Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemical and Synthetic Genetic Array Analysis Identifies Genes that Suppress Xylose Utilization and Fermentation in Saccharomyces cerevisiae

Though highly efficient at fermenting hexose sugars, Saccharomyces cerevisiae has limited ability to ferment five-carbon sugars. As a significant portion of sugars found in cellulosic biomass is the five-carbon sugar xylose, S. cerevisiae must be engineered to metabolize pentose sugars, commonly by the addition of exogenous genes from xylose fermenting fungi. However, these recombinant strains grow poorly on xylose and require further improvement through rational engineering or evolutionary adaptation. To identify unknown genes that contribute to improved xylose fermentation in these recombinant S. cerevisiae, we performed genome-wide synthetic interaction screens to identify deletion mutants that impact xylose utilization of strains expressing the xylose isomerase gene XYLA from Piromyces sp. E2 alone or with an additional copy of the endogenous xylulokinase gene XKS1. We also screened the deletion mutant array to identify mutants whose growth is affected by xylose. Our genetic network reveals that more than 80 nonessential genes from a diverse range of cellular processes impact xylose utilization. Surprisingly, we identified four genes, ALP1, ISC1, RPL20B, and BUD21, that when individually deleted improved xylose utilization of both S. cerevisiae S288C and CEN.PK strains. We further characterized BUD21 deletion mutant cells in batch fermentations and found that they produce ethanol even the absence of exogenous XYLA. We have demonstrated that the ability of laboratory strains of S. cerevisiae to utilize xylose as a sole carbon source is suppressed, which implies that S. cerevisiae may not require the addition of exogenous genes for efficient xylose fermentation.
SUPERNUMERARY TOOTH ASSOCIATED WITH CLEFT LIP AND PALATE.

A statistical study of the frequency of incidence of the supernumerary tooth associated with cleft lip and cleft palate was made in 1,168 patients examined at the department of oral surgery, Osaka University Dental School, Osaka, Japan, from 1958 to 1961. An additional 200 patients of whom a more detailed exami­ nation was possible were studied during the period of August, 1961, to March, 1962. I t was concluded that a supernu­ merary tooth was found much more often in the group of patients who had incom­ plete cleft lip with or without accom­ panying cleft palate than in the group of patients who had complete cleft lip with or without cleft palate. Cause and morphology of the supernumerary tooth and its positional relation to the site of the alveolar cleft are discussed in brief.
Electrotactile haptic display on the fingertips: preliminary results

Electrical stimulation of the sense of touch may be used to display pictorial information to blind computer users via a fingertip-scanned (haptic) touch tablet containing embedded electrodes. This might be particularly useful to users of systems with graphical user interfaces, or with drawing and layout software. Electrotactile (electrocutaneous) stimulation on the fingertip, however, differs substantially from that on other body locations. We discuss the implications of designing a practical graphics haptic display by addressing the high-resistance and variable nature of the fingertip electrode-skin interface. <<ETX>>
Modifying effects of low-intensity extremely high-frequency electromagnetic radiation on content and composition of fatty acids in thymus of mice exposed to X-rays

