Miracle-dz/UniFAR-FTUs huggingface dataset:
Controlling DNA-end resection: a new task for CDKs

DNA double-strand breaks (DSBs) are repaired by two major pathways: homologous recombination (HR) and non-homologous end-joining (NHEJ). The choice between HR and NHEJ is highly regulated during the cell cycle. DNA-end resection, an evolutionarily conserved process that generates long stretches of single-stranded DNA, plays a critical role in pathway choice, as it commits cells to HR, while, at the same time, suppressing NHEJ. As erroneous DSB repair is a major source of genomic instability-driven tumorigenesis, DNA-end resection factors, and in particular their regulation by post-translational modifications, have become the subject of extensive research over the past few years. Recent work has implicated phosphorylation at S/T-P motifs by cyclin-dependent kinases (CDKs) as a major regulatory mechanism of DSB repair. Intriguingly, CDK activity was found to be critically important for the coordinated and timely execution of DNA-end resection, and key players in this process were subsequently identified as CDK substrates. In this mini review, we provide an overview of the current understanding of how the DNA-end resection machinery in yeast and human cells is controlled by CDK-mediated phosphorylation.
Underwater locomotion in a terrestrial beetle: combination of surface de-wetting and capillary forces

For the first time, we report the remarkable ability of the terrestrial leaf beetle Gastrophysa viridula to walk on solid substrates under water. These beetles have adhesive setae on their feet that produce a secretory fluid having a crucial role in adhesion on land. In air, adhesion is produced by capillary forces between the fluid-covered setae and the substrate. In general, capillary forces do not contribute to adhesion under water. However, our observations showed that these beetles may use air bubbles trapped between their adhesive setae to walk on flooded, inclined substrata or even under water. Beetle adhesion to hydrophilic surfaces under water was lower than that in air, whereas adhesion to hydrophobic surfaces under water was comparable to that in air. Oil-covered hairy pads had a pinning effect, retaining the air bubbles on their feet. Bubbles in contact with the hydrophobic substrate de-wetted the substrate and produced capillary adhesion. Additional capillary forces are generated by the pad's liquid bridges between the foot and the substrate. Inspired by this idea, we designed an artificial silicone polymer structure with underwater adhesive properties.
Efficacy of crizotinib in ALK fusion variants.

In 1995, rearrangement of the anaplastic lymphoma kinase ( ALK ) gene was first reported as a fusion gene in anaplastic large cell non-Hodgkin lymphoma, and in 2005 it was again on focus when Mano et al. reported that echinoderm microtubule-associated protein-like4 (EML4)-ALK fusion gene is a powerful oncogene in lung cancer (1,2).
Resonators with integrated CMOS circuitry for mass sensing applications, fabricated by electron beam lithography

A resonator system has been fabricated directly on a pre-processed CMOS chip. The system is to be used for high sensitivity mass sensing applications in air and vacuum. The resonator system, corresponding of a cantilever and structures for electrostatic actuation and capacitive read-out, have been defined by electron beam lithography on top of a charge and radiation sensitive CMOS layer in predefined areas as a post-process step. This has been accomplished without affecting the electronic properties of the pre-processed CMOS circuits. The subsequent etching steps to fully release the cantilevers have been obtained without stiction of the cantilevers to the substrate. Cantilevers are driven at their mechanical resonance in a lateral mode, and the frequency is monitored by capacitive read-out on the chip. CMOS integration enables signal detection directly on the chip, which radically decreases the parasitic capacitances. Consequently, low-noise electrical measurements with a very high mass sensitivity are obtained. Fabricated resonator systems were characterized to have resonance frequencies of approximately 1.49 MHz, which is in good agreement with a theoretical estimation of 1.41 MHz. The theoretical mass resolution, , is approximately 17 ag Hz−1, using a Young modulus value of 160 GPa.
SELBERG'S TRACE FORMULA ON THE k-REGULAR TREE AND APPLICATIONS

