Miracle-dz/UniFAR-FTUs huggingface dataset:
Music Training, Working Memory, and Neural Oscillations: A Review

This review focuses on reports that link music training to working memory and neural oscillations. Music training is increasingly associated with improvement in working memory, which is strongly related to both localized and distributed patterns of neural oscillations. Importantly, there is a small but growing number of reports of relationships between music training, working memory, and neural oscillations in adults. Taken together, these studies make important contributions to our understanding of the neural mechanisms that support effects of music training on behavioral measures of executive functions. In addition, they reveal gaps in our knowledge that hold promise for further investigation. The current review is divided into the main sections that follow: (1) discussion of behavioral measures of working memory, and effects of music training on working memory in adults; (2) relationships between music training and neural oscillations during temporal stages of working memory; (3) relationships between music training and working memory in children; (4) relationships between music training and working memory in older adults; and (5) effects of entrainment of neural oscillations on cognitive processing. We conclude that the study of neural oscillations is proving useful in elucidating the neural mechanisms of relationships between music training and the temporal stages of working memory. Moreover, a lifespan approach to these studies will likely reveal strategies to improve and maintain executive function during development and aging.
Integrative Analysis for Identifying Co-Modules of Microbe-Disease Data by Matrix Tri-Factorization With Phylogenetic Information

Microbe-disease association relationship mining is drawing more and more attention due to its potential in capturing disease-related microbes. Hence, it is essential to develop new tools or algorithms to study the complex pathogenic mechanism of microbe-related diseases. However, previous research studies mainly focused on the paradigm of “one disease, one microbe,” rarely investigated the cooperation and associations between microbes, diseases or microbe-disease co-modules from system level. In this study, we propose a novel two-level module identifying algorithm (MDNMF) based on nonnegative matrix tri-factorization which integrates two similarity matrices (disease and microbe similarity matrices) and one microbe-disease association matrix into the objective of MDNMF. MDNMF can identify the modules from different levels and reveal the connections between these modules. In order to improve the efficiency and effectiveness of MDNMF, we also introduce human symptoms-disease network and microbial phylogenetic distance into this model. Furthermore, we applied it to HMDAD dataset and compared it with two NMF-based methods to demonstrate its effectiveness. The experimental results show that MDNMF can obtain better performance in terms of enrichment index (EI) and the number of significantly enriched taxon sets. This demonstrates the potential of MDNMF in capturing microbial modules that have significantly biological function implications.
Dynamics of Sentence Handwriting in Dyslexia: The Impact of Frequency and Consistency

Previous literature has indicated that linguistic and motor processes influence each other during written sentence production, and that the scope of this influence varies according to spelling ability or cognitive resources available. This study investigated how the spelling deficits associated with dyslexia affect the dynamics of the interaction between central and peripheral processes and the level of anticipation that can be observed in word spelling in the context of a sentence to dictation task. Children 9–12-year-olds with and without dyslexia wrote sentences to dictation in which the lexical frequency and phonology-to-orthography consistency of the last word (target) were manipulated. Analyses of kinematic measures (writing durations, in-air pen duration, and peaks of speed) revealed that children with dyslexia showed lexical frequency effects evident in within-word pauses (in-air pen) in the article and noun production. In addition, both children with and without dyslexia showed a phonology-to-orthography consistency effect in the pause before the target word. This effect tended to continue affecting the execution of the syllable prior to the inconsistency only in the group with dyslexia. Results support the influence of linguistic processes on motor execution. In addition, the study provides evidence of the impact of spelling deficits on the dynamics of handwriting in children with dyslexia.
Discovery and Mapping of the Triton Seep Site, Redondo Knoll: Fluid Flow and Microbial Colonization Within an Oxygen Minimum Zone