Abstract Purpose: The effects of extremely high-frequency electromagnetic radiation (EHF EMR) on thymus weight and its fatty acids (FA) content and FA composition in X-irradiated mice were studied to test the involvement of FA in possible protective effects of EHF EMR against ionizing radiation. Materials and methods: Mice were exposed to low-intensity pulse-modulated EHF EMR (42.2 GHz, 0.1 mW/cm2, 20 min exposure, 1 Hz modulation) and/or X-rays at a dose of 4 Gy with different sequences of the treatments. In 4–5 hours, 10, 30, and 40 days after the last exposure, the thymuses were weighed; total FA content and FA composition of the thymuses were determined on days 1, 10, and 30 using a gas chromatography. Results: It was shown that after X-irradiation of mice the total FA content per mg of thymic tissue was significantly increased in 4–5 h and decreased in 10 and 30 days after the treatment. On days 30 and 40 after X-irradiation, the thymus weight remained significantly reduced. The first and tenth days after X-rays injury independently of the presence and sequence of EHF EMR exposure were characterized by an increased content of polyunsaturated FA (PUFA) and a decreased content of monounsaturated FA (MUFA) with unchanged content of saturated FA (SFA). Exposure of mice to EHF EMR before or after X-irradiation prevented changes in the total FA content in thymic tissue, returned the summary content of PUFA and MUFA to the control level and decreased the summary content of SFA on the 30th day after the treatments, and promoted the restoration of the thymus weight of X-irradiated mice to the 40th day of the observations. Conclusions: Changes in the content and composition of PUFA in the early period after treatments as well as at the restoration of the thymus weight under the combined action of EHF EMR and X-rays indicate to an active participation of FA in the acceleration of post-radiation recovery of the thymus by EHF EMR exposure.
In vitro antidiabetic effects of selected fruits and vegetables against glycosidase and aldose reductase

Abstract In vitro antidiabetic effect of fruits and vegetables with reports as folk remedies were investigated. The antidiabetic effects were evaluated by comparing the inhibitory properties of α‐glycosidase, aldose reductase, and antioxidant activity. The results indicated that lychee extract exhibited the best dose‐dependent inhibitory activity against α‐glycosidase with IC 50 of 10.4 mg/mL, and lemon peel extract exhibited aldose reductase inhibitory potential with IC 50 value at 3.63 mg/mL. Besides, the result also showed that the inhibitory effects of blueberry and plum against α‐glycosidase were strong among the fruits samples. Bitter gourd and eggplant demonstrated significant inhibitory potential against aldose reductase, with IC 50 values at 8.55 mg/mL and 8.06 mg/mL, respectively. The result from correlation analysis part showed that the antioxidant activities of selected fruits and vegetables were found related to their health beneficial effects, as there was positive correlations between total flavonoids content (TFC) and aldose reductase inhibitory activity (r 2 = 0.556).
A knowledge based approach to matching human neurodegenerative disease and animal models

Neurodegenerative diseases present a wide and complex range of biological and clinical features. Animal models are key to translational research, yet typically only exhibit a subset of disease features rather than being precise replicas of the disease. Consequently, connecting animal to human conditions using direct data-mining strategies has proven challenging, particularly for diseases of the nervous system, with its complicated anatomy and physiology. To address this challenge we have explored the use of ontologies to create formal descriptions of structural phenotypes across scales that are machine processable and amenable to logical inference. As proof of concept, we built a Neurodegenerative Disease Phenotype Ontology (NDPO) and an associated Phenotype Knowledge Base (PKB) using an entity-quality model that incorporates descriptions for both human disease phenotypes and those of animal models. Entities are drawn from community ontologies made available through the Neuroscience Information Framework (NIF) and qualities are drawn from the Phenotype and Trait Ontology (PATO). We generated ~1200 structured phenotype statements describing structural alterations at the subcellular, cellular and gross anatomical levels observed in 11 human neurodegenerative conditions and associated animal models. PhenoSim, an open source tool for comparing phenotypes, was used to issue a series of competency questions to compare individual phenotypes among organisms and to determine which animal models recapitulate phenotypic aspects of the human disease in aggregate. Overall, the system was able to use relationships within the ontology to bridge phenotypes across scales, returning non-trivial matches based on common subsumers that were meaningful to a neuroscientist with an advanced knowledge of neuroanatomy. The system can be used both to compare individual phenotypes and also phenotypes in aggregate. This proof of concept suggests that expressing complex phenotypes using formal ontologies provides considerable benefit for comparing phenotypes across scales and species.
Evolution of the Multi-Domain Structures of Virulence Genes in the Human Malaria Parasite, Plasmodium falciparum

