Miracle-dz/UniFAR-FTUs huggingface dataset:
A unique T cell receptor discovered in marsupials

T cells recognize antigens by using T cell receptors (TCRs) encoded by gene segments, called variable (V), diversity (D), and joining (J), that undergo somatic recombination to create diverse binding specificities. Four TCR chains (α, β, γ, and δ) have been identified to date, and, as T cells develop in the thymus, they express exclusively either an αβTCR or a γδTCR heterodimer. Here, we show that marsupials have an additional TCR (TCRμ) that has V, D, and J that are either somatically recombined, as in conventional TCRs, or are already prejoined in the germ-line DNA in a manner consistent with their creation by retrotransposition. TCRμ does not have a known homolog in eutherian mammals but has features analogous to a recently described TCRδ isoform in sharks. TCRμ is expressed in at least two mRNA isoforms that appear capable of encoding a full-length protein, both of which are transcribed in the thymus and spleen. One contains two variable domains: a somatically recombined V and a prejoined V. This appears to be the dominant isoform in peripheral lymphoid tissue. The other isoform contains only the prejoined V and is structurally more similar to conventional TCR chains, however invariant. Unlike other TCRs, TCRμ uses prejoined gene segments and is likely present in all marsupials. Its similarity to a TCR isoform in sharks suggests that it, or something similar, may be present in other vertebrate lineages and, therefore, may represent an ancient receptor system.
Members of the Rid protein family have broad imine deaminase activity and can accelerate the Pseudomonas aeruginosa D-arginine dehydrogenase (DauA) reaction in vitro

The Rid (YjgF/YER057c/UK114) protein family is a group of small, sequence diverse proteins that consists of eight subfamilies. The archetypal RidA subfamily is found in all domains, while the Rid1-7 subfamilies are present only in prokaryotes. Bacterial genomes often encode multiple members of the Rid superfamily. The best characterized member of this protein family, RidA from Salmonella enterica, is a deaminase that quenches the reactive metabolite 2-aminoacrylate generated by pyridoxal 5’-phosphate-dependent enzymes and ultimately spares certain enzymes from damage. The accumulation of 2-aminoacrylate can damage enzymes and lead to growth defects in bacteria, plants, and yeast. While all subfamily members have been annotated as imine deaminases based on the RidA characterization, experimental evidence to support this annotation exists for a single protein outside the RidA subfamily. Here we report that six proteins, spanning Rid subfamilies 1–3, deaminate a variety of imine/enamine substrates with differing specific activities. Proteins from the Rid2 and Rid3 subfamilies, but not from the RidA and Rid1 subfamilies deaminated iminoarginine, generated in situ by the Pseudomonas aeruginosa D-arginine dehydrogenase DauA. These data biochemically distinguished the subfamilies and showed Rid proteins have activity on a metabolite that is physiologically relevant in Pseudomonas and other bacteria.
Helicobacter pylori infection appears essential for stomach carcinogenesis: Observations in Semarang, Indonesia

The gastric cancer incidence in Semarang, Indonesia, is exceedingly low: only approximately 1/100th of the level in Japan. To elucidate the reason, we carried out an ecological study recruiting 69 male and 102 female participants from the general populace in January 2005. Positive urea breath tests were 0% for both men and women, and Helicobacter pylori (H. pylori) IgG antibodies were found in 2% (0–5, 95% confidence interval) of men and 2% (0–4) of women, significantly lower than the 62% (58–65) and 57% (53–60), respectively, in Japan. Furthermore, there were no positive findings with the pepsinogen tests in Semarang, again significant in comparison with the 23% (22–25) and 22% (20–23) in Japan. Variation in smoking levels and consumption of NaCl, vegetables and fruit were found, but not to an extent that would allow explanation of the major differences in gastric cancer incidence. We may conclude that the very low prevalence of H. pylori infection and thus chronic atrophic gastritis account for the rarity of stomach cancer in Semarang, Indonesia. (Cancer Sci 2005; 96: 873–875)
Small Non-coding Transfer RNA-Derived RNA Fragments (tRFs): Their Biogenesis, Function and Implication in Human Diseases

tRNA-derived RNA fragments (tRFs) are an emerging class of non-coding RNAs (ncRNAs). A growing number of reports have shown that tRFs are not random degradation products but are functional ncRNAs made of specific tRNA cleavage. They play regulatory roles in several biological contexts such as cancer, innate immunity, stress responses, and neurological disorders. In this review, we summarize the biogenesis and functions of tRFs.
Retrospective study of prognostic value of DNA ploidy and proliferative activity in neuroblastoma.

