Miracle-dz/UniFAR-FTUs huggingface dataset:
PARENTAL AND DEVELOPMENTAL TEMPERATURE EFFECTS ON THE THERMAL DEPENDENCE OF FITNESS IN DROSOPHILA MELANOGASTER

Abstract Cross-generational effects refer to nongenetic influences of the parental phenotype or environment on offspring phenotypes. Such effects are commonly observed, but their adaptive significance is largely unresolved. We examined cross-generational effects of parental temperature on offspring fitness (estimated via a serial-transfer assay) at different temperatures in a laboratory population of Drosophila melanogaster. Parents were reared at 18°C, 25°C, or 29°C (Tpar) and then their offspring were reared at 18°C, 25°C, or 29°C (Toff) to evaluate several competing hypotheses (including an adaptive one) involving interaction effects of parental and offspring temperature on offspring fitness. The results clearly show that hotter parents are better; in other words, the higher the temperature of the parents, the higher the fitness of their offspring, independent of offspring thermal environment. These data contradict the adaptive cross-generational hypothesis, which proposes that offspring fitness is maximal when the offspring thermal regime matches the parental one. Flies with hot parents have high fitness seemingly because their own offspring develop relatively quickly, not because they have higher fecundity early in life. Corresponding Editor: W. T. Starmer
A Genetic Algorithm with repair and local search mechanisms able to find minimal length addition chains for small exponents

In this paper, we present an improved Genetic Algorithm (GA) that is able to find the shortest addition chains for a given exponent e. Two new variation operators (special two-point crossover and a local-search-like mutation) are proposed as a means to improve the GA search capabilities. Furthermore, the usage of an improved repair mechanism is applied to the process of generating the initial population of the algorithm. The proposed approach is compared on a set of test problems with two state-of-the-art evolutionary heuristic-based approaches recently published. Finally, the modified GA is used to find the optimal addition chain length for a small collection of “hard” exponents. The results obtained are competitive and even better in the more difficult instances of the exponentiation problem that were considered here.
Metazoan rDNA enhancer acts by making more genes transcriptionally active

Enhancers could, in principle, function by increasing the rate of reinitiation on individual adjacent active promoters or by increasing the probability that an adjacent promoter is activated for transcription. We have addressed this issue for the repetitive metazoan rDNA enhancer by microinjecting Xenopus oocytes with enhancer-less and enhancer-bearing genes and determining by EM the frequency that each gene type forms active transcription units and their transcript density. We use conditions where transcription requires the normal rDNA promoter and is stimulated 30-50-fold by the enhancer. (In contrast, at saturating template conditions as used in previous EM studies, an aberrant mode of transcription is activated that is not affected by the rDNA enhancer or by the generally recognized rDNA promoter). The active transcription units on enhancer-less genes are found to be as densely packed with nascent transcripts and polymerases as those on enhancer- bearing genes and on the endogenous rRNA genes. Significantly, the enhancer-bearing genes are approximately 30-50-fold more likely to form such active transcription units than enhancer-less genes, consistent with their amounts of transcript. Complementary studies confirm that the enhancer does not affect elongation rate, the stability of the transcription complex, or transcript half-life. These data demonstrate that the repetitive metazoan rDNA enhancer causes more genes to be actively transcribed and does not alter the reinitiation rate on individual active genes.
Non-blocking binary search trees

This paper describes the first complete implementation of a non-blocking binary search tree in an asynchronous shared-memory system using single-word compare-and-swap operations. The implementation is linearizable and tolerates any number of crash failures. Insert and Delete operations that modify different parts of the tree do not interfere with one another, so they can run completely concurrently. Find operations only perform reads of shared memory.
Cage Matching: Head to Head Competition Experiments of an Invasive Plant Species from Different Regions as a Means to Test for Differentiation