The var gene family of Plasmodium falciparum encodes the immunodominant variant surface antigens PfEMP1. These highly polymorphic proteins are important virulence factors that mediate cytoadhesion to a variety of host tissues, causing sequestration of parasitized red blood cells in vital organs, including the brain or placenta. Acquisition of variant-specific antibodies correlates with protection against severe malarial infections; however, understanding the relationship between gene expression and infection outcome is complicated by the modular genetic architectures of var genes that encode varying numbers of antigenic domains with differential binding specificities. By analyzing the domain architectures of fully sequenced var gene repertoires we reveal a significant, non-random association between the number of domains comprising a var gene and their sequence conservation. As such, var genes can be grouped into those that are short and diverse and genes that are long and conserved, suggesting gene length as an important characteristic in the classification of var genes. We then use an evolutionary framework to demonstrate how the same evolutionary forces acting on the level of an individual gene may have also shaped the parasite's gene repertoire. The observed associations between sequence conservation, gene architecture and repertoire structure can thus be explained by a trade-off between optimizing within-host fitness and minimizing between-host immune selection pressure. Our results demonstrate how simple evolutionary mechanisms can explain var gene structuring on multiple levels and have important implications for understanding the multifaceted epidemiology of P. falciparum malaria.
Imaging brain tumor proliferative activity with [124I]iododeoxyuridine.

Iododeoxyuridine (IUdR) uptake and retention was imaged by positron emission tomography (PET) at 0-48 min and 24 h after administration of 28.0-64.4 MBq (0.76-1.74 mCi) of [124I]IUdR in 20 patients with brain tumors, including meningiomas and gliomas. The PET images were directly compared with gadolinium contrast-enhanced or T2-weighted magnetic resonance images. Estimates for IUdR-DNA incorporation in tumor tissue (Ki) required pharmacokinetic modeling and fitting of the 0-48 min dynamically acquired data to correct the 24-h image data for residual, nonincorporated radioactivity that did not clear from the tissue during the 24-h period after IUdR injection. Standard uptake values (SUVs) and tumor:brain activity ratios (Tm:Br) were also calculated from the 24-h image data. The Ki, SUV, and Tm/Br values were related to tumor type and grade, tumor labeling index, and survival after the PET scan. The plasma half-life of [124I]IUdR was short (2-3 min), and the arterial plasma input function was similar between patients (48 +/- 12 SUV*min). Plasma clearance of the major radiolabeled metabolite ([124I]iodide) varied somewhat between patients and was markedly prolonged in one patient with renal insufficiency. It was apparent from our analysis that a sizable fraction (15-93%) of residual nonincorporated radioactivity (largely [124I]iodide) remained in the tumors after the 24-h washout period, and this fraction varied between the different tumor groups. Because the SUV and Tm:Br ratio values reflect both IUdR-DNA incorporated and exchangeable nonincorporated radioactivity, any residual nonincorporated radioactivity will amplify their values and distort their significance and interpretation. This was particularly apparent in the meningioma and glioblastoma multiforme groups of tumors. Mean tumor Ki values ranged between 0.5 +/- 0.9 (meningiomas) and 3.9 +/- 2.3 microl/min/g (peak value for glioblastoma multiforme, GBM). Comparable SUV and Tm:Br values at 24 h ranged from 0.13 +/- 0.03 to 0.29 +/- 0.19 and from 2.0 +/- 0.6 to 6.1 +/- 1.5 for meningiomas and peak GBMs, respectively. Thus, the range of values was much greater for Ki (approximately 8-fold) compared with that for SUV (approximately 2.2-fold) and Tm:Br (approximately 3-fold). The expected relationships between Ki, SUV, and Tm:Br and other measures of tumor proliferation (tumor type and grade, labeling index, and patient survival) were observed. However, greater image specificity and significance of the SUV and Tm:Br values would be obtained by achieving greater washout and clearance of the exchangeable fraction of residual (background) radioactivity in the tumors, i.e., by increased hydration and urinary clearance and possibly by imaging later than 24 h after [124I]IUdR administration.
The National Comprehensive Cancer Network

