Miracle-dz/UniFAR-FTUs huggingface dataset:
Creation and Removal of Embedded Ribonucleotides in Chromosomal DNA during Mammalian Okazaki Fragment Processing*

Mammalian RNase HI has been shown to specifically cleave the initiator RNA of Okazaki fragments at the RNA-DNA junction, leaving a single ribonucleotide attached to the 5′-end of the downstream DNA segment. This monoribonucleotide can then be removed by the mammalian 5′- to 3′-exo-/endonuclease, a RAD2 homolog-1 (RTH-1) class nuclease, also known as flap endonuclease-1 (FEN-1). Although FEN-1/RTH-1 nuclease often requires an upstream primer for efficient activity, the presence of an upstream primer is usually inhibitory or neutral for removal of this 5′-monoribonucleotide. Using model Okazaki fragment substrates, we found that DNA ligase I can seal a 5′-monoribonucleotide into DNA. When both ligase and FEN-1/RTH-1 were present simultaneously, some of the 5′-monoribonucleotides were ligated into DNA, while others were released. Thus, a 5′-monoribonucleotide, particularly one that is made resistant to FEN-1/RTH-1-directed cleavage by extension of an inhibitory upstream primer, can be ligated into the chromosome, despite the presence of FEN-1/RTH-1 nuclease. DNA ligase I was able to seal different monoribonucleotides into the DNA for all substrates tested, with an efficiency of 1–13% that of ligating DNA. These embedded monoribonucleotides can be removed by the combined action of RNase HI, cutting on the 5′-side, and FEN-1/RTH-1 nuclease, cleaving on the 3′-side. After FEN-1/RTH-1 action and extension by polymerization, DNA ligase I can join the entirely DNA strands to complete repair.
Contingent convertible bonds : a catastrophe insurance for banks ?

This paper justifies, in an agency context, the existence of hybrid securities that appeared very recently on the organised market: CoCo bonds (contingent convertible bonds). Like straight debt, CoCos make it possible to profit from the tax benefits of debt. And, like stocks, they provide protection against financial distress. Although CoCos cannot completely protect banks against bankruptcy, they significantly reduce their probability of failure independently of regulator actions. The structural model shows that CoCos allow increased valorisation of the banks without jeopardising their stability. However, special attention must be paid to their design on penalty of the inability to provide an efficient means of financing to investors. Particular attention should be paid to fixing the value of the “trigger”. Its optimal value is highly dependent on the environment (structure and amount of bankruptcy costs, extent of dilution of shareholder claims, tax environment and so on).
Implementing a Primary Prevention Social Skills Intervention in Urban Preschools: Factors Associated with Quality and Fidelity

Research Findings: Preschool behavior problems are of increasing concern to early childhood educators. Preventive interventions are being developed, but implementation in underresourced child care programs is challenging. This study describes the implementation of an adapted Second Step curriculum to increase children's social skills and decrease behavior problems in preschool classrooms. Teacher training/coaching, organizational supports, and procedures for sustainability are described. Measures included baseline classroom characteristics, lesson completion and fidelity, and teacher satisfaction. Teachers completed 88% of the lessons across 2 years. Follow-up monitoring in Year 3, once all training was terminated, found that 95% of lessons were delivered with higher fidelity than in the first 2 years. Teachers were satisfied with the training, felt that the curriculum improved children's social skills, and stated that they would continue to use the curriculum. Lesson completion and fidelity were associated with various teacher characteristics, training attendance, classroom characteristics, teacher and child turnover, and the percentage of children with developmental delays in the classroom. Practice or Policy: The results support the implementation strategy and suggest that paying attention to teacher morale, general skill development, and a period of ongoing support for training is important and will lead to sustainable and high implementation rates.
Role of the peripheral anionic site on acetylcholinesterase: inhibition by substrates and coumarin derivatives.