We survey graph theoretic analogues of the Selberg trace and pretrace formulas along with some applications. This paper includes a review of the basic geometry of a k-regular tree Ξ (symmetry group, geodesics, horocycles, and the analogue of the Laplace operator). A detailed discussion of the spherical functions is given. The spherical and horocycle transforms are considered (along with three basic examples, which may be viewed as a short table of these transforms). Two versions of the pretrace formula for a finite connected k-regular graph X � Γ \Ξ are given along with two applications. The first application is to obtain an asymptotic formula for the number of closed paths of length r in X (without backtracking but possibly with tails). The second application is to deduce the chaotic properties of the induced geodesic flow on X (which is analogous to a result of Wallace for a compact quotient of the Poincare upper half plane). Finally, the Selberg trace formula is deduced and applied to the Ihara zeta function of X, leading to a graph theoretic analogue of the prime number theorem.
Delay Analysis of a Two-Queue, Nonuniform Message Channel

A Message Channel is defined as a tandem connection of single server queues in which the successive service times experienced by any particular customer are scaled versions of the same random variable, and thus it serves as a model for sparsely connected store-and-forward data communications networks (or network segments) where messages typically preserve their lengths as they traverse the system . A particular instance of sucha nonstandard queueing model is analyzed in this paper. The system consists of two single server queues in tandem subject tao Poisson arrival process (at the first queue) and providing service according to scaled versions of a sequence of two-level, discrete random variables. A set of recursive equations that can be used to solve the model for any given scaling factor at the second queue (normalized with respect to the first queue service) is explicitly derived. In addition, complete solutions are displayed for several cases of interest, and the equilibrium mean cumulative waiting times for these instances are compared as a method of indicating the impact of the scaling factor on the operation of the system. The extension of several results to systems with more general service time processes is discussed.
Retroviruses use CD169-mediated trans-infection of permissive lymphocytes to establish infection

A close up view of retrovirus spreading Viral infections typically begin with a small number of viral particles gaining access to the host at a specific tissue site. But how do viruses that cause systemic infections, such as HIV, spread more widely? Sewald et al. visualized how the retroviruses murine leukemia virus (MLV) and HIV spread within lymph nodes in mice (see the Perspective by Hope). Specific macrophages that line the lymph-draining sinuses in lymph nodes first captured the virus using the carbohydrate-binding protein CD169. These macrophages subsequently transferred virus to the B1 subclass of B lymphocytes, which migrated further into the lymph node, disseminating the virus more widely. Science, this issue p. 563; see also p. 511 Local macrophages and a subclass of B cells promote retroviral spread in lymph nodes. [Also see Perspective by Hope] Dendritic cells can capture and transfer retroviruses in vitro across synaptic cell-cell contacts to uninfected cells, a process called trans-infection. Whether trans-infection contributes to retroviral spread in vivo remains unknown. Here, we visualize how retroviruses disseminate in secondary lymphoid tissues of living mice. We demonstrate that murine leukemia virus (MLV) and human immunodeficiency virus (HIV) are first captured by sinus-lining macrophages. CD169/Siglec-1, an I-type lectin that recognizes gangliosides, captures the virus. MLV-laden macrophages then form long-lived synaptic contacts to trans-infect B-1 cells. Infected B-1 cells subsequently migrate into the lymph node to spread the infection through virological synapses. Robust infection in lymph nodes and spleen requires CD169, suggesting that a combination of fluid-based movement followed by CD169-dependent trans-infection can contribute to viral spread.
Contingency Locus in ctsR of Listeria monocytogenes Scott A: a Strategy for Occurrence of Abundant Piezotolerant Isolates within Clonal Populations

