Miracle-dz/UniFAR-FTUs huggingface dataset:
Change Blindness Is Influenced by Both Contrast Energy and Subjective Importance within Local Regions of the Image

Our visual system receives an enormous amount of information, but not all information is retained. This is exemplified by the fact that subjects fail to detect large changes in a visual scene, i.e., change-blindness. Current theories propose that our ability to detect these changes is influenced by the gist or interpretation of an image. On the other hand, stimulus-driven image features such as contrast energy dominate the representation in early visual cortex (De Valois and De Valois, 1988; Boynton et al., 1999; Olman et al., 2004; Mante and Carandini, 2005; Dumoulin et al., 2008). Here we investigated whether contrast energy contributes to our ability to detect changes within a visual scene. We compared the ability to detect changes in contrast energy together with changes to a measure of the interpretation of an image. We used subjective important aspects of the image as a measure of the interpretation of an image. We measured reaction times while manipulating the contrast energy and subjective important properties using the change blindness paradigm. Our results suggest that our ability to detect changes in a visual scene is not only influenced by the subjective importance, but also by contrast energy. Also, we find that contrast energy and subjective importance interact. We speculate that contrast energy and subjective important properties are not independently represented in the visual system. Thus, our results suggest that the information that is retained of a visual scene is both influenced by stimulus-driven information as well as the interpretation of a scene.
Association study of a functional Toll-like receptor 4 polymorphism with susceptibility to gastric mucosa-associated lymphoid tissue lymphoma

Toll-like receptor 4, as part of innate immune response, is the main receptor for lipopolysaccharide on marginal zone B cells. The rare allele of TLR4 Asp299Gly attenuates receptor signaling and diminishes the inflammatory response. We genotyped 87 patients with gastric mucosa-associated lymphoid tissue (MALT) lymphoma, 594 Helicobacter pylori positive controls and 358 healthy blood donors to investigate an association of TLR4 Asp299Gly in the development of gastric MALT lymphoma. Heterozygote genotype was significantly less frequent in patients with gastric MALT lymphoma compared to H. pylori-infected controls (4.6% vs. 11.6%, Fischer's exact P=0.019, odds ratio=0.37, 95% confidence interval 0.13-1.03). Because 10% of caucasians are carriers of the rare allele G TLR4 Asp299Gly appears to be only one factor in the genetic susceptibility to gastric lymphoma. Further studies in larger samples are needed to confirm our findings and fully elucidate the role of TLR4 and its genetic variants in the pathophysiology of H. pylori infection and gastric lymphoma.
Association of gene polymorphism with serum levels of inflammatory and angiogenic factors in Pakistani patients with age-related macular degeneration

Purpose To study the association of serum levels of inflammatory mediators and angiogenic factors with genetic polymorphism in Pakistani age-related macular degeneration (AMD) patients. Methods This was a cross-sectional and case-control study that included 90 AMD patients diagnosed through slit-lamp examination, fundoscopy, and ocular coherence tomography. For reference and comparison purposes, 100 healthy age-matched subjects (controls) were also recruited. IL-6, IL-8, VEGF, and CRP levels were estimated in the serum samples of patients and control subjects. Using restriction fragment length polymorphism, single nucleotide polymorphisms were studied in IL-6 (rs1800795, rs1800796, rs1800797), IL-8 (rs4073, rs2227306, rs2227543), VEGF (rs3025039, rs699947), and CRP genes (rs1205, rs1130864). Since the data were obtained from a sample population, the Box–Cox transformation algorithm was applied to reduce heterogeneity of error. Multivariate analyses of variance (M-ANOVA) were applied on the transformed data to investigate the association of serum levels of IL-6, IL-8, VEGF, and CRP with AMD. Genotype and allele frequencies were compared through χ2 tests applying Hardy–Weinberg equilibrium. The serum concentrations of IL-6 and IL-8, VEGF, and CRP between homozygotes and heterozygotes were compared through one-way ANOVA. Significance level was p<0.05. Results Compared to control subjects, serum IL-6 (p<0.0001), IL-8 (p<0.0001), VEGF (p<0.0001), and CRP (p<0.0001) levels were significantly elevated in the AMD patients. For rs1800795, patients with the GG genotype showed significantly raised levels of IL-6 compared to those with GC and CC genotypes (p<0.0001). Serum IL-8 levels were significantly higher in patients with the GG genotype compared to the GC and CC genotypes for the single nucleotide polymorphism (SNP) rs2227543 (p<0.002). Similarly, significantly higher VEGF levels were detected for genotype TT for rs3025039 SNP (p<0.038). However, no significant alteration in serum CRP levels was detected in hetero- or homozygotes for rs1205 and rs1130864 SNPs. Conclusions Serum IL-6, IL-8, and VEGF levels are substantially increased in AMD, and the levels coincide with polymorphism in the respective gene. No such relationship appears to exist with regard to SNPs of CRP.
Keratinocyte junctions and the epidermal barrier

