Miracle-dz/UniFAR-FTUs huggingface dataset:
Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the Fossil Record

Abstract We assembled a dataset of 192 carefully selected species—51 extinct and 141 extant—and 976 apomorphies distributed among 610 phenotypic characters to investigate the phylogeny of Squamata (“lizards,” including snakes and amphisbaenians). These data enabled us to infer a tree much like those derived from previous morphological analyses, but with better support for some key clades. There are also several novel elements, some of which pose striking departures from traditional ideas about lizard evolution (e.g., that mosasaurs and polyglyphanodontians are on the scleroglossan stem, rather than parts of the crown, and related to varanoids and teiids, respectively). Long-bodied, limb-reduced, “snake-like” fossorial lizards—most notably dibamids, amphisbaenians and snakes—have been and continue to be the chief source of character conflict in squamate morphological phylogenetics. Carnivorous lizards (especially snakes, mosasaurs and varanoids) have proven a close second. Genetic data, presumably less burdened by the potential for adaptive convergence related to fossoriality, were expected to resolve these conflicts. Although recent gene phylogenies seem to do so, they also differ radically from any phylogeny based on the phenotype, especially for the most ancient crown squamate divergences that occured during the latter half of the Mesozoic. Our study relied on traditionally prepared specimens as well as high-resolution computed tomography scans that afforded unprecendented access to the cranial anatomy of Squamata. This, along with the inclusion of stem fossils, provided an unparalleled sample of the phenotype enabling us to more fully explore the extreme incongruences between molecular and morphological topologies for the squamate tree of life. Despite this extensive new database, we were unable to find morphological support for the major rearrangement of the deep divergences in Squamata proposed by recent molecular studies. Instead, our data strongly support the same fundamental topology suggested by most previous morphological studies—an Iguania-Scleroglossa basal split, a sister-group relationship between Gekkota and Autarchoglossa, and the divergence between Anguimorpha and Scincomorpha—and documents the extreme degree of morphological homoplasy required by those molecular topologies.
Survivability, Growth and Body Measurements of Awassi and Tahirova×Awassi (F1) Lambs

Abstract Kul, S. , Seker, I. and Yildirim, O. 2006. Survivability, growth and body measurements of Awassi and Tahirova×Awassi (F1) lambs. J. Appl. Anim. Res., 29: 121–124. This study was undertaken to compare the growth rate, survivability and some body measurements of Awassi and Tahirova (75% East Friesian and 25% Kivircik) x Awassi (F1 crossbred lambs. The mean body weight of Awassi and crossbred lambs were 4.06 and 4.57 kg at birth, and 14.56 and 19.17 kg (P<0.05) at weaning, respectively. The average survivability until weaning were 90.00% and 78.95% (P<0.01), respectively. The body length of Awassi and crossbred lambs were 64.11 and 66.17 cm; withers height 63.67 and 59.67 cm, pelvic width 23.11 and 25.83 cm (P<0.05), chest circumference 97.89 and 82.00 cm (P<0.01), leg height 34.00 and 31.17 cm (P<0.01), respectively. It may be concluded that Tahirova x Awassi (F1) lambs had higher body weight but lower survivability especially during weaning period as compared to Awassi lambs.
Risk of dementia in Parkinson’s disease: A community-based, prospective study

ObjectiveTo calculate the incidence of and determine possible risk factors for dementia in PD. BackgroundDementia has important clinical consequences for patients with PD and their caregivers, but the incidence is unknown. MethodsA population-based cohort of nondemented patients with PD (n = 171) from the county of Rogaland, Norway, was assessed at baseline and 4.2 years later with a comprehensive evaluation of motor, cognitive, and neuropsychiatric symptoms. The diagnosis of dementia was made according to the Diagnostic and Statistical Manual of Mental Disorders, 3rd edition, revised (DSM-III-R) criteria, based on interview of the patient and a caregiver, cognitive rating scales, and neuropsychologic tests. A representative sample of 3,062 nondemented elderly subjects without PD served as control group. ResultsForty-three patients with PD were demented at follow-up evaluation, equivalent to an incidence rate of 95.3 per 1,000 person-years (95% CI, 68.2 to 122.0). The risk for the development of dementia in patients with PD relative to the control subjects after adjusting for age, sex, and education was 5.9 (95% CI, 3.9 to 9.1). Predictive factors at baseline for dementia in PD in addition to age were Hoehn & Yahr score >2 (OR, 3.4; 95% CI, 1.3 to 8.6) and Mini-Mental State Examination score <29 (OR, 3.3; 95% CI, 1.3 to 8.2). ConclusionsPatients with PD have an almost sixfold increased risk for becoming demented compared with subjects without PD.
Visual field constriction: Accumulation of vigabatrin but not tiagabine in the retina