Many hypotheses are prevalent in the literature predicting why some plant species can become invasive. However, in some respects, we lack a standard approach to compare the breadth of various studies and differentiate between alternative explanations. Furthermore, most of these hypotheses rely on ‘changes in density’ of an introduced species to infer invasiveness. Here, we propose a simple method to screen invasive plant species for potential differences in density effects between novel regions. Studies of plant competition using density series are a fundamental tool applied to virtually every aspect of plant population ecology to better understand evolution. Hence, we use a simple density series with substitution contrasting the performance of Centaurea solstitialis in monoculture (from one region) to mixtures (seeds from two regions). All else being equal, if there is no difference between the introduced species in the two novel regions compared, Argentina and California, then there should be no competitive differences between intra and inter-regional competition series. Using a replicated regression design, seeds of each species were sown in the greenhouse at 5 densities in monoculture and mixed and grown till onset of flowering. Centaurea seeds from California had higher germination while seedlings had significantly greater survival than Argentina. There was no evidence for density dependence in any measure for the California region but negative density dependence was detected in the germination of seeds from Argentina. The relative differences in competition also differed between regions with no evidence of differential competitive effects of seeds from Argentina in mixture versus monoculture while seeds from California expressed a relative cost in germination and relative growth rate in mixtures with Argentina. In the former instance, lack of difference does not mean ‘no ecological differences’ but does suggest that local adaptation in competitive abilities has not occurred. Importantly, this method successfully detected differences in the response of an invasive species to changes in density between novel regions which suggests that it is a useful preliminary means to explore invasiveness.
The power density spectrum of NGC 5548 and the nature of its variability

ABSTRA C T We derive power density spectra in the optical and X-ray bands in the time-scale range from several yr down to ,1 d. We suggest that the optical power density spectrum consists of two separate components: long time-scale variations and short time-scale variations, with the dividing time-scale around 100 d. The shape of the short time-scale component is similar to the X-ray power density spectrum, which is consistent with the interpretation of short time-scale optical variations being caused by X-ray reprocessing. We show that the observed optical long time-scale variability is consistent with thermal pulsations of the accretion disc.
A new approach to a bridging tensor

Bridging Model is an efficient micromechanical theory which can be used to predict the effective thermomechanical as well as strength properties of a fiber reinforced composite. The key to the Bridging Model is a bridging tensor, which was obtained on Eshelby's inclusion method [Huang and Zhou, Strength of Fibrous Composites, Vol. 53, Zhejiang University Press, Springer, Hangzhou, (2011)]. A different approach to the closed-form expressions for the elements of a bridging tensor is presented in this work. The method is based on averaging the stress fields of a single-fiber inclusion embedded within an infinite matrix subjected to various load conditions. By solving the bridging equations between the averaged stress components in the fiber and those in the matrix, the exact expressions for the bridging tensor elements are obtained. The Bridging Model can be established by neglecting some small quantities in the bridging tensor elements. Effective elastic moduli of a unidirectional (UD) composite are expressed as functions of a bridging tensor. Comparisons of predicted elastic properties of a total number of 18 UD composites on simplified and the exact bridging tensors are made. POLYM. COMPOS. , 36:1417–1431, 2015. © 2014 Society of Plastics Engineers
Effect of Garlic Oil and Modified Atmosphere Packaging on the Quality of Chilled Shrimp

This research aimed to investigate the effect of essential oils extracted from garlic (Allium sativum L.) and modified atmospheric (MA) conditions on maintaining the quality of chilled Pacific white shrimps (Litopenaeus vannamei). Clean fresh shrimps (headless, shell‐off and devein) were dipped into 15 mg/ml of garlic oil for 15 min. Approximately 100 g of shrimps with or without dipping into the garlic oil was placed on polyethylene terephthalate trays and packed under two MA conditions (modified atmosphere packaging 1: 40% CO2 + 60% N2 and modified atmosphere packaging 2: 60% CO2 + 40% N2) using nylon/PE pouches. The shrimps with or without dipping into the garlic oil packed under normal atmospheric condition using PE pouches were prepared as the control. The samples were then stored at 8°C ± 2°C for three weeks and taken every two times a week. Shrimp samples were subjected to physical, chemical and microbiological analysis as well as sensory evaluation. The results showed that either garlic oil or MA conditions had proven to help preserving the quality of chilled white shrimps because they slowed down both chemical degradation and microbial spoilage. The shrimps dipped in garlic oil and/or packed under MA conditions had lower pH, total volatile base nitrogen and trimethylamine values as well as total viable counts than the control sample. 60% CO2 + 40% N2 in combination of garlic oil helped prolonging the shelf life of the shrimps stored at 8°C ± 2°C from 6 to 18 days. Thus, applying both garlic oil and low O2 atmospheric conditions were more effective on maintaining shrimp quality than applying only garlic oil or MA conditions. Copyright © 2013 John Wiley & Sons, Ltd.
Contribution of fimbrial operons to attachment to and invasion of epithelial cell lines by Salmonella typhimurium

