Phase synchronization during the processing of taxonomic and thematic relations

Semantic relations include "taxonomic" relations based on shared features and "thematic" relations based on co-occurrence in events. The "dual-hub" account proposes that the anterior temporal lobe (ATL) is functionally specialized for taxonomic relations and the inferior parietal lobule (IPL) for thematic relations. This study examined this claim by analyzing the intra- and inter-region phase synchronization of intracranial EEG data from electrodes in the ATL, IPL, and two subregions of the semantic control network: left inferior frontal gyrus (IFG) and posterior middle temporal gyrus (pMTG). Ten participants with epilepsy completed a semantic relatedness judgment task during intracranial EEG recording and had electrodes in at least one hub and at least one semantic control region. Theta band phase synchronization was partially consistent with the dual-hub account: synchronization between the ATL and IFG/pMTG increased when processing taxonomic relations, and synchronization within the IPL and between IPL and pMTG increased when processing thematic relations.

Phytoliths analysis in root, culm, leaf and synflorescence of Rostraria cristata (Poaceae)

Phytoliths (siliceous structures) present in the plants have been employed in the fields of taxonomy and archaeology for many decades. Rostraria cristata is an economically important grass species (Poaceae) which accumulates silica in its different organs in the form of phytoliths. In order to understand the pattern of phytolith production and biochemical architecture of silica in R. cristata, leaf epidermis (blade) using the clearing solution method and different organs using the dry ashing method, X-ray diffraction and Fourier-transform infrared spectroscopy techniques were analyzed. Both abaxial and adaxial leaf epidermis showed the presence of acute bulbosus, rectangular sinuate and stomata phytolith morphotypes. Leaf including sheath and blade had the highest silica content. Characteristic phytolith morphotypes were present in different organs. A total of 34 phytolith morphotypes were present among which nine (9) were articulated and 25 were isolated forms. The most abundant were elongate scrobiculate (48.20%) in root and rectangular sinuate (26.16%) in leaf part. Other common phytolith morphotypes present in different organs of R. cristata were articulated elongate irregular, articulated elongate scrobiculate, acute bulbosus, and polygonal rondel etc. Leaf and synflorescence had the highest similarity based on presence/absence of phytolith morphotypes (Jaccard's similarity index). XRD studies revealed the presence of cristobalite, quartz, tridymite, zeolite etc. forms of silica in different organs. FTIR spectra showed that inplane stretching vibration of Si-C was unique to root, anti-symmetric stretching vibration of C-H was unique to leaf and Al2O3.SiO2 was found in synflorescence only. Our results show the characteristic pattern of phytoliths production in R. cristata.

Temporal effects of fine sediment deposition on benthic macroinvertebrate community structure, function and biodiversity likely reflects landscape setting

Globally, excessive fine sediment (particles <2 mm) deposition is acknowledged to have deleterious effects on aquatic biodiversity. However, the impacts are often equivocal possibly reflecting landscape context, although this is rarely considered. To address this, we examined the temporal response of macroinvertebrate taxonomic and functional diversity to experimental fine sediment clogging in a prealpine (Italy) and lowland setting (UK). Colonisation devices were installed insitu with either clean or clogged substrates and examined for short (7-14 days), medium (21-28 days) and long (56-63 days) timescales. Clogging resulted in altered taxonomic community composition in both the lowland and prealpine rivers and modified functional community composition in the prealpine river. Nestedness was consistently found to be the dominant process driving differences in taxonomic composition between the clean and clogged substrates in the prealpine environment, with clogged substrates forming a nested community. No dominant component structured lowland taxonomic communities. Functional community composition was driven by nestedness in both environments but was heavily dominant in the case of the prealpine river, possibly reflecting low functional redundancy. Widely employed community richness metrics (EPT, taxa and functional richness) only displayed a response to fine sediment loading in the prealpine environment but taxa characterized as sensitive to fine sediment as well as some functional feeding groups did exhibit differences in both settings. In the prealpine environment, the effects of fine sediment intensified over time for several community metrics. Although further research is required to corroborate our findings and extend our observations across more rivers and typologies, excessive fine sediment is a pervasive stressor affecting macroinvertebrate communities in prealpine and lowland environments. However, the biodiversity facets that responded to clogging differed between the two landscape settings probably reflecting wider environmental filtering. Monitoring and managing fine sediment loading likely requires context specific approaches to maximise ecological benefits.