This paper examines a deep-water (∼900 m) cold-seep discovered in a low oxygen environment ∼30 km off the California coast in 2015 during an E/V Nautilus telepresence-enabled cruise. This Triton site was initially detected from bubble flares identified via shipboard multibeam sonar and was then confirmed visually using the remotely operated vehicle (ROV) Hercules. High resolution mapping (to 1 cm resolution) and co-registered imaging has provided us with a comprehensive site overview – both of the geologic setting and the extent of the associated microbial colonization. The Triton site represents an active cold-seep where microorganisms can act as primary producers at the base of a chemosynthesis-driven food chain. But it is also located near the core of a local oxygen minimum zone (OMZ), averaging <0.75 μM oxygen, which is significantly below average ocean levels (180–270 μM) and, indeed, extreme even among OMZs as a whole which are defined to occur at all oxygen concentrations <22 μM. Extensive microbial mats, extending for >100 m across the seafloor, dominate the site, while typical seep-endemic macro-fauna were noticeably absent from our co-registered photographic and high-resolution mapping surveys – especially when compared to all adjacent seep sites within the same California Borderlands region. While such absences of abundant macro-fauna could be attributable to variations in the availability of dissolved oxygen in the overlying water column this need not necessarily be the case. An alternate possibility is that the zonation in microbial activity that is readily observable at the seafloor at Triton reflects, instead, a concentric pattern of radially diminishing fluxes of reductants from the underlying seafloor. This unusual but readily accessible discovery, in close proximity to Los Angeles harbor, provides an intriguing new natural laboratory at which to examine biogeochemical and microbiological interactions associated with the functioning of cold seep ecosystems within an OMZ.
Restored Fire and Grazing Regimes Influence Nest Selection and Survival in Brewer's Blackbirds Euphagus cyanocephalus

Abstract. Grassland fire suppression causes numerous ecological changes including increases in woody vegetation, reduced biodiversity, and population declines of grassland species. Elimination of vegetation structure created and maintained by fire is a major driver of these changes. In this study, we documented a seldom-described nesting preference in Brewer's Blackbirds Euphagus cyanocephalus through the discovery of 56 nests in recently burned (0 and 1 years-since-fire) mixed-grass prairie. After locating nests via systematic rope dragging, we monitored them to characterize fates and then measured vegetation characteristics at and near nests to determine how vegetation structure influences nest survival. Most Brewer's Blackbird nests were located in patches burned within 1.5 years of the nesting attempt, though such patches made up 21% of the landscape. Nests were located on the ground and consisted of fine grasses lined with animal hair. Site selection analysis showed that Brewer's Blackbirds were 38 and 34 times more likely to nest in 0 and 1 year-since-fire patches than unburned patches, respectively. Nest survival analysis indicated a daily survival rate of 0.96 (0.32 overall survival). Lower survival rates were associated with higher bare ground and litter cover at the microsite (5 m from nest) and nest site (at nest), respectively. These results demonstrate that Brewer's Blackbirds exploit fire-associated vegetation structure in tree-limited landscapes. This research suggests that restored grassland disturbance regimes extend broad benefits to non-obligate taxa, as well as reveals previously repressed fire-associated behaviors of wildlife.
The influence of enrichment on spatial pattern separation in zebrafish (Danio rerio)

Abstract. For any animal, learning to distinguish between very similar spatial cues in the environment is a fundamental skill to acquire, because it can ultimately lead to a live or die situation. However, it is cognitively demanding to learn to discriminate between very similar spatial environments (as opposed to distinct ones). Spatial pattern separation is the cognitive process that keeps similar, overlapping memories distinct, and is thought to underlie many spatial tasks used in behavioral studies. In captivity, it has been shown that environmental enrichment can lead to enhanced spatial learning in fish, however, a task that utilizes spatial pattern separation has never been conducted on fish. In the current study, we used the delayed non-matching to place Radial Arm Maze (RAM) to determine if there were differences in spatial pattern separation in zebrafish (Danio rerio) housed with or without enrichment. In the delayed non-matching to place RAM, the animal has to discriminate between low spatially separated stimuli (near, similar) and high spatially separated stimuli (far, distinct). Our results show that environmental enrichment enhanced spatial learning at both low and high separation (i.e. at both spatially similar and distinct maze locations). Thus, enrichment did not selectively enhance zebrafish learning only at spatially similar cues as we expected, but rather zebrafish housed with enrichment were better learners overall. Given the growing use of zebrafish as a research model for behavioral research, these data will help us to understand how different housing and rearing methods influence spatial learning in captive lab fish, and ultimately will help to inform welfare guidelines on best practices for housing fish in captivity.
Mitochondrial DNA Analyses of Invasive Raccoons (Procyon lotor) in the Boso Peninsula, Japan