AIM--To assess the prognostic value of age and stage at diagnosis, site of primary tumour, cell ploidy and N-myc copy number in children with neuroblastoma. METHODS--Flow cytometry was used to determine the cellular DNA content of paraffin wax embedded archival material from 69 cases of neuroblastoma and was successful in 52. RESULTS--The age, stage, and survival distribution of the sampled cases was not significantly different from that in a larger population based series. There were seven diploid ("non-aneuploid") and 45 aneuploid (including two tetraploid and four triploid) tumours. The 10 year survival was significantly better for cases of aneuploid rather than diploid tumours (p < 0.05). An important new finding was that 10 year survival was also significantly better for tumours with a low percentage of cells in S phase (p < 0.03). CONCLUSION--The percentage of cells in S phase, a measure of the proliferative activity of the tumour, correlated with prognosis in neuroblastoma. This should be measured with other biological features of the disease, such as N-myc copy number, when prognostic indicators are being assessed.
Assessing Measurement Invariance of Behavioral Tendency Model for College and University Students Participating in In-line Hockey between Male and Female Groups

Ajzen’s (1985) Theory of Planned Behavior (TPB) was referred to as the architecture by this study, using SEM to construct the behavioral tendency causal model for university students participating in in-line hockey. The university students participating in in-line hockey were taken as the research subjects and Ajzen’s (1985) Theory of Planned Behavior was used as the reference. In addition, the modified planned behavior scale of behavior attitude scale for college and university students participating in tennis proposed by Chang and Lai (2005) were adopted as the research tool. The scale was found to feature good convergent validity, discriminate validity and composite reliability. The research results indicate that H1 attitude of university students participating in in-line hockey has a positive impact towards behavioral tendency with a path coefficient of . 43 (p<.01), and so H1 is supported. H2 subjective norm of university students participating in in-line hockey has a positive impact towards behavioral tendency with a path coefficient of . 16 (p>.01), and so H2 is not supported. H3 perceived behavioral control of university students participating in in-line hockey has a positive impact towards behavioral tendency with a path coefficient of . 54 (p<.01), and so H3 is supported. The results have verified that the measurement invariance assessment for college and university students participating in in-line hockey is incongruence between male and female groups.
Genome-wide analysis of thyroid hormone receptors shared and specific functions in neural cells

Significance This article presents a unique genome-wide transcriptome and cistrome analysis for thyroid hormone receptors. It defines 3,3′,5-triiodo-L-thyronine (T3) target genes in a neural cell line expressing either TRα1 or TRβ1. A substantial fraction of the T3 target genes display a marked preference for one of the two receptors. However, receptor-selective regulation of T3 target genes does not result from receptor-selective chromatin occupancy of their promoter regions. We conclude that modification of TRα1 and TRβ1 intrinsic properties contributes to the divergent evolution of the receptors’ function. TRα1 and TRβ1, the two main thyroid hormone receptors in mammals, are transcription factors that share similar properties. However, their respective functions are very different. This functional divergence might be explained in two ways: it can reflect different expression patterns or result from different intrinsic properties of the receptors. We tested this second hypothesis by comparing the repertoires of 3,3′,5-triiodo-L-thyronine (T3)-responsive genes of two neural cell lines, expressing either TRα1 or TRβ1. Using transcriptome analysis, we found that a substantial fraction of the T3 target genes display a marked preference for one of the two receptors. So when placed alone in identical situations, the two receptors have different repertoires of target genes. Chromatin occupancy analysis, performed at a genome-wide scale, revealed that TRα1 and TRβ1 cistromes were also different. However, receptor-selective regulation of T3 target genes did not result from receptor-selective chromatin occupancy of their promoter regions. We conclude that modification of TRα1 and TRβ1 intrinsic properties contributes in a large part to the divergent evolution of the receptors’ function, at least during neurodevelopment.
Qualitative assessment of the diet of European eel larvae in the Sargasso Sea resolved by DNA barcoding