Although intercellular junctions are known to be the major regulators of permeability of simple epithelia, they had not been thought to be important in regulating the permeability of stratified mammalian epithelia. Furuse et al. (2002)(this issue) demonstrate that functional tight junctions may indeed be a necessary part of the permeability barrier of the skin.
Gene regulation and speciation in house mice

One approach to understanding the process of speciation is to characterize the genetic architecture of post-zygotic isolation. As gene regulation requires interactions between loci, negative epistatic interactions between divergent regulatory elements might underlie hybrid incompatibilities and contribute to reproductive isolation. Here, we take advantage of a cross between house mouse subspecies, where hybrid dysfunction is largely unidirectional, to test several key predictions about regulatory divergence and reproductive isolation. Regulatory divergence between Mus musculus musculus and M. m. domesticus was characterized by studying allele-specific expression in fertile hybrid males using mRNA-sequencing of whole testes. We found extensive regulatory divergence between M. m. musculus and M. m. domesticus, largely attributable to cis-regulatory changes. When both cis and trans changes occurred, they were observed in opposition much more often than expected under a neutral model, providing strong evidence of widespread compensatory evolution. We also found evidence for lineage-specific positive selection on a subset of genes related to transcriptional regulation. Comparisons of fertile and sterile hybrid males identified a set of genes that were uniquely misexpressed in sterile individuals. Lastly, we discovered a nonrandom association between these genes and genes showing evidence of compensatory evolution, consistent with the idea that regulatory interactions might contribute to Dobzhansky-Muller incompatibilities and be important in speciation.
Associations between pre-pregnancy obesity and asthma symptoms in adolescents

Background The high prevalence of children's asthma symptoms, worldwide, is unexplained. We examined the relation between maternal pre-pregnancy weight and body mass index (BMI), and asthma symptoms in adolescents. Methods Data from 6945 adolescents born within the Northern Finland Birth Cohort 1986 were used. Prospective antenatal and birth outcome data, including maternal pre-pregnancy weight and BMI, and asthma symptoms in adolescent offspring at age 15–16 years, were employed. Logistic regression analyses were performed to examine the associations between relevant prenatal factors and asthma symptoms during adolescence. Results Current wheeze (within the past year) was reported by 10.6% of adolescents, and physician-diagnosed asthma by 6.0%. High maternal pre-pregnancy BMI was a significant predictor of wheeze in the adolescents (increase per kilogram per square metre unit; 2.7%, 95% CI 0.9 to 4.4 for ever wheeze; 3.5%, 95% CI 1.3 to 5.8 for current wheeze), and adjusting for potential confounders further increased the risk (2.8%, 95% CI 0.5 to 5.1; 4.7%, 95% CI 1.9 to 7.7, respectively). High maternal pre-pregnancy weight, in the top tertile, also significantly increased the odds of current wheeze in the adolescent by 20% (95% CI 4 to 39), and adjusting for potential confounders further increased the risk (OR=1.52, 95% CI 1.19 to 1.95). Results were similar for current asthma. Furthermore, these significant associations were observed only among adolescents without parental history of atopy but not among those with parental history of atopy. Conclusions The association demonstrated here between maternal pre-pregnancy overweight and obesity, and asthma symptoms in adolescents suggests that increase in asthma may be partly related to the rapid rise in obesity in recent years.
Gene expression of immunologically important factors in blood cells, milk cells, and mammary tissue of cows.

