Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Salinity on Bacterioplankton Communities from the Brazilian Rain Forest to the Coastal Atlantic Ocean

Background Planktonic bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems, however, the taxa that make up these communities are poorly known. The aim of this study was to investigate bacterial communities in aquatic ecosystems at Ilha Grande, Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic rain forest and how they correlate with a salinity gradient going from terrestrial aquatic habitats to the coastal Atlantic Ocean. Methodology/Principal Findings We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore) and three freshwater (water spring, river, and mangrove) environments. A total of 836 sequences were analyzed by MOTHUR, yielding 269 freshwater and 219 marine operational taxonomic units (OTUs) grouped at 97% stringency. Richness and diversity indexes indicated that freshwater environments were the most diverse, especially the water spring. The main bacterial group in freshwater environments was Betaproteobacteria (43.5%), whereas Cyanobacteria (30.5%), Alphaproteobacteria (25.5%), and Gammaproteobacteria (26.3%) dominated the marine ones. Venn diagram showed no overlap between marine and freshwater OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed marked differences between the freshwater and marine libraries suggesting the importance of salinity as a driver of community composition in this habitat. The phylogenetic analysis of marine and freshwater libraries showed that the differences in community composition are consistent. Conclusions/Significance Our data supports the notion that a divergent evolutionary scenario is driving community composition in the studied habitats. This work also improves the comprehension of microbial community dynamics in tropical waters and how they are structured in relation to physicochemical parameters. Furthermore, this paper reveals for the first time the pristine bacterioplankton communities in a tropical island at the South Atlantic Ocean.
Romantic love: An fMRI study of a neural mechanism for mate choice

Scientists have described myriad traits in mammalian and avian species that evolved to attract mates. But the brain mechanisms by which conspecifics become attracted to these traits is largely unknown. Yet mammals and birds express mate preferences and make mate choices, and data suggest that this “attraction system” is associated with the dopaminergic reward system. It has been proposed that intense romantic love, a cross‐cultural universal, is a developed form of this attraction system. To determine the neural mechanisms associated with romantic love we used functional magnetic resonance imaging (fMRI) and studied 17 people who were intensely “in love” (Aron et al. [2005] J Neurophysiol 94:327–337). Activation specific to the beloved occurred in the right ventral tegmental area and right caudate nucleus, dopamine‐rich areas associated with mammalian reward and motivation. These and other results suggest that dopaminergic reward pathways contribute to the “general arousal” component of romantic love; romantic love is primarily a motivation system, rather than an emotion; this drive is distinct from the sex drive; romantic love changes across time; and romantic love shares biobehavioral similarities with mammalian attraction. We propose that this attraction mechanism evolved to enable individuals to focus their mating energy on specific others, thereby conserving energy and facilitating mate choice—a primary aspect of reproduction. Last, the corticostriate system, with its potential for combining diverse cortical information with reward signals, is an excellent anatomical substrate for the complex factors contributing to romantic love and mate choice. J. Comp. Neurol. 493:58–62, 2005. © 2005 Wiley‐Liss, Inc.
Graph-based sinogram denoising for tomographic reconstructions

Limited data and low-dose constraints are common problems in a variety of tomographic reconstruction paradigms, leading to noisy and incomplete data. Over the past few years, sinogram denoising has become an essential preprocessing step for low-dose Computed Tomographic (CT) reconstructions. We propose a novel sinogram denoising algorithm inspired by signal processing on graphs. Graph-based methods often perform better than standard filtering operations since they can exploit the signal structure. This makes the sinogram an ideal candidate for graph based denoising since it generally has a piecewise smooth structure. We test our method with a variety of phantoms using different reconstruction methods. Our numerical study shows that the proposed algorithm improves the performance of analytical filtered back-projection (FBP) and iterative methods such as ART (Kaczmarz), and SIRT (Cimmino). We observed that graph denoised sinograms always minimize the error measure and improve the accuracy of the solution, compared to regular reconstructions.
Superconductivity in room-temperature stable electride and high-pressure phases of alkali metals

