Miracle-dz/UniFAR-FTUs huggingface dataset:
Polymorphisms in Cinnamoyl CoA Reductase (CCR) Are Associated With Variation in Microfibril Angle in Eucalyptus spp.

Linkage disequilibrium (LD) mapping using natural populations results in higher resolution of marker-trait associations compared to family-based quantitative trait locus (QTL) studies. Depending on the extent of LD, it is possible to identify alleles within candidate genes associated with a trait. Analysis of a natural mutant in Arabidopsis has shown that mutations in cinnamoyl CoA reductase (CCR), a key lignin gene, affect physical properties of the secondary cell wall such as stiffness and strength. Using this gene, we tested whether LD mapping could identify alleles associated with microfibril angle (MFA), a wood quality trait affecting stiffness and strength of wood. We identified 25 common single-nucleotide polymorphism (SNP) markers in the CCR gene in Eucalyptus nitens. Using single-marker and haplotype analyses in 290 trees from a E. nitens natural population, two haplotypes significantly associated with MFA were found. These results were confirmed in two full-sib families of E. nitens and Eucalyptus globulus. In an effort to understand the functional significance of the SNP markers, we sequenced the cDNA clones and identified an alternatively spliced variant from the significant haplotype region. This study demonstrates that LD mapping can be used to identify alleles associated with wood quality traits in natural populations of trees.
Effects of Different Levels of Water Stress on Yield and Quality of Lemon Trees

Three levels of water stress were caused by using the 'forzatura' technique to determine its effects on summer and winter crops. In summer fruits about to be harvested when the stress occurred, high percentage of drop was noticed after the resumption of irrigation in the most stressed treatment. Fruit drop was also observed in winter crop, and yield in the most severely stressed treatment was lower. In the new summer crop obtained under water stress, the number of flowers/m3 was clearly higher in the most stressed treatment, indicating a relationship between the severity of stress and the flowering response. Fruit set, on the other hand, was very low, so that no difference in yield was observed.
Enhancing the functional maturity of induced pluripotent stem cell–derived human hepatocytes by controlled presentation of cell–cell interactions in vitro

Induced pluripotent stem cell‐derived human hepatocyte‐like cells (iHeps) could provide a powerful tool for studying the mechanisms underlying human liver development and disease, testing the efficacy and safety of pharmaceuticals across different patients (i.e., personalized medicine), and enabling cell‐based therapies in the clinic. However, current in vitro protocols that rely upon growth factors and extracellular matrices (ECMs) alone yield iHeps with low levels of liver functions relative to adult primary human hepatocytes (PHHs). Moreover, these low hepatic functions in iHeps are difficult to maintain for prolonged times (weeks to months) in culture. Here, we engineered a micropatterned coculture (iMPCC) platform in a multiwell format that, in contrast to conventional confluent cultures, significantly enhanced the functional maturation and longevity of iHeps in culture for at least 4 weeks in vitro when benchmarked against multiple donors of PHHs. In particular, iHeps were micropatterned onto collagen‐coated domains of empirically optimized dimensions, surrounded by 3T3‐J2 murine embryonic fibroblasts, and then sandwiched with a thin layer of ECM gel (Matrigel). We assessed iHep maturity by global gene expression profiles, hepatic polarity, secretion of albumin and urea, basal cytochrome P450 (CYP450) activities, phase II conjugation, drug‐mediated CYP450 induction, and drug‐induced hepatotoxicity. Conclusion: Controlling both homotypic interactions between iHeps and heterotypic interactions with stromal fibroblasts significantly matures iHep functions and maintains them for several weeks in culture. In the future, iMPCCs could prove useful for drug screening, studying molecular mechanisms underlying iHep differentiation, modeling liver diseases, and integration into human‐on‐a‐chip systems being designed to assess multiorgan responses to compounds. (Hepatology 2015;61:1370–1381)
Variable efficacy of passive antibody administration against diverse Cryptococcus neoformans strains

