Miracle-dz/UniFAR-FTUs huggingface dataset:
A codon model of nucleotide substitution with selection on synonymous codon usage

The quality of phylogenetic inference made from protein-coding genes depends, in part, on the realism with which the codon substitution process is modeled. Here we propose a new mechanistic model that combines the standard M0 substitution model of Yang (1997) with a simplified model from Gilchrist (2007) that includes selection on synonymous substitutions as a function of codon-specific nonsense error rates. We tested the newly proposed model by applying it to 104 protein-coding genes in brewer’s yeast, and compared the fit of the new model to the standard M0 model and to the mutation-selection model of Yang and Nielsen (2008) using the AIC. Our new model provided significantly better fit in approximately 85% of the cases considered for the basic M0 model and in approximately 25% of the cases for the M0 model with estimated codon frequencies, but only in a few cases when the mutation-selection model was considered. However, our model includes a parameter that can be interpreted as a measure of the rate of protein production, and the estimates of this parameter were highly correlated with an independent measure of protein production for the yeast genes considered here. Finally, we found that in some cases the new model led to the preference of a different phylogeny for a subset of the genes considered, indicating that substitution model choice may have an impact on the estimated phylogeny.
Primary Muscular Hydatidosis Mimicking Soft Tissue Tumour: A Report of Five Cases

Primary muscular hydatidosis is rare and usually presents as an asymptomatic, slowly growing mass mimicking a soft tissue tumour. Adequate preoperative planning and wide excision is recommended, as incomplete excision may lead to anaphylactic reactions and local recurrence. It should be considered in the differential diagnosis of soft tissue tumours especially in regions endemic for the parasite.
Flavonoid Rutin Alters the Viability and Function of Mitogen-Stimulated Splenocytes and Thymocytes Compared with Non Stimulated Cells

Rutin is a flavonoid obtained from Dimorphandra mollis (Benth.), a medicinal Brazilian plant used as antioxidative, antihemorrhagic, and blood vessel protector. The present study has examined its effects on the viability and function of immune system cells in vitro. Rat spleen and thymus cells were cultured with 10 nM, 1 μM, and 10 μM of the drug in the presence or absence of PWM, LPS, or ConA mitogens. Cellular proliferation was analyzed by H3-thymidin uptake and IFN-γ and IL-10 were measured by ELISA after 48 and 72 hr. Viability was measured by flow cytometry using Annexin V and PI after 24 and 48 hr. The flavonoid rutin inhibited splenocytes and thymocytes proliferation under ConA stimulation observed by an increase on apoptosis levels of thymocytes stimulated with PWM in 24 hr and on splenocytes stimulated with PWM in 48 hr. Function studies showed a decrease on IFN-γ production by splenocytes and thymocytes stimulated with PWM or ConA. Spleen cells cultured with LPS and rutin showed a decrease on apoptosis after 24 hr and an increase on the IL-10 levels after 48 hr. There was no significant variation on the necrosis rate, viability, and function of cells treated with rutin in the absence of mitogenic stimulus.
A Semi-Blind Watermarking Scheme for Images using a Tree Structure

In this paper, we embed the watermark in a tree structure in the Discrete Wavelet Transform domain. For watermark embedding, the two level DWT decomposition of an NxN gray scale image I is computed. The same PRN sequence is embedded into the DWT coefficients higher than a given threshold T1 in the LL2 and HH2 bands. The watermark is also embedded into the children of DWT coefficients. The original DWT coefficients are replaced by the modified DWT coefficients. The final step is to compute the inverse DWT to obtain the watermarked image I. For watermark detection, the DWT of the watermarked and possibly attacked image I* is computed. All the DWT coefficients higher than a given threshold T2 in the LL2 and HH2 bands are selected. Then the sum Z of all attacked DWT coefficients multiplied by either the embedded watermark or other random PRN sequence is computed, divided by the length of the PRN sequence. The sum is also computed for the children of modified DWT coefficients. A predefined threshold T is chosen for LL2 and HH2 bands and the HH1 band. In each band, if Z exceeds T, the conclusion is that the watermark is present.
Mineralogy of Iron Microbial Mats from Loihi Seamount

