Miracle-dz/UniFAR-FTUs huggingface dataset:
The effects of transcription and recombination on mutational dynamics of short tandem repeats

Abstract Short tandem repeats (STR) are ubiquitous components of the genomic architecture of most living organisms. Recent work has highlighted the widespread functional significance of such repeats, particularly around gene regulation, but the mutational processes underlying the evolution of these highly abundant and highly variable sequences are not fully understood. Traditional models assume that strand misalignment during replication is the predominant mechanism, but empirical data suggest the involvement of other processes including recombination and transcription. Despite this evidence, the relative influences of these processes have not previously been tested experimentally on a genome-wide scale. Using deep sequencing, we identify mutations at >200 microsatellites, across 700 generations in replicated populations of two otherwise identical sexual and asexual Saccharomyces cerevisiae strains. Using generalized linear models, we investigate correlates of STR mutability including the nature of the mutation, STR composition and contextual factors including recombination, transcription and replication origins. Sexual capability was not a significant predictor of microsatellite mutability, but, intriguingly, we identify transcription as a significant positive predictor. We also find that STR density is substantially increased in regions neighboring, but not within, recombination hotspots.
Quality and Safety of General Anesthesia with Propofol and Sevoflurane in Children Aged 1-14 Based on Laboratory Parameters

Introduction: Knowledge of anatomic, physiological, biochemical and physical characteristics of children of all age groups, the existing illness and possible pathological response of the organism to the existing situation, require a pediatric anesthesiologist to participate in the preparation of a child for surgical treatment, to choose the best anesthesia technique and medications, and manipulative techniques to enable the scheduled surgical treatment with minimum anesthesia risks. The aim of this clinical study was to prove reliability and quality of propofol or sevoflurane general anesthesia in children in the age group of 1-14 years from the ASA I group and in the elective surgical treatments in duration of 60 minutes, based on preoperative and postoperative levels of laboratory findings (transaminases, blood sugar, urea and creatinine). Materials and methods: the study included 160 patients randomized in two groups based on different approaches: total intravenous anesthesia was used for the propofol group (n=80) (TIVA) and the inhalation technique was used for the sevoflurane group (n=80). Results: statistical evaluation of the obtained results indicates stability of laboratory findings in the immediate postoperative course (after 24 hours) in respect to the preoperative period. Based on the Mann Whitney test (P), preoperative and postoperative blood sugar levels in the sevoflurane vs. propofol group were P=0.152 vs. 0.021; creatinine levels P=0.113 vs. 0.325; urea levels P= 0.016 vs. 0.900; AST levels P=0,031 vs. 0,268 and ALT levels P=0.021 vs. 0.058. Level of significance was P<0.5. Conclusion: Analysis of the examined laboratory parameters show that propofol and sevoflurane provide full security and quality of general anesthesia in children age group 1-14 years, from the ASA I group. All analyzed laboratory levels in the postoperative course remained in their referential values in both groups of participants.
Aedes vittatus (Bigot) mosquito: An emerging threat to public health

Aedes vittatus (Bigot) mosquito is a voracious biter of humans and has a geographical distribution throughout tropical Asia, Africa and the Mediterranean region of Europe. It is predominantly a rock-hole breeder, though it can breed in diverse macro- and micro-habitats. The mosquito plays an important role in the maintenance and transmission of yellow fever (YFV), dengue (DENV), chikungunya (CHIKV) and Zika (ZIKV) viruses. It has been implicated as an important vector of YFV in several African countries as evidenced by repeated virus isolations from the mosquito and its potential to transmit the virus experimentally. Similarly, DENV-2 has been isolated from wild caught Ae. vittatus mosquitoes in Senegal, Africa which has been shown to circulate the virus in sylvatic populations without causing human infection. Experimental studies have shown replication of the virus at a low scale in naturally infected mosquitoes while high rate of infection and dissemination have been reported in parenterally infected mosquitoes. Natural isolation of ZIKV has been reported from Senegal and Cote d’Ivoire from these mosquitoes. They were found highly competent to transmit the virus experimentally and the transmission rate is at par with Ae. leuteocephalus, the primary vector of ZIKV. A few CHIKV isolations have also been reported from the mosquitoes in Senegal and other countries in Africa. Experimental studies have demonstrated high susceptibility, early dissemination and efficient transmission of CHIKV by Ae. vittatus mosquitoes. The mosquitoes with their high susceptibility and competence to transmit important viruses, viz. YFV, DENV, CHIKV and ZIKV pose a major threat to public health due to their abundance and anthropophilic behaviour.
Sherlock: Lightweight Detection of Performance Interference in Containerized Cloud Services