The efficacy of monoclonal antibody (MAb 2H1) against diverse strains of Cryptococcus neoformans was studied in a murine model of intravenous infection. For six of eight strains, administration of MAb prior to infection prolonged survival of mice. For two strains, 371 and SB4A, administration of MAb prior to infection did not prolong survival in multiple experiments with inocula ranging from 10(2) to 10(6) yeast cells per mouse. Mice infected with strains 371 and SB4A had fewer CFU than non-MAb-treated controls, but the CFU reduction was not sufficient to affect survival. Serum glucuronoxylomannan (GXM) levels varied for the different C. neoformans strains. For mice that did not receive MAb 2H1, there was a positive correlation between lung fungal burden and serum GXM levels. MAb 2H1-treated mice had significantly reduced serum GXM levels. The results indicate that the efficacy of MAb 2H1 administration in prolonging survival and/or reducing organ CFU varies with the C. neoformans strain.
Dry habitats were crucibles of domestication in the evolution of agriculture in ants

The evolution of ant agriculture, as practised by the fungus-farming ‘attine’ ants, is thought to have arisen in the wet rainforests of South America about 55–65 Ma. Most subsequent attine agricultural evolution, including the domestication event that produced the ancestor of higher attine cultivars, is likewise hypothesized to have occurred in South American rainforests. The ‘out-of-the-rainforest’ hypothesis, while generally accepted, has never been tested in a phylogenetic context. It also presents a problem for explaining how fungal domestication might have occurred, given that isolation from free-living populations is required. Here, we use phylogenomic data from ultra-conserved element (UCE) loci to reconstruct the evolutionary history of fungus-farming ants, reduce topological uncertainty, and identify the closest non-fungus-growing ant relative. Using the phylogeny we infer the history of attine agricultural systems, habitat preference and biogeography. Our results show that the out-of-the-rainforest hypothesis is correct with regard to the origin of attine ant agriculture; however, contrary to expectation, we find that the transition from lower to higher agriculture is very likely to have occurred in a seasonally dry habitat, inhospitable to the growth of free-living populations of attine fungal cultivars. We suggest that dry habitats favoured the isolation of attine cultivars over the evolutionary time spans necessary for domestication to occur.
Leveraging Machine Readable Dictionaries in Discriminative Sequence Models

Many natural language processing tasks make use of a lexicon  typically the words collected from some annotated training data along with their associated properties. We demonstrate here the utility of corpora-independent lexicons derived from machine readable dictionaries. Lexical information is encoded in the form of features in a Conditional Random Field tagger providing improved performance in cases where: i) limited training data is made available ii) the data is case-less and iii) the test data genre or domain is different than that of the training data. We show substantial error reductions, especially on unknown words, for the tasks of part-of-speech tagging and shallow parsing, achieving up to 20% error reduction on Penn TreeBank part-of-speech tagging and up to a 15.7% error reduction for shallow parsing using the CoNLL 2000 data. Our results here point towards a simple, but effective methodology for increasing the adaptability of text processing systems by training models with annotated data in one genre augmented with general lexical information or lexical information pertinent to the target genre (or domain).
Storage and retrieval properties of dual codes for pictures and words in recognition memory.

Storage and retrieval properties of pictures and words were studied within a recognition memory paradigm. Storage was manipulated by instructing subjects either to image or to verbalize to both picture and word stimuli during the study sequence. Retrieval was manipulated by representing a proportion of the old picture and word items in their opposite form during the recognition test (i.e., some old pictures were tested with their corresponding words and vice versa). Recognition performance for pictures was identical under the two instructional conditions, whereas recognition performance for words was markedly superior under the imagery instruction condition. It was suggested that subjects may engage in dual coding of simple pictures naturally, regardless of instructions, whereas dual coding of words may occur only under imagery instructions. The form of the test item had no effect on recognition performance for either type of stimulus and under either instructional condition. However, change of form of the test item markedly reduced item-by-item correlations between the two instructional conditions. It is tentatively proposed that retrieval is required in recognition, but that the effect of a form change is simply to make the retrieval process less consistent, not less efficient.
Microstructural investigation of gas shale in Longmaxi Formation, Lower Silurian, NE Sichuan Basin, China

