Miracle-dz/UniFAR-FTUs huggingface dataset:
Shuttling along DNA and directed processing of D-loops by RecQ helicase support quality control of homologous recombination

Significance RecQ helicase and its eukaryotic homologs are thought to play crucial roles in the quality control of homologous recombination (HR)-based DNA repair. These enzymes have multiple functions in processes that can either promote or suppress HR. A major role suggested for RecQ is the selective inhibition of illegitimate recombination events that could lead to loss of genome integrity. How can RecQ enzymes perform an exceptionally wide range of activities and selectively inhibit potentially harmful recombination events? Here, we propose a model in which the conserved domain architecture of RecQ senses and responds to the geometry of DNA substrates to achieve HR quality control. Cells must continuously repair inevitable DNA damage while avoiding the deleterious consequences of imprecise repair. Distinction between legitimate and illegitimate repair processes is thought to be achieved in part through differential recognition and processing of specific noncanonical DNA structures, although the mechanistic basis of discrimination remains poorly defined. Here, we show that Escherichia coli RecQ, a central DNA recombination and repair enzyme, exhibits differential processing of DNA substrates based on their geometry and structure. Through single-molecule and ensemble biophysical experiments, we elucidate how the conserved domain architecture of RecQ supports geometry-dependent shuttling and directed processing of recombination-intermediate [displacement loop (D-loop)] substrates. Our study shows that these activities together suppress illegitimate recombination in vivo, whereas unregulated duplex unwinding is detrimental for recombination precision. Based on these results, we propose a mechanism through which RecQ helicases achieve recombination precision and efficiency.
Poly (N‐acryloxysuccinimide‐co‐ethylene glycol dimethacrylate) precursor monolith and its post polymerization modification with alkyl ligands, trypsin and lectins for reversed‐phase chromatography, miniaturized enzyme reactors and lectin affinity chromatography, respectively

This investigation was aimed at introducing a monolithic precursor that can be conveniently grafted with the desired chromatographic ligand via the process of post polymerization modification (PPM). The precursor was obtained by the in‐situ polymerization of N‐acryloxysuccinimide (NAS) and ethylene glycol dimethacrylate (EDMA) in a narrow bore stainless steel column of 1 mm i.d. yielding a poly(NAS‐co‐EDMA) monolithic column designated as the poly(NAS‐co‐EDMA) monolith (NASM) column. In a first PPM, the NASM column was bonded with octadecyl (OD) ligands yielding a nonpolar NASM‐OD column that proved useful for reversed phase chromatography (RPC) of proteins in gradient elution at increasing %ACN in the mobile phase. NASM‐OD resulted from the reaction between the N‐hydroxysuccinimide of NASM with octadecyl amine. In a second PPM, NASM was surface immobilized with trypsin generating a proteolytic narrow bore enzyme reactor called NASM‐trypsin immobilized enzyme reactor (IMER) that permitted the online digestion of proteins in a 20‐min single pass through the IMER incorporated in a setup equipped with a short RPC column to achieve simultaneously a peptide tryptic map. This constituted a rapid turnover whereby ∼95% of the protein was hydrolyzed by the immobilized trypsin. In a third PPM, the NASM column was surface immobilized with three different lectins (LCA, Con A and RCA) having complementary affinities toward serum glycoproteins thus permitting the capture of a wide range of glycoproteins/glycoforms. The three NASM‐lectin columns when operated in a tandem format led to assessing the level of the various glycoforms in human serum via LC‐MS/MS analysis of the captured protein fractions by each NASM‐lectin column.
GPS Assisted Broadcasting in Mobile Ad-Hoc Networks

Broadcast protocols play a vital role in building services and applications for multihop, mobile, wireless ad hoc networks (MANET). This paper describes the design, implementation and evaluation of a new broadcast protocol for a multihop, mobile wireless ad hoc network that provides signiﬁcantly better performance than the currently existing protocols. In particular, this protocol provides lower end-to-end delivery latency and higher coverage than the existing protocols. It requires relatively small number of message exchanges, minimizes collisions, and tolerates dramatic changes in the network due to node movement. The protocol uses the unit disk graph model and a clever combination of FDMA and TDMA.
rRNA Operon Copy Number Can Explain the Distinct Epidemiology of Hospital-Associated Methicillin-Resistant Staphylococcus aureus