The National Comprehensive Cancer Network (NCCN) has developed an extensive set of practice guidelines that cover approximately 90% of all cancer patients. These guidelines are steadily becoming the standard for clinical and coverage policy. The guideline development process is integrated directly with the development of a multiinstitutional data base that will permit measurement of adherence of practice to the NCCN guidelines and provide important clinical and other outcomes data. The NCCN is forming partnerships with managed care companies in the guideline/data base area to facilitate the delivery of more effective and efficient care in oncology. Cancer 1998;82:2057‐60. © 1998 American Cancer Society.
Tensile Creep of Concrete: Study of Its Sensitivity to Basic Parameters

There is little data available in regard to concrete tensile creep, a property which can considerably influence shrinkage-induced cracking, for instance, in repair works. The authors examine findings of testing to evaluate the influence, on concrete tensile creep, of paste content, steel fiber reinforcement, age at loading, and stress level. The results indicate that concrete creep in tension, as in compression, sharply increases under drying conditions. The results also show that with age at loading, there is a decrease in tensile creep coefficient, and that, either under sealed or drying conditions, and up to half of the ultimate short-term strength, concrete tensile creep varies linearly with applied load. Compressive creep is apparently less sensitive to fiber reinforcement than tensile creep, and it was observed that as paste content decreased, tensile creep increased. Particularly to determine ultimate creep capacity, further research is necessary, but there are indications through reported data that optimization of cement-based repair materials could be possible to reduce cracking potential when subjected to restrained shrinkage.
Priority classification based fast intra mode decision for High Efficiency Video Coding

The latest High-Efficiency Video Coding (HEVC) video coding standard version 1 offers 50% bit rate reduction against the H.264/AVC at the same visual quality. However, HEVC encoder complexity is tremendously increased. It is therefore important to develop efficient encoding algorithms for the success of HEVC based applications. In this paper, we propose a priority classification based fast intra mode decision to speed up the HEVC intra encoder. Each prediction unit (PU) is given a priority label out of four based on its spatial and temporal neighbor PU information as well as the predicted PU depth. Different processing strategy will be applied to different priority class, under the assumption that more computing resource should be allocated to the high priority class since its corresponding PU has the high potential to be chosen as the optima. Experiments are performed using all the common test sequences, and results show that, the encoder complexity is significantly reduced by about 46% for All Intra configuration with BD-Rate (Bjontegaard Delta Rate) increase less than 0.9% for luma component. Meanwhile, compared with several recent works, our proposed solution demonstrates the well trade-off between the coding efficiency and complexity reduction.
Robust Pulse Rate From Chrominance-Based rPPG

Remote photoplethysmography (rPPG) enables contactless monitoring of the blood volume pulse using a regular camera. Recent research focused on improved motion robustness, but the proposed blind source separation techniques (BSS) in RGB color space show limited success. We present an analysis of the motion problem, from which far superior chrominance-based methods emerge. For a population of 117 stationary subjects, we show our methods to perform in 92% good agreement (±1.96σ) with contact PPG, with RMSE and standard deviation both a factor of 2 better than BSS-based methods. In a fitness setting using a simple spectral peak detector, the obtained pulse-rate for modest motion (bike) improves from 79% to 98% correct, and for vigorous motion (stepping) from less than 11% to more than 48% correct. We expect the greatly improved robustness to considerably widen the application scope of the technology.
Age Dependence of Myocardial Na+‐K+‐ ATPase Activity and Digitalis Intoxication in the Dog and Guinea Pig

