Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutational signatures of redox stress in yeast single-strand DNA and of aging in human mitochondrial DNA share a common feature

Redox stress is a major hallmark of cancer. Analysis of thousands of sequenced cancer exomes and whole genomes revealed distinct mutational signatures that can be attributed to specific sources of DNA lesions. Clustered mutations discovered in several cancer genomes were linked to single-strand DNA (ssDNA) intermediates in various processes of DNA metabolism. Previously, only one clustered mutational signature had been clearly associated with a subclass of ssDNA-specific apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) cytidine deaminases. Others remain to be elucidated. We report here deciphering of the mutational spectra and mutational signature of redox stress in ssDNA of budding yeast and the signature of aging in human mitochondrial DNA. We found that the predominance of C to T substitutions is a common feature of both signatures. Measurements of the frequencies of hydrogen peroxide–induced mutations in proofreading-defective yeast mutants supported the conclusion that hydrogen peroxide–induced mutagenesis is not the result of increased DNA polymerase misincorporation errors but rather is caused by direct damage to DNA. Proteins involved in modulation of chromatin status play a significant role in prevention of redox stress–induced mutagenesis, possibly by facilitating protection through modification of chromatin structure. These findings provide an opportunity for the search and identification of the mutational signature of redox stress in cancers and in other pathological conditions and could potentially be used for informing therapeutic decisions. In addition, the discovery of such signatures that may be present in related organisms should also advance our understanding of evolution.
Rapid prototyping with a local geolocation API

Geolocation technology provides the ability to target content and services to users visiting specific locations. There is an expanding growth of device features and Web Application Programming Interfaces (APIs) supporting the development of applications with geolocation services on mobile platforms. However, to be effective, these applications rely on the availability of broadband networks which are not readily available in various developing countries, especially Africa. We propose a geolocation API for the Orange Emerginov Platform which keeps geolocation data in an offline environment and periodically synchronises with its online database. The API also has a set of new features like categorisation and shortest path. It has been successfully implemented and tested with geolocation data of Mauritius, consumed by mobile applications. Our result demonstrates reduction of response time around 80% for some features, when compared with other online Web APIs.
A content-aware hybrid architecture for answering questions from open-domain texts

The current work blends the different paradigms of Question Answering systems and presents a content-aware hybrid architecture for an open-domain factoid questions. It combines a knowledge-based, information extraction-based and a web-based approach in a pipelined architecture to construct an answer to a question keeping the context and discourse of the question in view. The proposed semantic-aware hybrid architecture was compared with other QA systems designed over standard benchmark data. The work has shown enough potential in terms of accuracy and time domain complexity and can be used effectively as a semantic understanding-based QA system.
iPhone-based portable brain control wheelchair

A novel system which uses brain computer interface (BCI) technology and an iPhone to control wheelchair is developed. This system is developed with an aim to assist people suffering from spinal cord injuries (SCI), and amyotrophic lateral sclerosis (ALS), due to the inability to move limbs and body caused by death of nerve cells. The proposed system uses an iPhone to process the brain signals (EEG), specifically the attention signals, and direct corresponding commands to an assistive device, such as wheelchair, wirelessly. Comparing to other BCI system comprises of a bulky laptop and multi-electrodes, the proposed system is portable, cost-effective and ease of use. Potentially, not only people who are suffering from spinal cord injuries can benefit from this system, it extended to assisting elderly or people suffering from limb muscle disorder. The system structure and experimental results will be illustrated in this paper. No similar system is reported yet.
Expression of Ca2+-Binding Buffer Proteins in the Human and Mouse Retinal Neurons

