Miracle-dz/UniFAR-FTUs huggingface dataset:
Trichostomatid Ciliates (Alveolata, Ciliophora, Trichostomatia) Systematics and Diversity: Past, Present, and Future

The gastrointestinal tracts of most herbivorous mammals are colonized by symbiotic ciliates of the subclass Trichostomatia, which form a well-supported monophyletic group, currently composed by ∼1,000 species, 129 genera, and 21 families, distributed into three orders, Entodiniomorphida, Macropodiniida, and Vestibuliferida. In recent years, trichostomatid ciliates have been playing a part in many relevant functional studies, such as those focusing in host feeding efficiency optimization and those investigating their role in the gastrointestinal methanogenesis, as many trichostomatids are known to establish endosymbiotic associations with methanogenic Archaea. However, the systematics of trichostomatids presents many inconsistencies. Here, we stress the importance of more taxonomic works, to improve classification schemes of this group of organisms, preparing the ground to proper development of such relevant applied works. We will present a historical review of the systematics of the subclass Trichostomatia highlighting taxonomic problems and inconsistencies. Further on, we will discuss possible solutions to these issues and propose future directions to leverage our comprehension about taxonomy and evolution of these symbiotic microeukaryotes.
A Pilot Study Examining Neural Response to Pain in Adolescents With and Without Chronic Pain

Introduction: Chronic pain is common in adolescence and is associated with both pain and prevalence of mental illness later in life. While previous functional neuroimaging work has informed knowledge of neural alterations associated with chronic pain, these findings have been primarily limited to adult samples, and it is unclear if similar patterns of altered brain activation are present in the developing adolescent brain. Objectives: The purpose of this study was to pilot a noxious pressure task during functional neuroimaging to assess brain response to pain in adolescents with and without chronic pain. Methods: Adolescents (ages 11–16) with (n = 9, 7 females) and without (n = 9, 7 females) chronic pain, matched on age, sex, IQ, and parental history of chronic pain, completed a noxious mechanical pressure task to assess subjective pain thresholds. This was followed by randomized presentation of subjective equivalent pressure applications (adolescents' pain 4/0–10), and two objectively equivalent pressures (0.25 and 1.5 kg/cm2), during functional magnetic resonance imaging, using an event-related task design. Results: Findings revealed that adolescents with chronic pain demonstrated significantly greater activation in the posterior cingulate compared to controls. Further, all adolescents demonstrated significant pain-related brain response in brain regions implicated in pain neurocircuitry, as well as in several regions of the default mode network. Similar patterns of neural response were also noted during pain anticipation. Conclusion: These findings are important for not only understanding the neurocircuitry involved in adolescent chronic pain, but may prove beneficial to future pain treatment efforts that seek to alter pain neurocircuitry.
Gut Microbiota Are Associated With Psychological Stress-Induced Defections in Intestinal and Blood–Brain Barriers

Altered gut microbiota has been identified during psychological stress, which causes severe health issues worldwide. The integrity of the intestinal barrier and blood–brain barrier regulates the process of bacterial translocation and can supply the nervous system with real-time information about the environment. However, the association of gut microbiota with psychological stress remains to be fully interpreted. In this study, we established a psychological stress model using an improved communication box and compared the expression of tight junction proteins in multiple regions of the intestinal (duodenum, jejunum, ileum) and blood–brain (amygdala, hippocampus) barriers between model and control rats. We also conducted fecal microbiota analysis using 16S rRNA gene sequencing. Expression levels of the stress-related indicators adrenocorticotropic hormone, NR3C1,2, and norepinephrine were increased in the model group compared to control group. Psychological stress reduced brain and intestinal levels of tight junction proteins, including claudin5, occludin, α-actin, and ZO-1. Microbiota analysis revealed elevated microbial diversity and fecal proportions of Intestinimonas, Catenisphaera, and Globicatella in the model group. Further analysis indicated a negative correlation of Allisonella and Odoribacter, as well as a positive correlation of norank_f__Peptococcaceae, Clostridium_sensu_stricto_1, and Coprococcus_2, with claudin5, occludin, α-actin, and ZO-1. Our use of a rodent model to explore the association between compromised intestinal and blood–brain barriers and altered fecal microbiota under psychological stress improves our understanding of the gut–brain axis. Here, cues converge to control basic developmental processes in the intestine and brain such as barrier function. This study provides new directions for investigating the pathogenesis of emotional disorders and the formulation of clinical treatment.
Arabidopsis PARC6 Is Critical for Plastid Morphogenesis in Pavement, Trichome, and Guard Cells in Leaf Epidermis