Abstract. Ecological genetic analyses have recently been applied to the field of biological invasions to describe the genetic background of the invasive species. The raccoon (Procyon lotor) is a medium-sized mammal that is native to North and Central America and has been naturalized into several countries worldwide. In the Boso Peninsula, Japan, raccoons were estimated to have been introduced during the 1990s. We collected DNA samples from 139 raccoons in seven administrative districts and sequenced a part of the mitochondrial D-loop region. We identified two haplotypes of the mitochondrial DNA, which differed by three single nucleotide polymorphisms; therefore, the raccoon population in Boso was founded by at least two females. Although the two haplotypes were identified in all districts, genetic differentiation analysis showed that the northern population was genetically different from the southern population. This genetic gap might not be affected by the landscape, but instead by the expansion history of raccoons. One of the probable hypotheses suggests that the expansion of raccoons may have occurred twice in Boso, a second expansion occurring after raccoons had already spread across Boso. Although this is consistent with historical distribution records, further studies using nuclear microsatellite markers are necessary to validate this hypothesis.
Genetic differentiation in mountain-dwelling clam shrimp, Paralimnadia (Crustacea : Branchiopoda : Spinicaudata), in eastern Australia

Abstract. The majority of Australian Spinicaudata Linder, 1945 inhabit the (semi)arid deserts of Australia’s lowlands. However, several closely related species of Paralimnadia Sars, 1896 inhabit small temporary habitats throughout the Great Dividing Range in eastern Australia. By combining analyses of mitochondrial cytochrome c oxidase subunit I (COI) with double-digest restriction-site associated DNA (ddRAD) data, we studied the species diversity and genetic diversity of this group of mountain-dwelling branchiopods. Levels of genetic differentiation in COI are relatively low between putative species (mostly between 1.5 and 6.7%), complicating COI-based species delimitation. Depending on the applied threshold, three to six species are inferred in the studied area, with most putative species being geographically restricted. Particularly notable are the high levels of population differentiation indicated by ddRAD analyses between nearby populations within putative species. This suggests that gene flow is limited, even between populations separated only by a few kilometres. This may lead to fast population differentiation, which in turn might drive speciation. Our data suggest that the species diversity of Paralimnadia in the Great Dividing Range is much higher than currently appreciated.
Short-Term Fruiting Phenology Affects the Diet of an Omnivorous Carnivoran, the Tsushima Marten Martes melampus tsuensis

Abstract. The availability of fruits, but not animal prey, to consumer species is strictly limited to the fruiting period of specific plant species. This study aimed to identify the short-term fruit consumption of an omnivorous carnivoran in relation to daily phenological changes in the number of ripe fruits of multiple fruiting species during peak fruiting seasons (spring and fall). We collected the scats of the Tsushima marten (Martes melampus tsuensis) and documented changes in their diet according to the fruiting phenology of plants (spring and fall: five and three fruit species, respectively) at 1–2-day intervals. Four fruiting species were foraged by martens as soon as they started fruiting, while the other four fruiting species were rarely consumed. The high overlap in the fruiting period of different fruiting species in the study area resulted in martens preferentially feeding on certain fruits. Unlike the other fruiting species, persimmon (Diospyros kaki) exhibited an asynchronous fruiting pattern, with martens foraging on this plant intermittently throughout the fall. In conclusion, martens adjusted the type and quantity of fruits they consumed in relation to the daily fruiting patterns of different plant species and the extent of overlap in the fruiting period across fruiting species.
New Species and New Records of Xiphydriid Woodwasps (HYmenoptera: Xiphydriidae) from Southeastern Asia