The purpose of this paper is to probe into the nature and variability in vertical microstructure within Longmaxi gas shales of well WX2, Lower Silurian, located in the NE Sichuan Basin of China. To understand the pore system of these rocks, the total porosity, pore size distribution (PSD), surface area, organic geochemistry, and mineralogy, some image analyses by electron microscopy are performed. The obtained results indicated the following. (1) Gas shales have a complex pore structure. Total porosity from helium pycnometry ranges between 0.75% and 4.62%. Total organic content ranges between 3.4 wt. % and 11 wt. %, and vitrinite reflectance measured between 2.5% and 3.1%. The gas shales are quartz and clay rich. (2) Focused ion beam milling and field emission scanning electron microscopy provide high-resolution images of pores distribution and types. Three primary types of pores, organic matter (OM)-hosted pores, mineral-hosted pores, and micro-fractures, and 11 subgroups have been recognized. (3) The N2 isotherm curves are grouped into two types, II b as well as IV a, with the hysteresis loop belonging to Type B, reflecting the morphology of slits pores, and Type A, presenting cylinder pores. Combination of N2 and CO2 isotherm curve shows bimodal in two diameter sections, 0.3–1 nm and 2–5 nm, revealing meso-pores play important role in pore volume, whereas the micro-pores have great influence on pore specific surface area. (4) Total organic carbon (TOC) is considered to be the dominant contributor to total porosity and pore types, with the proportion of OM-hosted pores following the upward decreasing tendency of TOC. In plane, pore types are controlled by sedimentary facies. The OM-hosted pores are more prevalent in deep shelf facies within lower part of shale other than upper formation, instead of shallow shelf facies.
B‐Lymphocyte Precursors in Immunodeficient, Autoimmune and Anemic Mice

There are now several promising approaches to understanding B-lymphocyte heterogeneity and development. Among these is the use of monoclonal antibodies directed to cell surface antigens. Appropriate reagents are available for identifying cells in embryonic and adult murine hemopoietic tissues which are destined to quickly become functional B cells. This makes it possible to enumerate and manipulate such precursors before placing them in culture or an appropriate recipient animal where their further maturation can occur. One immediate application of these methods is to the study of animal models where genetic defects influence development ofthe humoral immune system. These are likely to reveal new cell types and functions that are critical to B-cell formation and provide examples of compensatory changes which can take place in response to primary immunological lesions. The purpose of this article will be to summarize our recent observations on the incidence and nature of B-cell precursors in several well-studied strains of mice which have abnormalities affecting humoral immunity.
Nanotechnology in the targeted drug delivery for bone diseases and bone regeneration

Nanotechnology is a vigorous research area and one of its important applications is in biomedical sciences. Among biomedical applications, targeted drug delivery is one of the most extensively studied subjects. Nanostructured particles and scaffolds have been widely studied for increasing treatment efficacy and specificity of present treatment approaches. Similarly, this technique has been used for treating bone diseases including bone regeneration. In this review, we have summarized and highlighted the recent advancement of nanostructured particles and scaffolds for the treatment of cancer bone metastasis, osteosarcoma, bone infections and inflammatory diseases, osteoarthritis, as well as for bone regeneration. Nanoparticles used to deliver deoxyribonucleic acid and ribonucleic acid molecules to specific bone sites for gene therapies are also included. The investigation of the implications of nanoparticles in bone diseases have just begun, and has already shown some promising potential. Further studies have to be conducted, aimed specifically at assessing targeted delivery and bioactive scaffolds to further improve their efficacy before they can be used clinically.
A Qualified ITU-T G.729EV Codec Candidate for Hierarchical Speech and Audio Coding

We present an embedded and hierarchical 8-32 kbit/s speech and audio coding algorithm that has been successfully submitted to the ITU-T as a candidate for ITU-T Rec. G.729. 1 (ex G.729EV). The submitting consortium consisted of Siemens AG, Matsushita Electric Industrial Co. Ltd., and Mindspeed Technologies Inc. This contribution gives a comprehensive overview of the proposed codec, describes the implemented algorithms, and states a detailed characterization as well as results of the official G.729EV qualification tests
Left Ventricular Systolic Dysfunction and the Risk of Ischemic Stroke in a Multiethnic Population

