Miracle-dz/UniFAR-FTUs huggingface dataset:
Transactivation of the epidermal growth factor receptor by cag+ Helicobacter pylori induces upregulation of the early growth response gene Egr-1 in gastric epithelial cells

Background and aims:Helicobacter pylori, in particular cytotoxin associated gene (cag)+ strains, have been shown to enhance gastric epithelial cell proliferation in vivo, an effect that likely contributes to gastric carcinogenesis. Early growth response gene 1 (Egr-1) is a crucial regulator of cell growth, differentiation, and survival, which is known to play a role in carcinogenesis and cancer progression. The aims of this study were to: (1) examine whether H pylori could upregulate Egr-1 in gastric epithelial cell lines; (2) determine whether there was a differential response to infection with different strains; (3) examine the role of the cag pathogenicity island in this process; and (4) elucidate the molecular mechanisms leading to Egr-1 upregulation. Methods and results: We found that infection of AGS cells with cag+H pylori resulted in a rapid (1–2 hours) but transient increase in Egr-1 mRNA and protein levels whereas coculture with cag− isolates did not elicit this response. Furthermore, two independent cagE− isogenic mutants of H pylori also demonstrated impaired ability to upregulate Egr-1. Upregulation of Egr-1 protein was inhibited by the extracellular regulated kinase (ERK)1/2 inhibitor PD98059 and overexpression of dominant negative MEK1 downregulated Egr-1 luciferase reporter gene activity. Treatment of AGS cells with the epidermal growth factor receptor (EGFR) kinase inhibitors PD153035 and AG1478 resulted in a reduction in H pylori mediated Egr-1 upregulation, demonstrating that EGFR transactivation plays a role in this early cellular process. Conclusions: Our findings show that cag+H pylori cause rapid induction of Egr-1 in gastric epithelial cells which may contribute to H pylori mediated pathogenesis.
An ECoG-Based Binary Classification of BCI Using Optimized Extreme Learning Machine

In order to improve the accuracy of brain signal processing and accelerate speed meanwhile, we present an optimal and intelligent method for large dataset classification application in this paper. Optimized Extreme Learning Machine (OELM) is introduced in ElectroCorticoGram (ECoG) feature classification of motor imaginary-based brain-computer interface (BCI) system, with common spatial pattern (CSP) to extract the feature. When comparing it with other conventional classification methods like SVM and ELM, we exploit several metrics to evaluate the performance of all the adopted methods objectively. The accuracy of the proposed BCI system approaches approximately 92.31% when classifying ECoG epochs into left pinky or tongue movement, while the highest accuracy obtained by other methods is no more than 81%, which substantiates that OELM is more efficient than SVM, ELM, etc. Moreover, the simulation results also demonstrate that OELM will significantly improve the performance with p value being far less than 0.001. Hence, the proposed OELM is satisfactory in addressing ECoG signal.
A quantitative real-time PCR assay for detection of Colletotrichum lindemuthianum in navy bean seeds

Bean anthracnose is a seedborne disease of common bean (Phaseolus vulgaris) caused by the fungal pathogen Colletotrichum lindemuthianum. Using seed that did not test positive for the pathogen has been proven to be an effective strategy for bean anthracnose control. To quantify the extent of anthracnose seed infection, a real-time PCR-based diagnostic assay was developed for detecting C. lindemuthianum in seeds of the commercial bean class navy bean. The ribosomal DNA (rDNA) region consisting of part of the18S rDNA, 5.8S rDNA, internal transcribed spacers (ITS) 1, 2 and part of the 28S rDNA of seven races of C. lindemuthianum, 21 isolates of Colletotrichum species and nine other bean pathogens were sequenced with the universal primer set ITS5/ITS4. Based on the aligned sequence matrix, one primer set and a probe were designed for a SYBR Green dye assay and a TaqMan MGB (minor groove binder) assay. The primer set was demonstrated to be specific for C. lindemuthianum and showed a high sensitivity for the target pathogen. The detection limit of both assays was 5 fg of C. lindemuthianum genomic DNA. To explore the correlation between the lesion area and the DNA amount of C. lindemuthianum in bean seed, seeds of the navy bean cultivar Navigator with lesions of different sizes, as well as symptomless seeds, were used in both real-time PCR assays.
Using Poisson Disk Sampling to Render Oil Particles at Sea