BackgroundThe antiepileptic drug (AED) vigabatrin (VGB) causes concentric visual field constriction. Anecdotal reports involving tiagabine (TGB) have implied that this may be a class effect of all AEDs with &ggr;-aminobutyric acid (GABA)–related actions. We investigated the pharmacokinetic and pharmacodynamic profiles of VGB and TGB in rat brain and eye. MethodsAdult male rats (n = 8) were administered 0.9% saline (control), VGB (500 or 1,000 mg/kg), or TGB (5, 10, or 20 mg/kg). At 1 (TGB) and 4 hours (VGB) postdosing, the animals were killed, a blood sample was obtained, their brains were dissected into five anatomic regions, and the retina and vitreous humor were isolated from each eye. Samples were analyzed for GABA concentrations and the activity of the enzyme GABA-transaminase (GABA-T). Plasma and tissue drug concentrations were also determined. ResultsVGB treatment produced a decrease in the activity of GABA-T and a rise in GABA concentrations in all tissues investigated. This effect was most pronounced in the retina. VGB concentrations were as much as fivefold higher in the retina than in the brain. TGB was without effect on GABA concentrations and activity of GABA-T. TGB concentrations were notably lower in the retina than in the brain. ConclusionsAccumulation of VGB in the retina, with or without an increase in GABA, may be responsible for the visual field constriction reported clinically. In contrast, TGB had no effect on GABA concentrations and did not accumulate in the retina. These results suggest that TGB is unlikely to cause visual field defects in humans.
Directing gene expression to cerebellar granule cells using γ-aminobutyric acid type A receptor α6 subunit transgenes

Expression of the γ-aminobutyric acid type A receptor α6 subunit gene is restricted to differentiated granule cells of the cerebellum and cochlear nucleus. The mechanisms underlying this limited expression are unknown. Here we have characterized the expression of a series of α6-based transgenes in adult mouse brain. A DNA fragment containing a 1-kb portion upstream of the start site(s), together with exons 1–8, can direct high-level cerebellar granule cell-specific reporter gene expression. Thus powerful granule cell-specific determinants reside within the 5′ half of the α6 subunit gene body. This intron-containing transgene appears to lack the cochlear nucleus regulatory elements. It therefore provides a cassette to deliver gene products solely to adult cerebellar granule cells.
Effect of nitrate and ammonium nutrition on the metabolism of the ectomycorrhizal basidiomycete, Hebeloma cylindrosporum Romagn

SUMMARY Hebeloma cylindrosporum Romagn. grown on a nitrate medium exhibits a growth rate ten times greater than that on an ammonium medium lacking organic acids. Nitrate reduction is accompanied by a low rate of synthesis of organic anions and an elevated excretion of OH− ions into the external medium. The addition of a Krebs cycle organic acid, e.g., malate, citrate, succinate or pyruvate to the ammonium medium induces a strong increase in the growth of the thalli which then equals that obtained on a nitrate medium. The absorption of such precursors to 2-oxoglutarate could permit the recharging of the Krebs cycle, otherwise inhibited because the assimilation of ammonium causes an important re-routing of 2-oxoglutarate. In these thalli, the soluble nitrogen content shows a clear reduction compared with the thalli cultured on ammonium medium lacking organic acids. The poor growth observed on an ammonium medium may be due in part to insufficient CO2 fixation by anaplerotic reactions which, in Hebeloma cylindrosporum Romagn. , is carried out by phosphoenolpyruvate carboxykinase.
Alpha-1 Antitrypsin: Its Role in Health and Disease