ABSTRACT The distinct epidemiology of original hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) and early community-associated MRSA (CA-MRSA) is largely unexplained. S. aureus carries either five or six rRNA operon copies. Evidence is provided for a scenario in which MRSA has adapted to the hospital environment by rRNA operon loss (six to five copies) due to antibiotic pressure. Early CA-MRSA, in contrast, results from wild-type methicillin-susceptible S. aureus (MSSA) that acquired mecA without loss of an rRNA operon. Of the HA-MRSA isolates (n = 77), 67.5% had five rRNA operon copies, compared to 23.2% of the CA-MRSA isolates (n = 69) and 7.7% of MSSA isolates (n = 195) (P < 0.001). In addition, 105 MSSA isolates from cystic fibrosis patients were tested, because these patients are repeatedly treated with antibiotics; 32.4% of these isolates had five rRNA operon copies. For all subsets, a correlation between resistance profile and rRNA copy number was found. Furthermore, we showed that in vitro antibiotic pressure may result in rRNA operon copy loss. We also showed that without antibiotic pressure, S. aureus isolates containing six rRNA copies are more fit than isolates with five copies. We conclude that HA-MRSA and cystic fibrosis isolates most likely have adapted to an environment with high antibiotic pressure by the loss of an rRNA operon copy. This loss has facilitated resistance development, which promoted survival in these niches. However, strain fitness decreased, which explains their lack of success in the community. In contrast, CA-MRSA isolates retained six rRNA operon copies, rendering them fitter and thereby able to survive and spread in the community.
Hydrogen and helium implants for obtaining high-resistance layers in n-type 4H silicon carbide

The effect of light ion implantation damage on the resistivity of n-type 4H-silicon carbide was investigated using hydrogen and helium. Resistivity variation as a function of post-implant annealing temperature and measurement temperature was studied. Maximum resistivities of the order of 10/sup 7/ and 10/sup 8/ /spl Omega/-cm were observed for hydrogen and helium implanted samples, respectively, at room temperature. With increasing measurement temperature, resistivities decreased with activation energies of 0.36 and 0.16 eV for hydrogen and helium, respectively. Resistivities start to decrease after annealing at /spl ges/600/spl deg/C. Rutherford backscattering measurements show implantation damage in the high-resistivity samples.
Tailoring of Perpendicular Magnetic Anisotropy in Dy13Fe87 Thin Films with Hexagonal Antidot Lattice Nanostructure

In this article, the magnetic properties of hexagonally ordered antidot arrays made of Dy13Fe87 alloy are studied and compared with corresponding ones of continuous thin films with the same compositions and thicknesses, varying between 20 nm and 50 nm. Both samples, the continuous thin films and antidot arrays, were prepared by high vacuum e-beam evaporation of the alloy on the top-surface of glass and hexagonally self-ordered nanoporous alumina templates, which serve as substrates, respectively. By using a highly sensitive magneto-optical Kerr effect (MOKE) and vibrating sample magnetometer (VSM) measurements an interesting phenomenon has been observed, consisting in the easy magnetization axis transfer from a purely in-plane (INP) magnetic anisotropy to out-of-plane (OOP) magnetization. For the 30 nm film thickness we have measured the volume hysteresis loops by VSM with the easy magnetization axis lying along the OOP direction. Using magnetic force microscopy measurements (MFM), there is strong evidence to suggest that the formation of magnetic domains with OOP magnetization occurs in this sample. This phenomenon can be of high interest for the development of novel magnetic and magneto-optic perpendicular recording patterned media based on template-assisted deposition techniques.
Dynamic item-based recommendation algorithm with time decay

Nowadays, the customers involved in e-commercial business are increasing rapidly. To meet their needs, many famous companies, like Amazon and Netflix, place building and optimizing e-commerce recommender systems as their priority. Recommender systems aim to provide personalized advice through mining and discovering the interests and consuming patterns of customers. Generally speaking, recommender systems use two strategies to provide recommendations, namely content-based and collaborative filtering (CF). Furthermore, two primary approaches, namely user-based and item-based, are widely used to build the CF-based top-N recommender systems. Item-based approaches have been empirically proved to provide comparable or even better recommendations than those provided by user-based approaches. In this paper, we first introduce the concept of “time decay” by giving its mathematical definition and redefine the item-to-item similarity function based on time decay. Then we study three patterns of time decay and show their effects on recommendations. Based on the above work, finally we present the dynamic item-based top-N recommendation algorithm that uses time decay to build models and provide recommendations. Our experiments on real data show that the proposed algorithm provides better recommendations.
Selective weakening and post-tensioning for retrofit of non-ductile R.C. exterior beam-column joints

A counter-intuitive “selective weakening” (SW) seismic retrofit strategy for non-ductile RC frame is presented. By focusing on increasing the global displacement and ductility capacity, simple retrofit interventions such as selective weakening of the beams and external post-tensioning of the beam-column joints could change the local inelastic mechanism and result in improved global lateral and energy dissipation capacities. After an overview of the SW retrofit concept, this paper presents the experimental and numerical investigations of SW retrofit techniques for non-ductile RC exterior joints. The experimental results of nine 2/3-scaled exterior joint subassemblies– as-built and SW retrofitted tests are briefly presented. Parameters considered in the tests included the presence of column lap-splice, slab and transverse beams, level of post-tensioning forces and location of beam weakening. Numerical investigation using 3D micro-plane concrete model within smeared fracture mechanics finite-element modelling is demonstrated for SW retrofitted joints. Lastly, a preliminary design procedure is outlined for the design of SW retrofit for exterior beam-column joints. With its economical, non-invasive and low-technology intensity approach, SW retrofit has potential for a wide implementation.
Temporal Human Action Segmentation via Dynamic Clustering