Fluid simulation is one of the most complex tasks in three-dimensional simulation. Specifically, in the case of oil spills at sea, the oil film constantly interacts and is influenced by the environment, thus making its composition and properties change over time. In this paper, we tackle this problem by using both Lehr's spreading model and Hoult's drifting model to build the oil spill physical model. Unlike previous studies that only applied the Poisson disk algorithm to static and solid objects, we applied it in a three-dimensional space to divide the oil film into fluid particles. The track of oil particles under the influence of waves, wind, and currents is rendered by the Unity3D tool with C# programming language, which vividly and realistically simulates the collision of oil particles on the ocean scene with obstacles such as buoys and small islands. The result of this research can be used to predict oil spill direction, thus providing the solution to respond and minimize the damage caused by oil spills at sea. We also discuss some improvements to our model by using the Marching cube algorithm to render the Metaball model.
Spatio-temporal variation in surf zone fish communities at Ilha do Cardoso State Park, São Paulo, Brazil

In order to analyze the time-space variation of the fish fauna in the surf zone fish communities at Ilha do Cardoso State Park, Sao Paulo, Brazil, four consecutive hauls were done over a year on three beaches with different degrees of exposure, at low and high tide. To evaluate the influence of each abiotic variable over the fish community, a Canonical Correspondence Analysis was conducted. We identified 7,286 individuals belonging to 20 families and 47 species, most specimens collected were juveniles. At low tide, the highest diversity and richness values were calculated while the highest dominance was obtained at high tide. As for the number of species collected at the three beaches, stood out for the lower values the cooler months, between June and September. Abiotic variables explained 41.3% of the variability of biological data, where 11.4% corresponds to the spatial variation. Meanwhile the temporal variables accounted for 31.9% of the variation in abundance, where 26.3% of the variance explained nycthemeral variation. Additionally two groups were clearly observed between months with low and high temperature. However in this variable, the tidal variation, excluding the seasonal effect, explained 6.2%, while seasonality, excluding tide effect, explained 26.3%. Although the main measurable seasonal changes were related to temperature, water temperature showed a low percentage of explanation in the fish fauna variability (2.7%). Finally, it is emphasized that the seasonal changes in surf zone fish community primarily reflect patterns of recruitment determined by the reproductive activity and coastal circulation.
Climate and the Evolution of Group-Living Behaviour in the Armadillo Lizard (Ouroborus cataphractus)

We evaluated the hypothesis that the regular use of the southern harvester termite, Microhodotermes viator, as food source by the armadillo lizard, Ouroborus cataphractus, originated as an adaptation to survive the summer dry season in a climatic regime where rainfall is highly seasonal. To do so, we determined the most important climatic predictors of the geographical range of this species. Climatic data were obtained for 130 localities where O. cataphractus is known to occur and 168 adjacent localities where it is known to be absent. For each locality, data for 10 climatic variables were extracted from the South African Atlas of Agrohydrology and Climatology database. We constructed a forward stepwise logistic regression model of the probability of O. cataphractus occurrence, based on the set of 10 climatic variables. The best model included, in order of importance, average monthly summer rainfall, mean annual precipitation, average monthly solar radiation, and the ratio of winter rainfall over summer rainfall as most significant predictors. The selected model predicted 88.80% of the presences correctly and 85.52% of the absences. In essence, O. cataphractus is restricted to the winter rainfall zone of South Africa, excluding the high-rainfall southwestern section. We postulate that the highly predictable seasonal rainfall and the ameliorating effect of the Atlantic Ocean on climates in the Namaqualand region, in particular, have provided a unique selective regime for the origin of group-living in O. cataphractus. Dependence on M. viator as food source developed to survive the summer-autumn period of low food availability and resulted in the evolution of heavy armour and group-living behaviour. The moderate winters and early spring temperatures allowed full capitalization on high arthropod abundance during winter—spring, thereby overriding the negative impacts of armour and groupliving on foraging efficiency at the home crevice.
Dispositional Envy

