Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploiting protein structure data to explore the evolution of protein function and biological complexity

New directions in biology are being driven by the complete sequencing of genomes, which has given us the protein repertoires of diverse organisms from all kingdoms of life. In tandem with this accumulation of sequence data, worldwide structural genomics initiatives, advanced by the development of improved technologies in X-ray crystallography and NMR, are expanding our knowledge of structural families and increasing our fold libraries. Methods for detecting remote sequence similarities have also been made more sensitive and this means that we can map domains from these structural families onto genome sequences to understand how these families are distributed throughout the genomes and reveal how they might influence the functional repertoires and biological complexities of the organisms. We have used robust protocols to assign sequences from completed genomes to domain structures in the CATH database, allowing up to 60% of domain sequences in these genomes, depending on the organism, to be assigned to a domain family of known structure. Analysis of the distribution of these families throughout bacterial genomes identified more than 300 universal families, some of which had expanded significantly in proportion to genome size. These highly expanded families are primarily involved in metabolism and regulation and appear to make major contributions to the functional repertoire and complexity of bacterial organisms. When comparisons are made across all kingdoms of life, we find a smaller set of universal domain families (approx. 140), of which families involved in protein biosynthesis are the largest conserved component. Analysis of the behaviour of other families reveals that some (e.g. those involved in metabolism, regulation) have remained highly innovative during evolution, making it harder to trace their evolutionary ancestry. Structural analyses of metabolic families provide some insights into the mechanisms of functional innovation, which include changes in domain partnerships and significant structural embellishments leading to modulation of active sites and protein interactions.
Cryopreservation of semen from genetic resource chicken lines

The objective of the present study was to establish an effective semen freezing procedure to set up a cryobank for chicken breeds and genetic lines of special interest. The fowls used in the experiments originated from White Leghorn lines maintained as conservation flocks. In this study, different protocols were evaluated in terms of differences in the fertilization success. 1 A) Comparison of slow and fast freezing procedures using a cryoprotectant containing Mix 2 (1 part 6.5% Dimethyl formamide + 2 parts 6.5% Methyl acetamide). The slow freezing procedure in a programmable freezer included two steps from 0 °C to -35 °C with a freezing rate of -3 °C/min, and from -35 °C to -130 °C with a freezing rate of -50 °C/ min. Fast freezing was carried out in a box by exposing the straws to liquid nitrogen vapour at 4 to 4.5 cm above liquid nitrogen surface (-40 °C/min). 1 B) Test of insemination procedures with one or two straws with semen frozen slowly with Mix 2, and 2) comparing three cryoprotectants Mix 1 (1 part 6.5% DMF + 1 part 6.5% MA), Mix 2 and MA only (6.5%). The base extender was the trehalose containing HS1-diluent to Hanzawa et al. (2006). The cryoprotectant-diluted semen was packaged in 0.25 ml plastic straws after dilution to a standardized number of spermatozoa (300 million/straw). All samples were thawed in a water bath at 4 °C. The females were inseminated intravaginal with a dose of 300 million (1 straw) or 600 million sperm (2 straws). The respective results were: the slow freezing procedure was superior to fast freezing and resulted in 49.3% compared to 11.5% fertility. There was no significant fertility difference between inseminations with one (43.6%) and two straws (52.1%). The fertility of both Mix 1 (77.3%) and Mix 2 (81.1%) showed higher fertilization rate than MA only (39.8%). In conclusion, the slow freezing procedure with Mix 2 media is an applicable method for establishing a sperm cryobank in chicken genetic resource populations.
Biodegradability and Toxicity of Pharmaceuticals in Biological Wastewater Treatment Plants