Recently, a recessive Arabidopsis thaliana mutant with abundant stromules in leaf epidermal pavement cells was visually screened and isolated. The gene responsible for this mutant phenotype was identified as PARC6, a chloroplast division site regulator gene. The mutant allele parc6-5 carried two point mutations (G62R and W700stop) at the N- and C-terminal ends of the coding sequence, respectively. Here, we further characterized parc6-5 and other parc6 mutant alleles, and showed that PARC6 plays a critical role in plastid morphogenesis in all cell types of the leaf epidermis: pavement cells, trichome cells, and guard cells. Transient expression of PARC6 transit peptide (TP) fused to the green fluorescent protein (GFP) in plant cells showed that the G62R mutation has no or little effect on the TP activity of the PARC6 N-terminal region. Then, plastid morphology was microscopically analyzed in the leaf epidermis of wild-type (WT) and parc6 mutants (parc6-1, parc6-3, parc6-4 and parc6-5) with the aid of stroma-targeted fluorescent proteins. In parc6 pavement cells, plastids often assumed aberrant grape-like morphology, similar to those in severe plastid division mutants, atminE1, and arc6. In parc6 trichome cells, plastids exhibited extreme grape-like aggregations, without the production of giant plastids (>6 µm diameter), as a general phenotype. In parc6 guard cells, plastids exhibited a variety of abnormal phenotypes, including reduced number, enlarged size, and activated stromules, similar to those in atminE1 and arc6 guard cells. Nevertheless, unlike atminE1 and arc6, parc6 exhibited a low number of mini-chloroplasts (< 2 µm diameter) and rarely produced chloroplast-deficient guard cells. Importantly, unlike parc6, the chloroplast division site mutant arc11 exhibited WT-like plastid phenotypes in trichome and guard cells. Finally, observation of parc6 complementation lines expressing a functional PARC6-GFP protein indicated that PARC6-GFP formed a ring-like structure in both constricting and non-constricting chloroplasts, and that PARC6 dynamically changes its configuration during the process of chloroplast division.
Active Turnover of Heme in Hibernation Period in Mammals

Heme oxygenase (HO)-1 plays an important role during hibernation by catalyzing the degradation of heme to biliverdin/bilirubin, ferrous iron, and carbon monoxide, which activates the protective mechanisms against stress. In this context, it was important to analyze the metabolic processes of heme. Nevertheless, to date, no study has approached on biosynthesis of heme. Therefore, our study aims to understand the process of heme biosynthesis, which regulates cell survival in conditions of hypothermia and calorie restriction (CR). During hibernation, the mRNA levels of enzymes responsible for de novo heme biosynthesis were increased in the liver tissue of a Syrian hamster model of hibernation. Moreover, heme trafficking and iron metabolism were found to be more active, as assessed based on the changes in the levels of heme transporter and ferroportin mRNA. The levels of HO-1, a powerful antioxidant, were also upregulated during hibernation. Additionally, increased levels of Sirt-1 mRNA were also observed. These enzymes are known to act as cellular metabolic sensors that activate the cytoprotective mechanisms. These results indicate that HO-1 induction, brought about by the upregulation of heme during the pre-hibernation period, may protect against external stress. Here, we describe heme catabolism during hibernation by analyzing the regulation of the key molecular players involved in heme metabolism. Therefore, this study offers a new strategy for the better regulation of intracellular heme concentrations during hypothermia and other stresses.
Connexins in Astrocyte Migration