Abstract. Hyperxiphia flava Smith, n. sp. and H. semilutea Smith, n. sp. are described from Laos. Hyperxiphia funicornis (Konow 1897), previously only known from Myanmar, is newly recorded from Laos. Euxiphydria vietnamensis Smith and Shinohara 2011, previously known only from Vietnam, is recorded from Laos and the male is described for the first time. Gryponeura quadrimaculata (Cameron 1899), previously only known from Assam, India, is newly recorded from Laos and China. Lataxiphyda nodai (Togashi 1982), known only from southern Japan, is recorded from Laos.
Two New Deep-Sea Species of Burrowing Anemones (Cnidaria: Actiniaria: Edwardsiidae) from Whittard Canyon Off the Southwestern Coast of Ireland

ABSTRACT Burrowing sea anemones have a simple morphology with an elongate body and a round aboral end that anchors the animal into mud, sand, or gravel, leaving only the tentacle crown exposed. Edwardsiids are easily differentiated from other burrowing sea anemones by their distinctive mesentery arrangement of eight unpaired macrocnemes at midcolumn with microcnemes restricted to the distal column at the base of the tentacles. Though edwardsiids may be frequently collected in biodiversity surveys, oceanographic expeditions, and ecological monitoring projects, their identification is particularly hampered by their small size, the need for histology, the high number of undescribed species, and the few specialists able to identify them. Scolanthus belongs to the subfamily Edwardsiinae, which is characterized by nemathybomes; it is differentiated from other members of the subfamily by having nemathybomes with basitrichs and periderm in the proximal end, at least eight microcnemes, and 16 or more tentacles in adults. The 14 valid species of Scolanthus are distributed worldwide, but only four species have been recorded from waters deeper than 100 m (S. ingolfi, 1461 m; S. nidarosiensis, 125–150 m; S. intermedius, 223 m; S. triangulus, 71–271 m). Here we describe Scolanthus shrimp, sp. nov., and S. celticus, sp. nov., the first two sea anemones recorded from the deep-sea Whittard Canyon off the coast of Ireland. We provide detailed morphological descriptions of the new species, including micro-CT scanning of S. celticus, and differentiate them from other species in the genus. We also generate a phylogeny using five molecular markers (12S, 16S, 18S, 28S, CO3) to establish the phylogenetic position of the new species. Based on our results, we discuss the relationship of Scolanthus to other edwardsiid genera and implications for the morphology and evolution of the group.
The Role of Gut Microbiome Perturbation in Fatigue Induced by Repeated Stress from Chemoradiotherapy: A Proof of Concept Study

Objectives The objectives of this proof of concept study were to (a) examine the temporal changes in fatigue and diversity of the gut microbiome over the course of chemoradiotherapy (CRT) in adults with rectal cancers; (b) investigate whether there are differences in diversity of the gut microbiome between fatigued and nonfatigued participants at the middle and at the end of CRT; and (c) investigate whether there are differences in the relative abundance of fecal microbiota at the phylum and genus levels between fatigued and nonfatigued participants at the middle and at the end of CRT. Methods Stool samples and symptom ratings were collected prior to the inception of CRT, at the middle (after 12–16 treatments) and at the end (after 24–28 treatments) of the CRT. Descriptive statistics and Mann–Whitney U test were computed for fatigue. Gut microbiome data were analyzed using the QIIME2 software. Results Participants (N = 29) ranged in age from 37 to 80 years. The median fatigue score significantly changed at the end of CRT (median = 23.0) compared with the median score before the initiation of CRT for the total sample (median = 17.0; p ≤ 0.05). At the middle of CRT, the alpha diversity (abundance of Operational Taxonomic Units) was lower for fatigued participants (149.30 ± 53.1) than for nonfatigued participants (189.15 ± 44.18, t(23) = 2.08, p ≤ 0.05). At the middle of CRT, the alpha diversity (abundance of Operational Taxonomic Units) was lower for fatigued participants (149.30 ± 53.1) than for nonfatigued participants (189.15 ± 44.18, Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla for fatigued participants, and Escherichia, Bacteroides, Faecalibacterium, and Oscillospira were the most abundant genera for fatigued participants. Conclusion CRT-associated perturbation of the gut microbiome composition may contribute to fatigue.
Bayesian and Frequentist Analytical Approaches Using Log-Normal and Gamma Frailty Parametric Models for Breast Cancer Mortality