Although many scholars have argued that individual differences in proneness to envy can have wide-ranging implications for social interactions, the empirical testing of these claims is largely undeveloped. We created a single-factor Dispositional Envy Scale (DES) to measure individual differences in tendencies to envy, and examined some of the implications of such differences. Study 1 indicated that the DES is a reliable, stable measure, containing items suiting theoretical criteria for the makeup of dispositional envy. Study 2 supported the construct validity of the DES by showing that it is correlated with other individual difference measures in theoretically compatible ways. Studies 3 and 4 supplied diverse ways of establishing the criterion-related validity of the DES by showing that it moderated envious responses to another person’s superiority and that it predicted envy beyond other correlated individual measures of neuroticism, self-esteem, cynical hostility, and socially desirable responding.
Molecular cloning and characterisation of serum lysozyme gene in Muzaffarnagri breed of sheep

The present study was carried out to characterise the serum lysozyme gene in Muzaffarnagri sheep. Total RNA was extracted from the white blood cells and serum lysozyme cDNA was synthesised by Reverse transcription-polymerase chain reaction, then cloned using pGEMT-cloning vector and sequenced. The sequencing of cDNA revealed that the length of serum lysozyme gene was 447 bp with 46% Guanine and Cytosine (GC) content. The comparative sequence analysis of serum lysozyme gene of cattle and buffalo with sheep revealed differences at 24 and 21 places, respectively. The molecular weight of serum lysozyme of sheep is 16.48 kDa. The sheep serum lysozyme cDNA sequence was 94.6% similar to cattle gene sequence, whereas it was 95.3% similar to buffalo gene sequence. Similarly, the derived amino acid sequence of sheep cDNA showed 90.6% similarity with cattle and 92.6% similarity with buffalo. Phylogenetic analysis revealed that sheep and buffalo sequences formed a cluster and evolutionary closer than the cattle sequences.
The Growth and Activity of Genetically Diverse Prochlorococcus

The Growth and Activity of Genetically Diverse Prochlorococcus by Yajuan Lin Marine Science and Conservation Duke University Date:_______________________ Approved: ___________________________ Zackary Johnson, Supervisor ___________________________ Erik Zinser ___________________________ Dana Hunt ___________________________ Jennifer Wernegreen An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Marine Science and Conservation in the Graduate School of Duke University 2013 Copyright by Yajuan Lin 2013
The form and function of the oesophageal region of the insect parasite Tetradonema plicans (Nematoda: Tetradonematidae)

The tetrad and companion cells, in association with the oesophagus and dorsal tract of tissue, of Tetradonema plicans, have been investigated in the host Bradysia paupera. The companion cells contain glycogen and mucopolysaccharide. The tetrad cells are rich in RNA and probably synthesize protein and secrete some as enzymes. The gut is functional and the oesophagus is in connexion with the tetrad. The dorsal tract is not connected with the oesophagus or tetrad and contains lipid with characteristics similar to that found in the eggs. It is suggested that the tetrad and companion cells are homologous with the stichocytes present in the Trichuroidea and some members of the Mermithoidea. I am grateful to Professor T. R. E. Southwood in whose department this work was carried out. I should like to thank Dr N. A. Croll for supervising and encouraging this work and Dr T. Jenkins for his helpful criticism and advice. The work was supported by the Agricultural Research Council.
DNA and meristic evidence for two species of giant stargazer (Teleostei: Uranoscopidae: Kathetostoma) in New Zealand waters