Ca2+-binding buffer proteins (CaBPs) are widely expressed by various neurons throughout the central nervous system (CNS), including the retina. While the expression of CaBPs by photoreceptors, retinal interneurons and the output ganglion cells in the mammalian retina has been extensively studied, a general description is still missing due to the differences between species, developmental expression patterns and study-to-study discrepancies. Furthermore, CaBPs are occasionally located in a compartment-specific manner and two or more CaBPs can be expressed by the same neuron, thereby sharing the labor of Ca2+ buffering in the intracellular milieu. This article reviews this topic by providing a framework on CaBP functional expression by neurons of the mammalian retina with an emphasis on human and mouse retinas and the three most abundant and extensively studied buffer proteins: parvalbumin, calretinin and calbindin.
Learning Relevance of Web Resources across Domains to Make Recommendations

Most traditional recommender systems focus on the objective of improving the accuracy of recommendations in a single domain. However, preferences of users may extend over multiple domains, especially in the Web where users often have browsing preferences that span across different sites, while being unaware of relevant resources on other sites. This work tackles the problem of recommending resources from various domains by exploiting the semantic content of these resources in combination with patterns of user browsing behavior. We overcome the lack of overlaps between domains by deriving connections based on the explored semantic content of Web resources. We present an approach that applies Support Vector Machines for learning the relevance of resources and predicting which ones are the most relevant to recommend to a user, given that the user is currently viewing a certain page. In real-world datasets of semantically-enriched logs of user browsing behavior at multiple Web sites, we study the impact of structure in generating accurate recommendations and conduct experiments that demonstrate the effectiveness of our approach.
An online noise filter for eye-tracker data recorded in a virtual environment

A Recursive Online Weight Average filter (ROWA) is proposed to remove and replace noisy data obtained from eye tracker. Since the filter can be implemented online, it can detect and replace noisy data using solely past records. Simulations results indicate that the filter achieved the same performance compared to other standard offline filters while being simpler.
Cost-Effective PEDOT:PSS Temperature Sensors Inkjetted on a Bendable Substrate by a Consumer Printer

In this work, we report on a fabrication protocol to produce fully inkjet-printed temperature sensors on a bendable polyethylene terephthalate (PET) substrate. The sensing layer is made of polymer-based Poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) ink that is electrically contacted by an underlying interdigitated electrode (IDE) structure based on a silver nanoparticle (AgNP) ink. Both inks are available commercially, and no further ink processing is needed to print them using a cost-effective consumer printer with standard cartridges. The fabricated sensor modules are tested for different IDE dimensions and post-deposition treatments of the AgNP film for their response to a temperature range of 20 to 70 °C and moisture range of 20 to 90% RH (relative humidity). Attributed to the higher initial resistance, sensor modules with a larger electrode spacing of 200 µm show a higher thermal sensitivity that is increased by a factor of 1.8 to 2.2 when compared to sensor modules with a 150 µm-spacing. In all cases, the sensors exhibit high linearity towards temperature and a response comparable to state of the art.
Glioblastoma vs temozolomide: can the red queen race be won?

ABSTRACT Glioblastoma is the most invasive form of brain tumor. Although temozolomide chemotherapy has been shown to significantly improve survival in patients with GBM, this increase is only trivial. The underlying cause is that many GBMs do not respond to temozolomide, and the rest produces resistance. In the past two decades, many attempts have been made to understand resistance mechanisms and to combine other treatments with temozolomide to maximize patient benefit. Unfortunately, it seems to be a red queen game, and the speed of disease development is as fast as the progress in the field. In order to win this game, a comprehensive approach is needed to decipher the details of the resistance mechanism and to transfer the basic research to the clinic. This article reviews the following: temozolomide discovery, chemistry, and mechanism of action, and mechanisms of resistance, as well as combination therapy with other strategies.
Embolisation of branches of the superior mesenteric artery in the treatment of haemosuccus pancreaticus