The role of the Salmonella typhimurium fimbrial operons, lpf, fim, and pef, in adhesion to and invasion of epithelial cell lines was investigated. An S. typhimurium lpfC mutant was unable to adhere to or to invade HEp-2 cells, while an S. typhimurium fim deletion mutant did not attach to or enter HeLa cells. These results suggest that adhesion is a prerequisite for invasion and that distinct fimbrial adhesins select different target cells for invasion by S. typhimurium.
From Exemplar to Grammar: A Probabilistic Analogy-Based Model of Language Learning

While rules and exemplars are usually viewed as opposites, this paper argues that they form end points of the same distribution. By representing both rules and exemplars as (partial) trees, we can take into account the fluid middle ground between the two extremes. This insight is the starting point for a new theory of language learning that is based on the following idea: If a language learner does not know which phrase-structure trees should be assigned to initial sentences, s/he allows (implicitly) for all possible trees and lets linguistic experience decide which is the "best" tree for each sentence. The best tree is obtained by maximizing "structural analogy" between a sentence and previous sentences, which is formalized by the most probable shortest combination of subtrees from all trees of previous sentences. Corpus-based experiments with this model on the Penn Treebank and the Childes database indicate that it can learn both exemplar-based and rule-based aspects of language, ranging from phrasal verbs to auxiliary fronting. By having learned the syntactic structures of sentences, we have also learned the grammar implicit in these structures, which can in turn be used to produce new sentences. We show that our model mimicks children's language development from item-based constructions to abstract constructions, and that the model can simulate some of the errors made by children in producing complex questions.
Prevalence of depression in consecutive patients with type 2 diabetes mellitus of 5-year duration and its impact on glycemic control

Context: Type 2 diabetes mellitus doubles the odds of suffering from depressive illness. Co-morbid depression is associated with poorer outcomes in diabetes mellitus in terms of glycemic control, medication adherence, quality of life, physical activity, and blood pressure control. Aim: The present study aims to estimate the prevalence of depression among a consecutive group of patients with type 2 diabetes and assess its impact on glycemic and blood pressure control. Setting: Outpatient department of the endocrinology department of a university affiliated teaching hospital in north India. Subjects: Consecutive adult patients (18–65 years) with type 2 diabetes mellitus of over 5-year duration with no prior history of psychiatric illnesses or intake of anti-depressants. Materials and Methods: A semi-structured questionnaire was used for demographic data, HbA1c was obtained to assess glycemic control, and blood pressure was recorded twice during patient interview to assess blood pressure control. Depression was assessed with the Major Depression Inventory and scores obtained were classified as consistent with mild, moderate and severe depression. Data was analyzed with SPSS v16, and multiple logistical regression test was done to compare the effect of depression on glycemic control after adjusting for age and sex. Results: Of the 80 patients interviewed, 31 (38.8%) had depressive symptoms. Among them 20 (25%) had mild depression, 10 (12.5%) had moderate depression, and 1 (1.3%) had severe depression. Conclusions: Over one third of patients with type 2 diabetes mellitus of over 5-year duration had depressive symptoms. The presence of depressive symptoms was associated with a significant worsening of glycemic control.
Dissimilar immunogenicities of human papillomavirus E7 and adenovirus E1A proteins influence primary tumor development.