S-band metals such as alkali and alkaline earth metals do not undergo a superconducting transition (SCT) at ambient pressure, but their high-pressure phases do. By contrast, room-temperature stable electride [Ca24Al28O64]4+⋅4e− (C12A7:e−) in which anionic electrons in the crystallographic sub-nanometer-size cages have high s-character exhibits SCT at 0.2–0.4 K at ambient pressure. In this paper, we report that crystal and electronic structures of C12A7:e− are close to those of the high-pressure superconducting phase of alkali and alkaline earth metals and the SCT of both materials is induced when electron nature at Fermi energy (EF) switches from s- to sd-hybridized state.
Diaphragm pacing improves sleep in patients with amyotrophic lateral sclerosis

Abstract In amyotrophic lateral sclerosis (ALS) patients, respiratory insufficiency is a major burden. Diaphragm conditioning by electrical stimulation could interfere with lung function decline by promoting the development of type 1 muscle fibres. We describe an ancillary study to a prospective, non-randomized trial (NCT00420719) assessing the effects of diaphragm pacing on forced vital capacity (FVC). Sleep-related disturbances being early clues to diaphragmatic dysfunction, we postulated that they would provide a sensitive marker. Stimulators were implanted laparoscopically in the diaphragm close to the phrenic motor point in 18 ALS patients for daily conditioning. ALS functioning score (ALSFRS), FVC, sniff nasal inspiratory pressure (SNIP), and polysomnographic recordings (PSG, performed with the stimulator turned off) were assessed before implantation and after four months of conditioning (n = 14). Sleep efficiency improved (69 ± 15% to 75 ± 11%, p = 0.0394) with fewer arousals and micro-arousals. This occurred against a background of deterioration as ALSFRS-R, FVC, and SNIP declined. There was, however, no change in NIV status or the ALSFRS respiratory subscore, and the FVC decline was mostly due to impaired expiration. Supporting a better diaphragm function, apnoeas and hypopnoeas during REM sleep decreased. In conclusion, in these severe patients not expected to experience spontaneous improvements, diaphragm conditioning improved sleep and there were hints at diaphragm function changes.
Effect of Hyperhomocysteinemia on Plasma or Tissue Adenosine Levels and Renal Function

Background—Hyperhomocysteinemia (hHcys) is considered an independent risk factor of cardiovascular diseases. Recent studies in our laboratory have shown that hHcys produced glomerular dysfunction and sclerosis independently of hypertension. However, the mechanism mediating these pathogenic effects of homocysteine (Hcys) is poorly understood. Because Hcys and adenosine (Ado) are simultaneously produced via hydrolysis of S-adenosylhomocysteine (SAH), we hypothesized that hHcys may produce its pathogenic effects by decrease in plasma or tissue Ado concentrations. Methods and Results—l-Hcys (1.5 &mgr;mol/min per kilogram) was infused intravenously for 60 minutes to produce acute hHcys in Sprague-Dawley rats. Plasma Hcys levels increased from 6.7±0.4 to 14.7±0.5 &mgr;mol/L, but Ado decreased from 141.7±15.1 to 52.4±6.8 nmol/L in these rats with acute hHcys. This hHcys-induced reduction of Ado was also observed in the kidney dialysate. In rats with chronic hHcys, plasma Ado levels were also significantly decreased. By kinetic analysis of the enzyme activities, decrease in renal Ado levels in hHcys was shown to be associated with inhibition of SAH hydrolase but not 5′-nucleotidase. Functionally, intravenous infusion of Hcys was found to decrease renal blood flow, glomerular filtration rate, and sodium and water excretion, which could be blocked by the Ado receptor antagonist 8-SPT. Conclusions—These results strongly suggest that hHcys decreases plasma and tissue Ado concentrations associated with inhibition of SAH hydrolase. Decrease in plasma and tissue Ado may be an important mechanism mediating the pathogenic effects of Hcys.
Abscisic Acid Flux Alterations Result in Differential Abscisic Acid Signaling Responses and Impact Assimilation Efficiency in Barley under Terminal Drought Stress1[C][W][OPEN]