We present an effective dynamic clustering algorithm for the task of temporal human action segmentation, which has comprehensive applications such as robotics, motion analysis, and patient monitoring. Our proposed algorithm is unsupervised, fast, generic to process various types of features, and applicable in both the online and offline settings. We perform extensive experiments of processing data streams, and show that our algorithm achieves the state-of-the-art results for both online and offline settings.
Getting ready to use control: Advances in the measurement of young children’s use of proactive control

A key developmental transition in executive function is in the temporal dynamics of its engagement: children shift from reactively calling to mind task-relevant information as needed, to being able to proactively maintain information across time in anticipation of upcoming demands. This transition is important for understanding individual differences and developmental changes in executive function; however, methods targeting its assessment are limited. We tested the possibility that Track-It, a paradigm developed to measure selective sustained attention, also indexes proactive control. In this task children must track a target shape as it moves unpredictably among moving distractors, and identify where it disappears, which may require proactively maintaining information about the target or goal. In two experiments (5–6 year-olds, Ns = 33, 64), children's performance on Track-It predicted proactive control across two established paradigms. These findings suggest Track-It measures proactive control in children. Theoretical possibilities regarding how proactive control and selective sustained attention may be related are also discussed.
Biosynthetic Genes for the Tetrodecamycin Antibiotics

ABSTRACT We recently described 13-deoxytetrodecamycin, a new member of the tetrodecamycin family of antibiotics. A defining feature of these molecules is the presence of a five-membered lactone called a tetronate ring. By sequencing the genome of a producer strain, Streptomyces sp. strain WAC04657, and searching for a gene previously implicated in tetronate ring formation, we identified the biosynthetic genes responsible for producing 13-deoxytetrodecamycin (the ted genes). Using the ted cluster in WAC04657 as a reference, we found related clusters in three other organisms: Streptomyces atroolivaceus ATCC 19725, Streptomyces globisporus NRRL B-2293, and Streptomyces sp. strain LaPpAH-202. Comparing the four clusters allowed us to identify the cluster boundaries. Genetic manipulation of the cluster confirmed the involvement of the ted genes in 13-deoxytetrodecamycin biosynthesis and revealed several additional molecules produced through the ted biosynthetic pathway, including tetrodecamycin, dihydrotetrodecamycin, and another, W5.9, a novel molecule. Comparison of the bioactivities of these four molecules suggests that they may act through the covalent modification of their target(s). IMPORTANCE The tetrodecamycins are a distinct subgroup of the tetronate family of secondary metabolites. Little is known about their biosynthesis or mechanisms of action, making them an attractive subject for investigation. In this paper we present the biosynthetic gene cluster for 13-deoxytetrodecamycin in Streptomyces sp. strain WAC04657. We identify related clusters in several other organisms and show that they produce related molecules.
Dissimilar Crystal Proteins Cry5Ca1 and Cry5Da1 Synergistically Act against Meloidogyne incognita and Delay Cry5Ba-Based Nematode Resistance

ABSTRACT Cry proteins of Bacillus thuringiensis (Bt) have been successfully used as biopesticides and in transgenic crops throughout the world. However, resources against the most serious agricultural pathogens, plant root-knot nematodes, are limited. The genomes of several highly nematicidal virulent Bt strains from our laboratory have been sequenced, facilitating the identification of novel Cry proteins and other virulence factors. We identified two novel Cry proteins, Cry5Ca1 and Cry5Da1, that exhibit high toxicity against Meloidogyne incognita. Using the Caenorhabditis elegans model, the two Cry5 toxins were shown to negatively affect nematode life span, fertility, and survival. The 50% lethal concentrations (LC50s) of Cry5Ca1 and Cry5Da1 were 57.22 μg/ml and 36.69 μg/ml, respectively. Moreover, a synergistic effect (synergism factor, 1.61 to 2.04) was observed for nematicidal toxicity of Cry5Ca1 and Cry5Da1, which is accordant with the phylogenetic results suggesting that domain II of the two novel Cry5 toxins evolved into two independent clades. Through comparison of the depressed degree of toxicity in the β-methylgalactoside detoxification test, we found that the novel toxin Cry5D possesses a different galactose-binding epitope; meanwhile, the finding that Cry5D does not share a motif (GXXXE) in the corresponding loop of domain II with Cry5B could explain the different galactose binding performance. Additionally, low-level cross-resistance of C. elegans bre mutant strains was evident between Cry5B and Cry5D. These results suggest that Cry5D can be used as an alternative to delay the potential resistance of nematodes to Cry5B. IMPORTANCE Although proper gene resources for Bt crops against the most serious agricultural pathogens, plant root-knot nematodes, are limited, we have identified two novel nematicidal toxins, Cry5Ca1 and Cry5Da1, against M. incognita, which have supplied more gene candidates for Bt crops designed against nematodes. Moreover, the association of the dissimilarity between Cry5Da1 and Cry5Ba1 and their low cross-resistance can be attributed not only to a low sequence similarity of domain II but also to the structural difference of the key motif and receptor-binding epitope in the loops. This association facilitates the selection of a proper candidate for the prospective design of pyramided Bt crops that can delay potential resistance.
Deconstructing racial differences: the effects of quality of education and cerebrovascular risk factors.