Astrocytes have long been considered the supportive cells of the central nervous system, but during the last decades, they have gained much more attention because of their active participation in the modulation of neuronal function. For example, after brain damage, astrocytes become reactive and undergo characteristic morphological and molecular changes, such as hypertrophy and increase in the expression of glial fibrillary acidic protein (GFAP), in a process known as astrogliosis. After severe damage, astrocytes migrate to the lesion site and proliferate, which leads to the formation of a glial scar. At this scar-forming stage, astrocytes secrete many factors, such as extracellular matrix proteins, cytokines, growth factors and chondroitin sulfate proteoglycans, stop migrating, and the process is irreversible. Although reactive gliosis is a normal physiological response that can protect brain cells from further damage, it also has detrimental effects on neuronal survival, by creating a hostile and non-permissive environment for axonal repair. The transformation of astrocytes from reactive to scar-forming astrocytes highlights migration as a relevant regulator of glial scar formation, and further emphasizes the importance of efficient communication between astrocytes in order to orchestrate cell migration. The coordination between astrocytes occurs mainly through Connexin (Cx) channels, in the form of direct cell-cell contact (gap junctions, GJs) or contact between the extracellular matrix and the astrocytes (hemichannels, HCs). Reactive astrocytes increase the expression levels of several proteins involved in astrocyte migration, such as αvβ3 Integrin, Syndecan-4 proteoglycan, the purinergic receptor P2X7, Pannexin1, and Cx43 HCs. Evidence has indicated that Cx43 HCs play a role in regulating astrocyte migration through the release of small molecules to the extracellular space, which then activate receptors in the same or adjacent cells to continue the signaling cascades required for astrocyte migration. In this review, we describe the communication of astrocytes through Cxs, the role of Cxs in inflammation and astrocyte migration, and discuss the molecular mechanisms that regulate Cx43 HCs, which may provide a therapeutic window of opportunity to control astrogliosis and the progression of neurodegenerative diseases.
Thalidomide and Phosphodiesterase 4 Inhibitors as Host Directed Therapeutics for Tuberculous Meningitis: Insights From the Rabbit Model

Tuberculous meningitis (TBM) is the most devastating form of extrapulmonary Mycobacterium tuberculosis infection in humans. Severe inflammation and extensive tissue damage drive the morbidity and mortality of this manifestation of tuberculosis (TB). Antibiotic treatment is ineffective at curing TBM due to variable and incomplete drug penetration across the blood-brain barrier (BBB) and blood-cerebrospinal fluid (CSF) barriers. Adjunctive corticosteroid therapy, used to dampen the inflammation, and the pathologic manifestation of TBM, improves overall survival but does not entirely prevent the morbidity of the disease and has significant toxicities, including immune-suppression. The rabbit has served as a fit for purpose experimental model of human TBM since the early 1900s due to the similarity in the developmental processes of the brain, including neuronal development, myelination, and microglial functions between humans and rabbits. Consistent with the observations made in humans, proinflammatory cytokines, including TNF-α, play a critical role in the pathogenesis of TBM in rabbits focusing the attention on the utility of TNF-α inhibitors in treating the disease. Thalidomide, an inhibitor of monocyte-derived TNF-α, was evaluated in the rabbit model of TBM and shown to improve survival and reduce inflammation of the brain and the meninges. Clinical studies in humans have also shown a beneficial response to thalidomide. However, the teratogenicity and T-cell activation function of the drug limit the use of thalidomide in the clinic. Thus, new drugs with more selective anti-inflammatory properties and a better safety profile are being developed. Some of these candidate drugs, such as phosphodiesterase-4 inhibitors, have been shown to reduce the morbidity and increase the survival of rabbits with TBM. Future studies are needed to assess the beneficial effects of these drugs for their potential to improve the current treatment strategy for TBM in humans.
Cross-Cancer Pleiotropic Analysis Reveals Novel Susceptibility Loci for Lung Cancer