Abstract The taxonomic status of the banded giant stargazer in New Zealand waters is uncertain. Mitochondrial DNA partial sequences of the cytochrome b gene and the control region, along with three meristic characters (numbers of dorsal fin rays, anal fin rays, and vertebrae), were compared among six recognised species of Kathetostoma and specimens of the banded giant morph. New Zealand specimens referred to as banded giant stargazer were shown to be a discrete species distinguished from the giant stargazer K. giganteum from New Zealand and the banded K. laeve and K. canaster from Australia, by cytochrome b and control region sequences and meristic counts. This undescribed species occurs over a wide geographic range from the Snares shelf (48°S) to the Norfolk Ridge (32°S) in the Tasman Sea, and is largely sympatric with K. giganteum. The two New Zealand species occupy different depth ranges, with the banded giant stargazer generally occurring in shallower water (<320m) than K. giganteum (12–1000 m).
Molecular aspects of growth and fruiting of the edible mushroom Agaricus bisporus

The research described in this thesis was part of a project aimed at the isolation of marker genes and the development of a genetic map of the white button mushroom Agaricus bisporus. The thesis concentrates on molecular aspects of growth and fruiting of A. bisporus. In order to study the genetic processes that are involved in fruiting of A. bisporus, we focused on the cloning and characterisation of genes that are specifically expressed during fruit body development and maturation. Two fruit body specific genes identified by differential screening techniques appeared to encode small hydrophobic cell wall proteins belonging to the fungal family of surface-active hydrophobins. One of those proteins, HYPA, is part of a protective layer surrounding the mushroom caps. It showed, like other fungal hydrophobins, a self-assembling behaviour which was shown by in vitro studies using Atomic Force Microscopy. Additionally, to study genetic aspects of compost utilisation by A. bisporus, we aimed at the cloning of genes involved in the release of sugars from the plant polysaccharides present in compost. Cloning and characterisation of one of such genes, the xlnA gene encoding an endo-1,4-`-xylanase, gave us a better insight in the regulation of enzymes that can degrade lignocellulosic compounds of compost. Expression studies with xlnA and cel3, encoding a cellobiohydrolase, showed that both genes are strongly induced on compost and the regulation of their transcription seems to be an elegant example of adaptation of a fungus to its natural niche. Furthermore, experiments were focused on the isolation and characterisation of housekeeping genes. Cloning of the housekeeping genes pgkA, pkiA and aldA enabled us to compare the structure of A. bisporus genes with homologous genes of related organisms and to monitor their expression in different parts of mature mushrooms. The cloning of large number of genes combined with chromosome separation techniques forms a solid base for the development of a gene-based linkage map and will make A. bisporus more amenable for breeding purposes
High-Fat Diet Enhances Working Memory in the Y-Maze Test in Male C57BL/6J Mice with Less Anxiety in the Elevated Plus Maze Test

Obesity is characterized by massive adipose tissue accumulation and is associated with psychiatric disorders and cognitive impairment in human and animal models. However, it is unclear whether high-fat diet (HFD)-induced obesity presents a risk of psychiatric disorders and cognitive impairment. To examine this question, we conducted systematic behavioral analyses in C57BL/6J mice (male, 8-week-old) fed an HFD for 7 weeks. C57BL/6J mice fed an HFD showed significantly increased body weight, hyperlocomotion in the open-field test (OFT) and Y-maze test (YMZT), and impaired sucrose preference in the sucrose consumption test, compared to mice fed a normal diet. Neither body weight nor body weight gain was associated with any of the behavioral traits we examined. Working memory, as assessed by the YMZT, and anxiety-like behavior, as assessed by the elevated plus maze test (EPMT), were significantly correlated with mice fed an HFD, although these behavioral traits did not affect the entire group. These results suggest that HFD-induced obesity does not induce neuropsychiatric symptoms in C57BL/6J mice. Rather, HFD improved working memory in C57BL/6J mice with less anxiety, indicating that an HFD might be beneficial under limited conditions. Correlation analysis of individual traits is a useful tool to determine those conditions.
Prognostic value of left ventricular remodelling index in idiopathic dilated cardiomyopathy.