Alpha-1 Antitrypsin (AAT) is a 52 kDa glycoprotein that is principally synthesized by the liver. It is the archetype of the serine protease inhibitor (Serpin) superfamily of proteins, which has a major role in inactivating neutrophil elastase and other proteases to retain protease – antiprotease equilibrium. AAT deficiency is a rare monogenic disorder characterized by low levels of AAT in serum and the lungs and it is well known to be associated with emphysema and liver disease. Inadequate knowledge of AAT deficiency might be due to under-recognition of this protein. To date, the exact role of AAT deficiency in various diseases has not been extensively elucidated. In this review, the current knowledge regarding the role AAT in various disorders will be discussed.
UKnowledge UKnowledge

Cellular mechanisms that achieve protein diversity in eukaryotes are multifaceted, including transcriptional components such as RNA splicing. Through alternative splicing, a single protein-coding gene can generate multiple mRNA transcripts and protein isoforms, some of which are tissue-specific. We have conducted qualitative and quantitative analyses of the Bodymap 2.0 messenger RNA-sequencing data from 16 human tissue samples and identified 209,363 splice junctions. Of these, 22,231 (10.6%) were not previously annotated and 21,650 (10.3%) were expressed in a tissue-restricted pattern. Tissue-restricted alternative splicing was found to be widespread, with approximately 65% of expressed multi-exon genes containing at least one tissue-specific splice junction. Interestingly, we observed many tissue-specific splice junctions not only in genes expressed in one or a few tissues, but also from gene loci with a broad pattern of expression.
Oscillating reproductive strategies of herring in the western Atlantic in response to changing environmental conditions

Melvin, G. D. , Stephenson, R. L. , and Power, M. J. 2009. Oscillating reproductive strategies of herring in the western Atlantic in response to changing environmental conditions. - ICES Journal of Marine Science, 66: 1784-1792.Herring are broadly distributed in the western Atlantic, but reproductive activity is restricted to the central portion, from Cape Cod to northern Newfoundland. Spawning extends from early spring to late autumn. Two spawning types are recognized: spring spawners and autumn spawners. At the southern extreme, spawning occurs almost exclusively in autumn, whereas in the north, spring spawners prevail. Mid-range, both strategies are common, with spawning occurring throughout the entire season. We postulate that the temporal intra-stock dominance of spawning type is an adaptive reproductive strategy to changing environmental conditions. A conceptual model is presented to describe how reproductive success can oscillate between spawning strategies. In most years, environmental conditions appear to favour one type or the other, although strong year classes can co-occur when conditions are right. The recent change in environmental conditions, characterized by a general warming trend, favours autumn spawners and is consistent with our model. At the distributional extremes, stocks are restricted to a single spawning strategy, and broad-scale environmental changes can introduce large interannual variability and limit the reproductive and recovery potential of a stock. The dependence of a stock on a single spawning season may result in longer times to recover to target levels.
Towards a real-time demand response framework for smart communities using clustering techniques

type. These characteristics are then used to distinguish the clusters that would be most likely to aid with the DR schemes would ﬁt each cluster. Finally, we conceptualize a DR system that combines forecasting, clustering and a price-based demand projection engine to produce daily individualized DR recommendations and pricing policies for prosumers participating in the program. The results of this study can be useful for network operators and utilities that aim to develop targeted DR programs for groups of prosumers within ﬂexible energy communities
Low blood selenium: A probable factor in essential hypertension

The possible association between selenium and essential hypertension was investigated in this study. Blood selenium (BSe) and plasma glutathione peroxidase (plGSH-Px) activity were measured as biochemical markers of selenium status of 103 hypertensive patients (44 males and 59 females) and 88 apparently healthy subjects (40 males and 48 females). The hypertensive patients were classified into three groups based on the severity of the disease namely: mild (Group 1), moderate (Group 2) and severe (Group 3). The healthy and the hypertensive subjects were recruited from Abeokuta and Ibadan (South-Western Nigeria). The mean age of the hypertensive patients was 41.9 ± 10.3 (range 21 – 68) years, while the mean age of the healthy subjects was 37.8 ± 8.6 (range 18 – 52) years. The weight, height, blood pressure and pulse rates of all subjects were measured and their body mass indices (BMI) computed. BSe was determined by atomic absorption spectrophotometry (AAS) while plGSH-Px activity was measured by spectrophotometric method. The mean BSe concentration was significantly lower in the hypertensive patients (0.136 ± 0.028 mg/L) than in the healthy group (0.188 ± 0.026 mg/L) (P differences in the BSe levels of Group 2 and Group 3 patients (P of the healthy group. This suggests that BSe may exist in another functional form, which plays a role in the pathogenesis or prognosis of the disease.
Peroxidase biocatalysis in water-soluble ionic liquids: activity, kinetic and thermal stability