ABSTRACT In a recent study we demonstrated that a high-hydrostatic-pressure-tolerant isolate of Listeria monocytogenes lacks a codon in the class 3 heat shock regulator gene ctsR. This mutation in the region that encodes four consecutive glycines was directly responsible for the observed piezotolerance, increased stress resistance, and reduced virulence. The aim of the present study was to determine whether mutations in ctsR are frequently associated with piezotolerance in L. monocytogenes. Wild-type cultures of L. monocytogenes were therefore exposed to 350 MPa for 20 min, and the piezotolerance of individual surviving isolates was assessed. This rendered 33 isolates with a stable piezotolerant phenotype from a total of 84 survivors. Stable piezotolerant mutants were estimated to be present in the initial wild-type population at frequencies of >10−5. Subsequent sequencing of the ctsR gene of all stable piezotolerant isolates revealed that two-thirds of the strains (i.e., n = 21) had mutations in this gene. The majority of the mutations (16 of 21 strains) consisted of a triplet deletion in the glycine-encoding region of ctsR, identical to what was found in our previous study. Interestingly, 2 of 21 mutants contained a codon insertion in this repeat region. The remaining three stable piezotolerant strains showed a 19-bp insertion in the glycine repeat region, a 16-bp insertion downstream of the glycine repeat area (both leading to frameshifts and a truncated ctsR), and an in-frame 114-bp deletion encoding a drastically shortened carboxy terminus of CtsR. In four instances it was not possible to generate a PCR product. A piezotolerant phenotype could not be linked to mutations in ctsR in 8 of 33 isolates, indicating that other thus-far-unknown mechanisms also lead to stable piezotolerance. The present study highlights the importance of ctsR in piezotolerance and stress tolerance of L. monocytogenes, and it demonstrates that short-sequence repeat regions contribute significantly to the occurrence of a piezotolerant and stress-tolerant subpopulation within L. monocytogenes cultures, thus playing an important role in survival.
Endogenous Retrovirus ev21 Dose Not Recombine with ALV-J and Induces the Expression of ISGs in the Host

Avian leukosis virus subgroup J (ALV-J) infection can cause tumors and immunosuppression. Endogenous viruses integrate into host genomes and can recombine with exogenous avian leukosis virus (ALV). In this study, we analyzed the interaction of endogenous retrovirus 21 (ev21) with the ALV-J in late-feathering Chinese yellow chicken. Two ALV-J strains M180 and K243 were isolated from late-feathering and fast-feathering Chinese yellow chicken flocks, respectively. The env gene of the two strains showed 94.2–94.8% nucleotide identity with reference ALV-J strains. Compared with the env gene and the LTR of ev21 and M180, the nucleotide identity of LTR was 69.7% and env gene was 58.4%, respectively, especially the amino acid identity of env gene as low as 14.2%. Phylogenetic analysis of the nucleotide sequence of the env gene and the 3′LTR showed that M180 was closely related to ALV-J, and was located in a distinct group with ev21 in the phylogenetic tree. Using co-immunoprecipitation (co-IP), we next demonstrate that the envelope protein of ev21 does not interact with the M180 envelope protein. We further show that the envelope protein of ev21 cannot activate ALV-J LTR promoter activity using luciferase-reporter assays. qPCR and western blot analysis revealed that envelope protein of endogenous ev21 can facilitate the expression of PKR at 6h post ALV-J infection (hpi) and facilitate the expression of ISG12 and CH25H at 24 hpi. However, the expression of the env gene of M180 strain was not significantly at 6 and 24 hpi. We conclude that there is no evidence of recombination between endogenous retrovirus ev21 and ALV-J strain M180 in late-feathering Chinese yellow chicken, and envelope protein of ev21 can affect the expression of host ISGs, but appears not to influence the replication of ALV-J strain M180. This is the first report of interaction among the endogenous retrovirus ev21, ALV-J and the late-feathering chicken.
Violence against young women attending primary care services in Spain: prevalence and health consequences.

BACKGROUND There are a significant number of studies assessing the negative health consequences of violence against women. However, a limited number of studies analyse the health consequences of violence committed against young women by different types of aggressors. OBJECTIVES The goal of this study is to assess the prevalence of interpersonal violence against young women in Spain and analyse its impact on the physical and mental health of the victims. METHODS A total of 1076 women aged 18-25 years attending Spanish primary care services were selected. We estimated the prevalence of interpersonal violence and compared the health data and demographic characteristics of abused and non-abused young women, multi-logistic regression models were fitted. The Wald test was used to assess whether there were differences in the negative health consequences of intimate partner (IPV) versus non-IPV. RESULTS As many as 27.6% young women reported a history of abuse, of whom 42.7% had been assaulted by their partner, 41.1% by someone other than their partner and 16.2% both by their partner and another person. The distribution of social and demographic characteristics was similar for IPV and non-IPV victims. Young abused women were three times more likely to suffer psychological distress and have somatic complaints, and they were four times more likely to use medication as compared to non-abused women. CONCLUSION Our results suggest that all forms of violence compromise young women's health seriously. Including patients' history of abuse in their health record may help make more informed clinical decisions and provide a more integrated care.
Role of lipoprotein lipase in lipid metabolism