Haemosuccus pancreaticus (HP) is an uncommon cause of upper gastrointestinal (GI) bleeding, most often intermittent, making it difficult to diagnose, becoming fatal. It usually occurs in patients with chronic pancreatitis and is caused by the rupture of a visceral aneurysm within the main pancreatic duct. The association between pseudoaneurysm formation and pancreatitis is well established. Pseudoaneurysm occurs in 3.5%–10% of pancreatitis cases and its rupture is a rare but life-threatening complication of chronic pancreatitis occurring in 6%–8% of patients with pseudocysts and corresponds to less than 1% of cases of GI bleeding. Its diagnosis is challenging, given the intermittent nature of bleeding. Angiographic therapy is considered the first-choice treatment, especially in patients who are stable haemodynamically. We present a case of embolisation of inferior pancreaticoduodenal branches with polyvinyl alcohol microparticles in the treatment of HP.
E2EProf: Automated End-to-End Performance Management for Enterprise Systems

Distributed systems are becoming increasingly complex, caused by the prevalent use of Web services, multi-tier architectures, and grid computing, where dynamic sets of components interact with each other across distributed and heterogeneous computing infrastructures. For these applications to be able to predictably and efficiently deliver services to end users, it is therefore, critical to understand and control their runtime behavior. In a datacenter environment, for instance, understanding the end-to-end dynamic behavior of certain IT subsystems, from the time requests are made to when responses are generated and finally, received, is a key prerequisite for improving application response, to provide required levels of performance, or to meet service level agreements (SLAs). The E2EProf toolkit enables the efficient and nonintrusive capture and analysis of end-to-end program behavior for complex enterprise applications. E2EProf permits an enterprise to recognize and analyze performance problems when they occur - online, to take corrective actions as soon as possible and wherever necessary along the paths currently taken by user requests - end-to-end, and to do so without the need to instrument applications - nonintrusively. Online analysis exploits a novel signal analysis algorithm, termed pathmap, which dynamically detects the causal paths taken by client requests through application and backend servers and annotates these paths with end-to-end latencies and with the contributions to these latencies from different path components. Thus, with pathmap, it is possible to dynamically identify the bottlenecks present in selected servers or services and to detect the abnormal or unusual performance behaviors indicative of potential problems or overloads. Pathmap and the E2EProf toolkit successfully detect causal request paths and associated performance bottlenecks in the RUBiS ebay-like multi-tier Web application and in one of the datacenter of our industry partner, Delta Air Lines.
ON THE PIECEWISE SMOOTHNESS OF ENTROPY SOLUTIONS TO SCALAR CONSERVATION LAWS

The behavior and structure of entropy solutions of scalar convex conservation laws are studied. It is well kn0a.n that such entropy solutioris consist of at most countable number of C1-smooth regions. We obtain new upper. bounds on the higher order derivatives of the entropy solution in any one of its C1-smoothness regions. These bounds enable us to measure the hzgh order piecewise smoothness of the entropy solution. To this end we introduce an appropriate new Cn-semi norm - localized to the smooth part of the entropy solution. and we show that the entropy solution is stable with respect to this norm. \Ye also address the question regarding the number of C1-smoothness pieces, we show that if the initial speed has a finite number of decreasing inflection points then it bounds the number of future shock discontinuities. Loosely speaking this says that in the case of such generic initial data the entropy solution consists of a finite number of smooth pieces, each of which is as smooth as the data permits. It is this type of pzecewise smoothness which is assumed - sometime implicitly - in many finite-dimensional computations for such discontinuous problems.
Evaluations of short-range wireless communications employing ultrasound wave

In recent years, short range wireless communications have been used more and more frequently in our life. But the electromagnetic fields waves also have some disadvantages. One of these disadvantages is health problems. Many studies shows the electromagnetic field waves using for communication may damage our health. And in most hospitals, they also have bans on the use of mobile phones and wide area networks because of Electromagnetic Interference. So in this paper, we studied the use of ultrasound for wireless communication in air, instead of using electromagnetic field wave. An Alternating-Direction Implicit Finite-Difference Time-Domain (ADI-FDTD) method is developed to simulate the ultrasonic wave communication system. The ADI-FDTD simulations make it possible to better understand the behavior of an ultrasonic signal. Experimental data is also presented to compare with simulation. The results show that such a system is feasible in principle for communications using ultrasound.
A method for topology conformance tests under logical constraints