Propidium has been demonstrated in previous studies to be a selective ligand for the peripheral anionic site on acetylcholinesterase (EC 3.1.1.7). Its association with this site can be advantageously monitored by direct fluorescent titration. We have measured the ability of acetylcholine, acetylthiocholine, haloxon [di-(2-chloroethyl)3-chloro-4-methylcoumarin-7-ylphosphate] , and a coumarin derivative (3-chloro-7-hydroxy-4-methylcoumarin) to dissociate propidium from the peripheral anionic site of Torpedo californica acetylcholinesterase. Measurements were made by back-titration of propidium after complete inhibition of the active center with diisopropylfluorophosphate. Both acetylcholine and acetylthiocholine show substrate inhibition at high substrate concentrations. The concentrations required for occupation of the peripheral site, as ascertained by competition with propidium, correlated well with the concentration dependence for the kinetics of substrate inhibition. These observations are consistent with substrate inhibition being due to binding of acetylcholine or acetylthiocholine at a peripheral anionic site. Displacement of propidium by haloxon and coumarin indicated that these inhibitors also bind to the peripheral anionic site. The dissociation constants ascertained from peripheral site occupation are in agreement with the constants obtained from inhibition kinetics. Evidence is presented that competition with propidium obtained by direct fluorescence titrations, when combined with inhibition kinetics, provides a more reliable means for ascertaining site selectivity of various inhibitors than does a kinetic analysis alone.
Prediction of Loop Regions in protein Sequence

We suggest an algorithm that inputs a protein sequence and outputs a decomposition of the protein chain into a regular part including secondary structures and a nonregular part corresponding to loop regions. We have analyzed loop regions in a protein dataset of 3,769 globular domains and defined the optimal parameters for this prediction: the threshold between regular and nonregular regions and the optimal window size for averaging procedures using the scale of the expected number of contacts in a globular state and entropy scale as the number of degrees of freedom for the angles phi, psi, and chi for each amino acid. Comparison with known methods demonstrates that our method gives the same results as the well-known ALB method based on physical properties of amino acids (the percentage of true predictions is 64% against 66%), and worse prediction for regular and nonregular regions than PSIPRED (Protein Structure Prediction Server) without alignment of homologous proteins (the percentage of true predictions is 73%). The potential advantage of the suggested approach is that the predicted set of loops can be used to find patterns of rigid and flexible loops as possible candidates to play a structure/function role as well as a role of antigenic determinants.
Thaumarchaeal Ammonia Oxidation in an Acidic Forest Peat Soil Is Not Influenced by Ammonium Amendment

ABSTRACT Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and “deep peat” lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen.
A V-band power amplifier using Marchand balun for power combining in 90n-nm CMOS process

A fully integrated power amplifier (PA) which is implemented in the 90-nm CMOS process technology for V-band applications is presented in this paper. The proposed PA is composed of three-stage common-source configuration and adopts Marchand baluns for power dividing/combining in the third stage. The CMOS PA delivers a 9-dBm saturated output power (i.e. Psat) and has a 7.3-dBm output 1-dB compression point (OP1dB) at 60 GHz. It performs a maximum power gain of 5.4 dB and a peak power-added efficiency (PAE) of 1.81%. The proposed PA draw a power consumption of 215 mW from the 1.2-V supply.
Factors associated with use of falls risk–increasing drugs among patients of a geriatric oncology outpatient clinic in Australia: a cross‐sectional study†

Older people with cancer are at increased risk of falling. Falls risk-increasing drugs (FRIDs), comprising psychotropics and medications that cause orthostatic hypotension, are a potentially modifiable risk factor for falls. The objective of this study was to determine the prevalence and factors associated with use of FRIDs in older people with cancer. Patients aged ≥70 years who presented to a hospital outpatient clinic between January 2009 and July 2010 were included in the study. Information on current medication use, falls in previous 6 months, and frailty criteria was collected. Multinomial logistic regression was used to compute odds ratios (OR) and 95% confidence intervals (CIs) for factors associated with levels of FRID use. Overall, 76.1% (n = 293) of 383 patients used FRIDs. This comprised psychotropics (31.2%, n = 120) and medications causing orthostatic hypotension (69.9%, n = 269). In total, 24.0% (n = 92) patients reported falling in the previous 6 months. Risk factors for falling were associated with use of psychotropics but not orthostatic hypotension drugs. Patients with a history of falls had increased odds of using psychotropics (≥3 psychotropics; OR 13.50; 95%CI, 2.64-68.94). Likewise, frail patients had increased odds of using psychotropics (≥3 psychotropics; OR 27.78; 95%CI, 6.06-127.42). Risk factors for falling were associated with the use of psychotropics. This suggests that clinicians either do not recognize or underestimate the contribution of medications to falls in this high-risk patient group. Further efforts are needed to rationalize medication regimens at the time of patients' first presentation to outpatient oncology services.
A system for real-time synthesis of subtle expressivity for life-like MPEG-4 based virtual characters