In this experimental study both biological treatability of pharmaceuticals and their potential toxic effect in biological processes were evaluated. The pharmaceuticals were selected among those that are present at higher concentration in the Italian wastewater treatment plant effluents and widely used as antiulcer (ranitidine), β-blocker (atenolol) and antibiotic (lincomycin). The present paper is the continuation of a work already presented,[1] which used a synthetic wastewater fed to laboratory scale SBR (Sequencing Batch Reactor) operated with different sludge ages (8 and 14 days), different biochemical conditions (aerobic or anoxic-aerobic mode) and several influent drug concentrations (2, 3 and 5 mg/L). In this case a real municipal wastewater was used as influent to the SBR. In parallel, batch tests were conducted to determine the removal kinetics of drugs and nitrogen. Toxicity tests using a titrimetric biosensor to verify possible inhibition on microorganisms were also performed. Finally, the possible adsorption of the pharmaceuticals on activated sludge was evaluated. The drugs under investigation showed different behaviours in terms of both biodegradability and toxicity effect on nitrifiers. Ranitidine showed generally low removal efficiencies (17–26%) and a chronic inhibition on nitrification. Atenolol showed generally higher removal efficiencies than ranitidine, even if the fairly good efficiency obtained in the previous experimentation with synthetic wastewater (up to 90%) was not attained with real wastewater (36%). No inhibition on nitrification was observed on both acclimated and non acclimated microorganisms with a high nitrification activity, whilst it was present with activated sludge characterised by a lower nitrification activity. Consistently with his pharmaceutical properties, lincomycin showed significant inhibition on nitrification activity.
Effects of electrode contact on geometry structure and transport properties of the graphene-based nanomolecule Devices

A series of graphene-based nanomolecule devices are constructed by connecting the graphene nanodot to two Au electrodes through different bond length between the electrodes and molecules. The geometric structure and electronic properties are studied by using density functional theory calculations. Basing on the optimized structure, we calculate the quantum conductance of the system by using the Green's function method. We find that the geometry structures of the molecule and the transport properties are sensitive to the bond length dAu-H. The plane of carbon atoms increasingly bends with the decrease of the dAu-H. The ISD-VSD curves have the same threshold value under different dAu-H.
Flow cytometric investigation of neutrophil oxidative burst and apoptosis in physiological and pathological situations

Flow cytometric analysis provides a rapid screen for abnormalities of polymorphonuclear neutrophils (PMN) function and reflect their behavior in vivo more accurately. This review summarizes the major fluorescent probes used to study PMN oxidative burst and apoptosis using flow cytometry (FCM). We also provide examples of FCM studies in physiological and pathological situations, illustrating the advantages of FCM for assessment of PMN oxidative burst and PMN apoptosis. These data point to the role of FCM in detecting primary immunodeficiencies such as IRAK4 deficiency and support the use of the assessment of the PMN oxidative burst for routine testing in patients with bacterial infections. We also demonstrate the utility of whole‐blood analysis using FCM for a better understanding of PMN functionality, i.e., tuning PMN responses to inflammatory stimuli. Finally, FCM permits a simultaneous analysis of phenotypic, functional and morphometric parameters assessing whole‐blood PMN apoptosis, in particular in response to Toll‐like receptor agonists and during simian immunodeficiency virus infection. © 2009 International Society for Advancement of Cytometry
Simulation and experimental analysis of a ZigBee sensor network with fault detection and reconfiguration mechanism

In this paper, the networking architecture of wireless sensor system is studied and proposed by simulation analysis and experimental testing to implement the fault detection and reconfiguration mechanism on ZigBee network. The tool software NS2 is used to simulate and analyze the networking topologies and transmission characteristics for ZigBee network system. By way of simulation analysis of different networking topologies, the system performance of ZigBee sensor network is discussed and recognized individually for the mesh and tree routing algorithms, respectively. Moreover, the CC2430 development kit of Texas Instrument (TI) is used to develop the ZigBee nodes including the coordinator, router, and end-devices to form a specific application scenario for disaster prevention and warning system. By applying the Inter-PAN conception and algorithm, the networking architecture of ZigBee sensor system is proposed and exercised to carry out the fault detection and reconfiguration functions which may increase the reliability of data transmission on ZigBee network. Finally, through the various and practical experiments, the proposed networking topologies are implemented and tested to illustrate and evaluate the system feasibility and performance of proposed ZigBee network for wireless sensor system.
The Association Between Adiposity and the Response to Resistance Training Among Pre- and Early-Pubertal Boys