One of the major causes of death among females in Saudi Arabia is breast cancer. Newly diagnosed cases of breast cancer among the female population in Saudi Arabia is 19.5%. With this high incidence, it is crucial that we explore the determinants associated with breast cancer among the Saudi Arabia populace—the focus of this current study. The total sample size for this study is 8312 (8172 females and about 140 representing 1.68% males) patients that were diagnosed with advanced breast cancer. These are facility-based cross-sectional data collected over a 9-year period (2004 to 2013) from a routine health information system database. The data were obtained from the Saudi Cancer Registry (SCR). Both descriptive and inferential (Cox with log-normal and gamma frailties) statistics were conducted. The deviance information criterion (DIC), Watanabe–Akaike information criterion (WAIC), Bayesian information criterion (BIC), and Akaike information criterion were used to evaluate or discriminate between models. For all the six models fitted, the models which combined the fixed and random effects performed better than those with only the fixed effects. This is so because those models had smaller AIC and BIC values. The analyses were done using R and the INLA statistical software. There are evident disparities by regions with Riyadh, Makkah, and Eastern Province having the highest number of cancer patients at 28%, 26%, and 20% respectively. Grade II (46%) and Grade III (45%) are the most common cancer grades. Left paired site laterality (51%) and regional extent (52%) were also most common characteristics. Overall marital status, grade, and cancer extent increased the risk of a cancer patient dying. Those that were married had a hazard ratio of 1.36 (95% CI: 1.03–1.80) while widowed had a hazard ratio of 1.57 (95% CI: 1.14–2.18). Both the married and widowed were at higher risk of dying with cancer relative to respondents who had divorced. For grade, the risk was higher for all the levels, that is, Grade I (Well diff) (HR = 7.11, 95% CI: 3.32–15.23), Grade II (Mod diff) (HR = 7.89, 95% CI: 3.88–16.06), Grade III (Poor diff) (HR = 5.90, 95% CI (2.91–11.96), and Grade IV (Undiff) (HR = 5.44, 95% (2.48–11.9), relative to B-cell. These findings provide empirical evidence that information about individual patients and their region of residence is an important contributor in understanding the inequalities in cancer mortalities and that the application of robust statistical methodologies is also needed to better understand these issues well.
Epigenetic Therapy as a Putative Molecular Target to Modulate B Cell Biology and Behavior in the Context of Immunological Disorders

Histone Deacetylase- (HDAC-) dependent epigenetic mechanisms have been widely explored in the last decade in different types of malignancies in preclinical studies. This effort led to the discovery and development of a range of new HDAC inhibitors (iHDAC) with different chemical properties and selective abilities. In fact, hematological malignancies were the first ones to have new iHDACs approved for clinical use, such as Vorinostat and Romidepsin for cutaneous T cell lymphoma and panobinostat for multiple myeloma. Besides these promising already approved iHDACs, we highlight a range of studies focusing on the HDAC-dependent epigenetic control of B cell development, behavior, and/or function. Here, we highlight 21 iHDACs which have been studied in the literature in the context of B cell development and/or dysfunction mostly focused on B cell lymphomagenesis. Regardless, we have identified 55 clinical trials using 6 out of 21 iHDACs to approach their putative roles on B cell malignancies; none of them focuses on peritoneal B cell populations. Since cells belonging to this peculiar body compartment, named B1 cells, may contribute to the development of autoimmune pathologies, such as lupus, a better understanding of the HDAC-dependent epigenetic mechanisms that control its biology and behavior might shed light on iHDAC use to manage these immunological dysfunctions. In this sense, iHDACs might emerge as a promising new approach for translational studies in this field. In this review, we discuss a putative role of iHDACs in the modulation of peritoneal B cell subpopulation's balance as well as their role as therapeutic agents in the context of chronic diseases mediated by peritoneal B cells.