Cytokines, eicosanoids, and lactoferrin are involved in the mammary gland's immune response to invading microorganisms. The goal of this work was to investigate the synthesis of these immunologically important factors in somatic milk cells, blood cells, and mammary tissue of cows with different somatic cell count levels, i.e., different immunological activity. On the level of mRNA expression, the cytokine tumor necrosis factor alpha (TNFalpha), lactoferrin (Lf), and specific key enzymes of leukotriene and prostaglandin biosynthesis, 5-lipoxygenase (5-LO), and cyclooxygenase-1 (COX-1) and -2 (COX-2), respectively, were determined. All 15 experimental cows were clinically healthy with no visible mammary disease. Eight cows were defined as control group with all quarters <150,000 cells/ml (C), whereas seven cows had partially elevated quarter somatic cell counts, with at least one quarter >150,000 cells/ml (H) and one quarter <150,000 cells/ml (L). Total quarter milk from one quarter of control group and from two quarters of cows with partially elevated cell counts (one of H and one of L) was collected at one milking and a blood sample was taken simultaneously. In addition, mammary tissue samples were taken from the respective quarters on the following day during slaughter. Total RNA from milk, blood, and tissue cells was isolated and reverse transcription and quantitative polymerase chain reaction was carried out. All factors investigated were not significantly different between groups in blood cells and between C and L quarters in milk cells and mammary tissue. TNFalpha and COX-2 mRNA expression was higher in milk cells and mammary tissue of H than in L quarters, except for COX-2 in mammary tissue. Generally, TNFalpha and COX-2 showed their highest expression in milk cells, 5-LO in blood cells, whereas lactoferrin was mainly expressed by the mammary tissue. COX-1 was similarly expressed in all tested samples.
Learning Graph-Level Representation for Drug Discovery

Predicating macroscopic influences of drugs on human body, like efficacy and toxicity, is a central problem of small-molecule based drug discovery. Molecules can be represented as an undirected graph, and we can utilize graph convolution networks to predication molecular properties. However, graph convolutional networks and other graph neural networks all focus on learning node-level representation rather than graph-level representation. Previous works simply sum all feature vectors for all nodes in the graph to obtain the graph feature vector for drug predication. In this paper, we introduce a dummy super node that is connected with all nodes in the graph by a directed edge as the representation of the graph and modify the graph operation to help the dummy super node learn graph-level feature. Thus, we can handle graph-level classification and regression in the same way as node-level classification and regression. In addition, we apply focal loss to address class imbalance in drug datasets. The experiments on MoleculeNet show that our method can effectively improve the performance of molecular properties predication.
WIDTH AND MODE OF THE PROFILE FOR SOME RANDOM TREES OF LOGARITHMIC HEIGHT

We propose a new, direct, correlation-free approach based on central moments of profiles to the asymptotics of width (size of the most abundant level) in some random trees of logarithmic height. The approach is simple but gives precise estimates for expected width, central moments of the width and almost sure convergence. It is widely applicable to random trees of logarithmic height, including recursive trees, binary search trees, quad trees, plane-oriented ordered trees and other varieties of increasing trees. 1. Introduction. Most random trees in the discrete probability literature have height either of order √ n or of order log n (n being the tree size); see [1]. For simplicity, we call these trees square-root trees and log trees, respectively. Profiles (number of nodes at each level of the tree) of random square-root trees have a rich connection to diverse structures in combinatorics and in probability, and have been extensively studied. In contrast, profiles of random log trees, arising mostly from data structures and computer algorithms, were less addressed and only quite recently were their limit distributions, drastically different from those of square-root trees, better understood; see [3, 12, 13, 21, 27] and the references therein. We study in this paper the asymptotics of width, which is defined to be the size of the most abundant level, and its close connection to the profile. There are many results on first-order asymptotics of profiles for standard log trees, such as binary search trees, random recursive trees, m-ary search trees and quad trees. In some cases, quite accurate asymptotic expressions are known for the expected profile. There is already a paucity of results with regard to
Protection against experimental salmonellosis in mice and sheep by immunisation with aromatic-dependent Salmonella typhimurium.