ABA homeostasis achieved in the tolerant lines is closely coupled to readjustment in ABA receptors, which enables this line to maintain a favorable WUE and photoassimilate accumulation when challenged by terminal drought. Abscisic acid (ABA) is a central player in plant responses to drought stress. How variable levels of ABA under short-term versus long-term drought stress impact assimilation and growth in crops is unclear. We addressed this through comparative analysis, using two elite breeding lines of barley (Hordeum vulgare) that show senescence or stay-green phenotype under terminal drought stress and by making use of transgenic barley lines that express Arabidopsis (Arabidopsis thaliana) 9-cis-epoxycarotenoid dioxygenase (AtNCED6) coding sequence or an RNA interference (RNAi) sequence of ABA 8′-hydroxylase under the control of a drought-inducible barley promoter. The high levels of ABA and its catabolites in the senescing breeding line under long-term stress were detrimental for assimilate productivity, whereas these levels were not perturbed in the stay-green type that performed better. In transgenic barley, drought-inducible AtNCED expression afforded temporal control in ABA levels such that the ABA levels rose sooner than in wild-type plants but also subsided, unlike as in the wild type , to near-basal levels upon prolonged stress treatment due to down-regulation of endogenous HvNCED genes. Suppressing of ABA catabolism with the RNA interference approach of ABA 8′-hydroxylase caused ABA flux during the entire period of stress. These transgenic plants performed better than the wild type under stress to maintain a favorable instantaneous water use efficiency and better assimilation. Gene expression analysis, protein structural modeling, and protein-protein interaction analyses of the members of the PYRABACTIN RESISTANCE1/PYRABACTIN RESISTANCE1-LIKE/REGULATORY COMPONENT OF ABA RECEPTORS, TYPE 2C PROTEIN PHOSPHATASE Sucrose non-fermenting1-related protein kinase2, and ABA-INSENSITIVE5/ABA-responsive element binding factor family identified specific members that could potentially impact ABA metabolism and stress adaptation in barley.
Synthesis of murine leukemia virus proteins differentiating Friend erythroleukemia cells.

In agreement with previous observations, the Friend 745 line of virus-induced erythroleukemia cells can be induced by dimethyl sulfoxide to synthesize hemoglobin and to increase simultaneously their content of morphologically recognizable virus particles, especially in cytoplasmic vesicles. In apparent contrast to the electron microscopic results, the cellular content of the major murine leukemia virus (MuLV) proteins p30 (the major internal core protein) and gp70 (the envelope glycoprotein) were measured by radioimmunoassay and were found to be approximately the same in control and in induced cells. Control and induced cells are also approximately as active in the synthesis of the protein precursors of p30, reverse transcriptase, and gp70 in the processing of these precursors by proteolysis and glycosylation. Furthermore, the noninfectious MuLV synthesized by this cell line is released into the culture medium to the same extent by control and induced cells. Although some of the virions formed in induced Friend 745 cells bud into cytoplasmic vesicles that are absent from control cells, this intravesicular budding is not associated with a major increase in the synthesis, processing, or cellular content of virion proteins. MuLV synthesis by Friend 745 cells was compared with that of Ostertag-derived F46/K erythroleukemia cells that produce infectious virus. The synthesis and processing of MuLV-specific proteins were very similar in these independently isolated cell lines, despite the major difference in infectivity of the virus produced.
Putting concepts to work: Some thoughts for the twentyfirst century. Author's reply

Fodor's theory makes thinking prior to doing. It allows for an inactive agent or pure reflector, and for agents whose actions in various ways seem to float free of their own conceptual repertoires. We show that naturally evolved creatures are not like that. In the real world, thinking is always and everywhere about doing. The point of having a brain is to guide the actions of embodied beings in a complex material world. Some of those actions are, to be sure, more recondite-than others. But in every case the contents of thoughts still look to depend, in some non-unique but vitally important way, on the kinds of doings they support.
Oil Characterization and Lipids Class Composition of Pomegranate Seeds