Abstract The activity and stability of commercial peroxidase was investigated in the presence of five 1-alkyl-3-methylimidazolium-based ionic liquids (ILs) with either bromide or chloride anions: [Cxmim][X]. The peroxidase activity and stability were better for the shorter alkyl chain lengths of the ILs and peroxidase was more stable in the presence of the bromide anion, rather than chloride. The thermal inactivation profile was studied from 45 to 60 °C in [C4mim][Cl] and [C4mim][Br]. The activation energy was also determined. Kinetic analysis of the enzyme in the presence of the [C4mim][Br] or control (buffer solution) showed that the KM value increased 5-fold and Vm decreased 13-fold in the presence of the IL. The increase in KM indicates that this IL can reduce the binding affinity between substrate and enzyme.
Long-Term Trout Production Dynamics inValley Creek, Minnesota

Abstract Long-term studies in Valley Creek, Minnesota, continued from April 1965 to April 1986. Initially, the brook trout Salvelinus fontinalis was the only trout species present, but both rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta later entered the study section. Brook trout declined after severe floods, recovered, declined again after an extreme sedimentation, and continued to decline while brown trout increased. Brook trout biomass, initially at 184 kg/ha, decreased to 4 kg/ha at the end of the period, a reduction of 98%. Rainbow trout entered the study section when floods overflowed private ponds, but their population did not reach high levels. After its entrance, the brown trout increased to predominate the trout fauna with a final biomass of 201 kg/ha. At the end of the study period, brook trout biomass remained at 2% of all trout species, rainbow trout at 5%, and brown trout at 93%. Maximum annual production by brook trout, near the beginning of the 21-year period, was 171 kg/h.
HCV core antigen detection in seropositive samples

Detection of antibodies to HCV is typically the primary test utilized to identify HCV‐infected individuals. Seropositive individuals may then be tested for HCV RNA by nucleic acid testing (NAT) to determine if the individual is actively infected with HCV. In addition, NAT assays that are based on quantitation of HCV RNA copies/ml, are utilized to determine the effectiveness of antiviral therapy. Over the last several years, HCV core antigen tests have been developed that have shown utility both for the identifying active HCV infection and for monitoring antiviral therapy. Although these assays are relatively simple and rapid, the HCV core antigen tests have not been widely accepted mostly due to their lack of sensitivity. Recently developed assays have shown improved sensitivity, and may represent an alternative or adjunct to HCV NAT both for identifying active HCV infection and for monitoring antiviral therapy. J. Med. Virol. 79:S52–S53, 2007. © 2007 Wiley‐Liss, Inc.
Monoclonal antibodies against the FhuA (TonA) protein of the Escherichia coli outer membrane

Outer membranes of Escherichia coli K-12 were used to isolate hybridoma cell lines that produce monoclonal antibodies against the FhuA (TonA) protein. Two monoclonal antibodies were obtained from independent immunization and fusion experiments. The antibodies belonged to the subclass IgG1 and κ, and IgG2b and κ, respectively. The latter antibody was purified by affinity chromatography on protein A-Sepharose. The culture supernatants of the hybridoma cell lines and the isolated antibody inhibited adsorption of the phages T5 and T1 to E. coli cells while binding of phage o80, which also uses the FhuA protein as a receptor, remained unaffected. The specificity of the antibodies to the FhuA protein was supported by the prevention of killing of cells by colicin M and by the lack of inhibition of colicin B and of phage BG23. Transport of iron(III) as ferrichrome complex was not inhibited by the isolated antibody. However, partial competition with the adsorption of the phages T2, TuIb and T6 was observed which may indicate an organization of certain functional phage receptors into clusters.
Physiological, biochemical and molecular responses of the halophilic cyanobacterium Aphanothece halophytica to Pi-deficiency

