Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic parameters for lignin, extractives and decay in Eucalyptus globulus

Eucalyptus globulus is grown in temperate regions of the world for pulp production. The chemical and physical properties of its wood make it highly suited to this purpose. This study analysed genetic variation in lignin content, extractives content and decay, for nine localities of E. globulus. Heritability estimates were also obtained, and the relationships between these traits and physical wood traits and growth were examined. Significant genetic variation was found between localities for lignin content (Klason lignin and acid-soluble lignin contents) and decay. The only trait for which significant variation between families within locality was detected was acid-soluble lignin content, which resulted in this trait also having the highest narrow-sense heritability (0.51 ± 0.26). However, family means heritabilities were high for lignin content, extractives content and decay (0.42-0.64). The chemical wood traits were strongly correlated with each other both phenotypically and genetically, with important correlations found with density and microfibril angle. Correlations suggested that during selection for the breeding objective traits, it is likely that favourable states in the chemical wood traits, decay resistance and fibre properties are concurrently being selected, whereas growth may be selected for independently. This initial study provides a stepping stone for future studies where particular localities of the breeding population may be characterised further. correlation / eucalypt / genetic variation / heritability / lignin
The adipokine C1q TNF related protein 3 (CTRP3) is elevated in the breast milk of obese mothers

Background C1q TNF related protein 3 (CTRP3) is a relatively novel hormonal factor primarily derived from adipose tissue and has anti-diabetic properties. To determine if CTRP3 could play a role in early childhood development, the purpose of this study was to establish the presence of CTRP3 in breast milk (BM) and to determine whether CTRP3 levels were correlated with pregravid obesity status of the mother. Methods Breast milk was collected from breast-feeding mothers who had a pregravid body mass index (BMI) classification of normal weight (BMI 18–25 kg/m2, n = 23) or obese (BMI > 30 kg/m2, n = 14). Immunoprecipitation followed by immunoblot analysis confirmed the presence of CTRP3 in BM. The concentration of CTRP3 in BM samples was determined by ELISA. Additional bioactive components were also measured by commercially available assays: ghrelin, insulin, leptin, adiponectin, interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), and glucose. Bioactive components in normal weight and obese mothers were compared using unpaired t-test (parametric) and Mann–Whitney U-test (non-parametric), as appropriate. Results The primary findings of this study are that the adipokine CTRP3 is present in BM and CTRP3 levels are increased with pregravid obesity. Additionally, this study independently confirmed previous work that BM from obese mothers has a higher concentration of insulin and leptin. Further, no differences were observed in BM between obese and normal weight mothers in ghrelin, adiponectin, IL-6, TNF-α, or glucose levels. Conclusion This study identified a novel factor in BM, CTRP3, and showed that BM CTRP3 levels higher in obese mothers. Because of the purported insulin sensitizing effect of CTRP3, it is possible that the elevated levels of CTRP3 in the BM of obese mothers may offset negative effects of elevated leptin and insulin levels in the BM of obese mothers. Future studies will need to be conducted to determine the relevance of CTRP3 in BM and to examine the presence of other adipose tissue-derived hormonal factors.
Control of Tissue Growth and Cell Transformation by the Salvador/Warts/Hippo Pathway

The Salvador-Warts-Hippo (SWH) pathway is an important regulator of tissue growth that is frequently subverted in human cancer. The key oncoprotein of the SWH pathway is the transcriptional co-activator, Yes-associated protein (YAP). YAP promotes tissue growth and transformation of cultured cells by interacting with transcriptional regulatory proteins via its WW domains, or, in the case of the TEAD1-4 transcription factors, an N-terminal binding domain. YAP possesses a putative transactivation domain in its C-terminus that is necessary to stimulate transcription factors in vitro, but its requirement for YAP function has not been investigated in detail. Interestingly, whilst the WW domains and TEAD-binding domain are highly conserved in the Drosophila melanogaster YAP orthologue, Yorkie, the majority of the C-terminal region of YAP is not present in Yorkie. To investigate this apparent conundrum, we assessed the functional roles of the YAP and Yorkie C-termini. We found that these regions were not required for Yorkie's ability to drive tissue growth in vivo, or YAP's ability to promote anchorage-independent growth or resistance to contact inhibition. However, the YAP transactivation domain was required for YAP's ability to induce cell migration and invasion. Moreover, a role for the YAP transactivation domain in cell transformation was uncovered when the YAP WW domains were mutated together with the transactivation domain. This shows that YAP can promote cell transformation in a flexible manner, presumably by contacting transcriptional regulatory proteins either via its WW domains or its transactivation domain.
ARMDN: Associative and Recurrent Mixture Density Networks for eRetail Demand Forecasting