This study aims to investigate the physicochemical characteristics, phenolics content, and oil composition of pomegranate oil seeds (PSO). Quality indices, pigments, phenolics content, and antioxidant activity were determined. PSO was fractioned into polar lipids: glycolipids (GL) and phospholipids (PL). Sterols profile and fatty acids composition of total lipids (TL), GL, and PL were determined by GC/FID. The free acidity, the peroxide value, and the specific extinction coefficients were, respectively, 1.69%, 3.42 in milliequivalents of active oxygen per kilogram of oil, 4.15, and 3.95. PSO is rich in phenols (93.42 mg/Kg) but poor in pigments. The sterols markers were β-sitosterol (77.94%), Δ5-avenasterol (7.45%), and campesterol (6.35%). Oil content was 12.2%, wherein 23.9% were GL and 24.35% were PL. TL were rich in unsaturated fatty acids (63.17%), while saturated fatty acids were more present in PL and GL (71.97% and 66.29%, resp.). Conjugated fatty acids were about 13.30%, 2.03%, and 4.91%, respectively, in TL, PL, and GL. The cis/trans ratio of TL, PL, and GL was, respectively, 49.82%, 42.91%, and 27.39%. Monounsaturated fatty acids were more bound in PL, whereas polyunsaturated fatty acids were more bound in GL. PSO is a good source of essential fatty acids, phenolics compounds, phytosterols, and lipid-soluble fractions.
The Type I Collagen Fragments ICTP and CTX Reveal Distinct Enzymatic Pathways of Bone Collagen Degradation

Bone resorption may generate collagen fragments such as ICTP and CTX, which can be quantified in serum and/or urine by using specific immunoassays, and which are used as clinical markers. However, the relative abundance of ICTP and CTX varies according to the type of bone pathology, suggesting that these two fragments are generated through distinct collagenolytic pathways. In this study, we analyzed the release of ICTP and CTX from bone collagen by the proteinases reported to play a role in the solubilization of bone matrix. Cathepsin K released large amounts of CTX, but did not allow a detectable release of ICTP. Conversely, the matrix metalloproteinases (MMPs) MMP‐2, ‐9, ‐13, or ‐14 released ICTP, but did not allow a detectable release of CTX. Next we analyzed the release of ICTP and CTX from bone explants cultured in the presence of well‐established inhibitors of these proteinases and of matrix solubilization. An inhibitor of cysteine proteinases including cathepsin K, inhibited the release of CTX, but not the release of ICTP. MMP inhibitors inhibited the release of ICTP, but also that of CTX, in agreement with the putative role of MMPs in the initiation of bone resorption in addition to matrix solubilization. Similarly the treatment of mice bearing bone metastasis with an MMP inhibitor led to a significant reduction of serum ICTP and CTX, and osteolytic lesions. We conclude that the generation of ICTP and CTX depends on different collagenolytic pathways. This finding may explain why these two markers may discriminate between different bone pathologies.
Youth offending : resilience and protective factors

The assessment and rehabilitation of young offenders is an important area within forensic Psychology, however knowledge regarding resilience and youth offending is deficient as outlined in Chapter One. Chapter Two is a systematic review of the literature examining the relevance of protective factors in young people’s desistance from crime. A number of protective factors were found to significantly discriminate between re-offenders and desisters, and an interactive relationship between risk and protective factors received most support. In Chapter Three the strengths and limitations of a psychometric tool to assess personal resiliency are discussed. In Chapter Four this measure was used to examine whether resiliency differed between males who had nonsexually offended, sexually offended, and not offended. Differences in personal resiliency were found between and within these groups. Limitations and implications for practice and future research are discussed in Chapter Five. It is concluded that the inclusion of protective factors and personal resiliency, alongside risk factors, improves the prediction of offending behaviour. Furthermore, these positive factors appear to be instrumental to the rehabilitation of young offenders.
Neuro-motor deficits in six- to eight-year old learners with ADHD and DAMP