Mice immunised by the oral or intraperitoneal route with a live aromatic-dependent strain of Salmonella typhimurium exhibited significantly less protection against oral challenge with 50 LD50 of an ovine isolate of S. typhimurium (12313) than when a bovine isolate with the same O antigens and phage-type as strain 12313 was used as the challenge organism. When challenged with 10 LD50, however, protection against both strains was significantly better than that obtained when mice were vaccinated with killed vaccines (heat-killed, acetone-killed or irradiated) even when the antigenic mass of the killed vaccine was increased by up to 500-fold in an attempt to compensate for the expected limited multiplication of the mutant organism. Sheep immunised with the live mutant strain by either the intramuscular or oral route were protected against oral challenge with the virulent ovine isolate of S. typhimurium; unimmunised sheep died of acute enteritis within 7 days, although there was no evidence of systemic invasion by the challenge organism. After challenge, immunised animals ate more food than the unimmunised controls and suffered only transient, mild diarrhoea. Serum antibody titres against O and H antigens measured by direct or antiglobulin tests were significantly higher in sheep immunised by the intramuscular route than in those immunised orally. Sheep in both immunised groups developed skin swellings within 30 min after intradermal inoculation with purified homologous lipopolysaccharide indicating development of immediate-type hypersensitivity, but only those immunised by the intramuscular route showed significant indurated skin swellings characteristic of delayed-type hypersensitivity 48 and 72 h post-inoculation. (ABSTRACT TRUNCATED AT 250 WORDS)
Heat inactivation of Salmonella typhimurium DT104 in beef as affected by fat content

The heat resistance of an eight‐strain cocktail of Salmonella typhimurium DT104 was determined at 58–65 °C in beef containing 7, 12, 18 or 24% fat. Inoculated beef was packaged in bags completely immersed in a circulating water bath and held at 58, 60, 62·5 and 65 °C for a predetermined length of time. The surviving cell population was enumerated by spiral plating heat‐treated samples onto tryptic soy agar supplemented with 0·6% yeast extract and 1% sodium pyruvate. Preliminary studies on thermal inactivation of the Salmonellae isolates in chicken broth indicated no correlation between heat resistance and origin of the isolates. While linear survival curves were observed in chicken broth, inactivation kinetics in beef showed deviations from the first order kinetics, represented by an initial lag period or shoulder before any death occurred with time. Overall, increased fat levels in beef resulted in longer lag periods and lower D‐values, suggesting that the lag periods must be taken into account and added to the D‐values for calculating the time required at a specific temperature for achieving a specific lethality for Salm. typhimurium DT104 in beef. Thermal death times from this study will assist the retail food industry to design cooking regimes that ensure safety of beef contaminated with Salm. typhimurium DT104.
Tobacco mosaic virus-directed reprogramming of auxin/indole acetic acid protein transcriptional responses enhances virus phloem loading

Significance For plant viruses a successful infection correlates with the ability to access the vascular phloem and move systemically into distal tissues. However, how viruses gain access to and usurp vascular tissues is poorly understood. Here we show how tobacco mosaic virus (TMV) enhances its access to the phloem of mature plant tissues through the targeted disruption of auxin/indole acetic acid (Aux/IAA) transcriptional regulators that control expression of host genes involved in virus cell-to-cell movement, plasmodesmata gating, and defense. TMV’s ability to disrupt Aux/IAA function successfully confers a significant advantage in the systemic spread of this virus, allowing it to outcompete nondisrupting viruses. In summary, TMV interacts with Aux/IAA proteins to reprogram the vascular phloem, making it more conducive to systemic movement. Vascular phloem loading has long been recognized as an essential step in the establishment of a systemic virus infection. In this study, an interaction between the replication protein of tobacco mosaic virus (TMV) and phloem-specific auxin/indole acetic acid (Aux/IAA) transcriptional regulators was found to modulate virus phloem loading in an age-dependent manner. Promoter expression studies show that in mature tissues TMV 126/183-kDa–interacting Aux/IAAs predominantly express and accumulate within the nuclei of phloem companion cells (CCs). Furthermore, CC Aux/IAA nuclear localization is disrupted upon infection with an interacting virus. In situ analysis of virus spread shows that the inability to disrupt Aux/IAA CC nuclear localization correlates with a reduced ability to load into the vascular tissue. Subsequent systemic movement assays also demonstrate that a virus capable of disrupting Aux/IAA localization is significantly more competitive at moving out of older plant tissues than a noninteracting virus. Similarly, CC expression and overaccumulation of a degradation-resistant Aux/IAA-interacting protein was found to inhibit TMV accumulation and phloem loading selectively in flowering plants. Transcriptional expression studies demonstrate a role for Aux/IAA-interacting proteins in the regulation of salicylic and jasmonic acid host defense responses as well as virus-specific movement factors, including pectin methylesterase, that are involved in regulating plasmodesmata size-exclusion limits and promoting virus cell-to-cell movement. Combined, these findings indicate that TMV directs the reprogramming of auxin-regulated gene expression within the vascular phloem of mature tissues as a means to enhance phloem loading and systemic spread.
Quantitative imaging and microlocalization of boron-10 in brain tumors and infiltrating tumor cells by SIMS ion microscopy: relevance to neutron capture therapy.