Accurate demand forecasts can help on-line retail organizations better plan their supply-chain processes. The challenge, however, is the large number of associative factors that result in large, non-stationary shifts in demand, which traditional time series and regression approaches fail to model. In this paper, we propose a Neural Network architecture called AR-MDN, that simultaneously models associative factors, time-series trends and the variance in the demand. We first identify several causal features and use a combination of feature embeddings, MLP and LSTM to represent them. We then model the output density as a learned mixture of Gaussian distributions. The AR-MDN can be trained end-to-end without the need for additional supervision. We experiment on a dataset of an year's worth of data over tens-of-thousands of products from Flipkart. The proposed architecture yields a significant improvement in forecasting accuracy when compared with existing alternatives.
Rhythms of the Night: Spatiotemporal Inequalities in the Nighttime Economy

The authors seek to extend the literature on inequalities and exclusion in the nighttime economy through a rhythmic analysis of visitor presence in public space in nightlife districts in the city centres of the Dutch cities of Groningen, Utrecht, and Rotterdam. Substantial inequalities in visitor presence, based on race/ethnicity and gender, are demonstrated. In the cities considered, racial/ethnic inequalities vary more in spatial terms, and gender inequalities fluctuate more heavily over the course of the night. Overall, however, the findings support the argument that exclusion from the nighttime economy needs to be understood in temporal—ecological terms. Multiple drivers, or pacemakers, of rhythmic inequalities rooted in race/ethnicity and gender are identified, including opening hours and revellers' collective habits. For advocates of greater diversity among nighttime-economy participants, the analysis suggests that neither a more varied supply of nightlife premises, nor more surveillance and policing, are straightforward solutions: a strong orientation of premises toward university students and urban professionals may promote gender-based inclusion, but deters nonwhite revellers, and more police on the street may empower women to move through a nightlife district unaccompanied yet reduce the inclination to do so among racial/ethnic minorities
The Effects of Nutrient Dynamics on Root Patch Choice

Plants have been recognized to be capable of allocating more roots to rich patches in the soil. We tested the hypothesis that in addition to their sensitivity to absolute differences in nutrient availability, plants are also responsive to temporal changes in nutrient availability. Different roots of the same Pisum sativum plants were subjected to variable homogeneous and heterogeneous temporally – dynamic and static nutrient regimes. When given a choice, plants not only developed greater root biomasses in richer patches; they discriminately allocated more resources to roots that developed in patches with increasing nutrient levels, even when their other roots developed in richer patches. These results suggest that plants are able to perceive and respond to dynamic environmental changes. This ability might enable plants to increase their performance by responding to both current and anticipated resource availabilities in their immediate proximity.
Construct Validity of the WISC-III for White and Black Students from the WISC-III Standardization Sample and for Black Students Referred for Psychological Evaluation

Abstract This study used both exploratory (EFA) and confirmatory factor analyses (CFA) to examine the factor structure of the WISC-III among White and Black students from the WISC-III standardization sample and a sample of 348 Black students referred for psychological evaluation. Results of the EFA provided evidence of a large first principal factor as well as the expected Verbal and Performance components across all three groups. Empirical support for the Freedom from Distractibility dimension was provided only from the confirmatory factor analyses. Although the four factor confirmatory model exhibited the best overall statistical fit, inspection of specific factor loadings revealed anomalies with the third and fourth factors, especially for the Referred Black sample. Implications for school psychologists are presented and recommendations for future research are provided.
EZH2 Codon 641 Mutations are Common in BCL2-Rearranged Germinal Center B Cell Lymphomas