Resistance training has been shown to be effective in enhancing muscle strength among prepubertal and adolescent boys. Lately, it has been recommended for obese children. We hypothesized that resistance training will be similarly effective among boys of different adiposity. Thirty boys, aged 9.2 +/- 0.3 years, participated in progressive resistance training twice weekly during the first and second school years and thrice weekly during the third year. Training sessions included 1-4 sets of 3-6 exercises, with 5-30 repetitions/set. The mean load was 50-60% of 1 repetition maximum. Subjects were divided into responders (R--upper tertile) and non-responders (NR--lower tertile), according to the three-year improvement in muscle strength, as assessed by means of changes in concentric strength of knee flexors and extensors. Differences between groups were observed at baseline (p <0.05) in all variables reflecting adiposity (mean +/- SD): % body fat (14.1 +/- 2.6 vs 23.5 +/- 7.5% for R and NR, respectively), sum of four skinfolds (25.4 +/- 4.7 vs 47.8 +/- 21.6 mm for R and NR, respectively), BMI (15.5 +/- 1.1 vs 18.6 +/- 2.6 kg x m(-2) for R and NR, respectively). Additionally, the changes in adiposity were inversely related to the training effect (r = -0.60 to -0.34). No differences were observed in initial height and maturation between R and NR groups and there was no difference in linear growth and physical maturation with time between groups. These data suggest that resistance-training loads which may be appropriate to increase strength of knee flexors and extensors in normal-weight children may be insufficient to do so in overweight children. More research is required to elucidate the efficacy of resistance training among overweight children.
Subdivision of the cardiac Nkx2.5 expression domain into myogenic and nonmyogenic compartments.

Nkx2.5 is expressed in the cardiogenic mesoderm of avian, mouse, and amphibian embryos. To understand how various cardiac fates within this domain are apportioned, we fate mapped the mesodermal XNkx2.5 domain of neural tube stage Xenopus embryos. The lateral portions of the XNkx2.5 expression domain in the neural tube stage embryo (stage 22) form the dorsal mesocardium and roof of the pericardial cavity while the intervening ventral region closes to form the myocardial tube. XNkx2.5 expression is maintained throughout the period of heart tube morphogenesis and differentiation of myocardial, mesocardial, and pericardial tissues. A series of microsurgical experiments showed that myocardial differentiation in the lateral portion of the field is suppressed during normal development by signals from the prospective myocardium and by tissues located more dorsally in the embryo, in particular the neural tube. These signals combine to block myogenesis downstream of XNkx2.5 and at or above the level of contractile protein gene expression. We propose that the entire XNkx2.5/heart field is transiently specified as cardiomyogenic. Suppression of this program redirects lateral cells to adopt dorsal mesocardial and dorsal pericardial fates and subdivides the field into distinct myogenic and nonmyogenic compartments.
Purification and characterization of Pseudomonas aeruginosa alkaline phosphatase.

Alkaline phosphatase and a subunit form of the enzyme have been isolated from Pseudomonas aeruginosa. The enzyme is pure as judged by molecular-sieve chromatography, sodium dodecyl gel electrophoresis, and ultracentrifugation. The enzyme possesses the following properties: (a) existence of three forms: monomer mol. wt. 39 000, dimer mol. wt. 68 000, and tetramer mol. wt. 139 000; (b) pH optimum 10.5; (c) Michaelis constant Km = 6.6 × 10−5 M p-nitrophenyl phosphate; and (d) energy of activation 5647 cal/mol. Amino acid analysis indicates a protein that is hydrophobic. Its physical behavior in solution supports this conclusion. These results explain the observed association of alkaline phosphatase and lipopolysaccharide and substantiate the current theory that the alkaline phosphatase of P. aeruginosa is bound to the outer cell wall in vivo.
Space diversity parameters of MIMO systems small antenna array for mobile terminal