Event related potential exploration of the organizational structure of abstract versus concrete words in neurologically intact younger adults

The purpose of this study was to test the effects of concreteness and relationship type (similarity vs. association) on semantic processing using event-related potentials (ERP). Neurophysiological evidence has been found for the concreteness effect and for an effect of relationship type. This study replicated and extended these findings by investigating the interaction of concreteness and relationship type. Twenty-four neurologically healthy young adults performed lexical decision and semantic relatedness tasks while continuous scalp EEG was recorded. Larger N400 effects were found for concrete words in associative relationships than for concrete words in similarity relationships and abstract words in either type of relationship. The results are discussed in relation to the different representational frameworks account for abstract and concrete word processing.

Fibrivirga algicola gen. nov., sp. nov., an algicidal bacterium isolated from a freshwater river

An aerobic, gram-stain-negative, pink-colored, non-motile and rod-shaped algicidal bacterium, designated as JA-25^T was isolated from freshwater in Geumgang River, Republic of Korea. Strain JA-25^T grew at 15-30 °C and pH 6-9, and did not require NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JA-25^T belongs to the family 'Spirosomaceae' and is most closely related to Fibrella aestuarina BUZ 2^T (93.6%). Strain JA-25^T showed < 90% sequence similarity to other members of the family 'Spirosomaceae'. The average nucleotide identity(ANI), in silico DNA-DNA hybridization and average amino acid identity(AAI) values based on the genomic sequences of JA-25^T and F. aestuarina BUZ 2^T were 74.4, 20.5, and 73.6%, respectively. Strain JA-25^T showed an algicidal effect on the marine flagellate alga Heterocapsa triquetra, but no effect on fresh water cyanobacterium (Nostoc). In genome analysis, RIPP-like peptides were detected and predicted to resemble the indolmycin biosynthetic gene cluster, which possibly influence its algicidal effect. Furthermore, a bacteriorhodopsin gene with photoheterotrophic characteristics was detected. The genomic DNA G + C content was 52.5 mol%. The major cellular fatty acids were summed feature 3 (C16:1 ω6c/C16:1 ω7c), C16:1 ω5c, C16:0 (> 10%). The major respiratory quinone was menaquinone 7 and major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two phospholipids, and five unidentified lipids. Considering the phylogenetic inference, phenotypic, and chemotaxonomic data, strain JA-25^T should be classified as a novel species in the novel genus Fibrivirga, with the proposed name Fibrivirga algicola sp. nov. The type strain is JA-25^T (= KCCM 43334^T = NBRC 114259^T).

Intracranial EEG evidence of functional specialization for taxonomic and thematic relations

The dual-hub account posits that the neural organization of semantic knowledge is segregated by the type of semantic relation with anterior temporal lobe (ATL) specializing for taxonomic relations and inferior parietal lobule (IPL) for thematic relations. This study critically examined this account by recording intracranial EEG from an array of depth electrodes within ATL, IPL, and two regions within the semantic control network, inferior frontal gyrus (IFG) and posterior middle temporal gyrus (pMTG), while 17 participants with refractory epilepsy completed a semantic relatedness judgment task. We observed a significant difference between relation types in ATL and IPL approximately 600-800 ms after trial presentation, and no significant differences in IFG or pMTG. Within this time window, alpha and theta suppression indexing cognitive effort and memory retrieval was observed in ATL for taxonomic trials and in IPL for thematic trials. These results suggest taxonomic specialization in ATL and thematic specialization in IPL, consistent with the dual-hub account of semantic cognition.

The Role of Co-Occurrence Statistics in Developing Semantic Knowledge

The organization of our knowledge about the world into an interconnected network of concepts linked by relations profoundly impacts many facets of cognition, including attention, memory retrieval, reasoning, and learning. It is therefore crucial to understand how organized semantic representations are acquired. The present experiment investigated the contributions of readily observable environmental statistical regularities to semantic organization in childhood. Specifically, we investigated whether co-occurrence regularities with which entities or their labels more reliably occur together than with others (a) contribute to relations between concepts independently and (b) contribute to relations between concepts belonging to the same taxonomic category. Using child-directed speech corpora to estimate reliable co-occurrences between labels for familiar items, we constructed triads consisting of a target, a related distractor, and an unrelated distractor in which targets and related distractors consistently co-occurred (e.g., sock-foot), belonged to the same taxonomic category (e.g., sock-coat), or both (e.g., sock-shoe). We used an implicit, eye-gaze measure of relations between concepts based on the degree to which children (N = 72, age 4-7 years) looked at related versus unrelated distractors when asked to look for a target. The results indicated that co-occurrence both independently contributes to relations between concepts and contributes to relations between concepts belonging to the same taxonomic category. These findings suggest that sensitivity to the regularity with which different entities co-occur in children's environments shapes the organization of semantic knowledge during development. Implications for theoretical accounts and empirical investigations of semantic organization are discussed.

