250 research outputs found
Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case
Classifications and phylogenetic inferences of organismal groups change in
light of new insights. Over time these changes can result in an imperfect
tracking of taxonomic perspectives through the re-/use of Code-compliant or
informal names. To mitigate these limitations, we introduce a novel approach
for aligning taxonomies through the interaction of human experts and logic
reasoners. We explore the performance of this approach with the Perelleschus
use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies
published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of
names individuated according to their respective source publications), and 75
expert-asserted Region Connection Calculus articulations (e.g., congruence,
proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is
used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous
constraints and interpretations. The reasoning workflow optimizes the logical
consistency and expressiveness of the input and infers the set of maximally
informative relations among the entailed taxonomic concepts. The latter are
then used to produce merge visualizations that represent all congruent and
non-congruent taxonomic elements among the aligned input trees. In this small
use case with 6-53 input concepts per alignment, the information gained through
the reasoning process is on average one order of magnitude greater than in the
input. The approach offers scalable solutions for tracking provenance among
succeeding taxonomic perspectives that may have differential biases in naming
conventions, phylogenetic resolution, ingroup and outgroup sampling, or
ostensive (member-referencing) versus intensional (property-referencing)
concepts and articulations.Comment: 30 pages, 16 figure
Correlation of 3'-phosphoadenosine-5'-phosphosulfate synthase 1 (PAPSS1) expression with clinical parameters and prognosis in esophageal squamous cell carcinoma
Background. In recent years, 3'-
phosphoadenosine-5'-phosphosulfate synthase 1
(PAPSS1) has been found to be highly expressed in
some cancers and significantly associated with
prognosis. Nevertheless, the role of PAPSS1 in
esophageal squamous cell carcinoma (ESCC) is poorly
understood.
Methods. In this study, PAPSS1 expression in ESCC
samples was researched through real-time quantitative
polymerase chain reaction (qPCR), immunohistochemistry (IHC), and western blot (WB) techniques.
siRNA technology was then used to inhibit PAPSS1
expression in ESCC cells, and cytologic tests were
conducted to research gene affection on cell apoptosis,
proliferation, and migration. Then, the expression of
Bcl2, Ki67, and Snail was detected using qPCR and WB
tests. These experimental data were analyzed by
GraphPad software, where the P-value <0.05 was
statistically significant.
Results. The results showed that PAPSS1 expression
level in ESCC tissues was higher than in the adjacent
tissues. The data also showed that PAPSS1 was
significantly correlated with N stage, and that the
patients with high expressions had longer survival time.
After transfection for 48 hours, the cell apoptosis rate of
siRNA-PAPSS1 transfected groups decreased
significantly, whereas the cell proliferation rate and
migration ability increased relative to the control. At the
same time, the expression levels of Bcl2, Ki67 and Snail
were all upregulated by siRNA-PAPSS1. PAPSS1,
however, was suppressed.
Conclusions. PAPSS1 may be an ESCC suppressor
gene, and its specific molecular mechanism in ESCC
needs to be further studied
Gray matter asymmetry atypical patterns in subgrouping minors with autism based on core symptoms
Abnormal gray matter (GM) asymmetry has been verified in autism spectrum disorder (ASD), which is characterized by high heterogeneity. ASD is distinguished by three core symptom domains. Previous neuroimaging studies have offered support for divergent neural substrates of different core symptom domains in ASD. However, no previous study has explored GM asymmetry alterations underlying different core symptom domains. This study sought to clarify atypical GM asymmetry patterns underlying three core symptom domains in ASD with a large sample of 230 minors with ASD (ages 7–18 years) and 274 matched TD controls from the Autism Brain Imaging Data Exchange I (ABIDE I) repository. To this end, the scores of the revised autism diagnostic interview (ADI-R) subscales were normalized for grouping ASD into three core-symptom-defined subgroups: social interaction (SI), verbal communication (VA), and restricted repetitive behaviors (RRB). We investigated core-symptom-related GM asymmetry alterations in ASD resulting from advanced voxel-based morphometry (VBM) by general linear models. We also examined the relationship between GM asymmetry and age and between GM