Common Criteria(CC) provides only the standard for evaluating information security product or system. Conformance test is considered from a statistical point of view, while the determination of whether the topology is consistent with the standard depends on a conformance test. CC based topology conformance test is in trouble without an effective method. In this paper, a method for topology conformance test was presented and an algorithm for topology conformance test under logical constraints was introduced. In our method, the topology is described by a matrix and the logical constraints are stored using Binary Decision Diagrams (BDDs) data structure. From the experimental results, we can see the method is efficient enough for topology conformance test.
Communication-limited stabilisability of Jump Markov linear systems

This paper investigates the control of fully observed, scalar jump Markov linear systems in which feedback is transmitted at ﬁnite data rates over noiseless digital channels. In particular, the objective is to ﬁnd the inﬁmum data rate, over all causal coding and control laws, at which such a system may be asymptotically stabilised in m th absolute output moment. The control problem is ﬁrst shown to be equivalent to quantisation of the initial output under a mean-m th-power-error criterion. Quantisation methods are then applied to derive the smallest stabilising data rate in terms of the Perron-Frobenius eigenvalue of a matrix deﬁned by the transition probabilities, the dynamic parameters and the power m .
Efficacy of Er

AIM To evaluate the adjunctive efficacy of Er:YAG laser use with mechanical scaling and root planing (SRP) for non-surgical treatment of periodontitis. MATERIALS AND METHODS In a randomized, single-blinded, controlled trial, 27 patients were recruited. Using a split-mouth design, two quadrants were randomly allocated into either a test group or a control group. The test quadrants received Er:YAG laser (ERL; 100 mJ/pulse; 15 Hz to hard tissue and 50 mJ/pulse; 30 Hz to soft tissue) plus SRP treatment, while the control quadrants received SRP only. We evaluated periodontal indexes, including probing depth (PD), clinical attachment level (CAL), bleeding index (BI), and plaque index (PLI) at baseline, 3 months, and 6 months. RESULTS The PD and CAL means in the ERL + SRP group were significantly lower than those in the SRP group at 3-month follow-up (PD: 2.98 ± 0.38 mm vs. 3.09 ± 0.35 mm; CAL: 4.51 ± 0.69 mm vs. 4.72 ± 0.67 mm) and 6-month follow-up (PD: 2.91 ± 0.31 mm vs. 3.02 ± 0.30 mm; CAL: 4.52 ± 0.65 mm vs. 4.72 ± 0.66 mm; p = 0.03 for both PD and CAL). There were no significant differences in BI and PLI between two groups. CONCLUSIONS The Er:YAG laser treatment combined with conventional SRP significantly improved PD and CAL compared to SRP therapy alone; however, these differences were very small and, as a result, the adjunctive effect of Er:YAG laser is likely to be minimal clinically important.
Smyd2 conformational changes in response to p53 binding: role of the C‐terminal domain

Smyd2 lysine methyltransferase regulates monomethylation of histone and nonhistone lysine residues using S‐adenosylmethionine cofactor as the methyl donor. The nonhistone interactors include several tumorigenic targets, including p53. Understanding this interaction would allow the structural principles that underpin Smyd2‐mediated p53 methylation to be elucidated. Here, we performed μ‐second molecular dynamics (MD) simulations on binary Smyd2‐cofactor and ternary Smyd2‐cofactor‐p53 peptide complexes. We considered both unmethylated and monomethylated p53 peptides (at Lys370 and Lys372). The results indicate that (a) the degree of conformational freedom of the C‐terminal domain of Smyd2 is restricted by the presence of the p53 peptide substrate, (b) the Smyd2 C‐terminal domain shows distinct dynamic properties when interacting with unmethylated and methylated p53 peptides, and (c) Lys372 methylation confines the p53 peptide conformation, with detectable influence on Lys370 accessibility to the cofactor. These MD results are therefore of relevance for studying the biology of p53 in cancer progression.
Manganese Mediated Formic Acid Dehydrogenation.