The cost of switching between taxonomic and thematic semantics

Current models and theories of semantic knowledge primarily capture taxonomic relationships (DOG and WOLF) and largely do not address the role of thematic relationships in semantic knowledge (DOG and LEASH). Recent evidence suggests that processing or representation of thematic relationships may be distinct from taxonomic relationships. If taxonomic and thematic relations are distinct, then there should be a cost associated with switching between them even when the task remains constant. This hypothesis was tested using two different semantic-relatedness judgment tasks: Experiment 1 used a triads task and Experiment 2 used an oddball task. In both experiments, participants were faster to respond when the same relationship appeared on consecutive trials than when the relationship types were different, even though the task remained the same and the specific relations were different on each trial. These results are consistent with the theory that taxonomic and thematic relations rely on distinct processes or representations.

Can we resolve the taxonomic bias in spider venom research?

The rate of discovery of new spider species greatly exceeds the rate of spider venom characterisation, leading to an increasing number of species with unstudied venoms. However, recent advances in proteomics and genomics that enable the study of venoms from smaller species has expanded the accessible taxonomic range. Thus, although the number of unstudied spider venoms is likely to further increase, future research should focus on the characterisation of venoms and toxins from previously unstudied spider families.

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The rate of discovery of new spider species by far exceeds the rate of spider venom characterisation.

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Advances in proteomics and genomics techniques now allow the study of venoms from a much wider taxonomic range.

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Closing the taxonomic gap at the family level should be the main focus for toxinologists over the next decade.

Isolation and characterization of a novel mesonivirus from Culex mosquitoes in China

A new insect nidovirus (named Yichang virus) from the family Mesoniviridae was isolated, identified, and characterized from Culex mosquitoes in Hubei, China. Results showed a high number of viral RNA copies (up to 10¹¹ copies/ml) within 48 h in C6/36 cells. In addition, the titers of the Yichang virus reached maximal levels of 10⁷ PFU/mL at 6 d post-infection (dpi). The virus produced moderate cytopathic effects when the multiplicity of infection ranged from 0.001–0.1 at 6 dpi, but did not replicate in mammalian cells. Under electron microscopy, the virion of the Yichang virus appeared as spherical particles with diameters of ∼80 nm and large club-shaped projections. Although subsequent genomic sequence analysis revealed that the Yichang virus had similar protein patterns as those of other mesoniviruses, the nucleotide acids shared less than 20% BLAST query coverage with known viruses in the family Mesoniviridae, and showed a maximum sequence identity of 67% for RNA-dependent RNA polymerase (RdRp). The putative protein sequences showed slightly higher identity (28%–68%), and the most conserved domain was RdRp. Based on the phylogenetic and pairwise evolutionary distance analyses, the Yichang virus should be considered a new species belonging to a currently unassigned genus within the family Mesoniviridae.

Description of a new anaerobic thermophilic bacterium, Thermoanaerobacterium butyriciformans sp. nov

Strain USBA-019^T, an anaerobic and thermophilic strain, was identified as a new member of the genus Thermoanaerobacterium. USBA-019^T cells are gram-positive, strictly anaerobic, thermophilic, chemoorganotrophic, moderately acidophilic, non-motile, endospore-forming, slightly curved, and rod-shaped. Cells measure 0.4×3.0-7.0μm. Optimal growth occurs at 50-55°C (35-65°C). Optimum pH is 5.0-5.5 (4.0-8.5). Thiosulfate, elemental sulfur and nitrate were utilized as electron acceptors. Fermentation of glucose, lactose, cellobiose, galactose, arabinose, xylose, starch and xylan primarily produced acetate and butyrate. Xylan, starch and cellobiose produced ethanol and starch, cellobiose, galactose, arabinose and mannose produced lactic acid. Phylogenetic analyses based on 16S rRNA gene sequence comparison and genomic relatedness indices show the close relation of USBA-019^T to Thermoanaerobacterium thermostercoris and Thermoanaerobacterium aotearoense (similarity value: 99%). Hybridization of USBA-019^T, Th. thermostercoris DSM22141^T and Th. aotearoense DMS10170^T found DNA-DNA relatedness of 33.2% and 18.2%, respectively. Based on phenotypic, chemotaxonomic and phylogenetic evidence, along with low identity at whole genome level, USBA-019^T is a novel species of the genus Thermoanaerobacterium which we propose to name Thermoanaerobacterium butyriciformans sp. nov. The type strain is USBA-019^T (=CMPUJ U-019^T=DSM 101588^T).