Cloud instances are usually virtual machines hosted on shared hardware. Containers are often used to deploy services in cloud instances. However, excessive consumption of shared hardware resources by some VMs may lead to unpredictability in the performance of containers running in co-located VMs. Existing techniques to detect performance interference in applications are either too expensive in terms of profiling or applicable only from the perspective of the infrastructure owner. In this paper, we propose Sherlock, a lightweight subscriber-centric mechanism to detect performance interference and estimate its impact on cloud services. Sherlock does not require access to hardware counters and can work on unmodified clouds without any support from the cloud provider or changes to the hypervisor. Sherlock uses a simple profiling technique which is performed only for a short duration before deployment. When interference from co-resident VMs is observed, Sherlock notifies the cloud subscriber, so that any remedial actions can be taken. We also define a metric IScore, which is an estimate of the impact of interference on a service. Experiments on the real-world web benchmark CloudSuite show that our approach is able to detect interference with accuracy ranging from 89% to 98.4%, and with very less false positives ( 8%).
Intransitive noninterference in nondeterministic systems

This paper addresses the question of how TA-security, a semantics for intransitive information-flow policies in deterministic systems, can be generalized to nondeterministic systems. Various definitions are proposed, including definitions that state that the system enforces as much of the policy as possible in the context of attacks in which groups of agents collude by sharing information through channels that lie outside the system. Relationships between the various definitions proposed are characterized, and an unwinding-based proof technique is developed. Finally, it is shown that on a specific class of systems, access control systems with local non-determinism, the strongest definition can be verified by checking a simple static property.
3D visual fatigue: Interaction between ranges of binocular disparity and interocular crosstalk

We investigated biomedical effects of stereoscopic 3D (s3D) images on visual fatigue, especially the effects of binocular disparity range and interocular crosstalk. Fifteen observers, aged from 22 to 59, watched s3D images for approx. 10 minutes performing visual searches of a target moving in depth among 90 distracters. The results showed that for larger crosstalk and larger disparity range, (i) search time was longer, (ii) subjective score of uncomfortability was larger, and (iii) total score of visual fatigue questionnaire was larger. Moreover, the search time and the scores increased more drastically with disparity range when crosstalk is smaller.
Met promotes the formation of double minute chromosomes induced by Sei-1 in NIH-3T3 murine fibroblasts

Background Sei-1 is an oncogene capable of inducing double minute chromosomes (DMs) formation. DMs are hallmarks of amplification and contribute to oncogenesis. However, the mechanism of Sei-1 inducing DMs formation remains unelucidated. Results DMs formation significantly increased during serial passage in vivo and gradually decreased following culture in vitro. micro nuclei (MN) was found to be responsible for the reduction. Of the DMs-carrying genes, Met was found to be markedly amplified, overexpressed and highly correlated with DMs formation. Inhibition of Met signaling decreased the number of DMs and reduced the amplification of the DMs-carrying genes. We identified a 3.57Mb DMs representing the majority population, which consists of the 1.21 Mb AMP1 from locus 6qA2 and the 2.36 Mb AMP2 from locus 6qA2-3. Materials and Methods We employed NIH-3T3 cell line with Sei-1 overexpression to monitor and characterize DMs in vivo and in vitro. Array comparative genome hybridization (aCGH) and fluorescence in situ hybridization (FISH) were performed to reveal amplification regions and DMs-carrying genes. Metaphase spread was prepared to count the DMs. Western blot and Met inhibition rescue experiments were performed to examine for involvement of altered Met signaling in Sei-1 induced DMs. Genomic walking and PCR were adopted to reveal DMs structure. Conclusions Met is an important promotor of DMs formation.
Endoscopic Transorbital Superior Eyelid Approach for the Management of Selected Spheno-orbital Meningiomas: Preliminary Experience.

BACKGROUND Feasibility and safety of spheno-orbital meningioma resection by means of endoscopic-assisted transorbital route. OBJECTIVE To evaluate the feasibility and outcomes of the transorbital endoscopic management of selected spheno-orbital meningiomas. As secondary aims, symptom improvement and tumor volume removed were evaluated. METHODS Retrospective chart evaluation of patients with spheno-orbital meningiomas treated by means of endoscopic transorbital superior eyelid approach in 3 referral centers over the last 4 yr. RESULTS Fourteen cases were included in this study. In 4 patients, the transorbital endoscopic approach was combined with an endonasal route. Mean age was 51 and male-to-female ratio was 1:6. In 8 patients (57.1%), an intraorbital involvement was observed, 3 of them (21.4%) showed significant intraconal disease. No patient presented significant cavernous sinus infiltration. Main presenting symptoms were proptosis, diplopia, and visual impairment in 14, 6, and 6 patients, respectively. Mean proptosis improvement was 2 mm (standard deviation 2.3). We observed no major postoperative complications. CONCLUSION Our preliminary clinical experience seems to demonstrate that selected spheno-orbital meningiomas can be safely managed by means of an endoscopic transorbital route through a superior eyelid approach. Patients with orbital or cavernous sinus infiltration are at highest risk of persistence.
High power density superconducting rotating machines—development status and technology roadmap

