Miracle-dz/UniFAR-FTUs huggingface dataset:
Post-transcriptional gene silencing triggered by sense transgenes involves uncapped antisense RNA and differs from silencing intentionally triggered by antisense transgenes

Although post-transcriptional gene silencing (PTGS) has been studied for more than a decade, there is still a gap in our understanding of how de novo silencing is initiated against genetic elements that are not supposed to produce double-stranded (ds)RNA. Given the pervasive transcription occurring throughout eukaryote genomes, we tested the hypothesis that unintended transcription could produce antisense (as)RNA molecules that participate to the initiation of PTGS triggered by sense transgenes (S-PTGS). Our results reveal a higher level of asRNA in Arabidopsis thaliana lines that spontaneously trigger S-PTGS than in lines that do not. However, PTGS triggered by antisense transgenes (AS-PTGS) differs from S-PTGS. In particular, a hypomorphic ago1 mutation that suppresses S-PTGS prevents the degradation of asRNA but not sense RNA during AS-PTGS, suggesting a different treatment of coding and non-coding RNA by AGO1, likely because of AGO1 association to polysomes. Moreover, the intended asRNA produced during AS-PTGS is capped whereas the asRNA produced during S-PTGS derives from 3′ maturation of a read-through transcript and is uncapped. Thus, we propose that uncapped asRNA corresponds to the aberrant RNA molecule that is converted to dsRNA by RNA-DEPENDENT RNA POLYMERASE 6 in siRNA-bodies to initiate S-PTGS, whereas capped asRNA must anneal with sense RNA to produce dsRNA that initiate AS-PTGS.
Cubic Regularization of Newton's Method for Convex Problems with Constraints

In this paper we derive efficiency estimates of the regularized Newton's method as applied to constrained convex minimization problems and to variational inequalities. We study a one-step Newton's method and its multistep accelerated version, which converges on smooth convex problems as O(1/k), where k is the iteration counter. We derive also the efficiency estimate of a second-order scheme for smooth variational inequalities. Its global rate of convergence is established on the level O (1/k).
Algorithmic Transparency via Quantitative Input Influence: Theory and Experiments with Learning Systems

Algorithmic systems that employ machine learning play an increasing role in making substantive decisions in modern society, ranging from online personalization to insurance and credit decisions to predictive policing. But their decision-making processes are often opaque-it is difficult to explain why a certain decision was made. We develop a formal foundation to improve the transparency of such decision-making systems. Specifically, we introduce a family of Quantitative Input Influence (QII) measures that capture the degree of influence of inputs on outputs of systems. These measures provide a foundation for the design of transparency reports that accompany system decisions (e.g., explaining a specific credit decision) and for testing tools useful for internal and external oversight (e.g., to detect algorithmic discrimination). Distinctively, our causal QII measures carefully account for correlated inputs while measuring influence. They support a general class of transparency queries and can, in particular, explain decisions about individuals (e.g., a loan decision) and groups (e.g., disparate impact based on gender). Finally, since single inputs may not always have high influence, the QII measures also quantify the joint influence of a set of inputs (e.g., age and income) on outcomes (e.g. loan decisions) and the marginal influence of individual inputs within such a set (e.g., income). Since a single input may be part of multiple influential sets, the average marginal influence of the input is computed using principled aggregation measures, such as the Shapley value, previously applied to measure influence in voting. Further, since transparency reports could compromise privacy, we explore the transparency-privacy tradeoff and prove that a number of useful transparency reports can be made differentially private with very little addition of noise. Our empirical validation with standard machine learning algorithms demonstrates that QII measures are a useful transparency mechanism when black box access to the learning system is available. In particular, they provide better explanations than standard associative measures for a host of scenarios that we consider. Further, we show that in the situations we consider, QII is efficiently approximable and can be made differentially private while preserving accuracy.
Chirality measurements using optical fibre long period gratings fabricated in high birefringent fibre