asymmetry and symptom severity assessed by the Autism Diagnostic Observation Schedule (ADOS). We found unique GM asymmetry alterations underlying three core-symptom-defined subgroups in ASD: more rightward asymmetry in the thalamus for SI, less rightward asymmetry in the superior temporal gyrus, anterior cingulate and caudate for VA, and less rightward asymmetry in the middle and inferior frontal gyrus for RRB. Furthermore, the asymmetry indexes in the thalamus were negatively associated with ADOS_SOCIAL scores in the general ASD group. We also showed significant correlations between GM asymmetry and age in ASD and TD individuals. Our results support the theory that each core symptom domain of ASD may have independent etiological and neurobiological underpinnings, which is essential for the interpretation of heterogeneity and the future diagnosis and treatment of ASD
Differential association of the Na+/H+ exchanger regulatory factor (NHERF) family of adaptor proteins with the raft- and the non-raft brush border membrane fractions of NHE3
Background/Aims: Trafficking, brush border membrane (BBM) retention, and signal-specific regulation of the Na+/H+ exchanger NHE3 is regulated by the Na+/H+ Exchanger Regulatory Factor (NHERF) family of PDZ-adaptor proteins, which enable the formation of multiprotein complexes. It is unclear, however, what determines signal specificity of these NHERFs. Thus, we studied the association of NHE3, NHERF1 (EBP50), NHERF2 (E3KARP), and NHERF3 (PDZK1) with lipid rafts in murine small intestinal BBM. Methods: Detergent resistant membranes ('lipid rafts') were isolated by floatation of Triton X-incubated small intestinal BBM from a variety of knockout mouse strains in an Optiprep step gradient. Acid-activated NHE3 activity was measured fluorometrically in BCECF-loaded microdissected villi, or by assessment of CO2/HCO3 - mediated increase in fluid absorption in perfused jejunal loops of anethetized mice. Results: NHE3 was found to partially associate with lipid rafts in the native BBM, and NHE3 raft association had an impact on NHE3 transport activity and regulation in vivo. NHERF1, 2 and 3 were differentially distributed to rafts and non-rafts, with NHERF2 being most raft-associated and NHERF3 entirely non-raft associated. NHERF2 expression enhanced the localization of NHE3 to membrane rafts. The use of acid sphingomyelinase-deficient mice, which have altered membrane lipid as well as lipid raft composition, allowed us to test the validity of the lipid raft concept in vivo. Conclusions: The differential association of the NHERFs with the raft-associated and the non-raft fraction of NHE3 in the brush border membrane is one component of the differential and signal-specific NHE3 regulation by the different NHERFs
Fashion, Cooperation, and Social Interactions
Fashion plays such a crucial rule in the evolution of culture and society
that it is regarded as a second nature to the human being. Also, its impact on
economy is quite nontrivial. On what is fashionable, interestingly, there are
two viewpoints that are both extremely widespread but almost opposite:
conformists think that what is popular is fashionable, while rebels believe
that being different is the essence. Fashion color is fashionable in the first
sense, and Lady Gaga in the second. We investigate a model where the population
consists of the afore-mentioned two groups of people that are located on social
networks (a spatial cellular automata network and small-world networks). This
model captures two fundamental kinds of social interactions (coordination and
anti-coordination) simultaneously, and also has its own interest to game
theory: it is a hybrid model of pure competition and pure cooperation. This is
true because when a conformist meets a rebel, they play the zero sum matching
pennies game, which is pure competition. When two conformists (rebels) meet,
they play the (anti-) coordination game, which is pure cooperation. Simulation
shows that simple social interactions greatly promote cooperation: in most
cases people can reach an extraordinarily high level of cooperation, through a
selfish, myopic, naive, and local interacting dynamic (the best response
dynamic). We find that degree of synchronization also plays a critical role,
but mostly on the negative side. Four indices, namely cooperation degree,
average satisfaction degree, equilibrium ratio and complete ratio, are defined
and applied to measure people's cooperation levels from various angles. Phase
transition, as well as emergence of many interesting geographic patterns in the
cellular automata network, is also observed.Comment: 21 pages, 12 figure
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Protein sequences of the ABCA transporters of the eight species. (XLSX 25 kb
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