Superconducting technology applications in electric machines have long been pursued due to their significant advantages of higher efficiency and power density over conventional technology. However, in spite of many successful technology demonstrations, commercial adoption has been slow, presumably because the threshold for value versus cost and technology risk has not yet been crossed. One likely path for disruptive superconducting technology in commercial products could be in applications where its advantages become key enablers for systems which are not practical with conventional technology. To help systems engineers assess the viability of such future solutions, we present a technology roadmap for superconducting machines. The timeline considered was ten years to attain a Technology Readiness Level of 6+, with systems demonstrated in a relevant environment. Future projections, by definition, are based on the judgment of specialists, and can be subjective. Attempts have been made to obtain input from a broad set of organizations for an inclusive opinion. This document was generated through a series of teleconferences and in-person meetings, including meetings at the 2015 IEEE PES General meeting in Denver, CO, the 2015 ECCE in Montreal, Canada, and a final workshop in April 2016 at the University of Illinois, Urbana-Champaign that brought together a broad group of technical experts spanning the industry, government and academia.
Removing Depth-Order Cycles among Triangles: An Efficient Algorithm Generating Triangular Fragments

More than 25 years ago, inspired by applications in computer graphics, Chazelle \etal (FOCS 1991) studied the following question: Is it possible to cut any set of n lines or other objects in \Reals^3 into a subquadratic number of fragments such that the resulting fragments admit a depth order? They managed to prove an O(n^{9/4}) bound on the number of fragments, but only for the very special case of bipartite weavings of lines. Since then only little progress was made, until a recent breakthrough by Aronov and Sharir (STOC 2016) who showed that O(n^{3/2}\polylog n) fragments suffice for any set of lines. In a follow-up paper Aronov, Miller and Sharir (SODA 2017) proved an O(n^{3/2+&#x2265;}) bound for triangles, but their method uses high-degree algebraic arcs to perform the cuts. Hence, the resulting pieces have curved boundaries. Moreover, their method uses polynomial partitions, for which currently no algorithm is known. Thus the most natural version of the problem is still wide open: Is it possible to cut any collection of n disjoint triangles in \Reals^3 into a subquadratic number of triangular fragments that admit a depth order? And if so, can we compute the cuts efficiently? We answer this question by presenting an algorithm that cuts any set of n disjoint triangles in \Reals^3 into O(n^{7/4}\polylog n) triangular fragments that admit a depth order. The running time of our algorithm is O(n^{3.69}). We also prove a refined bound that depends on the number, K, of intersections between the projections of the triangle edges onto the xy-plane: we show that O(n^{1+&#x2265;} + n^{1/4} K^{3/4}\polylog n) fragments suffice to obtain a depth order. This result extends to xy-monotone surface patches bounded by a constant number of bounded-degree algebraic arcs in general position, constituting the first subquadratic bound for surface patches. Finally, as a byproduct of our approach we obtain a faster algorithm to cut a set of lines into O(n^{3/2}\polylog n) fragments that admit a depth order. Our algorithm for lines runs in O(n^{5.38}) time, while the previous algorithm uses O(n^{8.77}) time.
Development and validation of the WASP classification system for optical diagnosis of adenomas, hyperplastic polyps and sessile serrated adenomas/polyps

Objective Accurate endoscopic differentiation would enable to resect and discard small and diminutive colonic lesions, thereby increasing cost-efficiency. Current classification systems based on narrow band imaging (NBI), however, do not include neoplastic sessile serrated adenomas/polyps (SSA/Ps). We aimed to develop and validate a new classification system for endoscopic differentiation of adenomas, hyperplastic polyps and SSA/Ps <10 mm. Design We developed the Workgroup serrAted polypS and Polyposis (WASP) classification, combining the NBI International Colorectal Endoscopic classification and criteria for differentiation of SSA/Ps in a stepwise approach. Ten consultant gastroenterologists predicted polyp histology, including levels of confidence, based on the endoscopic aspect of 45 polyps, before and after participation in training in the WASP classification. After 6 months, the same endoscopists predicted polyp histology of a new set of 50 polyps, with a ratio of lesions comparable to daily practice. Results The accuracy of optical diagnosis was 0.63 (95% CI 0.54 to 0.71) at baseline, which improved to 0.79 (95% CI 0.72 to 0.86, p<0.001) after training. For polyps diagnosed with high confidence the accuracy was 0.73 (95% CI 0.64 to 0.82), which improved to 0.87 (95% CI 0.80 to 0.95, p<0.01). The accuracy of optical diagnosis after 6 months was 0.76 (95% CI 0.72 to 0.80), increasing to 0.84 (95% CI 0.81 to 0.88) considering high confidence diagnosis. The combined negative predictive value with high confidence of diminutive neoplastic lesions (adenomas and SSA/Ps together) was 0.91 (95% CI 0.83 to 0.96). Conclusions We developed and validated the first integrative classification method for endoscopic differentiation of small and diminutive adenomas, hyperplastic polyps and SSA/Ps. In a still image evaluation setting, introduction of the WASP classification significantly improved the accuracy of optical diagnosis overall as well as SSA/P in particular, which proved to be sustainable after 6 months.
Simulation of dissimilar weld joints of steel P91