Boron neutron capture therapy (BNCT) is dependent on the selective accumulation of boron-10 in tumor cells relative to the contiguous normal cells. Ion microscopy was used to evaluate the microdistribution of boron-10 from p-boronophenylalanine (BPA) in the 9L rat gliosarcoma and the F98 rat glioma brain tumor models. Four routes of BPA administration were used: i.p. injection, intracarotid (i.c.) injection [with and without blood-brain barrier disruption (BBB-D)], and continuous timed i.v. infusions. i.p. injection of BPA in the 9L gliosarcoma resulted in a tumor-to-brain (T:Br) boron-10 concentration ratio of 3.7:1 when measured at the tumor-normal brain interface. In the F98 glioma, i.c injection of BPA resulted in a T:Br ratio of 2.9:1, and this increased to 5.4:1 when BBB-D was performed. The increased tumor boron uptake would potentially enhance the therapeutic ratio of BNCT by >25%. At present, ion microscopy is the only technique to provide a direct measurement of the T:Br boron-10 concentration ratio for tumor cells infiltrating normal brain. In the 9L gliosarcoma, this ratio was 2.9:1 after i.p. administration. In the F98 glioma, i.c injection resulted in a ratio of 2.2:1, and this increased to 3.0:1 after BBB-D. Ion microscopy revealed a consistent pattern of boron-10 microdistribution for both rat brain tumor models. The boron-10 concentration in the main tumor mass (MTM) was approximately twice that of the infiltrating tumor cells. One hour after a 2-h i.v. infusion of BPA in rats with the 9L gliosarcoma, tumor boron-10 concentrations were 2.7 times higher than that of infiltrating tumor cells [83 +/- 23 microg/g tissue versus 31 +/- 12 microg/g tissue (mean +/- SD)]. Continuous 3- and 6-h i.v. infusions of BPA in the 9L gliosarcoma resulted in similar high boron-10 concentrations in the MTM. The boron-10 concentration in infiltrating tumor cells was two times lower than the MTM after a 3-h infusion. After 6 h, the boron-10 concentration in infiltrating tumor cells had increased nearly 90% relative to the 2- and 3-h infusions. A 24-h i.v. infusion resulted in similar boron-10 levels between the MTM and the infiltrating tumor cells. Boron concentrations in the normal brain were similar for all four infusion times (approximately 20 microg/g tissue). These results are important for BNCT, because clinical protocols using a 2-h infusion have been performed with the assumption that infiltrating tumor cells contain equivalent amounts of boron-10 as the MTM. The results reported here suggest that this is not the case and that a 6-h or longer infusion of BPA may be necessary to raise boron-10 levels in infiltrating tumor cells to that in the MTM.
PHYSICOCHEMICAL CHARACTERIZATION OF SEED OIL OF JATROPHA CURCAS L.COLLECTED FROM DEHRADUN (UTTARAKHAND) INDIA

To study oil contents and fatty acid composition among the samples of Jatropha curcas L. seeds were collected from Dehradun, Uttarakhand. Soxhlet extraction method and gas chromatography (GC) were employed to determine the oil contents of Jatropha seeds and the fatty acid composition of Jatropha oil. The seed oil contents (dry basis) was 46.27% . Physicochemical properties shows acid value (36.46), iodine value (106.00 mg/g) and saponification value (194.70 mg/g.The evaluation of fatty acid composition using gas chromatography (GC) revealed that, oleic (44.93%), linoleic acid (33.40 %), Palmitic acid (15.39%) and Stearic acid (6.26%).