Purpose of review A major step in energy metabolism is hydrolysis of triacylglycerol-rich lipoproteins (TRLs) to release fatty acids that can be used or stored. This is accomplished by lipoprotein lipase (LPL) at ‘binding lipolysis sites’ at the vascular endothelium. A multitude of interactions are involved in this seemingly simple reaction. Recent advances in the understanding of some of these factors will be discussed in an attempt to build a comprehensive picture. Recent findings The first event in catabolism of TRLs is that they dock at the vascular endothelium. This requires LPL and GPIHBP1, the endothelial transporter of LPL. Kinetic studies in rats with labeled chylomicrons showed that once a chylomicron has docked in the heart it stays for minutes and a large number of triacylglycerol molecules are split. The distribution of binding between tissues reflects the amount of LPL, as evident from studies with mutant mice. Clearance of TRLs is often slowed down in metabolic disease, as was demonstrated both in mice and men. In mice, this was directly connected to decreased amounts of endothelial LPL. Summary The LPL system is central in energy metabolism and results from interplay between several factors. Rapid and exciting progress is being made.
Rigid body visual servoing using navigation functions

Visual servo controllers in the literature rarely achieve provably large domains of attraction, and seldom address two important sensor limitations: (i) susceptibility to self-occlusions and (ii) finite field of view (FOV). We tackle the problem of global, occlusion-free visual servoing of a fully actuated rigid body by recourse to navigation functions on a compact manifold which encode these restrictions as control obstacles. For occlusion free rigid body servoing, the manifold of interest is the "visible" set of rigid body configurations, that is, those for which the feature points are within the field of view and unoccluded by the body. For a set of coplanar feature points on one face of a convex polyhedron, we show that a slightly conservative subset of the visible set has a simple topology amenable to analytical construction of a navigation function. We construct the controller via a closed form coordinate transformation from our problem domain into the topological model space and conclude with simulation results.
Endothelium-Derived Nitric Oxide Modulates Renal Hemodynamics in the Developing Piglet

ABSTRACT: The developing mammal exhibits lower renal blood flow (RBF) and higher renal vascular resistance (RVR) than its adult counterpart. The maturational pattern of renal hemodynamics involves the synchronous increase in RBF and decrease in RVR with age. In spite of considerable investigation, the mechanisms involved in the regulation of renal hemodynamics in the developing animal remain largely unexplained. Specifically, the role of the vasodilator endothelium-derived nitric oxide (EDNO) in the regulation of developing renal hemodynamics is not known. These experiments examined the intrarenal effect on the renal hemodynamics of the developing piglet and adult pig of the EDNO competitive inhibitor N-nitro-L-arginine methylester (L-NAME) at three doses (50, 5, and 3 μg/kg/min). During basal conditions, the developing piglet exhibited lower RBF and higher RVR than the adult pig. All doses of intrarenal L-NAME produced significant decreases in RBF and increases in RVR in both groups. The 3-μg/kg/min L-NAME dose did not change mean arterial pressure. The developing piglet exhibited significantly greater changes at all doses. After the 50-μg/kg/min infusion, piglet RBF decreased 45% and adult pig RBF decreased 29%; piglet RVR increased 128% and adult pig RVR increased 51%. After a 5-μg/kg/min infusion, RBF decreased 28% in the piglet and 14% in the adult pig; RVR increased 75% in the piglet compared with 27% in the adult pig. After 3 μ/kg/min L-NAME, piglet RBF decreased 29% and adult RBF decreased 9%; RVR increased 47% in the piglet versus 13% in the adult pig. The results of this study suggest that EDNO participates in the regulation of basal renal hemodynamics in the developing piglet and adult pig. Furthermore, it appears that EDNO may play a greater role in maintaining basal renal hemodynamics in the developing piglet than in the adult pig.
Tap 'n' shake: gesture-based smartwatch-smartphone communications system