Mutations at codon 641 of EZH2 are recurrent in germinal center B cell lymphomas, and the most common variants lead to altered EZH2 enzymatic activity and enhanced tri-methylation of histone H3 at lysine 27, a repressive chromatin modification. As an initial step toward screening patients for cancer genotype-directed therapy, we developed a screening assay for EZH2 codon 641 mutations amenable for testing formalin-fixed clinical specimens, based on the sensitive SNaPshot single nucleotide extension technology. We detected EZH2 mutations in 12/55 (22%) follicular lymphomas (FL), 5/35 (14%) diffuse large B cell lymphomas with a germinal center immunophenotype (GCB-DLBCL), and 2/11 (18%) high grade B cell lymphomas with concurrent rearrangements of BCL2 and MYC. No EZH2 mutations were detected in cases of Burkitt lymphoma (0/23). EZH2 mutations were frequently associated with the presence of BCL2 rearrangement (BCL2-R) in both the FL (28% of BCL-R cases versus 0% of BCL2-WT cases, p<0.05) and GCB-DLBCL groups (33% of BCL2-R cases versus 4% of BCL2-WT cases, p<0.04), and across all lymphoma types excluding BL (27% of BCL2-R cases versus 3% of BCL2-WT cases, p<0.003). We confirmed gain-of-function activity for all previously reported EZH2 codon 641 mutation variants. Our findings suggest that EZH2 mutations constitute an additional genetic “hit” in many BCL2-rearranged germinal center B cell lymphomas. Our work may be helpful in the selection of lymphoma patients for future trials of pharmacologic agents targeting EZH2 and EZH2-regulated pathways.
Outcomes of outpatient breast cancer surgery at a private breast clinic

Advances in surgical and anesthetic techniques have allowed for outpatient treatment of breast cancer. We evaluated the feasibility, safety, efficacy, and surgical outcomes of outpatient surgery in 370 patients with breast cancer who underwent breast‐conserving surgery (BCS)/axillar lymph node (ALN) management. There were no deaths or severe intraoperative complications, but 41 complications were observed and disease recurrence occurred in 18 patients. The cumulative overall survival rate was 95.2%. Outpatient surgery was well tolerated, feasible, and safe in patients receiving BCS/ALN management.
Amplification of P. falciparum Cytoadherence through Induction of a Pro-Adhesive State in Host Endothelium

This study examined the ability of P.falciparum-infected erythrocytes (IE) to induce a pro-adhesive environment in the host endothelium during malaria infection, prior to the systemic cytokine activation seen in the later phase of disease. Previous work had shown increases in receptor levels but had not measured to actual impact on IE binding. Using a co-culture system with a range of endothelial cells (EC) and IE with different cytoadherent properties, we have characterised the specific expression of adhesion receptors and subsequent IE binding by FACS and adhesion assays. We have also examined the specific signalling pathways induced during co-culture that are potentially involved in the induction of receptor expression. The results confirmed that ICAM-1 is up-regulated, albeit at much lower levels than seen with TNF activation, in response to co-culture with infected erythrocytes in all three tissue endothelial cell types tested but that up-regulation of VCAM-1 is tissue-dependent. This small increase in the levels of EC receptors correlated with large changes in IE adhesion ability. Co-culture with either RBC or IE increased the potential of subsequent adhesion indicating priming/modulation effects on EC which make them more susceptible to adhesion and thereby the recruitment of IE. Trypsin surface digestion of IE and the use of a Pfsbp1-knockout (ko) parasite line abrogated the up-regulation of ICAM-1 and reduced IE binding to EC suggesting that PfEMP-1 and other molecules exported to the IE surface via the PfSBP1 pathway are major mediators of this phenotype. This was also supported by the higher induction of EC adhesion receptors by adherent IE compared to isogenic, non-adherent lines.
Going beyond intention: Integrating behavioral expectation into the unified theory of acceptance and use of technology

