combined coordination changes of Al and Si are estimated to total only about 1 to 2%, and are roughly constant with composition despite the large effects of Al content on the individual coordinations of the two cations. Thus, effects of other structural changes must be significant to the overall densification. Apparent equilibrium constants for reactions involving the generation of high-coordinated species show systematic behavior, which suggests an internal consistency to the observed Si and Al coordination number shifts.
A Measure of the Broad Substrate Specificity of Enzymes Based on ‘Duplicate’ Catalytic Residues

The ability of an enzyme to select and act upon a specific class of compounds with unerring precision and efficiency is an essential feature of life. Simultaneously, these enzymes often catalyze the reaction of a range of similar substrates of the same class, and also have promiscuous activities on unrelated substrates. Previously, we have established a methodology to quantify promiscuous activities in a wide range of proteins. In the current work, we quantitatively characterize the active site for the ability to catalyze distinct, yet related, substrates (BRASS). A protein with known structure and active site residues provides the framework for computing ‘duplicate’ residues, each of which results in slightly modified replicas of the active site scaffold. Such spatial congruence is supplemented by Finite difference Poisson Boltzmann analysis which filters out electrostatically unfavorable configurations. The congruent configurations are used to compute an index (BrassIndex), which reflects the broad substrate profile of the active site. We identify an acetylhydrolase and a methyltransferase as having the lowest and highest BrassIndex, respectively, from a set of non-homologous proteins extracted from the Catalytic Site Atlas. The acetylhydrolase, a regulatory enzyme, is known to be highly specific for platelet-activating factor. In the methyltransferase (PDB: 1QAM), various combinations of glycine (Gly38/40/42), asparagine (Asn101/11) and glutamic acid (Glu59/36) residues having similar spatial and electrostatic profiles with the specified scaffold (Gly38, Asn101 and Glu59) exemplifies the broad substrate profile such an active site may provide. ‘Duplicate’ residues identified by relaxing the spatial and/or electrostatic constraints can be the target of directed evolution methodologies, like saturation mutagenesis, for modulating the substrate specificity of proteins.
Enhancement of the Mehler-peroxidase Reaction in Salt-stressed Rumex K-1 Leaves

The effects of salt stress on photosynthesis, Mehler-peroxidase reaction (MPR) and the susceptibility of PSII to photoinhibition were investigated in Rumex K-1 leaves. Salt stress resulted in dramatic decrease in photosynthesis, but had no significant effect on maximal photochemistry of PSII (Fv/Fm). During photosynthetic induction, a considerable electron flow was transported to oxygen in MPR both in control and salt-stressed leaves. Under steady state photosynthesis, enhanced electron flow to oxygen in MPR was observed only in salt-stressed leaves. The enhanced MPR in salt-stressed leave was accompanied by enhanced activities of scavenging enzymes, i.e. superoxidase dismutase (SOD) and ascorbate peroxidase (APX). In the presence of saturating CO2, decreasing oxygen concentration from 21% to 2% did not affect the susceptibility to photoinhibition in control leaves, but largely increased the susceptibility to photoinhibition in salt-stressed leaves. Based on these results, it is concluded that the enhanced MPR in salt-stressed Rumex leaves serves as a sink to drain the excess electrons off the electron chain and thus mitigates photoinhibition.
Epicardial Mapping: How to Measure Local Activation?

Epicardial ventricular mapping was performed in 5 dogs during sinus rhythm with a sock array containing 41 electrodes. Maps were generated with a computer‐assisted mapping system using four different definitions of local epicardial activation: (1) maximal negative slope (intrinsic deflection) of the unipolar electrogram, (2) maximal slope of the bipolar electrogram, (3) maximal amplitude of the bipolar elecirogram, and (4) first onset by 45° from the baseline of the bipolar electrogram. The site of earliest and latest epicardial activation ivas identical with maximal negative slope in the unipolar electrogram and maximal slope and maximal amplitude of the bipolar electrogram in all jive animals. Times of earliest and latest epicardial activation calculated witb maximal amplitude of the bipolar electrogram were most similar to those evaluated with maximal negative slope of the unipolar electrogram. Using onset of the bipolar electrogram, activation times were measured 10 to 12 msec earlier than with each of the other three definitions of local activation, and in two of the five animals, first epicardial breakthrough was mapped to a different site than with the three other methods. Conclusions: (1) Maximal amplitude of the bipolar electrogram coincided with maximal negative slope of the unipolar electrogram; (2) Using onset of the bipolar electrogram, timing and location of earliest epicardial activation may be misinterpreted.
Fast fingerprinting based indoor localization by Wi-Fi signals

Indoor localization is vital for location based services as well as security purposes. Wireless local area network (WLAN) positioning systems based on fingerprints of received signal strength (RSS) measured from access points, can be used for localization. Due to the effectiveness of fingerprinting in indoor positioning, fingerprinting network designers try to lower the cost of using this technique in terms of time and energy. In this paper, a fast fingerprinting method is presented, using indoor path-loss model instead of using reference points with complicated measurement devices. The accuracy of the localization by the proposed model is compared with the experimental RSS data collected via smart-phones and the feasibility of the idea is proved.