A Long period grating (LPG) with a period of 111 μm was fabricated in the highly birefringent (Hi-Bi) optical fibre with the aim of developing a sensor for chirality measurements. The LPG sensor was exposed to different concentrations of glucose D(+) and fructose D(-) in water, which have similar structures but exhibit opposite optical rotations, i.e. chirality. The behaviour of the resonance bands of the submodes corresponding to the two orthogonal polarization states was different depending on the chirality of the compound, thus allowing discrimination between two compounds.
The Role of Vision in Attributing the Sense of Part- and Full-Body Ownership During Anomalous Conditions

Our bodies are arguably one of the most intimate things we will ever know. But the comfort of our own physical boundaries can be altered in various ways. In this analysis, we will look at how vision contributes to the sense of owning a body by analysing six abnormal conditions: the rubber hand illusion, phantom limbs, somatoparaphrenia, the body-swap illusion, out-of-body experiences, and heautoscopy. Examinations of these experimental or pathological conditions has granted a greater understanding of body-ownership. It was discovered that vision plays different modulatory roles, being more intricately involved in full-body ownership than in part-body ownership. Vision appears to be highly connected to self-location and first-person perspective, which both are contributing factors in projecting the sense of ownership to an external location. In part-body ownership, however, vision can be overruled by other senses, such as proprioception. Though it is still able to contribute to the illusion of projecting ownership and proprioceptive displacement to a rubber hand.
Familial Down syndrome: evidence supporting cytoplasmic inheritance

The frequently observed familial aggregation of Down syndrome (DS) 47,+21 and other aneuploidies and the phenomenon of double aneuploidy involving DS cannot be accounted for by chance alone. To clarify possible aetiological factors, pedigrees from all 7 affected families with repeated marriages referred to two regional genetics centres were examined. In each case the recurrence of aneuploidy was on the mother's side (p<0.01). Such a pattern suggests cytoplasmic inheritance of a risk factor. The hypothesis that mitochondrial DNA mutations have a role in the aetiology of DS is supported by other observations as well as by theoretical considerations.
Attention-Deﬁcit/Hyperactivity Disorder and Urinary Metabolites of Organophosphate Pesticides

OBJECTIVE: The goal was to examine the association between urinary concentrations of dialkyl phosphate metabolites of organophosphates and attention-deﬁcit/hyperactivity disorder (ADHD) in children 8 to 15 years of age. METHODS: Cross-sectional data from the National Health and Nutrition Examination Survey (2000–2004) were available for 1139 children, who were representative of the general US population. A structured interview with a parent was used to ascertain ADHD diagnostic status, on the basis of slightly modiﬁed criteria from the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition . RESULTS: One hundred nineteen children met the diagnostic criteria for ADHD. Children with higher urinary dialkyl phosphate concentrations, especially dimethyl alkylphosphate (DMAP) concentrations, were more likely to be diagnosed as having ADHD. A 10-fold increase in DMAP concentration was associated with an odds ratio of 1.55 (95% conﬁdence interval: 1.14–2.10), with adjustment for gender, age, race/eth-nicity, poverty/income ratio, fasting duration, and urinary creatinine concentration. For the most-commonly detected DMAP metabolite, dimethyl thiophosphate, children with levels higher than the median of detectable concentrations had twice the odds of ADHD (adjusted odds ratio: 1.93 [95% conﬁdence interval: 1.23–3.02]), compared with children
A metaregression analysis of the dose-response effect of aspirin on stroke.

BACKGROUND We evaluated whether the risk of stroke depends on aspirin dose in patients with a previous transient ischemic attack or stroke. METHODS We conducted a metaregression analysis of stroke by using published randomized, placebo-controlled trials. We analyzed studies of patients who had recently had a transient ischemic attack or stroke (ie, secondary prevention). We abstracted data on the treatment regimen and stroke. To evaluate the dose-response relationship, we conducted a metaregression analysis of study-specific risk ratios by means of weighted linear regression. RESULTS Eleven randomized, placebo-controlled trials contributed a total of 5228 patients randomized to aspirin only and 4401 patients randomized to placebo only. The slope of the dose-response curve was virtually flat across a wide range of aspirin doses from 50 to 1500 mg/d (P = .49 for test of slope not =0). Summarizing across studies, aspirin decreases the risk of stroke by about 15% (risk ratio, 0.85;95% confidence interval, 0.77-0.94). CONCLUSIONS Aspirin reduces the risk of stroke by approximately 15%, and this effect is uniform across aspirin doses from 50 to 1500 mg/d. The lowest effective aspirin dose has not yet been identified, but it could be lower than 50 mg/d.
Deductive database languages: problems and solutions