Research on information technology (IT) adoption and use, one of the most mature streams of research in the information science and information systems literature, is primarily based on the intentionality framework. Behavioral intention (BI) to use an IT is considered the sole proximal determinant of IT adoption and use. Recently, researchers have discussed the limitations of BI and argued that behavioral expectation (BE) would be a better predictor of IT use. However, without a theoretical and empirical understanding of the determinants of BE, we remain limited in our comprehension of what factors promote greater IT use in organizations. Using the unified theory of acceptance and use of technology as the theoretical framework, we develop a model that posits 2 determinants (i.e., social influence and facilitating conditions) of BE and 4 moderators (i.e., gender, age, experience, and voluntariness of use) of the relationship between BE and its determinants. We argue that the cognitions underlying the formation of BI and BE differ. We found strong support for the proposed model in a longitudinal field study of 321 users of a new IT. We offer theoretical and practical IT implications of our findings.
Enhanced Phosphorylation of Bax and Its Translocation into Mitochondria in the Brains of Individuals Affiliated with Alzheimer’s Disease

Background: Despite increased neuronal death, senile plaques, and neurofibrillary tangles observed in patients suffering from Alzheimer’s disease (AD), the detailed mechanism of cell death in AD is still poorly understood. Method: We hypothesized that p38 kinase activates and then phosphorylates Bax, leading to its translocation to mitochondria in AD brains compared to controls. The aim of this study was to investigate the role of p38 kinase in phosphorylation and sub-cellular localization of pro-apoptotic Bax in the frontal cortex of the brains from AD and control subjects. Increased oxidative stress in AD individuals compared to control was evaluated by measuring the levels of carbonylated proteins and oxidized peroxiredoxin, an antioxidant enzyme. The relative amounts of p38 kinase and phospho-Bax in mitochondria in AD brains and controls were determined by immunoblot analysis using the respective antibody against each protein following immunoprecipitation. Results: Our results showed that the levels of oxidized peroxiredoxin-SO3 and carbonylated proteins are significantly elevated in AD brains compared to controls, demonstrating the increased oxidative stress. Conclusion: The amount of phospho-p38 kinase is increased in AD brains and the activated p38 kinase appears to phosphorylate Thr residue(s) of Bax, which leads to its mitochondrial translocation, contributing to apoptosis and ultimately, neurodegeneration.
Solid bone tumors of the spine: Diagnostic performance of apparent diffusion coefficient measured using diffusion‐weighted MRI using histology as a reference standard

To assess the diagnostic performance of mean apparent diffusion coefficient (mADC) in differentiating benign from malignant bone spine tumors, using histology as a reference standard. Conventional magnetic resonance imaging (MRI) sequences have good reliability in evaluating spinal bone tumors, although some features of benign and malignant cancers may overlap, making the differential diagnosis challenging.
Decreased dendritic spine density on prefrontal cortical pyramidal neurons in schizophrenia.

BACKGROUND The pathophysiological characteristics of schizophrenia appear to involve altered synaptic connectivity in the dorsolateral prefrontal cortex. Given the central role that layer 3 pyramidal neurons play in corticocortical and thalamocortical connectivity, we hypothesized that the excitatory inputs to these neurons are altered in subjects with schizophrenia. METHODS To test this hypothesis, we determined the density of dendritic spines, markers of excitatory inputs, on the basilar dendrites of Golgi-impregnated pyramidal neurons in the superficial and deep portions of layer 3 in the dorsolateral prefrontal cortex (area 46) and in layer 3 of the primary visual cortex (area 17) of 15 schizophrenic subjects, 15 normal control subjects, and 15 nonschizophrenic subjects with a psychiatric illness (referred to as psychiatric subjects). RESULTS There was a significant effect of diagnosis on spine density only for deep layer 3 pyramidal neurons in area 46 (P = .006). In the schizophrenic subjects, spine density on these neurons was decreased by 23% and 16% compared with the normal control (P = .004) and psychiatric (P = .08) subjects, respectively. In contrast, spine density on neurons in superficial layer 3 in area 46 (P = .09) or in area 17 (P = .08) did not significantly differ across the 3 subject groups. Furthermore, spine density on deep layer 3 neurons in area 46 did not significantly (P = .81) differ between psychiatric subjects treated with antipsychotic agents and normal controls. CONCLUSION This region- and disease-specific decrease in dendritic spine density on dorsolateral prefrontal cortex layer 3 pyramidal cells is consistent with the hypothesis that the number of cortical and/or thalamic excitatory inputs to these neurons is altered in subjects with schizophrenia.
Genomes of the Most Dangerous Epidemic Bacteria Have a Virulence Repertoire Characterized by Fewer Genes but More Toxin-Antitoxin Modules