Genome-wide association studies (GWASs) have identified hundreds of single nucleotide polymorphisms (SNPs) associated with cancer risk, several of which have shown pleiotropic effects across cancers. Therefore, we performed a systematic cross-cancer pleiotropic analysis to detect the effects of GWAS-identified variants from non-lung cancers on lung cancer risk in 12,843 cases and 12,639 controls from four lung cancer GWASs. The overall association between variants in each cancer and risk of lung cancer was explored using sequential kernel association test (SKAT) analysis. For single variant analysis, we combined the result of specific study using fixed-effect meta-analysis. We performed functional exploration of significant associations based on features from public databases. To further detect the biological mechanism underlying identified observations, pathway enrichment analysis were conducted with R package “clusterProfiler. ” SNP-set analysis revealed the overall associations between variants of 8 cancer types and lung cancer risk. Single variant analysis identified 6 novel SNPs related to lung cancer risk after multiple correction (Pfdr < 0.10), including rs1707302 (1p34.1, OR = 0.93, 95% CI: 0.90–0.97, P = 7.60 × 10−4), rs2516448 (6p21.33, OR = 1.07, 95% CI: 1.03–1.11, P = 1.00 × 10−3), rs3869062 (6p22.1, OR = 0.91, 95% CI: 0.86–0.96, P = 7.10 × 10−4), rs174549 (11q12.2, OR = 0.90, 95% CI: 0.87–0.94, P = 1.00 × 10−7), rs7193541 (16q23.1, OR = 0.93, 95% CI: 0.90–0.96, P = 1.20 × 10−4), and rs8064454 (17q12, OR = 1.07, 95% CI: 1.03–1.11, P = 4.30 × 10−4). The eQTL analysis and functional annotation suggested that these variants might modify lung cancer susceptibility through regulating the expression of related genes. Pathway enrichment analysis showed that genes modulated by these variants play important roles in cancer carcinogenesis. Our findings demonstrate the pleiotropic associations between non-lung cancer susceptibility loci and lung cancer risk, providing important insights into the shared mechanisms of carcinogenesis across cancers.
Purification and characterization of antibodies against killifish HIF-1Î±

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STATUS OF CORAL REEFS OF MESOAMERICA – MEXICO , BELIZE , GUATEMALA , HONDURAS , NICARAGUA AND

The coral reefs of this region have changed considerably following a series of major natural disturbances and the impacts of human stresses. Reefs on the Atlantic side were battered by hurricanes in 2000, 2001 and 2002, which struck the reefs from the Mexican Yucatan Peninsula to Honduras, destroying corals with some losses up to 75% in Belize. These impacts follow closely on the heels of the extreme coral bleaching event and Hurricane Mitch in 1998, which also caused widespread damage to the region’s reefs. 303 PATRICIA ALMADA-VILLELA, MELANIE MCFIELD, PHILIP KRAMER, PATRICIA RICHARDS KRAMER AND ERNESTO ARIAS-GONZALEZ Status of Coral Reefs of the World: 2002 Throughout large parts of the region, there are intense fishing pressures and major threats to reefs from poor land-use practices and unregulated coastal development. A region-wide survey in 2001 found that coral cover had not increased since the 1998 disturbances and coral diseases were found throughout the region. The Mesoamerican Barrier Reef System (MBRS) Initiative has gathered considerable support for public and private conservation efforts in the region. This regional cooperation program between Belize, Guatemala, Honduras and Mexico is addressing: key aspects of marine protected areas (MPAs); environmental information systems; environmental monitoring of coral reefs and associated ecosystems; public awareness and formal and informal education. Capacity to monitor and manage coral reefs varies enormously in the region, from advanced to basic. The MBRS Initiative and the WWF Ecoregional Conservation Program are working with national, regional and international partners to improve management of the coral reefs and fisheries resources in these countries, and to understand and address land-based sources of marine pollution, and to resolve trans-boundary management issues.
Spatial Audio with Consumer Headphones : How its quality affects the immersion