Non-verbal behaviors have a key role in making a virtual character appear life-like. We describe an extensible system for the specification, control and real-time generation of facial expressions and gestures. The system approximates in a MPEG-4 based virtual character the wide expressive range, dynamism (an expression's meaning significantly depends on its temporal evolution) and variability (an emotion is never expressed exactly in the same way by different people, and even by the same person at different times), typical of human nonverbal behavior. The MPEG-4 standard only allows high-level control of 6 basic emotions and does not explicitly support the description of an expression temporal evolution. Our approach has been that of creating a hierarchical model of expressiveness; expressions are defined in term of parameterized functions controlling low-level animation parameters trajectories (by means of an XML-based expression definition markup language). The real-time generation of those expressions is performed by an expression synthesis engine. The system allows to effectively modulate expressivity both at design-time (the developer tweaks the parameters to give the character a given expressive style), and at run-time (the engine automatically changes the way in which an expression is performed each time), producing controllable, but non-deterministic, behavior patterns, a key factor for enhancing believability.
Ladon1: end-to-end authorisation support for resource-deprived environments

The authors present Ladon, an enhanced version of Kerberos which extends the original protocol with authorisation capacity and relaxes the necessity of clock synchronisation by adding to the protocol special limited-lifetime nonces. This way, although all entities need timers, only the clocks of the two servers that constitute the key distribution centre must be synchronised with each other. The design of this protocol is motivated by the emergence of a new trend of applications in which sensors and low-capacity devices become tiny information or application servers directly addressable by any Internet-connected entity. Despite the huge potential of these environments, security is probably the greatest barrier to their long-term success. To address this issue, Ladon allows for end-to-end pair-wise key establishment in an authenticated and authorised manner, while keeping the introduced storage, computational and communication overhead very low. The security analysis with the AVISPA formal validation tool shows that the protocol meets the stated security goals, whereas the performance analysis shows that the overhead of the protocol is bounded and comparable to that of other security protocols which provide even less functionalities.
Direct observation of s-wave atomic collisions.

We observe the angular distribution of {ital s}-wave scattering of Cs atoms in an atomic fountain by selecting and probing atomic velocities. At an average temperature of {ital T}=0.89 {mu}K the scattering is predominantly {ital s}-wave and we have a sensitivity to {ital p}-wave cross sections as small as 0.1% of the {ital s}-wave. The cross section is 4{times}10{sup {minus}11}cm{sup 2} for atoms in the {ital F}=3, {ital m}{sub {ital F}}=0 state colliding with atoms distributed among the {ital F}=4, {ital m}{sub {ital F}} states. We also demonstrate a multiply loaded magneto-optic trap and a temperature of 1.53(7) {mu}K.
Stability analysis for delta operator systems subject to state saturation

ABSTRACT In this paper, we investigate the problem of stability analysis for linear delta operator systems subject to state saturation. Both full state saturation and partial state saturation are investigated for the delta operator systems. Two equivalent necessary and sufficient conditions are identified such that the system with full state saturation is globally asymptotically stable. Based on the sufficient conditions, an iterative algorithm is proposed for testing global asymptotic stability of the system with full state saturation. A new globally asymptotically stable condition is also proposed for the partial state saturation system. Two numerical examples on a ball and beam model are given to show the effectiveness of the proposed method.
Controllability of nonlinear systems with multiple delays

In the present paper local constrained controllability problems for nonlinear system with constant delays in the control are formulated and discussed. Using some mapping theorems taken from functional analysis and linear approximation methods sufficient conditions for relative and absolute local constrained controllability in a given time interval are derived and proved. The present paper extends controllability conditions with unconstrained controls given in the literature to cover the case of nonlinear systems with delays in control and with constrained controls. Special case of semilinear systems without delays is also considered.
A modulatory action of divalent cations on transient outward current in cultured rat sensory neurones.