Extensive mats of Fe oxyhydroxides and associated Fe-oxidizing microbial organisms form in diverse geochemical settings – freshwater seeps to deep-sea vents – where ever opposing Fe(II)-oxygen gradients prevail. The mineralogy, reactivity, and structural transformations of Fe oxyhydroxides precipitated from submarine hydrothermal fluids within microbial mats remains elusive in active and fossil systems. In response, a study of Fe microbial mat formation at the Loihi Seamount was conducted to describe the physical and chemical characteristics of Fe-phases using extended X-ray absorption fine structure spectroscopy, powder X-ray diffraction, synchrotron radiation X-ray total scattering, low-temperature magnetic measurements, and Mössbauer spectroscopy. Particle sizes of 3.5–4.6 nm were estimated from magnetism data, and coherent scattering domain (CSD) sizes as small as 1.6 nm are indicated by pair distribution function (PDF) analysis. Disorder in the nanostructured Fe-bearing phases results in limited intermediate-range structural order: less than that of standard two-line ferrihydrite (Fh), except for the Pohaku site. The short-range ordered natural Fh (FhSRO) phases were stable at 4°C in the presence of oxygen for at least 1 year and during 400°C treatment. The observed stability of the FhSRO is consistent with magnetic observations that point to non-interacting nanoparticles. PDF analyses of total scattering data provide further evidence for FhSRO particles with a poorly ordered silica coating. The presence of coated particles explains the small CSD for the mat minerals, as well as the stability of the minerals over time and against heating. The mineral properties observed here provide a starting point from which progressively older and more extensively altered Fe deposits may be examined, with the ultimate goal of improved interpretation of past biogeochemical conditions and diagenetic processes.
Effects of the aqueous extract from Salvia miltiorrhiza Bge on the pharmacokinetics of diazepam and on liver microsomal cytochrome P450 enzyme activity in rats

The aim of this study was to determine the effects of the aqueous extract of Salvia miltiorrhiza Bge (danshen in Chinese) on the pharmacokinetics of diazepam and on liver microsomal cytochrome P450 enzyme activity in rats. Rats (n = 5) were pretreated with danshen extract (100 mg kg−1 per day, p.o.) for 15 consecutive days. Control rats (n = 5) received saline at the same time. Each rat was then administered a single oral dose of 15 mg kg−1 diazepam. The pharmacokinetic parameters of diazepam were significantly different between the two groups. In the danshen pretreated group, the maximum concentration of diazepam and the area under the plasma concentration–time curve were reduced to about 72.7% and 44.4%, respectively, while the total body clearance was markedly increased by 2‐fold. To help explain the results, liver microsomal suspensions were obtained from rats that were randomly divided into the control group (n = 10), and the low‐ (20 mg kg−1 for 15 days, p.o., n = 10) and high‐dose groups (100 mg kg−1 for 15 days, p.o., n = 10) pretreated with danshen extract. Compared with the control rats, the microsomal protein content, cytochrome P450 enzyme level and erythromycin N‐demethylase activity of pretreated rats were significantly increased. These results indicate that danshen extract can stimulate the activity of cytochrome P450 isoforms, and changes in the pharmacokinetics of diazepam resulting from danshen extract are related to an increase in metabolic activity of cytochrome P450.
Frameworks for studying the determinants of child survival.