European eels (Anguilla anguilla) undertake spawning migrations of more than 5000 km from continental Europe and North Africa to frontal zones in the Sargasso Sea. Subsequently, the larval offspring are advected by large-scale eastward ocean currents towards continental waters. However, the Sargasso Sea is oligotrophic, with generally low plankton biomass, and the feeding biology of eel larvae has so far remained a mystery, hampering understanding of this peculiar life history. DNA barcoding of gut contents of 61 genetically identified A. anguilla larvae caught in the Sargasso Sea showed that even the smallest larvae feed on a striking variety of plankton organisms, and that gelatinous zooplankton is of fundamental dietary importance. Hence, the specific plankton composition seems essential for eel larval feeding and growth, suggesting a linkage between eel survival and regional plankton productivity. These novel insights into the prey of Atlantic eels may furthermore facilitate eel larval rearing in aquaculture, which ultimately may replace the unsustainable use of wild-caught glass eels.
Phylogenomics Reshuffles the Eukaryotic Supergroups

Background Resolving the phylogenetic relationships between eukaryotes is an ongoing challenge of evolutionary biology. In recent years, the accumulation of molecular data led to a new evolutionary understanding, in which all eukaryotic diversity has been classified into five or six supergroups. Yet, the composition of these large assemblages and their relationships remain controversial. Methodology/Principle Findings Here, we report the sequencing of expressed sequence tags (ESTs) for two species belonging to the supergroup Rhizaria and present the analysis of a unique dataset combining 29908 amino acid positions and an extensive taxa sampling made of 49 mainly unicellular species representative of all supergroups. Our results show a very robust relationship between Rhizaria and two main clades of the supergroup chromalveolates: stramenopiles and alveolates. We confirm the existence of consistent affinities between assemblages that were thought to belong to different supergroups of eukaryotes, thus not sharing a close evolutionary history. Conclusions This well supported phylogeny has important consequences for our understanding of the evolutionary history of eukaryotes. In particular, it questions a single red algal origin of the chlorophyll-c containing plastids among the chromalveolates. We propose the abbreviated name ‘SAR’ (Stramenopiles+Alveolates+Rhizaria) to accommodate this new super assemblage of eukaryotes, which comprises the largest diversity of unicellular eukaryotes.
Optimism, Symptom Distress, Illness Appraisal, and Coping in Patients With Advanced-Stage Cancer Diagnoses Undergoing Chemotherapy Treatment.

PURPOSE/OBJECTIVES To explore the relationships between optimism, self-efficacy, symptom distress, treatment complexity, illness appraisal, coping, and mood disturbance in patients with advanced-stage cancer. DESIGN Cross-sectional study. SETTING Smilow Cancer Hospital at Yale New Haven in Connecticut, an outpatient comprehensive cancer center. SAMPLE A convenience sample of 121 adult patients with stages III-IV cancer undergoing active chemotherapy. METHODS Participants completed common self-report questionnaires to measure variables. Treatment hours and visits were calculated from data retrieved from medical record review. Mediation and path analysis were conducted to identify direct and indirect pathways from the significant antecedent variables to mood disturbance. MAIN RESEARCH VARIABLES Dispositional optimism, self-efficacy, social support, treatment complexity, symptom distress, illness appraisal, coping, and mood disturbance. FINDINGS Greater optimism and self-efficacy were associated with less negative illness appraisal, less avoidant coping, and decreased mood disturbance. Conversely, greater symptom distress was associated with greater negative illness appraisal, greater avoidant coping, and greater mood disturbance. In the final model, optimism and symptom distress had direct and indirect effects on mood disturbance. Indirect effects were partially mediated by illness appraisal. CONCLUSIONS Mood disturbance resulted from an interaction of disease stressors, personal resources, and cognitive appraisal of illness. Avoidant coping was associated with greater disturbed mood, but neither avoidant nor active coping had a significant effect on mood in the multivariate model. IMPLICATIONS FOR NURSING Illness appraisal, coping style, and symptom distress are important targets for intervention. Optimism is a beneficial trait and should be included, along with coping style, in comprehensive nursing assessments of patients with cancer.
Differential Intracellular Sorting of Immediate Early Gene mRNAs Depends on Signals in the mRNA Sequence