Infants and young animals tolerate higher doses of digitalis glycosides, relative to body weight, than adults. One possible explanation for this could be an age-dependent difference in the myocardial digitalis receptor, the Na+-K+-ATPase. Two functions of this enzyme were studied in adult, 1- and 6-week-old dogs and guinea pigs: in vitro myocardial uptake of rubidium (86Rb) and binding of ouabain. In guinea pigs, rubidium uptake (pmol Rb/mg LV per 15 min) was: 1 week old: 100.9 ± 7.1 (mean + SE); 6 week: 79.8 ± 6.7; adult: 55.2 ± 7.9; (1 week: 6 week: P< 0.025; 1 week: adult, P< 0.001; 6 week: adult, P < 0.025). Similarly in dogs, rubidium uptake was significantly greater at 1 week than at 6 weeks (208 ± 13 vs. 144 ± 9; P < 0.001) and the latter greater than in adults (111 ± 4) (P < 0.005). Other groups of anesthetized adult and 6-week-old dogs were given digoxin, 0.3 mg/kg, iv. The young dogs took significantly longer to become cardiotoxic (17.3 ± 3.4 min vs. 9.3 ± 1.4 min; P< 0.025), while their myocardial digoxin uptake was at least as great. Rubidium uptake showed an average decrease of 56% after digoxin but residual uptakes were not different in the two groups. Data for ouabain binding showed similar differences between the various groups of dogs studied. Increased myocardial Na+-K+-ATPase activity, reflected in greater active cation transport and specific enzyme binding, has been demonstrated in young animals and may be partly responsible for their greater tolerance to digitalis glycosides. Circ Res 48: 329-333, 1981
Objective Bayesian Analysis of Skew‐t Distributions

Abstract. We study the Jeffreys prior and its properties for the shape parameter of univariate skew‐t distributions with linear and nonlinear Student's t skewing functions. In both cases, we show that the resulting priors for the shape parameter are symmetric around zero and proper. Moreover, we propose a Student's t approximation of the Jeffreys prior that makes an objective Bayesian analysis easy to perform. We carry out a Monte Carlo simulation study that demonstrates an overall better behaviour of the maximum a posteriori estimator compared with the maximum likelihood estimator. We also compare the frequentist coverage of the credible intervals based on the Jeffreys prior and its approximation and show that they are similar. We further discuss location‐scale models under scale mixtures of skew‐normal distributions and show some conditions for the existence of the posterior distribution and its moments. Finally, we present three numerical examples to illustrate the implications of our results on inference for skew‐t distributions.
Multiple levels of single-strand slippage at cetacean tri- and tetranucleotide repeat microsatellite loci.

Between three and six tri- and tetranucleotide repeat microsatellite loci were analyzed in 3720 samples collected from four different species of baleen whales. Ten of the 18 species/locus combinations had imperfect allele arrays, i.e., some alleles differed in length by other than simple integer multiples of the basic repeat length. The estimate of the average number of alleles and heterozygosity was higher at loci with imperfect allele arrays relative to those with perfect allele arrays. Nucleotide sequences of 23 different alleles at one tetranucleotide repeat microsatellite locus in fin whales, Balaenoptera physalus, and humpback whales, Megaptera novaeangliae, revealed sequence changes including perfect repeats only, multiple repeats, and partial repeats. The relative rate of the latter two categories of mutation was estimated at 0.024 of the mutation rate involving perfect repeats only. It is hypothesized that single-strand slippage of partial repeats may provide a mechanism for counteracting the continuous expansion of microsatellite loci, which is the logical consequence of recent reports demonstrating directional mutations. Partial-repeat mutations introduce imperfections in the repeat array, which subsequently could reduce the rate of single-strand slippage. Limited computer simulations confirmed this predicted effect of partial-repeat mutations.
Pleiotropic Functions for Transcription Factor Zscan10

The transcription factor Zscan10 had been attributed a role as a pluripotency factor in embryonic stem cells based on its interaction with Oct4 and Sox2 in in vitro assays. Here we suggest a potential role of Zscan10 in controlling progenitor cell populations in vivo. Mice homozygous for a Zscan10 mutation exhibit reduced weight, mild hypoplasia in the spleen, heart and long bones and phenocopy an eye malformation previously described for Sox2 hypomorphs. Phenotypic abnormalities are supported by the nature of Zscan10 expression in midgestation embryos and adults suggesting a role for Zscan10 in either maintaining progenitor cell subpopulation or impacting on fate choice decisions thereof.