Am I looking at a cat or a dog? Gaze in the semantic variant of primary progressive aphasia is subject to excessive taxonomic capture

Object naming impairments or anomias are the most frequent symptom in aphasia, and can be caused by a variety of underlying neurocognitive mechanisms. Anomia in neurodegenerative or primary progressive aphasias (PPA) often appears to be based on taxonomic blurring of word meaning: words such as "dog" and "cat" are still recognized generically as referring to animals, but are no longer conceptually differentiated from each other, leading to coordinate errors in word-object matching. This blurring is the hallmark symptom of the "semantic variant" of PPA, who invariably show focal atrophy in the left anterior temporal lobe. In this study we used eye tracking to characterize information processing online (in real time) as non-aphasic controls, semantic and non-semantic PPA participants completed a word-to-object matching task. All participants (including controls) showed taxonomic capture of gaze, spending more time viewing foils that were from the same category as the target compared to unrelated foils, but capture was more extreme in the semantic PPA group. The semantic group showed heightened capture even on trials where they ultimately pointed to the correct target, demonstrating the superiority of eye movements over traditional testing methods in detecting subtle processing impairments. Heightened capture was primarily driven by a tendency to direct gaze back and forth, repeatedly, between a set of related foils on each trial, a behavior almost never shown by controls or non-semantic participants. This suggests semantic PPA participants were accumulating and weighing evidence for a probabilistic rather than definitive mapping between the noun and several candidate objects. Neurodegeneration in PPA thus appears to distort lexical concepts prior to extinguishing them altogether, causing uncertainty in recognition and word-object matching.

Groundwater ecosystem resilience to organic contaminations: microbial and geochemical dynamics throughout the 5-year life cycle of a surrogate ethanol blend fuel plume

The capacity of groundwater ecosystem to recover from contamination by organic chemicals is a vital concern for environmental scientists. A pilot-scale aquifer system was used to investigate the long-term dynamics of contaminants, groundwater geochemistry, and microbial community structure (by 16S rRNA gene pyrosequencing and quantitative real-time PCR) throughout the 5-year life cycle of a surrogate ethanol blend fuel plume (10% ethanol + 50 mg/L benzene + 50 mg/L toluene). Two-year continuous ethanol-blended release significantly changed the groundwater geochemistry (resulted in anaerobic, low pH, and organotrophic conditions) and increased bacterial and archaeal populations by 82- and 314-fold respectively. Various anaerobic heterotrophs (fermenters, acetogens, methanogens, and hydrocarbon degraders) were enriched. Two years after the release was shut off, all contaminants and their degradation byproducts disappeared and groundwater geochemistry completely restored to the pre-release states (aerobic, neutral pH, and oligotrophic). Bacterial and archaeal populations declined by 18- and 45-fold respectively (relative to the time of shut off). Microbial community structure reverted towards the pre-release states and alpha diversity indices rebounded, suggesting the resilience of microbial community to ethanol blend releases. We also found shifts from O2-sensitive methanogens (e.g., Methanobacterium) to methanogens that are not so sensitive to O2 (e.g., Methanosarcina and Methanocella), which is likely to contribute to the persistence of methanogens and methane generation following the source removal. Overall, the rapid disappearance of contaminants and their metabolites, rebound of geochemical footprints, and resilience of microbial community unequivocally document the natural capacity of groundwater ecosystem to attenuate and recover from a large volume of catastrophic spill of ethanol-based biofuel.

GenomePeek-an online tool for prokaryotic genome and metagenome analysis

As more and more prokaryotic sequencing takes place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.

Taxonomic and ad hoc categorization within the two cerebral hemispheres

A typicality effect refers to categorization which is performed more quickly or more accurately for typical than for atypical members of a given category. Previous studies reported a typicality effect for category members presented in the left visual field/right hemisphere (RH), suggesting that the RH applies a similarity-based categorization strategy. However, findings regarding the typicality effect within the left hemisphere (LH) are less conclusive. The current study tested the pattern of typicality effects within each hemisphere for both taxonomic and ad hoc categories, using words presented to the left or right visual fields. Experiment 1 tested typical and atypical members of taxonomic categories as well as non-members, and Experiment 2 tested typical and atypical members of ad hoc categories as well as non-members. The results revealed a typicality effect in both hemispheres and in both types of categories. Furthermore, the RH categorized atypical stimuli more accurately than did the LH. Our findings suggest that both hemispheres rely on a similarity-based categorization strategy, but the coarse semantic coding of the RH seems to facilitate the categorization of atypical members.