Deductive databases result from the integration of relational database and logic programming techniques. However, significant problems remain inherent in this simple synthesis from the language point of view. In this paper, we discuss these problems from four different aspects: complex values, object orientation, higher-orderness, and updates. In each case, we examine four typical languages that address the corresponding issues.
Driver compliance with route guidance advice: The evidence and its implications

This paper will present results from two sources; questionnaires conducted among drivers equipped with route guidance as part of the Berlin LISB trial and analysis of decisions made by users of the interactive route guidance simulator known as IGOR. The results from Berlin show a high level of commitment by participants in the trial but nevertheless show a general reduction in usage of the equipment over time. Adherence to advice is not high on regular journeys and reflects a low opinion of the quality of routes recommended by the system for such journeys. For finding new destinations or travelling in unfamiliar areas, opinions and usage are much higher. Overall driver behaviour has not been much influenced by LISB. Our surveys provide useful information on drivers' reasons for ignoring advice and their suggestions for system enhancement. The IGOR results provide strong quantitative evidence that acceptance of an item of advice is closely correlated with objective measures of its quality. It is also a function of the drivers' familiarity with the network, his previous experience of the reliability of advice and the degree of corroboration of advice by "external" evidence such as the orientation of the advice route relative to the destination, the absence of congestion and the behaviour of other drivers.
Recent and Ancient Signature of Balancing Selection around the S-Locus in Arabidopsis halleri and A. lyrata

Balancing selection can maintain different alleles over long evolutionary times. Beyond this direct effect on the molecular targets of selection, balancing selection is also expected to increase neutral polymorphism in linked genome regions, in inverse proportion to their genetic map distances from the selected sites. The genes controlling plant self-incompatibility are subject to one of the strongest forms of balancing selection, and they show clear signatures of balancing selection. The genome region containing those genes (the S-locus) is generally described as nonrecombining, and the physical size of the region with low recombination has recently been established in a few species. However, the size of the region showing the indirect footprints of selection due to linkage to the S-locus is only roughly known. Here, we improved estimates of this region by surveying synonymous polymorphism and estimating recombination rates at 12 flanking region loci at known physical distances from the S-locus region boundary, in two closely related self-incompatible plants Arabidopsis halleri and A. lyrata. In addition to studying more loci than previous studies and using known physical distances, we simulated an explicit demographic scenario for the divergence between the two species, to evaluate the extent of the genomic region whose diversity departs significantly from neutral expectations. At the closest flanking loci, we detected signatures of both recent and ancient indirect effects of selection on the S-locus flanking genes, finding ancestral polymorphisms shared by both species, as well as an excess of derived mutations private to either species. However, these effects are detected only in a physically small region, suggesting that recombination in the flanking regions is sufficient to quickly break up linkage disequilibrium with the S-locus. Our approach may be useful for distinguishing cases of ancient versus recently evolved balancing selection in other systems.
Analysis of Millimeter-Wave LC Oscillators Based on Two-Port Network Theory