This study characterizes the differential targeting of recently synthesized immediate early gene (IEG) mRNAs to neuronal cell bodies versus dendrites and tests the hypothesis that this targeting is based on signals in the encoded proteins. A single electroconvulsive seizure induces the expression of a number of IEG mRNAs in granule cells of the dentate gyrus. Most of these IEG mRNAs remain in the cell body, including two that are characterized in the present study (the mRNAs for NGFI-A and COX-2). In contrast, the mRNA for Arcmoved rapidly into dendrites at an apparent rate of ∼300 μm/hr. Inhibiting protein synthesis with cycloheximide did not disrupt the differential mRNA sorting, demonstrating that the differential targeting of mRNAs is not dependent on translation.
Immunocytochemical demonstration of alpha-tubulin modification during axonal maturation in the cerebellar cortex

Previous light microscopic immunocytochemical studies using two monoclonal antibodies that recognise alpha-tubulin (YOL/34 and YL1/2) but differ in their isotypic specificity have shown that the unmyelinated parallel fiber axons in the cerebellar cortex are labeled with only one of the antibodies (YOL/34). We now show that at 10 d postnatally the parallel fibers are labeled with both antibodies, and that during development YL1/2 (but not YOL/34) immunoreactivity disappears progressively from parallel fibers in the lower regions of the molecular layer upwards towards the external germinal layer. By approximately 28 d postnatally, the differential staining pattern of parallel fibers by the antibodies is established throughout the molecular layer. The time course, light microscopic, and ultrastructural staining distribution corresponds to a progressive change in alpha-tubulin immunoreactivity as the parallel fibers form synaptic contacts. This modification of alpha-tubulin (which was not observed in Purkinje cell dendrites or Bergmann glia) may be related to the formation of a basic isotype of alpha-tubulin within parallel fiber axons at maturation.
Intended use of informal long‐term care: the role of race and ethnicity

Objective. To examine the role of race/ethnicity in the use of informal long‐term care among African American and white elders, using an expanded Andersen model of health services use (Bradley et al., Health Services Research, vol. 37, pp. 1221–1242, 2002). Design. Four hundred respondents (n = 200 African American; n=200 white) aged 65 and older, who had been hospitalized within the last year. Data were collected using a cross‐sectional survey analyzed with ordered logistic regression. Independent variables included individuals' predisposing factors, enabling factors, need, and psychosocial factors. Intended use of informal long‐term care was defined based on responses to a hypothetical scenario of future use of unpaid services by family members, relatives, friends, or neighbors for help with daily needs. Results. African American respondents were more likely than white respondents to intend to use informal long‐term care. This effect persisted (p < 0.05) after controlling for predisposing, enabling, and need factors. However, race/ethnicity‐related differences in intended use were attenuated substantially (14–18%) after controlling for psychosocial differences. Further, in the fully adjusted models, race/ethnicity was no longer significantly associated with intended long‐term care use. Conclusions. Psychosocial factors, particularly social norms concerning family caregiving, mediated the relationship between race/ethnicity and intended use of informal long‐term care. A fuller appreciation of the multiple influences on healthcare decision making of older adults has the potential to inform policy efforts to appropriately meet the respective long‐term care needs of an ethnically diverse frail older population.
Occurrence of Serotonin Immunoreactivity in the Central Nervous System and Midgut of Adult Female Tabanus nigrovittatus (Diptera: Tabanidae)

Abstract Serotonin is an important neuromessenger used in a variety of signaling pathways throughout the animal kingdom. In insects, serotonin has been demonstrated to mediate feeding and feeding-related behaviors. In this study, serotonin antibody was localized in cells and processes throughout the central nervous system (CNS) and midgut of female horse fly Tabanus nigrovittatus Macquart. In the CNS, immunoreactivity was localized in cells and processes throughout the brain and ventral nerve cord. In the midgut, a fine network of immunoreactive processes was observed running along the outer surface of the midgut, with a decrease in innervation toward the posterior region of the midgut.
Frequent and specific immunity to the embryonal stem cell–associated antigen SOX2 in patients with monoclonal gammopathy