Looking back the optimism of the early 1980s that child survival could be improved rapidly and at low cost in all lowincome settings was at best premature. Although immunization programmes have greatly increased immunization levels and oral rehydration has been effective at reducing deaths from diarrhoea in some settings child mortality declines in the 1980s were not noticeably faster than those of the 1970s. The Mosley–Chen model however has stood the test of time remarkably well and still provides explicitly or implicitly the conceptual basis for many studies of child survival. The underlying ideas have influenced a wide range of health research. The basic proximate determinants framework is very similar to the household health production function in economics. The proposal of a single health status outcome measure combining both morbidity and mortality is picked up in studies of disease burden in the 1990s. Mosley & Chen correctly predicted that it would not be possible to develop their framework into a readily-quantifiable model whereby the effect on child health status of a given change in one of the proximate determinants could be estimated (in the way that Bongaarts had developed Davis & Blake’s framework for the study of fertility). However social science research on child mortality has benefitted greatly from the clarity of the conceptual framework proposed by Moseley & Chen. As their paper concludes the framework permits research that “. can not only assess the overall health impact of alternative development strategies but also more sharply define which among a number of specific factors amenable to change by health policymakers are of greatest consequence for child survival. ” This is just as true today as when the paper was written. (excerpt)
Reorganization of descending motor tracts in the rat spinal cord

Following lesion of the central nervous system (CNS), reinnervation of denervated areas may occur via two distinct processes: regeneration of the lesioned fibres or/and sprouting from adjacent intact fibres into the deafferented zone. Both regeneration and axonal sprouting are very limited in the fully mature CNS of higher vertebrates, but can be enhanced by neutralizing the neurite outgrowth inhibitory protein Nogo‐A. This study takes advantage of the distinct spinal projection pattern of two descending tracts, the corticospinal tract (CST) and the rubrospinal tract (RST), to investigate if re‐innervation of denervated targets can occur by sprouting of anatomically separate, undamaged tracts in the adult rat spinal cord. The CST was transected bilaterally at its entry into the pyramidal decussation. Anatomical studies of the RST in IN‐1 antibody‐treated rats showed a reorganization of the RST projection pattern after neutralization of the myelin associated neurite growth inhibitor Nogo‐A. The terminal arborizations of the rubrospinal fibres, which are normally restricted to the intermediate layers of the spinal cord, invaded the ventral horn but not the dorsal horn of the cervical spinal cord. Moreover, new close appositions were observed, in the ventral horn, onto motoneurons normally receiving CST projections. Red nucleus microstimulation experiments confirmed the reorganization of the RST system. These observations indicate that mature descending motor tracts are capable of significant intraspinal reorganization following lesion and suggests the expression of cues guiding and/or stabilizing newly formed sprouts in the adult, denervated spinal cord.
Reduced mitochondrial mass and function add to age‐related susceptibility toward diet‐induced fatty liver in C57BL/6J mice

Nonalcoholic fatty liver disease (NAFLD) is a major health burden in the aging society with an urging medical need for a better understanding of the underlying mechanisms. Mitochondrial fatty acid oxidation and mitochondrial‐derived reactive oxygen species (ROS) are considered critical in the development of hepatic steatosis, the hallmark of NAFLD. Our study addressed in C57BL/6J mice the effect of high fat diet feeding and age on liver mitochondria at an early stage of NAFLD development. We therefore analyzed functional characteristics of hepatic mitochondria and associated alterations in the mitochondrial proteome in response to high fat feeding in adolescent, young adult, and middle‐aged mice. Susceptibility to diet‐induced obesity increased with age. Young adult and middle‐aged mice developed fatty liver, but not adolescent mice. Fat accumulation was negatively correlated with an age‐related reduction in mitochondrial mass and aggravated by a reduced capacity of fatty acid oxidation in high fat‐fed mice. Irrespective of age, high fat diet increased ROS production in hepatic mitochondria associated with a balanced nuclear factor erythroid‐derived 2 like 2 (NFE2L2) dependent antioxidative response, most likely triggered by reduced tethering of NFE2L2 to mitochondrial phosphoglycerate mutase 5. Age indirectly influenced mitochondrial function by reducing mitochondrial mass, thus exacerbating diet‐induced fat accumulation. Therefore, consideration of age in metabolic studies must be emphasized.
The relationship between usual alcohol consumption and the content of association memory in young and mature social drinkers