OBJECTIVES To evaluate the effects of vascular conditions and education quality on cognition over time in White and African American (AA) older adults. METHOD We investigated cross-sectional and longitudinal racial differences in executive functioning (EF) and memory composites among Whites (n = 461) and AAs (n = 118) enrolled in a cohort study. We examined whether cerebrovascular risk factors and Shipley Vocabulary scores (a proxy for education quality) accounted for racial differences. RESULTS On average, AAs had lower quality of education and more cerebrovascular risk factors including hypertension, diabetes, and obesity. AAs had lower mean EF and memory at baseline, but there were no group differences in rates of decline. Cross-sectional racial differences in EF and memory persisted after controlling for vascular disease, but disappeared when controlling for Shipley Vocabulary. DISCUSSION Quality of education appears to be more important than cerebrovascular risk factors in explaining cross-sectional differences in memory and EF performance between White and AA older adults. Further investigation is needed regarding the relative contribution of education quality and cerebrovascular risk factors to cognitive decline among ethnically/racially diverse older adults.
Multi-Task Learning for Argumentation Mining in Low-Resource Settings

We investigate whether and where multi-task learning (MTL) can improve performance on NLP problems related to argumentation mining (AM), in particular argument component identification. Our results show that MTL performs particularly well (and better than single-task learning) when little training data is available for the main task, a common scenario in AM. Our findings challenge previous assumptions that conceptualizations across AM datasets are divergent and that MTL is difficult for semantic or higher-level tasks.
ERP Evidence for Implicit Priming of Top–Down Control of Attention

Proportion congruency effects are the observation that the magnitude of the Stroop effect increases as the proportion of congruent trials in a block increases. Contemporary work shows that proportion effects can be specific to a particular context. For example, in a Simon task in which items appearing above fixation are mostly congruent and items appearing below fixation are mostly incongruent, the Simon effect is larger for the items appearing at the top. There is disagreement as to whether these context-specific effects result from simple associative learning or, instead, a type of conflict-mediated associative learning. Here, we address this question in an ERP study using a Simon task in which the proportion congruency effect was context-specific, manipulating the proportion of congruent trials based on location (upper vs. lower visual field). We found significant behavioral proportion congruency effects that varied with the specific contexts. In addition, we observed that the N2 response of the ERPs to the stimuli was larger in amplitude for the high congruent (high conflict) versus low congruent (low conflict) conditions/contexts. Because the N2 is known to be greater in amplitude also for trials where conflict is high and is believed to be an electrical signal related to conflict detection in the medial frontal cortex, this supports the idea that conflict-mediated associative learning is involved in the proportion congruency effect.
Internet-supported versus face-to-face cognitive behavior therapy for depression

Major depression and depressive symptoms are highly prevalent and there is a need for different forms of psychological treatments that can be delivered from a distance at a low cost. In the present review the authors contrast face-to-face and Internet-delivered cognitive behavior therapy (ICBT) for depression. A total of five studies are reviewed in which guided ICBT was directly compared against face-to-face CBT. Meta-analytic summary statistics were calculated for the five studies involving a total of 429 participants. The average effect size difference was Hedge’s g = 0.12 (95% CI: −0.06–0.30) in the direction of favoring guided ICBT. The small difference in effect has no implication for clinical practice. The overall empirical status of clinician-guided ICBT for depression is commented on and future challenges are highlighted. Among these are developing treatments for patients with more severe and long-standing depression and for children, adolescents and the elderly. Also, there is a need to investigate mechanisms of change.
Secure comics: an interactive comic series for improving cyber security and privacy

Users could experience Secure Comics online2, and on iPads . Users select a comic to read from the title screen (Three comics are available. See Figure 1, A), and navigate by pressing a forward/backward button, or use the section buttons. Parts of the comic enable interactive exploration of the content (Two examples are provided in Figure 1). Each comic takes approximately 5 to 8 minutes for adults to read.