Background We conducted a comparative genomic study based on a neutral approach to identify genome specificities associated with the virulence capacity of pathogenic bacteria. We also determined whether virulence is dictated by rules, or if it is the result of individual evolutionary histories. We systematically compared the genomes of the 12 most dangerous pandemic bacteria for humans (“bad bugs”) to their closest non-epidemic related species (“controls”). Methodology/Principal Findings We found several significantly different features in the “bad bugs”, one of which was a smaller genome that likely resulted from a degraded recombination and repair system. The 10 Cluster of Orthologous Group (COG) functional categories revealed a significantly smaller number of genes in the “bad bugs”, which lacked mostly transcription, signal transduction mechanisms, cell motility, energy production and conversion, and metabolic and regulatory functions. A few genes were identified as virulence factors, including secretion system proteins. Five “bad bugs” showed a greater number of poly (A) tails compared to the controls, whereas an elevated number of poly (A) tails was found to be strongly correlated to a low GC% content. The “bad bugs” had fewer tandem repeat sequences compared to controls. Moreover, the results obtained from a principal component analysis (PCA) showed that the “bad bugs” had surprisingly more toxin-antitoxin modules than did the controls. Conclusions/Significance We conclude that pathogenic capacity is not the result of “virulence factors” but is the outcome of a virulent gene repertoire resulting from reduced genome repertoires. Toxin-antitoxin systems could participate in the virulence repertoire, but they may have developed independently of selfish evolution.
Trans-Generational Effect of Maternal Lactation during Pregnancy: A Holstein Cow Model

Epigenetic regulation in mammals begins in the first stages of embryogenesis. This prenatal programming determines, in part, phenotype expression in adult life. Some species, particularly dairy cattle, are conceived during the maternal lactation, which is a period of large energy and nutrient needs. Under these circumstances, embryo and fetal development compete for nutrients with the mammary gland, which may affect prenatal programming and predetermine phenotype at adulthood. Data from a specialized dairy breed were used to determine the transgenerational effect when embryo development coincides with maternal lactation. Longitudinal phenotypic data for milk yield (kg), ratio of fat-protein content in milk during first lactation, and lifespan (d) from 40,065 cows were adjusted for environmental and genetic effects using a Bayesian framework. Then, the effect of different maternal circumstances was determined on the residuals. The maternal-related circumstances were 1) presence of lactation, 2) maternal milk yield level, and 3) occurrence of mastitis during embryogenesis. Females born to mothers that were lactating while pregnant produced 52 kg (MonteCarlo standard error; MCs.e. = 0.009) less milk, lived 16 d (MCs.e. = 0.002) shorter and were metabolically less efficient (+0.42% milk fat/protein ratio; MCs.e.<0.001) than females whose fetal life developed in the absence of maternal lactation. The greater the maternal milk yield during embryogenesis, the larger the negative effects of prenatal programming, precluding the offspring born to the most productive cows to fully express their potential additive genetic merit during their adult life. Our data provide substantial evidence of transgenerational effect when pregnancy and lactation coincide. Although this effect is relatively low, it should not be ignored when formulating rations for lactating and pregnant cows. Furthermore, breeding, replacement, and management strategies should also take into account whether the individuals were conceived during maternal lactation because, otherwise, their performance may deviate from what it could be expected.