Abstract Results of computer simulations of long term service exposure for weldments of the CSN 15 128/P91 and SK3STC/P91 steels are presented and compared with corresponding results of phase and composition experiments. The welded material P91 (EU designation: X10CrMoVNb 9–1) represents progressive chromium steel alloyed with molybdenum, vanadium, carbon, and nitrogen. The CSN 15 128 (13CrMoV 2–5) material is low alloy Cr–Mo–V steel. The SK3STC alloy (12CrMo 10–10) represents the consumable electrode material. The stability of the weldment microstructure is investigated at elevated temperatures (500–700° C). The simulation method is based on the Calphad approach complemented with the theory of multicomponent bulk diffusion, local conditions of phase equilibrium, and the assumption that diffusion is the process that controls the rate of phase transformation. Significant phase profiles, concentration profiles, and phase transformation processes in the diffusion affected zone are simulated, investigated, and compared with experimental results. The potentially deleterious carbon depleted region inside each weld joint is discussed. The method described can be used to predict microstructure instability in weld joints.
The Spoken BNC2014: Designing and building a spoken corpus of everyday conversations

This paper introduces the Spoken British National Corpus 2014, an 11.5-million-word corpus of orthographically transcribed conversations among L1 speakers of British English from across the UK, recorded in the years 2012–2016. After showing that a survey of the recent history of corpora of spoken British English justifies the compilation of this new corpus, we describe the main stages of the Spoken BNC2014’s creation: design, data and metadata collection, transcription, XML encoding, and annotation. In doing so we aim to (i) encourage users of the corpus to approach the data with sensitivity to the many methodological issues we identified and attempted to overcome while compiling the Spoken BNC2014, and (ii) inform (future) compilers of spoken corpora of the innovations we implemented to attempt to make the construction of corpora representing spontaneous speech in informal contexts more tractable, both logistically and practically, than in the past.
Osteonecrosis of the Jaw After Bisphosphonates Treatment in Patients with Multiple Myeloma

Background: Bone lytic lesion in Multiple myeloma are the most commonly presented symptoms which require treatment with bisphosphonates (BPs). BPs are providing supportive care, reducing the rate of skeletal morbidity but evidently not abolishing it, the criteria for stopping their administration have to be different from those used for classic antineoplastic drugs, and they should not be stopped when metastatic bone disease is progressing. Osteonecrosis of the jaw (ONJ) has been associated recently with the use of BPs. Aim: The aim of these study is to evaluate the incidence of ONJ in patients with MM treated with mixed biphosphonates. Patients and methods: We analyzed total 296 myeloma patients (150 male and 146 female). Mostly effected age group with 58,1% is age more than 60 years up to 88 years, diagnosed in our institution in the period 2005-2015. We used intravenous or oral forms of biphosphonates such as pamidronate, ibandronate, clodronate and zolendronic acid. The patients were evaluated for ONJ. Results: The incidence of ONJ in our group of patients treated with Bps was 4,6% from our group of 260 patients 87,8% received BPs therapy and patients which haven’t received BPs 12,2%. From this group, 95,4% (248) didn’t show ONJ, and 4,6% (12) showed ONJ. The period of this treatment with BPs is an important risk factor for development of ONJ, average duration of BPs therapy in patients which show adverse effects is 26.8±13.7 months, from the total number of 12 patients that developed ONJ adverse effects, we have 8 patients which received treatment with Zolendronic acid and the remaining 4 patients which were treated with other BPs combinations without Zolendronic acid. Conclusions: All patients treated for MM must continue with the therapy with Zolendronic acid and Pamidronate, each patient must be individually treated according to his response of the treatment (dose, frequency and duration of therapy).
High rates of viral suppression in adults and children with high CD4+ counts using a streamlined ART delivery model in the SEARCH trial in rural Uganda and Kenya

Introduction: The 2015 WHO recommendation of antiretroviral therapy (ART) for all HIV‐positive persons calls for treatment initiation in millions of persons newly eligible with high CD4+ counts. Efficient and effective care models are urgently needed for this population. We evaluated clinical outcomes of asymptomatic HIV‐positive adults and children starting ART with high CD4+ counts using a novel streamlined care model in rural Uganda and Kenya.