Specific targets of cellular immunity in human premalignancy are largely unknown. Monoclonal gammopathy of undetermined significance (MGUS) represents a precursor lesion to myeloma (MM). We show that antigenic targets of spontaneous immunity in MGUS differ from MM. MGUS patients frequently mount a humoral and cellular immune response against SOX2, a gene critical for self-renewal in embryonal stem cells. Intranuclear expression of SOX2 marks the clonogenic CD138− compartment in MGUS. SOX2 expression is also detected in a proportion of CD138+ cells in MM patients. However, these patients lack anti-SOX2 immunity. Cellular immunity to SOX2 inhibits the clonogenic growth of MGUS cells in vitro. Detection of anti-SOX2 T cells predicts favorable clinical outcome in patients with asymptomatic plasmaproliferative disorders. Harnessing immunity to antigens expressed by tumor progenitor cells may be critical for prevention and therapy of human cancer.
Migratory and adhesive properties of Xenopus laevis primordial germ cells in vitro

Summary The directional migration of primordial germ cells (PGCs) to the site of gonad formation is an advantageous model system to study cell motility. The embryonic development of PGCs has been investigated in different animal species, including mice, zebrafish, Xenopus and Drosophila. In this study we focus on the physical properties of Xenopus laevis PGCs during their transition from the passive to the active migratory state. Pre-migratory PGCs from Xenopus laevis embryos at developmental stages 17–19 to be compared with migratory PGCs from stages 28–30 were isolated and characterized in respect to motility and adhesive properties. Using single-cell force spectroscopy, we observed a decline in adhesiveness of PGCs upon reaching the migratory state, as defined by decreased attachment to extracellular matrix components like fibronectin, and a reduced adhesion to somatic endodermal cells. Data obtained from qPCR analysis with isolated PGCs reveal that down-regulation of E-cadherin might contribute to this weakening of cell-cell adhesion. Interestingly, however, using an in vitro migration assay, we found that movement of X. laevis PGCs can also occur independently of specific interactions with their neighboring cells. The reduction of cellular adhesion during PGC development is accompanied by enhanced cellular motility, as reflected in increased formation of bleb-like protrusions and inferred from electric cell-substrate impedance sensing (ECIS) as well as time-lapse image analysis. Temporal alterations in cell shape, including contraction and expansion of the cellular body, reveal a higher degree of cellular dynamics for the migratory PGCs in vitro.
Diminished Perisomatic GABAergic Terminals on Cortical Neurons Adjacent to Amyloid Plaques

One of the main pathological hallmarks of Alzheimer's disease (AD) is the accumulation of plaques in the cerebral cortex, which may appear either in the neuropil or in direct association with neuronal somata. Since different axonal systems innervate the dendritic (mostly glutamatergic) and perisomatic (mostly GABAergic) regions of neurons, the accumulation of plaques in the neuropil or associated with the soma might produce different alterations to synaptic circuits. We have used a variety of conventional light, confocal and electron microscopy techniques to study their relationship with neuronal somata in the cerebral cortex from AD patients and APP/PS1 transgenic mice. The main finding was that the membrane surfaces of neurons (mainly pyramidal cells) in contact with plaques lack GABAergic perisomatic synapses. Since these perisomatic synapses are thought to exert a strong influence on the output of pyramidal cells, their loss may lead to the hyperactivity of the neurons in contact with plaques. These results suggest that plaques modify circuits in a more selective manner than previously thought.
Bioactive Materials for Regenerative Medicine: Zeolite‐Hydroxyapatite Bone Mimetic Coatings

We report the synthesis and characterization of a novel zeolite‐hydroxyapatite composite coating on titanium alloys and stainless steel. The zeolite‐hydroxyapatite coating is superhydrophilic and outperforms the state‐of‐the‐art Ti6Al4V alloys in corrosion resistance tests in aggressive pitting NaCl media, phosphate buffer solution with BSA protein, as well as highly complex DMEM cell culture media. And the composite coating also eliminates the elastic modulus mismatch between coating and bone. In addition, the composite coating has an osteoconductive and osteoinductive effect on hFOBs, indicating that it may enhance osteointegration of implants and speed up post‐surgical recovery, and thus reduce the need for recurring implant replacement surgeries. Replacing titanium with zeolite‐hydroxyapatite coated steel can also significantly reduce implant cost while improving implant lifespan.