The results from this study indicated that the accessibility of negative alcohol memory associations was higher in alcohol contexts as participants generated more alcohol-related responses to the negative alcohol-related behavioural outcomes. As no effect of context was observed for positive alcohol memory associations, it was postulated that this type of memory association might become activated prior to or during decisions to consume alcohol. In addition, the results indicated that activated negative memory associations might not exert an influential role over decisions to consume alcohol. The results form this study provided further support for the Alcohol-Related Association Memory model of alcohol use. The findings from the series of studies provided support for the Alcohol-Related Association Memory model of alcohol use. In addition to replicating previous research findings, concerning the relationship between alcohol use and positive outcomes of this behaviour, the research findings showed that a relationship between alcohol use and negative outcomes of this behaviour is evident when an appropriate assessment tool is used. In addition to demonstrating that alcohol memory associations are strengthened in relation to current alcohol consumption level, the results from Study 3 showed that the length of an alcohol consumption history relates to the strength and subsequent accessibility of positive and negative alcohol memory associations. It was also indicated that activated negative alcohol memory associations might not exert an influential role over behavioural decisions. Alcohol association memory research, conducted thus far, has shown that there is a relationship between alcohol consumption experience and strength of alcohol memory associations. However, the effect that activated memory associations have on actual alcohol consumption, has not yet been established. Therefore, future research suggestions address this issue.
The effect of service interaction orientation on customer satisfaction and behavioral intention

Purpose – The purpose of this paper is to investigate the relationships among interaction orientation, customer satisfaction and behavioral intentions across firms in the hospitality industry.Design/methodology/approach – A self‐administered survey was conducted with a convenience sample of 628 full‐service seafood restaurants.Findings – The empirical results indicate that interaction orientation has positive influences on customer satisfaction in first‐time and frequent diners; interaction orientation positively affects behavioral intentions in frequent diners; and customer satisfaction positively affects behavioral intentions in first‐time and frequent diners. In addition, customer satisfaction is a mediator between interaction orientation and behavioral intentions.Research limitations/implications – The research target of full‐service seafood restaurants limits the generalizability of the findings to a wider population.Originality/value – In addition to insights on how restaurant promotion strategies s.
Protective effects of Schisandra Lignans on myocardial ischemia-reperfusion injury in anesthetized rats

To examine the effects of schisandra lignans on arrhythmias and infarct area induce by ischemia and reperfusion in the anesthetized rats and to study the mechanisms involved. Wistar rats were randomly divided into control group; positive group; and three Schisandra Lignans-treated groups. After 14 days administration of drugs, rats underwent acute ischemia (30 min) and reperfusion (120 min). After reperfusion, hearts were taken for the measurement of MPO activities by Evens blue-TTC staining. As compared with control group, Schisandra Lignans decreased myocardial infarct area/ventricle area ratio, decreased MPO activities, prolonged the latent period of VT. There were no significant changes in blood pressure and heart rate. In conclusion, Schisandra Lignans has protective effects on myocardial ischemia and reperfusion injuries. The inhibition of inflammatory cell infiltration may be related to the protective effects. The present study provides a hopeful basis for the development of new drugs with Schisandra Lignans in the treatment ischemic diseases.
Clonogenic Multiple Myeloma Cells have Shared stemness Signature Associated with Patient Survival