Smartwatches have recently seen a surge in popularity, and the new technology presents a number of interesting opportunities and challenges, many of which have not been adequately dealt with by existing applications. Current smartwatch messaging systems fail to adequately address the problem of smartwatches requiring two-handed interactions. This paper presents Tap 'n' Shake, a novel gesture-based messaging system for Android smartwatches and smartphones addressing the problem of two-handed interactions by utilising various motion-gestures within the applications. The results of a user evaluation carried out with sixteen subjects demonstrated the usefulness and usability of using gestures over two-handed interactions for smartwatches. Additionally, the study provides insight into the types of gestures that subjects preferred to use for various actions in a smartwatch-smartphone messaging system.
Geo-Opportunistic Routing for Vehicular Networks

Road topology information has been recently used to assist geographic routing in urban vehicular environments to improve the overall routing performance. However, the unreliable nature of wireless channels due to motion and obstructions still makes road topology assisted geographic routing challenging. In this article, we begin by reviewing conventional road topology assisted geographic routing protocols and investigate the robust routing protocols that address and help overcome the unreliable wireless channels. We then present TOpology-assisted Geo-Opportunistic routing (TO-GO) that incorporates topology assisted geographic routing with opportunistic forwarding. That is, the routing protocol exploits the simultaneous packet receptions induced by the broadcast nature of wireless medium and performs opportunistic forwarding via a subset of the neighbors that have received the packet correctly. Our simulation results confirm TO-GO’s superior robustness to channel errors and collisions as compared to conventional topology-assisted geographic routing protocols.
Characterization of a NifS-Like Chloroplast Protein from Arabidopsis. Implications for Its Role in Sulfur and Selenium Metabolism1

NifS-like proteins catalyze the formation of elemental sulfur (S) and alanine from cysteine (Cys) or of elemental selenium (Se) and alanine from seleno-Cys. Cys desulfurase activity is required to produce the S of iron (Fe)-S clusters, whereas seleno-Cys lyase activity is needed for the incorporation of Se in selenoproteins. In plants, the chloroplast is the location of (seleno) Cys formation and a location of Fe-S cluster formation. The goal of these studies was to identify and characterize chloroplast NifS-like proteins. Using seleno-Cys as a substrate, it was found that 25% to 30% of the NifS activity in green tissue in Arabidopsis is present in chloroplasts. A cDNA encoding a putative chloroplast NifS-like protein, AtCpNifS, was cloned, and its chloroplast localization was confirmed using immunoblot analysis and in vitro import. AtCpNIFS is expressed in all major tissue types. The protein was expressed in Escherichia coli and purified. The enzyme contains a pyridoxal 5′ phosphate cofactor and is a dimer. It is a type II NifS-like protein, more similar to bacterial seleno-Cys lyases than to Cys desulfurases. The enzyme is active on both seleno-Cys and Cys but has a much higher activity toward the Se substrate. The possible role of AtCpNifS in plastidic Fe-S cluster formation or in Se metabolism is discussed.
Sudden Loss of Memory

part, together with the progressive and scientific development of the barbiturates and other anaesthetic and analgesic agents, in the recent remarkable advance in the methods of producing anaesthesia, muscular quiescence, and adjustment of the blood pressure, to meet the needs of surgery. It is obvious, I think, that these improvements, all dependent on a scientifically based medicinal therapeutics, together with the now rapidly improving methods of establishing and physiologically controlling an artificial circulation, are playing essential parts in the dramatically successful extensions of surgery to the heart and its great vessels, and to the other thoracic organs.
Persistence software: bridging object-oriented programming and relational databases

Building object-oriented applications which access relational data introduces a number of technical issues for developers who are making the transition to C++. We describe these issues and discuss how we have addressed them in Persistence, an application development tool that uses an automatic code generator to merge C++ applications with relational data. We use client-side caching to provide the application program with efficient access to the data.