A realistic sound immersion can be reproduced by high quality headphones. However, low quality consumer headphones are widely employed by common users. A weak frequency response, the distortion and the sensitivity disparity between the left and right transducers could be some of the degrading factors. In this work, we are studying how these factors affect spatial perception. A series or perceptual tests have been carried out with a virtual headphone listening test methodology. The first experiment focuses on the analysis of the disparity of sensitivity between the two transducers. The second test studies the influence of the frequency response relating perceived quality and spatial impression. The third test analyses the effects of distortion using a Volterra kernels scheme for the simulation of the distortion using convolutions. Finally, the fourth relate the quality of the frequency response with the accuracy on azimuth localization. The conclusions of the experiments are: the disparity between both transducers can affect the localization of the source; the perception of quality and spatial impression has a high correlation; the distortion produced by the range of headphones tested at a fixed level is not perceptible; and that some frequency bands have an important role in the front-back confusions.
The Link between Expenditure on Contraceptives and Number of Young Dependents in the Philippines

The growing population of the Philippines hinders the country from achieving economic development due to the limited resources available. The 2010 Census on Population and Housing (CPH) reports that the Philippine population has struck 92.1 million, a 15.8-million increase from the 76.3 million population size reported in 2000. Moreover, the relationship between population and family size, on the one hand, and poverty incidence on the other, has been established through econometric models showing the causality between presence of young dependents in a household and household welfare. Using the Family Income and Expenditure Survey (FIES) 2009 data, this study examines the factors affecting the number of young dependents in a household, and focuses in particular on the household’s level of contraceptive expenditure. The negative binomial regression model is used to quantify the effect of the factors and predict the average number of young dependents in a household. This model allows for overdispersion in the data. Results show that for every P10,000 increase in total expenditure on contraceptives for a period of six months, the mean number of young dependents decreases by 3.7%. Other demographic variables such as education of household head and income of the household are controlled for in the study.
Higher-order finite element de Rham complexes, partially localized flux reconstructions, and applications

We construct finite element de~Rham complexes of higher and possibly non-uniform polynomial order in finite element exterior calculus (FEEC). Starting from the finite element differential complex of lowest-order, known as the complex of Whitney forms, we incrementally construct the higher-order complexes by adjoining exact local complexes associated to simplices. We define a commuting canonical interpolant. On the one hand, this research provides a base for studying $hp$-adaptive methods in finite element exterior calculus. On the other hand, our construction of higher-order spaces enables a new tool in numerical analysis which we call"partially localized flux reconstruction". One major application of this concept is in the area of equilibrated a~posteriori error estimators: we generalize the Braess-Sch\"oberl error estimator to edge elements of higher and possibly non-uniform order.
On the Product of Two κ – μ Random Variables and its Application to Double and Composite Fading Channels

In this paper, we perform a systematic investigation of the statistics associated with the product of two independent and non-identically distributed κ–μ random variables. More specifically, we develop novel analytical formulations for many of the fundamental statistics of interest, namely, the probability density function, cumulative distribution function, and moment-generating function. Using these new results, closedform expressions are obtained for the higher order moments, amount of fading and channel quality estimation index, while analytical formulations are obtained for the outage probability, average channel capacity, average symbol error probability, and average bit error probability. These general expressions can be reduced to a number of fading scenarios, such as the double Rayleigh, double Rice, double Nakagami-m, κ–μ/Nakagami-m, and Rice/Nakagami-m, which all occur as special cases. Additionally, as a byproduct of the work performed here, formulations for the κ–μ/κ–μ composite fading model can also be deduced. To illustrate the efficacy of the novel expressions proposed here, we provide useful insights into the outage probability of a dualhop system used in body area networks, and demonstrate the suitability of the κ–μ/κ–μ composite fading for characterizing shadowed fading in device-to-device channels.