Although human papillomaviruses (HPV) and adenoviruses (Ad) both transform cells by expressing functionally related oncogenes (Ad-E1A/E1B; HPV-E7/E6), only HPV are oncogenic in humans. Prior studies have shown that HPV-transformed cells are resistant to NK cell lysis and E7- and E6-specific CTL are inefficiently generated in women with HPV-induced cervical cancer. Therefore, we postulated that the dissimilar oncogenicities of Ad and HPV may be caused by a protective NK and T cell response that is triggered by transformed cells expressing E1A, but not by E7. To test this hypothesis, mice that were either immunologically intact, lacked T cells, or lacked both NK and T cells were challenged with Ad serotype 5 (Ad5)-E1A- or HPV16-E7-transfected tumor cells. E7-expressing tumor cells were resistant to NK cell lysis in vitro and failed to elicit a measurable anti-tumor NK or T cell response in vivo. The concomitant expression of E6 did not change this phenotype. In contrast, E1A-expressing tumor cells were sensitive to NK lysis in vitro and triggered a protective NK and T cell immune response in vivo. These data suggest differences in the capacities of E1A or E7 oncoproteins to trigger protective anti-tumor immune responses may contribute to the dissimilar oncogenicities of Ad and HPV in humans.
The spectrum of use of rituximab in chronic lymphocytic leukemia

The monoclonal chimeric anti-CD20 antibody, rituximab, has considerably improved therapeutic outcome in B-cell chronic lymphocytic leukemia. Rituximab has limited clinical activity when used as a single agent. The combination of the monoclonal antibody with fludarabine-based regimens clearly demonstrated, in Phase II and randomized trials, an increase in clinical efficacy in previously untreated and pretreated patients. Furthermore the addition of rituximab enabled the eradication of minimal residual disease, which is correlated with the prognosis in a high proportion of patients. Although the combination of rituximab with fludarabine-based regimens increased myelosuppression and immunosuppression, incidence of infections did not increase. The benefit of adding rituximab to other purine analogs or other chemotherapeutic combination regimens has also been explored. Moreover there could be a role for achieving better quality of responses with the combination of different monoclonal antibodies, considering that they target different antigens and exert different mechanism of action. Although the role of rituximab as maintenance therapy in low grade non-Hodgkin’s lymphomas has been determined, the benefit and optimal schedule in chronic lymphocytic leukemia are still under investigation. This review brings together knowledge of the pharmacokinetics, mechanism of action and clinical use of rituximab in chronic lymphocytic leukemia.
Inducible Apoe Gene Repair in Hypomorphic ApoE Mice Deficient in the Low-Density Lipoprotein Receptor Promotes Atheroma Stabilization with a Human-Like Lipoprotein Profile

Objective—To study atherosclerosis regression in mice after plasma lipid reduction to moderately elevated apolipoprotein B (apoB)–lipoprotein levels. Approach and Results—Chow-fed hypomorphic Apoe mice deficient in low-density lipoprotein receptor expression (Apoeh/hLdlr–/–Mx1-cre mice) develop hyperlipidemia and atherosclerosis. These mice were studied before and after inducible cre-mediated Apoe gene repair. By 1 week, induced mice displayed a 2-fold reduction in plasma cholesterol and triglyceride levels and a decrease in the non–high-density lipoprotein:high-density lipoprotein-cholesterol ratio from 87%:13% to 60%:40%. This halted atherosclerotic lesion growth and promoted macrophage loss and accumulation of thick collagen fibers for up to 8 weeks. Concomitantly, blood Ly-6Chigh monocytes were decreased by 2-fold but lesional macrophage apoptosis was unchanged. The expression of several genes involved in extracellular matrix remodeling and cell migration was changed in lesional macrophages 1 week after Apoe gene repair. However, mRNA levels of numerous genes involved in cholesterol efflux and inflammation were not significantly changed at this time point. Conclusions—Restoring apoE expression in Apoeh/hLdlr–/–Mx1-cre mice resulted in lesion stabilization in the context of a human-like ratio of non–high-density lipoprotein:high-density lipoprotein-cholesterol. Our data suggest that macrophage loss derived in part from reduced blood Ly-6Chigh monocytes levels and genetic reprogramming of lesional macrophages.
Age-Specific Differences in Oncogenic Pathway Deregulation Seen in Human Breast Tumors