A robust and rapid manganese formic acid (FA) dehydrogenation catalyst is reported. The manganese is supported by the recently developed, hybrid backbone chelate ligand tBuPNNOP (tBuPNNOP = 2,6-(ditertbutylphosphinito)(ditertbutylphosphinamine)-pyridine) (1) and the catalyst is readily prepared with MnBrCO5 to form [(tBuPNNOP)Mn(CO)2][Br] (2). Dehydrohalogenation of 2 generated the neutral five coordinate complex (tBuPNNOP)Mn(CO)2 (3). Dehydrogenation of FA by 2 and 3 was found to be highly efficient, exhibiting turnover frequencies (TOFs) exceeding 8500 hr-1, rivaling many noble metal systems. The parent chelate, tBuPONOP (tBuPONOP = 2,6-bis(ditertbutylphosphinito)pyridine) or tBuPNNNP (tBuPNNNP = 2,6-bis (ditertbutylphosphinamine)pyridine), coordination complexes of Mn were synthesized respectively affording [(tBuPONOP)Mn(CO)2][Br] (4) and [(tBuPNNNP)Mn(CO)2][Br] (5). FA dehydrogenation with the hybrid-ligand supported 2 exhibits superior catalysis to 4 and 5.
The thermodynamic advantage of DNA oligonucleotide 'stacking hybridization' reactions: energetics of a DNA nick.

'Stacking hybridization reactions' wherein two or more short DNA oligomers hybridize in a contiguous tandem orientation onto a longer complementary DNA single strand have been employed to enhance a variety of analytical oligonucleotide hybridization schemes. If the short oligomers anneal in perfect head-to-tail register the resulting duplex contains a nick at every boundary between hybridized oligomers. Alternatively, if the short oligomers do not hybridize precisely in register, i.e. single strand regions on the longer strand are left unbound, gaps are formed between regions where short oligomers bind. The resulting gapped DNA duplexes are considerably less stable than their nicked duplex analogs. Formation of base pair stacking interactions between neighboring oligomers at the nicks that do not occur in gapped duplexes has been proposed as the source of the observed added stability. However, quantitative evidence supporting this hypothesis for DNA has not been reported. Until now, a direct comparison of the thermodynamics of DNA nicks versus DNA gaps has not been performed. In this communication we report such a comparison. Analysis of optical melting experiments in a well defined molecular context enabled quantitative evaluations of the relative thermodynamic difference between nicked and gapped DNA duplexes. Results of the analysis reveal that a nick may be energetically favored over a gap by at least 1.4 kcal/mol and perhaps as much as 2.4 kcal/mol. The presence of a 5'phosphate at a nick or gap fails to significantly affect their stabilities.
Life Cycle Effects of Job Displacement in Brazil

This paper estimates the consequences of the decline of the Brazilian manufacturing sector for displaced workers. I estimate that earnings decline by nearly 50% after displacement relative to one year prior. About a quarter of the initial earnings loss is attributable to reduced hours of work rather than lower wages. However, hours recover fully within one year of displacement, while wages remain about a third lower. Allowing the displacement effect to differ by age yields a surprising U-shaped curve. Middle aged workers are hit hardest by a layoff, with younger and older workers relatively better off. For workers aged 35-40, the initial earnings loss reaches 70%. This is a surprising finding because most theories of job loss predict a negative relationship between the wage loss on displacement and the length of tenure on the pre-displacement job, which is increasing in age. I account for these facts with a simple model in which the ratio of specific to general human capital reaches a peak at middle age. Young workers have little specific capital and a low specific-general human capital ratio. In the early years of one’s career, specific capital (whether due to investments in specific skills or in search) accumulates much more rapidly than general human capital. Around ages 35 to 40, this trend reverses and the returns to general skills rise more rapidly. Thus, the accumulation of general skills serves to reduce the effect of job displacement at older ages despite increasing average job tenure. These findings suggest that major market reforms may have larger than anticipated effects because the primary losers are workers in the middle of their working life. This is also important from a welfare perspective because these workers are the most likely to fall through the cracks of social safety nets, which typically target younger and older workers.