Background and Purpose— Left ventricular dysfunction (LVD) is associated with cardiovascular mortality. Its association with ischemic stroke has been mainly documented after myocardial infarction. The stroke risk associated with LVD, especially of mild degree, in the general population is unclear. The purpose of this study was to evaluate the relationship between LVD and ischemic stroke in a multiethnic cohort. Methods— LV systolic function was assessed by transthoracic 2-dimensional echocardiography in a subset of subjects from the Northern Manhattan Study (NOMAS), 270 patients with first ischemic stroke and 288 age-, gender- and race-matched community controls. LV ejection fraction was measured by a simplified cylinder-hemiellipsoid formula, and categorized as normal (>50%), mildly (41% to 50%), moderately (31% to 40%) or severely (≤30%) decreased. The association between impaired ejection fraction and ischemic stroke was evaluated by logistic regression analysis after adjustment for established stroke risk factors. Results— LVD of any degree was more frequent in stroke patients (24.1%) than in controls (4.9%; P<0.0001), as was moderate/severe LVD (13.3% versus 2.4%; P<0.001). A decreased ejection fraction was associated with ischemic stroke even after adjusting for other stroke risk factors. The adjusted odds ratio for any degree of LVD was 3.92 (95% CI, 1.93 to 7.97). The adjusted odds ratio for mild LVD was 3.96 (95% CI, 1.56 to 10.01) and for moderate/severe LVD 3.88 (95% CI, 1.45 to 10.39). The association between LVD of any degree and stroke was present in all age, gender and race-ethnicity subgroups. Conclusions— LVD, even of mild degree, is independently associated with an increased risk of ischemic stroke. The assessment of LV function should be considered in the assessment of the stroke risk.
Neuroanatomical Differences between First-Episode Psychosis Patients with and without Neurocognitive Deficit: A 3-Year Longitudinal Study

Background: The course of cognitive function in first-episode psychosis (FEP) patients suggests that some individuals are normal or near normal whereas some cases present a marked decline. The goal of the present longitudinal study was to identify neuroanatomical differences between deficit and non-deficit patients. Methods: Fifty nine FEP patients with neuroimage and neurocognitive information were studied at baseline and 3 year after illness onset. A global cognitive function score was used to classify deficit and non-deficit patients at baseline. Analysis of covariances and repeated-measures analysis were performed to evaluate differences in brain volumes. Age, premorbid IQ, and intracranial volume were used as covariates. We examined only volumes of whole brain, whole brain gray and white matter, cortical CSF and lateral ventricles, lobular volumes of gray and white matter, and subcortical (caudate nucleus and thalamus) regions. Results: At illness onset 50.8% of patients presented global cognitive deficit. There were no significant differences between neuropsychological subgroups in any of the brain regions studied at baseline [all F(1, 54) ≤ 3.42; all p ≥ 0.07] and follow-up [all F(1, 54) ≤ 3.43; all p ≥ 0.07] time points. There was a significant time by group interaction for the parietal tissue volume [F(1, 54) = 4.97, p = 0.030] and the total gray matter volume [F(1, 54) = 4.31, p = 0.042], with the deficit group showing a greater volume decrease. Conclusion: Our results did not confirm the presence of significant morphometric differences in the brain regions evaluated between cognitively impaired and cognitively preserved schizophrenia patients at the early stages of the illness. However, there were significant time by group interactions for the parietal tissue volume and the total gray matter volume during the 3-year follow-up period, which might indicate that cognitive deficit in schizophrenia would be associated with progressive brain volume loss.
Microhabitat Selection by Caribbean Damselfish in a Marine Protected Area, Bluefield's Bay, Jamaica