In this brief, a cross-coupled oscillator is analyzed based on the two-port network theory and the $Y$- parameter model for a transistor. Contrary to the previous works, the proposed analysis shows that LC cross-coupled oscillators have an additional and higher pure imaginary natural frequency at which the circuit cannot oscillate. The analysis investigates the sufficient condition at which the circuit is able to oscillate at this higher frequency. For the oscillation at the higher frequency mode, we propose adding an extra stage and making a three-stage ring oscillator. The equations obtained from this analysis indicate that the oscillation start-up condition depends on the oscillation frequency. Hence, increasing the speed of the oscillator does not satisfy the start-up condition of oscillators. Our analysis shows that the maximum frequency, in which the circuit stops oscillation in the ring oscillator, is higher than the cross-coupled oscillator and this maximum frequency is very close to the maximum frequency of the transistor.
O R I G I N a L C O N T R I B U T I O N Open Access

Assaults against U.S. law enforcement officers in the line-of-duty: situational context and predictors of lethality Abstract Background: Research on occupational safety of law enforcement officers (LEOs) has primarily focused on fatal assaults. Nonfatal assaults, however, have received little attention. The goal of this study was to describe the situational contexts in which LEOs are assaulted, and compare these contexts and risks between fatal and nonfatal assaults in the U.S. Analyzing both types of assaults provides a more complete understanding of occupational safety and opportunities for intervention. Methods: This study includes a descriptive epidemiology of fatal and nonfatal assaults of LEOs in the U.S. and a pooled cross-sectional analysis of risk factors contributing to the odds of lethal assault. Data were collected from the Law Enforcement Officers Killed and Assaulted database. Descriptive statistics were used to characterize fatal and nonfatal assaults. Odds ratios were generated to understand the odds that an assault would result in a fatality.
Production of alkaline protease from Cellulosimicrobium cellulans

Cellulosimicrobium cellulans is one of the microorganisms that produces a wide variety of yeast cell wall-degrading enzymes, β-1,3-glucanase, protease and chitinase. Dried cells of Saccharomyces cerevisiae were used as carbon and nitrogen source for cell growth and protease production. The medium components KH2PO4, KOH and dried yeast cells showed a significant effect (p<0.05) on the factorial fractional design. A second design was prepared using two factors: pH and percentage of dried yeast cells. The results showed that the culture medium for the maximum production of protease was 0.2 g/l of MgSO4.7H2O, 2.0 g/l of (NH4)2SO4 and 8% of dried yeast cells in 0.15M phosphate buffer at pH 8.0. The maximum alkaline protease production was 7.0 ± 0.27 U/ml over the center point. Crude protease showed best activity at 50ºC and pH 7.0-8.0, and was stable at 50ºC.
The inhibitory motoneurons of crayfish thoracic limbs: Identification, structures, and homology with insect common inhibitors

The three inhibitory motoneurons supplying crayfish thoracic limbs were identified, stained, and compared structurally. The inhibitors to the walking leg muscles (in Orconectes) were identified anatomically by a combination of immunocytochemical staining for gammaaminobutyric acid (GABA) or glutamate decarboxylase and differential backfill staining with nickel and cobalt ions. The cheliped inhibitors were identified intracellularly and injected with Lucifer Yellow (Pucifustucus) or cobalt (Procumbarus). The common inhibitor (CI) in each thoracic segment has a medial or slightly contralateral soma near the ganglion's posterior boundary, a gently curving primary neurite, an extensive ipsilateral dendritic tree, and an axon emerging through the anterior root. The stretcher‐closer inhibitor (SI) has a soma slightly anterior and ipsilateral to the CI's, a sharply bent proximal neurite, a smaller dendritic tree, and an axon in the posterior root. The opener inhibitor (OI) lies more laterally and often posterior to the CI; its diagonally directed neurite enters the posterior root. The inhibitors' structures were related to major neuroanatomical landmarks within the ganglion, to soma positions of excitatory motoneurons revealed by backfilling, and to soma locations of inhibitory interneurons revealed by GABA‐like immunoreactivity.
From relational verification to SIMD loop synthesis