The 2 × 2 MIMO system antenna consisting of two elements, each of which built-up of two like monopoles of the loop shape was numerically modeled and designed. It works in 1924.5-2200, 2836.5-3235.5 and 5629.5-5743.4 MHz bands of UMTS/LTE as well as the Bluetooth and WLAN systems. Insulation between the ports of the antenna is greater than 15dB, which confirms the excellent diversity operation on mobile terminal. Theoretical and experimental results agreed favorable.
Facultative sex allocation in snow skink lizards (Niveoscincus microlepidotus)

Mathematical models suggest that reproducing females may benefit by facultatively adjusting their relative investment into sons vs. daughters, in response to population‐wide shifts in operational sex ratio (OSR). Our field studies on viviparous alpine skinks (Niveoscincus microlepidotus) document such a case, whereby among‐ and within‐year shifts in OSR were followed by shifts in sex allocation. When adult males were relatively scarce, females produced male‐biased litters and larger sons than daughters. The reverse was true when adult males were relatively more common. That is, females that were courted and mated by few males produced mainly sons (and these were larger than daughters), whereas females that were courted and mated by many males produced mainly daughters (and these were larger than sons). Maternal body size and condition also covaried with sex allocation, and the shifting pattern of sexual size dimorphism at birth may reflect these correlated effects rather than a discrete component of an evolved sex‐allocation strategy.
A Fluorescent Probe for Imaging p53–MDM2 Protein–Protein Interaction

In this article, we describe a no‐wash small‐molecule fluorescent probe for detecting and imaging p53–MDM2 protein–protein interaction based on an environment‐sensitive fluorescent turn‐on mechanism. After extensive biological examination, this probe L1 exhibited practical activity and selectivity in vitro and in cellulo.
Localisation of cannabinoid receptors in the rat brain using antibodies to the intracellular C‐terminal tail of CB1

The CB1‐type cannabinoid receptor mediates physiologic effects of Δ9‐tetrahydrocannabinol, the psychoactive ingredient of the drug marijuana. In this report, the authors analyse the expression of CB1 in the rat brain by using antibodies to the C‐terminal 13 amino acids of the receptor. Western blot analysis of rat brain membranes revealed a prominent immunoreactive band with a molecular mass (≈53 kDa) consistent with that predicted for CB1 from the rat cDNA sequence. In addition, however, less intense immunoreactive bands corresponding to glycosylated (≈62 kDa) and putative N‐terminally shorter (≈45 kDa) isoforms of CB1 were detected. The distribution of CB1‐immunoreactivity in rat brain was similar to the distribution of binding sites for radiolabelled cannabinoids, with high levels of expression in the olfactory system, the hippocampal formation, the basal ganglia, the cerebellum, and the neocortex. This provides important evidence that CB1 is likely to be largely responsible for mediating effects of cannabinoids in the brain. CB1 immunoreactivity was associated with nerve fibre systems and axon terminals but was not detected in neuronal somata. This is consistent with the presynaptic inhibitory effects of cannabinoids on neurotransmitter release in the brain. Detailed immunocytochemical analysis of anatomically or functionally related regions of the brain revealed the location of CB1 receptors within identified neural circuits. Determination of the cellular and subcellular location of CB1 within known neuronal circuits of the brain provides an anatomic framework for interpretation of the neurophysiologic and behavioural effects of cannabinoids. J. Comp. Neurol. 422:159–171, 2000. © 2000 Wiley‐Liss, Inc.
Cartilage metabolism in osteoarthritis and the influence of viscosupplementation and steroid: a review

Osteoarthritis (O.A.) is the most common type of articular disease. This is an idiopathic joint disease characterized by an imbalance between synthesis and degradation of articular cartilage and subchondral bone accompanied by capsular fibrosis, osteophyte formation and variable grade of inflammation of synovial membrane. Joint lubrication is naturally provided by Hyaluronic acid in syovial fluid. Hyaluronan is present in abundance in normal young and healthy joints. In degenerative O.A. Hyaluronan is smaller in size, molecular weight and diminished in concentration. This decrease in joint lubrication and shock absorbing mechanism in O.A. can be remedied by intraarticular viscosupplementation. Alternatively the pain and secondary inflammation in O.A. can be relieved by intraarticular injection of steroids and long acting local anesthetics. Promt and effective reduction in local inflammation occurs after intra‐articular injection of corticosteriod. This article reviews the cartilage metabolism in O.A. , discusses the pros and cons of these treatments and provides a literature review of the studies which compare benefits and adverse reactions of viscosupplementation vs. intraarticular steroids with placebo treatment.
Effect of Steroid Milieu on Gonadotropin-Releasing Hormone-1 Neuron Firing Pattern and Luteinizing Hormone Levels in Male Mice1