This study investigated the nature of coordination, visual-motor integration and neurological functioning in children diagnosed with ADHD and whether the likelihood of motor impairment will increase with the presence of co-occurring DCD (DAMP). Ninety-five learners (60 boys; 35 girls) with a mean age of 6.9 years participated in the study. Four groups were compared: An ADHD only group (n=42); a group of typically developing children (n=18); a medicated group (n=14); and a DAMP group (n=21). The MABC-2, QNST-2 and the VMI-4 were used to assess the groups. Descriptive statistics (StatSoft, 2012), two-way frequency tables and an ANOVA were used to analyse the results. ADHD learners using medication had significantly poorer fine motor skills (p<0.05) than those with only ADHD or typical children. ADHD children using medication and DAMP learners displayed comparable fine motor skills and hand control, although both groups had more impaired fine motor skills than those with only ADHD or typical children. Overall coordination and selected sensory and perceptual impairments increased as a function of co-occurring DCD, indicating that motor coordination does account for overall motor coordination and perceptual and sensory deficits seen in ADHD. These results further confirm a link between ADHD and fine motor problems. Key words : ADHD; DAMP; DCD; Neuro-motor control; Fine motor skills; Visual-motor integration.
Protection against Autoimmune Diabetes by Silkworm-Produced GFP-Tagged CTB-Insulin Fusion Protein

In animals, oral administration of the cholera toxin B (CTB) subunit conjugated to the autoantigen insulin enhances the specific immune-unresponsive state. This is called oral tolerance and is capable of suppressing autoimmune type 1 diabetes (T1D). However, the process by which the CTB-insulin (CTB-INS) protein works as a therapy for T1D in vivo remains unclear. Here, we successfully expressed a green fluorescent protein- (GFP-) tagged CTB-Ins (CTB-Ins-GFP) fusion protein in silkworms in a pentameric form that retained the native ability to activate the mechanism. Oral administration of the CTB-Ins-GFP protein induced special tolerance, delayed the development of diabetic symptoms, and suppressed T1D onset in nonobese diabetic (NOD) mice. Moreover, it increased the numbers of CD4+CD25+Foxp3+ T regulatory (Treg) cells in peripheral lymph tissues and affected the biological activity of spleen cells. This study demonstrated that the CTB-Ins-GFP protein produced in silkworms acted as an oral protein vaccine, inducing immunological tolerance involving CD4+CD25+Foxp3+ Treg cells in treating T1D.
Geographic scale matters in detecting the relationship between neighbourhood food environments and obesity risk: an analysis of driver license records in Salt Lake County, Utah

Objectives Empirical studies of the association between neighbourhood food environments and individual obesity risk have found mixed results. One possible cause of these mixed findings is the variation in neighbourhood geographic scale used. The purpose of this paper was to examine how various neighbourhood geographic scales affected the estimated relationship between food environments and obesity risk. Design Cross-sectional secondary data analysis. Setting Salt Lake County, Utah, USA. Participants 403 305 Salt Lake County adults 25–64 in the Utah driver license database between 1995 and 2008. Analysis Utah driver license data were geo-linked to 2000 US Census data and Dun & Bradstreet business data. Food outlets were classified into the categories of large grocery stores, convenience stores, limited-service restaurants and full-service restaurants, and measured at four neighbourhood geographic scales: Census block group, Census tract, ZIP code and a 1 km buffer around the resident's house. These measures were regressed on individual obesity status using multilevel random intercept regressions. Outcome Obesity. Results Food environment was important for obesity but the scale of the relevant neighbourhood differs for different type of outlets: large grocery stores were not significant at all four geographic scales, limited-service restaurants at the medium-to-large scale (Census tract or larger) and convenience stores and full-service restaurants at the smallest scale (Census tract or smaller). Conclusions The choice of neighbourhood geographic scale can affect the estimated significance of the association between neighbourhood food environments and individual obesity risk. However, variations in geographic scale alone do not explain the mixed findings in the literature. If researchers are constrained to use one geographic scale with multiple categories of food outlets, using Census tract or 1 km buffer as the neighbourhood geographic unit is likely to allow researchers to detect most significant relationships.