Purpose To define the biology driving the aggressive nature of breast cancer arising in young women. Experimental Design Among 784 patients with early stage breast cancer, using prospectively-defined, age-specific cohorts (young ≤45 years; older ≥65 years), 411 eligible patients (n = 200≤45 years; n = 211≥65 years) with clinically-annotated Affymetrix microarray data were identified. GSEA, signatures of oncogenic pathway deregulation and predictors of chemotherapy sensitivity were evaluated within the two age-defined cohorts. Results In comparing deregulation of oncogenic pathways between age groups, a higher probability of PI3K (p = 0.006) and Myc (p = 0.03) pathway deregulation was observed in breast tumors arising in younger women. When evaluating unique patterns of pathway deregulation, a low probability of Src and E2F deregulation in tumors of younger women, concurrent with a higher probability of PI3K, Myc, and β-catenin, conferred a worse prognosis (HR = 4.15). In contrast, a higher probability of Src and E2F pathway activation in tumors of older women, with concurrent low probability of PI3K, Myc and β-catenin deregulation, was associated with poorer outcome (HR = 2.7). In multivariate analyses, genomic clusters of pathway deregulation illustrate prognostic value. Conclusion Results demonstrate that breast cancer arising in young women represents a distinct biologic entity characterized by unique patterns of deregulated signaling pathways that are prognostic, independent of currently available clinico-pathologic variables. These results should enable refinement of targeted treatment strategies in this clinically challenging situation.
A Novel Color Change Mechanism for Breast Cancer Biomarker Detection: Naphthoquinones as Specific Ligands of Human Arylamine N-Acetyltransferase 1

Human arylamine N-acetyltransferase 1 (hNAT1) has become an attractive potential biomarker for estrogen-receptor-positive breast cancers. We describe here the mechanism of action of a selective non-covalent colorimetric biosensor for the recognition of hNAT1 and its murine homologue, mNat2, over their respective isoenzymes, leading to new opportunities in diagnosis. On interaction with the enzyme, the naphthoquinone probe undergoes an instantaneous and striking visible color change from red to blue. Spectroscopic, chemical, molecular modelling and biochemical studies reported here show that the color change is mediated by selective recognition between the conjugate base of the sulfonamide group within the probe and the conjugate acid of the arginine residue within the active site of both hNAT1 and mNat2. This represents a new mechanism for selective biomarker sensing and may be exploited as a general approach to the specific detection of biomarkers in disease.
Amphotericin B lipid formulations in critically ill patients on continuous veno-venous haemofiltration.

OBJECTIVES The pharmacokinetics of lipid-formulated amphotericin B (AMB), and of AMB that has dissociated from its lipid moiety and bound to lipoproteins in plasma, were separately determined in critically ill patients. PATIENTS AND METHODS Eleven patients required continuous veno-venous haemofiltration (CVVH). Five of them were treated with liposomal AMB (AmBisome) and seven with AMB colloidal dispersion (Amphocil). Six of the critically ill were not undergoing CVVH (three of them treated with liposomal AMB and three with AMB colloidal dispersion). RESULTS Significant amounts of AMB are liberated from liposomes or colloidal dispersion during circulation in plasma, where pharmacokinetics mimic that of AMB deoxycholate. Elimination of the remaining lipid-formulated fraction is different and differentially affected by CVVH. Plasma levels of lipid-formulated AMB were significantly higher in patients treated with liposomal AMB than in those treated with AMB colloidal dispersion; clearance of liposomal AMB is enhanced by haemofiltration, whereas elimination of AMB colloidal dispersion is not significantly affected. CONCLUSIONS The pharmacokinetics of AMB that has been liberated from its lipid moiety is similar under treatment with either liposomal AMB or AMB colloidal dispersion. Since no significant influence of haemofiltration on the pharmacokinetics of liberated AMB has been found, a standard dose of lipid-formulated AMB can be recommended for patients on haemofiltration.