We studied the responses of a halophilic cyanobacterium Aphanothece halophytica at surplus (normal composition of growth medium containing 125 µM PO43−), sufficient (the minimum concentration supporting optimal growth, 22 µM PO43−) and deficient (no external supply of Pi) concentrations of inorganic phosphate (Pi). The cyanobacterium was able to grow well in Pi-deficient conditions until the end of incubation (14 days), though at a marginally reduced rate. The cellular P-quota in Pi-surplus cells at the end of incubation was 2.7 times that of their initial P-quota (0.75 µmol mg protein−1), and remained fairly high (0.442 µmol mg protein−1) even in Pi-deficient medium. However, cultures growing in Pi-sufficient medium (22 µM PO43−), upon transfer to Pi-deficient medium, exhibited a rapid decline in cellular P level. Furthermore, cells growing in Pi-surplus medium showed a rapid efflux of P into the external medium. Aphanothece halophytica exhibited a biphasic phosphate transport system involving both high- (Ks 2.06 µM) and low-affinity (Ks 17.85 µM) transporters. Cyanobacterial cells maintained a basal level (constitutively expressed and not affected by Pi availability) of alkaline phosphatase (APase) activity, which increased 5–7-fold under Pi-deficiency. Supplementation of phosphate to the medium caused gradual decline in the enzyme activity to the basal level. Pi-deficient cells showed an enhanced level of transcripts for PPi-dependent glycolytic enzymes. Though moderate, Pi-deficiency affected the respiration, photosynthetic rate and electron transport chain activity negatively. PS II activity was most sensitive to Pi-deficiency, followed by PSI and whole chain. Pi-replete A. halophytica cells showed a single high-affinity nitrate transport system. However, deficiency of Pi reduced the nitrate and nitrite reductase activities.
Biology of Rock Crab (Cancer irroratus) in Northumberland Strait

Divers hand-collected 342 rock crabs (Cancer irroratus) ranging from 4.2 mm carapace width to 97 mm (females) and 127 mm (males). The sex ratio (1.37:1) was biased in favour of males. Of 2929 crabs taken in commercial lobster fishing gear, 92% were above the minimum commercial size of 89 mm, and of these 99.1% were male. Smallest size at maturity was 60 mm for females and 69 mm for males. Breeding occurred in late summer and fall. Larvae were present in surface waters from June to September. Prey of crabs > 25 mm consisted principally of polychaetes, mussels, starfish, and sea urchins. Crabs less than about 65 mm inhabit rocky areas; larger crabs move out onto sand and mud. The fishable population is probably not in significant competition with lobsters for food or space.
Factors influencing spatial patterns of molluscs in a eutrophic tropical bay

Samples were collected from 10 stations distributed through three sectors in Guanabara Bay during two consecutive years, in order to determine factors that influence the spatial pattern of molluscs and to describe the structure and composition of this community in a eutrophic estuarine system on the Brazilian coast. Although only one species, the gastropod Heleobia australis, comprised 77% of mollusc abundance, 59 species were identified in the bay. In addition to H. australis, three other species were dominant: the gastropod Anachis isabellei and the bivalves Americuna besnardi and Ervilia concentrica. The mollusc communities were significantly influenced by the spatial gradient; the outermost sector has marine conditions, and the other sectors are typically estuarine, leading to differences in the composition and abundance of molluscs. The outermost sector showed the highest diversity, which gradually decreased towards the innermost sector where the dominance of a few opportunistic species is favoured by highly organic mud sediments. Sediment type was strongly correlated with mollusc occurrence in the bay. Guanabara Bay showed two indicator species: the bivalve E. concentrica of the outer sector, and the gastropod H. australis of the intermediate sector. Our results suggest that benthic molluscs in Guanabara Bay show characteristics related to levels of environmental impact. A monitoring programme based on this community is needed to evaluate the effects of human impacts on this community and to monitor changes in its biodiversity in Guanabara Bay.