Existing pattern-based compiler technology is unable to effectively exploit the full potential of SIMD architectures. We present a new program synthesis based technique for auto-vectorizing performance critical innermost loops. Our synthesis technique is applicable to a wide range of loops, consistently produces performant SIMD code, and generates correctness proofs for the output code. The synthesis technique, which leverages existing work on relational verification methods, is a novel combination of deductive loop restructuring, synthesis condition generation and a new inductive synthesis algorithm for producing loop-free code fragments. The inductive synthesis algorithm wraps an optimized depth-first exploration of code sequences inside a CEGIS loop. Our technique is able to quickly produce SIMD implementations (up to 9 instructions in 0.12 seconds) for a wide range of fundamental looping structures. The resulting SIMD implementations outperform the original loops by 2.0x-3.7x.
Forecasting performance of logistic STAR model: An alternative version to the original LSTAR models

This paper proposes an alternative representation of the original version of the Logistic (LSTAR) model. The LSTAR and ESTAR models are frequently used in empirical research. The LSTAR model describes asymmetrical nonlinear adjustment process, while the ESTAR model describes symmetrical nonlinear adjustment process [19] in Liews [10]. To Liews et al., the theoretical assumption that exchange rate adjustment is symmetric makes the LSTAR model inappropriate for modelling exchange rate movements. They claim that this is the reason the LSTAR model has being neglected in the modelling of exchange rate in the past. They proposed the ALSTAR model. This version they noted allows a V-shape symmetric adjustment in exchange rate behaviour. In this paper, we also propose a similar but better alternative to their model. The square logistic smooth transition auto-regressive model (SLSTAR) has a shape exactly similar to the inverted bell-shape of the exponential model which allows a symmetric adjustment in exchange rate behaviour. Simulation studies were carried out to investigate the sample performance of our model. We also demonstrated our model with life data.
Helicobacter pylori infection is identified as a cardiovascular risk factor in Central Africans

Background Helicobacter pylori is now incriminated in the pathogenesis of atherosclerosis. Objective To examine the importance of H. pylori infection as a cardiovascular disease (CVD) risk factor. Methods Two hundred five patients (128 with H. pylori infection [HP-seropositive] and 77 without) had a baseline assessment for other potential CVD risk factors and were followed prospectively for 10 years (1999–2008). They were assessed on a monthly basis for the outcomes of carotid plaque, angina pectoris, myocardial infarction, and stroke. In the HP-seropositive group, male sex and quartile 4 for IgG anti-H. pylori antibodies (anti-HP Ab) were correlated with traditional CVD risk factors, stroke, myocardial infarction, and angina pectoris. Results At the baseline assessment, the levels of carotid intima-media thickness, blood fibrinogen, total cholesterol, fasting plasma glucose, and uric acid were higher in H. pylori-infected patients than in the uninfected group. Serum HDL-cholesterol was significantly lower in the HP-seropositive group. Men had higher levels of IgG anti-HP Ab, waist circumference, blood pressure, uric acid, and total cholesterol than women. Within the HP-seropositive group, individuals in quartile 4 for IgG anti-HP Ab had higher rates of elevated fibrinogen, diabetes mellitus, low high-density lipoprotein cholesterol, arterial hypertension, and high total cholesterol than those in quartile 1. After adjusting for traditional CVD risk factors, H. pylori infection was the only independent predictor of incident carotid plaque (multivariate odds ratio [OR] = 2.3, 95% confidence interval [CI]: 1.2–7.2; P < 0.0001) and incident acute stroke (multivariate OR = 3.6, 95% CI: 1.4–8.2; P < 0.0001). Within the HP-seropositive group and after adjusting for traditional CVD risk factors, male sex was the only independent predictor of incident angina pectoris (multivariate OR = 3.5, 95% CI: 1.6–16; P < 0.0001), incident acute stroke (multivariate OR = 3.2, 95% CI: 1.4–28; P < 0.0001), and acute myocardial infarction (multivariate OR = 7.2, 95% CI: 3.1–18; P < 0.0001). Conclusion Our study provides evidence for an association among known CVD risk factors, carotid plaque, stroke, and H. pylori infection. Among infected individuals, there is a significant association among severity of HP-seropositivity, male sex, and CVD. The eradication of H. pylori infection may therefore reduce the emerging burden of CVD in Africa.