AIMS To evaluate the prognostic value of left ventricular (LV) remodelling index (RI) in idiopathic dilated cardiomyopathy (DCM) patients. METHODS AND RESULTS We prospectively enrolled 412 idiopathic DCM patients and 130 age- and sex-matched healthy volunteers who underwent cardiovascular magnetic resonance imaging between September 2013 and March 2018. RI was defined as the cubic root of the LV end-diastolic volume divided by the mean LV wall thickness on basal short-axis slice. The primary endpoint included all-cause mortality and heart transplantation. The secondary endpoint included the primary endpoint and heart failure (HF) readmission. During the median follow-up of 28.1 months (interquartile range: 19.3-43.0 months), 62 (15.0%) and 143 (34.7%) patients reached the primary and secondary endpoints, respectively. Stepwise multivariate Cox regression showed that RI [hazard ratio (HR) 1.20, 95% confidence interval (CI) 1.11-1.30, P < 0.001], late gadolinium enhancement (LGE) presence and log (N-terminal pro-B-type natriuretic peptide) were independent predictors of the primary endpoint, while RI (HR 1.15, 95% CI 1.08-1.23, P < 0.001) and extracellular volume were independent predictors of the secondary endpoint. The addition of RI to LV ejection fraction (EF) and LGE presence showed significantly improved global χ2 for predicting primary and secondary endpoints (both P < 0.001). Furthermore, RI derived from echocardiography also showed independent prognostic value for primary and secondary endpoints with clinical risk factors. CONCLUSIONS RI is an independent predictor of all-cause mortality, heart transplantation, and HF readmission in DCM patients and provides incremental prognostic value to LVEF and LGE presence.
A hidden message: Decoding artistic intent

Abstract Understanding how art makes impressions upon the perceiver has been a fundamental topic of philosophical interest since the time of ancient Greece. However, the extent of artistic perception and aesthetic appreciation has been the topic of empirical studies only recently, following the emergence of psychology as an independent field of science. The present study discusses the hypothesis that the impression created by artwork on the viewer can be predicted by examining activity of neuronal networks. In particular, we focus on neural activity evoked by abstract stimuli that matches elements of the viewers' previously learned conceptual dictionary. We show that artistic appreciation fundamentally depends on how easily the author's intent expressed in his or her artwork can be abstracted and decoded, on a neuronal level, into new or merged concept networks. More diverse intellectual and personal experiences—and their corollary neural networks—may facilitate the creation of new networks. These new networks, in turn, modulate the extent to which art can be apprehended and appreciated.
A Fast and Cost Effective Transfer Printing of Liquid Metal Inks for 3D Wiring in Flexible Electronics.

The fluidity and high electrical conductivity of liquid metal make it an excellent material for preparing flexible electronics. Here, we established a method utilizing widespread laser-printing technique to manufacture 3D flexible electronics. Through digital-constructing of liquid alloy-philic smooth toner on liquid alloy-phobic rough substrates, we have liquid metal selectively adhered to the designed pattern. The liquid metal circuit can then be transferred to uneven and deformable Ecoflex surface to form a 3D circuit. Computational fluid dynamics simulation was performed to interpret the printing mechanism of liquid metal on substrate with selected adhesion. Flexible electronics fabricated through this method reveal great performance and stability, opening up opportunities for office and home flexible electronics manufacture, especially for lighting, heating and logistics. By making the full use of the laser printers, our method not only saves the cost and time in preparation, but also identifies favorable prospects for the mature laser-printing industry to promote next generation flexible electronics fabrication.
LABORATORY BREEDING OF ASCOGASTER CARPOCAPSAE VIER. WITH NOTES ON BIOLOGY AND LARVAL MORPHOLOGY

Ascogaster carpocapsae Vier. was not known to have spread naturally over the mountain barriers into the apple growing districts of British Columbia, and it was considered that the introduction of this species might aid in the control of the codling moth (Cydia pomonella Linn.) which has become a serious pest in that area during recent years.