Abstract GnRH neuronal function is regulated by gonadal hormone feedback. In males, testosterone can act directly or be converted to either dihydrotestosterone (DHT) or estradiol (E2). We examined central steroid feedback by recording firing of green fluorescent protein (GFP)-identified GnRH neurons in brain slices from male mice that were intact, castrated, or castrated and treated with implants containing DHT, E2, or E2+DHT. Castration increased LH levels. DHT or E2 alone partially suppressed LH, whereas E2+DHT reduced LH to intact levels. Despite the inhibitory actions on LH, the combination of E2+DHT increased GnRH neuron activity relative to other treatments, reflected in mean firing rate, amplitude of peaks in firing rate, and area under the curve of firing rate vs. time. Cluster8 was used to identify peaks in firing activity that may be correlated with hormone release. Castration increased the frequency of peaks in firing rate. Treatment with DHT failed to reduce frequency of these peaks. In contrast, treatment with E2 reduced peak frequency to intact levels. The frequency of peaks in firing rate was intermediate in animals treated with E2+DHT, perhaps suggesting the activating effects of this combination partially counteracts the inhibitory actions of E2. These data indicate that E2 mediates central negative feedback in males primarily by affecting the pattern of GnRH neuron activity, and that androgens combined with estrogens have a central activating effect on GnRH neurons. The negative feedback induced by E2+DHT to restore LH to intact levels may mask an excitatory central effect of this combination.
Real-Time Multicast With Network Coding In Mobile Ad-Hoc Networks

Abstract In this paper, a Network Coding based Real-time Multicast (NCRM) protocol is proposed for real-time multicast services in Mobile Ad-hoc Networks (MANET). Through reducing the forwarding times for data packets in MANET, NCRM can not only decrease the energy consumption but also improve the throughput performance. To satisfy the maximum end-to-end delay deadline requirements for real-time services, NCRM adopts a mechanism with strict delay constraints. Simulation results show that, in those real-time multicast scenarios with many receivers and/or high node motilities, NCRM outperforms those traditional protocols such as PUMA and MAODV in terms of transmission reliability and energy consumption significantly.
A time series approach to design of a permanent magnet synchronous generator for a direct-drive wind turbine

The design of a permanent magnet generator for a wind turbine is studied. The best generator is chosen from a range of designs based on minimizing material cost and energy loss. The main loss mechanisms in an air-cored machine are copper and eddy current losses. The energy lost for each design is evaluated in the steady-state and then in the time domain so as to better take into account the thermal behavior of the machines.
Embryonic stem cell factors undifferentiated transcription factor‐1 (UFT‐1) and reduced expression protein‐1 (REX‐1) are widely expressed in human skin and may be involved in cutaneous differentiation but not in stem cell fate determination

Undifferentiated transcription factor‐1 (UTF‐1) and reduced expression protein‐1 (REX‐1) are used as markers for the undifferentiated state of pluripotent stem cells. Because no highly specific cytochemical marker for epidermal stem cells has yet been identified, we investigated the expression pattern of these markers in human epidermis and skin tumours by immunohistochemistry and in keratinocyte cell cultures. Both presumed stem cell markers were widely expressed in the epidermis and skin appendages. Distinct expression was found in the matrix cells of the hair shaft. Differentiation of human primary keratinocytes (KC) in vitro strongly downregulated UTF‐1 and REX‐1 expression. In addition, REX‐1 was upregulated in squamous cell carcinomas, indicating a possible role of this transcription factor in malignant tumour formation. Our data point to a role for these proteins not only in maintaining KC stem cell populations, but also in proliferation and differentiation of matrix cells of the shaft and also suprabasal KC.