Multiple myeloma is the abnormal clonal expansion of post germinal B cells in the bone marrow. It was previously reported that clonogenic myeloma cells are CD138−. Human MM cell lines RPMI8226 and NCI H929 contained 2-5% of CD138− population. In this study, we showed that CD138− cells have increased ALDH1 activity, a hallmark of normal and neoplastic stem cells. CD138−ALDH+ cells were more clonogenic than CD138+ALDH− cells and only CD138− cells differentiated into CD138+ population. In vivo tumor initiation and clonogenic potentials of the CD138− population was confirmed using NOG mice. We derived a gene expression signature from functionally validated and enriched CD138− clonogenic population from MM cell lines and validated these in patient samples. This data showed that CD138− cells had an enriched expression of genes that are expressed in normal and malignant stem cells. Differentially expressed genes included components of the polycomb repressor complex (PRC) and their targets. Inhibition of PRC by DZNep showed differential effect on CD138− and CD138+ populations. The ‘stemness’ signature derived from clonogenic CD138− cells overlap significantly with signatures of common progenitor cells, hematopoietic stem cells, and Leukemic stem cells and is associated with poorer survival in different clinical datasets.
Highly Collimated Molecular Hydrogen Jets near IRAS 05487+0255: Near-Infrared Imaging and Spectroscopy

We present new narrowband near-infrared images together with K-band spectra of highly collimated bipolar jets close to the IRAS 05487+0255 source. The jets are located ~50'' west of the Herbig-Haro 110 outflow. The jets are not visible at optical wavelengths and therefore do not fall into the "standard" Herbig-Haro object classification scheme. Nevertheless, they belong to an ever growing group of molecular hydrogen jets associated with young stellar objects that are optically undetected. The jets are very well collimated, with length-to-width ratios of ~10-20. The spectra of the jet and its counterjet in the K band show a limited number of H2 emission lines that make it difficult to obtain an accurate excitation temperature. We estimate Tex = 1104±67 K and Tex = 920±156 K for the red and blue jet components, respectively. The radial velocities of the jet and counterjet, based on the shift of the (1,0) S(1) 2.121 μm line, are ~-275 ± 50 km s-1 and ~180 ± 50 km s-1, respectively, suggesting an angle of ~30°-45° between the jet and the line of sight. The H2 emission of the entire jet extends for at least 40'', ~0.1 pc at the distance of Orion. If the flow velocity is comparable to that of the radial velocities, then the dynamical age of the system is quite short (~500 yr), consistent with a young jet arising from an embedded source. Entrainment in a turbulent mixing layer may explain this morphology and spectral character.
Grouping in object recognition: The role of a Gestalt law in letter identification

The Gestalt psychologists reported a set of laws describing how vision groups elements to recognize objects. The Gestalt laws “prescribe for us what we are to recognize ‘as one thing’” (Köhler, 1920). Were they right? Does object recognition involve grouping? Tests of the laws of grouping have been favourable, but mostly assessed only detection, not identification, of the compound object. The grouping of elements seen in the detection experiments with lattices and “snakes in the grass” is compelling, but falls far short of the vivid everyday experience of recognizing a familiar, meaningful, named thing, which mediates the ordinary identification of an object. Thus, after nearly a century, there is hardly any evidence that grouping plays a role in ordinary object recognition. To assess grouping in object recognition, we made letters out of grating patches and measured threshold contrast for identifying these letters in visual noise as a function of perturbation of grating orientation, phase, and offset. We define a new measure, “wiggle”, to characterize the degree to which these various perturbations violate the Gestalt law of good continuation. We find that efficiency for letter identification is inversely proportional to wiggle and is wholly determined by wiggle, independent of how the wiggle was produced. Thus the effects of three different kinds of shape perturbation on letter identifiability are predicted by a single measure of goodness of continuation. This shows that letter identification obeys the Gestalt law of good continuation and may be the first confirmation of the original Gestalt claim that object recognition involves grouping.
Qualitative research through case studies

What Is Qualitative Research? PART ONE: THE INTERPRETIVE TRADITION Addressing 'Lived Experience' Symbolic Interactionism and Ethnography Varieties of Symbolic Interactionism Grounded Theory and Dramaturgical Analysis Investigating Practices Ethnomethodological Ethnography Researching Language Conversation Analysis PART TWO: CRITICAL PERSPECTIVES From Description to Critique Feminism and Qualitative Research Postmodern Ethnography PART THREE: CONCLUSION The Craft of Qualitative Research