The main objective of this project was to determine if Caribbean damselfish select microhabitat based on coral morphology. Sampling sites were located within the Bluefield’s Bay Marine Sanctuary in Bluefield’s Bay, Jamaica. Four species of damselfish were selected, based on their abundance and ecological significance, and were sampled at 17 sites using a passive drift sampling technique in June, 2011. An underwater camera was utilized to capture associations between damselfish and the coral reef. Habitat composition was estimated by dividing the substrate into 14 categories based on morphology. Percent composition was estimated for each substrate group at 30 randomly selected positions within each transect and then averaged to provide an estimate across all 17 transects. Three chi-square goodness of fit tests were then utilized to examine the relationship between damselfish and microhabitat selection. The first included all observed substrate groups. The second excluded sand, and the third excluded all noncoral substrate groups. For all but one species (C. parasema), there was a significant difference between habitat selection and availability when analyzing all substrate types with and without sand. However, none of the four target species showed a habitat selection preference towards one group of live coral over another.
Mastery Learning Reconsidered

Several recent reviews and meta-analyses have claimed extraordinarily positive effects of mastery learning on student achievement, and Bloom (1984a , 1984b) has hypothesized that mastery-based treatments will soon be able to produce “2-sigma” (i.e., 2 standard deviation) increases in achievement. This article examines the literature on achievement effects of practical applications of group-based mastery learning in elementary and secondary schools over periods of at least 4 weeks, using a review technique, “best-evidence synthesis,” which combines features of meta-analytic and traditional narrative reviews. The review found essentially no evidence to support the effectiveness of group-based mastery learning on standardized achievement measures. On experimenter-made measures, effects were generally positive but moderate in magnitude, with little evidence that effects maintained over time. These results are discussed in light of the coverage versus mastery dilemma posed by group-based mastery learning.
Labor Market Policy: A Comparative View on the Costs and Benefits of Labor Market Flexibility

I review theories and evidence on labor market policies and institutions in an international context. These include collective bargaining, minimum wages, employment protection laws, unemployment insurance (UI), mandated parental leave, and active labor market policies. Scandinavia and Central Europe follow more interventionist policies than Canada, the UK and the US. Vulnerability to external market forces and ethnic homogeneity may explain such differences. While the interventionist model appears to reduce wage inequality and raise job security for incumbent workers, it also often relegates new entrants (disproportionately women, youth and immigrants) and the less skilled to temporary jobs or unemployment.
Histological results after maxillary sinus augmentation with Straumann® BoneCeramic, Bio-Oss®, Puros®, and autologous bone. A randomized controlled clinical trial.

OBJECTIVE This investigation focused on a comparison of clinical and histological characteristics after sinus floor augmentation with biphasic calcium phosphate (BCP, Straumann BoneCeramic(®) ), anorganic bovine bone (ABB, Geistlich Bio-Oss(®) ), mineralized cancellous bone allograft (MCBA, Zimmer Puros(®) ), or autologous bone (AB). MATERIALS AND METHODS Thirty consecutive patients with a posterior edentulous maxillary situation and a vertical bone height less than or equal to 4 mm were included in this study. A two-stage procedure was carried out. After augmentation of the maxillary sinus with ABB, BCP, MCBA, or AB followed by a healing period of 5 months, biopsies were taken with simultaneous implant placement. The samples were analyzed using microradiography and histology. RESULTS Ninety-four implants were placed in the augmented positions and 53 bone biopsies were taken and evaluated. The bone volume fraction of newly formed bone was measured as 30.28 ± 2.16% for BCP, 24.9 ± 5.67% for ABB, 41.74 ± 2.1% for AB, and 35.41 ± 2.78% for MCBA with significant increases in bone volume of AB vs. BCP and ABB, and MCBA vs. ABB samples. Significantly different residual bone substitute material was measured as 15.8 ± 2.1% in the BCP group and 21.36 ± 4.83% in the ABB group. CONCLUSION As it provides the highest rate of de novo bone formation, AB can be considered to remain the gold standard in sinus floor augmentation. All tested control materials showed comparable results and are suitable for maxillary sinus augmentation.