1. The effects of some divalent cations on the A‐current (IA) in cultured rat dorsal root ganglion cells (DRGs) were studied using whole‐cell patch recording. 2. IA was not affected by omission of calcium from the external medium; however it was significantly depressed by manganese (10 mM) applied by pressure ejection. This depressant effect of manganese resulted from a depolarizing shift of the activation curve by 17 mV, associated with only a slight reduction of the maximum conductance. At 10 mM manganese also caused a depolarizing shift of the steady‐state inactivation curve by 34 mV. Divalent cations other than manganese also gave positive shifts of the steady‐state activation and inactivation curves for IA but were of different potency; the sequence was: Cd2+ greater than Mn2+ = Co2+ greater than Mg2+. 3. A dose‐response curve for the depolarizing shift of the activation and inactivation curves of IA, as a function of manganese concentration, could be fitted by a single binding site model with an apparent dissociation constant of approximately 17 mM. The depolarizing shift of the inactivation curve was on average twice as large as that of the activation curve. 4. In contrast to its effect on IA, manganese (10 mM) did not cause any appreciable change in the voltage dependence of the activation curve for the delayed rectifier K+ current. 5. A low concentration of manganese (1 mM) increased the amplitude of IA recorded at pre‐pulse potentials ranging from ‐50 to ‐70 mV. This augmentation of IA resulted from a positive shift of the inactivation curve by 6 mV without an appreciable shift of the activation curve; as a result a population of A‐channels is released from inactivation over pre‐pulse potentials from ‐50 to ‐70 mV. 6. These results show that divalent cations can evoke a depolarizing shift of both the activation and inactivation gates controlling IA; this causes either depression or augmentation of IA, depending on the species and concentration of the divalent cation, and also on the pre‐ pulse potential used to de‐inactivate IA. This modulatory effect of divalent cations on the gating of IA appears to reflect binding to a specific, saturable site, either the A‐channel protein itself, or phospholipids electrically close to the gating apparatus.
Prevalence of alcohol related brain damage among homeless hostel dwellers in Glasgow.

BACKGROUND Over half of Glasgow's 4000 homeless people drink hazardously but the prevalence of alcohol-related brain damage (ARBD) has not been described. AIMS AND OBJECTIVES To determine the prevalence of ARBD among homeless hostel dwellers in Glasgow. METHODS A representative sample of homeless hostel dwellers was surveyed using validated survey instruments and clinical assessment. RESULTS From a sample of 266 hostel dwellers, 82% had cognitive impairment and 78% were drinking hazardously. The prevalence of ARBD among homeless hostel dwellers was 21%. CONCLUSIONS ARBD has a high prevalence among homeless hostel dwellers and treatment is usually effective. There is a need to actively identify and treat this population to help them move out of homelessness.
Conception et hybridation de l'environnement électronique des composants de puissance à structure verticale

Ces travaux de these portent sur l'integration heterogene des fonctions de commande pour des transistors de puissance verticaux a grille isolee. Ce travail a consiste en la conception des fonctions de commande pour un transistor de type MOSFET en technologie CMOS planar, puis en la conception du composant de puissance lui-meme, incluant des fonctions specifiques pour l'auto-alimentation de sa commande. Le deuxieme aspect de ce travail est l'etude et la realisation technologique de metallisations epaisses en surface de puces silicium pour l'hybridation en chip on chip de la partie commande et de la partie puissance. Ce memoire de these comporte trois chapitres equivalents : etudes theoriques et presentation des concepts, conception et validation experimentale de la partie commande puis conception de la partie puissance et developpements technologiques. Les champs d'application de ces travaux sont varies car ils couvrent un large domaine de l'electronique de puissance (convertisseurs hybrides).
Spectropolarimetry of the massive post -Red Supergiants IRC +10420 and HD 179821

We present medium resolution spectropolarimetry and long term photo-polarimetry of two massive post-red supergiants, IRC +10420 and HD 179821. The data provide new information on their circumstellar material as well as their evolution. In IRC +10420, the polarization of the Ha line is different to that of the continuum, which indicates that the electron-scattering region is not spherically symmetric. The observed long term changes in the polarimetry can be associated with an axi-symmetric structure, along the short axis of the extended reflection nebulosity. Long term photometry reveals that the star increased in temperature until the mid-nineties, after which the photospheric flux in the optical levelled off. As the photometric changes are mostly probed in the red, they do not trace high stellar temperatures sensitively. And so, it is not obvious whether the star has halted its increase in temperature or not. For HD 179821 we find no polarization effects across any absorption or emission lines, but observe very large polarization changes of order 5% over 15 years. During the same period, the optical photometry displayed modest variability at the 0.2 magnitude level. This is unexpected, because large polarization changes are generally accompanied by strong photometric changes. Several explanations for this puzzling fact are discussed. Most of which, involving asymmetries in the circumstellar material, seem to fail as there is no evidence for the presence of hot, dusty material close to the star. A caveat is that the sparsely available near-infrared photometry could have missed periods of strong polarization activity. Alternatively, the variations can be explained by the presence of a non-radially pulsating photosphere. Changes in the photometry hint at an increase in temperature corresponding to a change through two spectral subclasses over the past ten years.