Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacteria Getting into Shape: Genetic Determinants of E. coli Morphology

ABSTRACT Perturbation of cellular processes is a prevailing approach to understanding biology. To better understand the complicated biology that defines bacterial shape, a sensitive, high-content platform was developed to detect multiple morphological defect phenotypes using microscopy. We examined morphological phenotypes across the Escherichia coli K-12 deletion (Keio) collection at the mid-exponential growth phase, revealing 111 deletions perturbing shape. Interestingly, 64% of these were uncharacterized mutants, illustrating the complex nature of shape maintenance and regulation in bacteria. To understand the roles these genes play in defining morphology, 53 mutants with knockouts resulting in abnormal cell shape were crossed with the Keio collection in high throughput, generating 1,373 synthetic lethal interactions across 1.7 million double deletion mutants. This analysis yielded a highly populated interaction network spanning and linking multiple phenotypes, with a preponderance of interactions involved in transport, oxidation-reduction, and metabolic processes. IMPORTANCE Genetic perturbations of cellular functions are a prevailing approach to understanding cell systems, which are increasingly being practiced in very high throughput. Here, we report a high-content microscopy platform tailored to bacteria, which probes the impact of genetic mutation on cell morphology. This has particular utility in revealing elusive and subtle morphological phenotypes associated with blocks in nonessential cellular functions. We report 111 nonessential mutations impacting E. coli morphology, with nearly half of those genes being poorly annotated or uncharacterized. Further, these genes appear to be tightly linked to transport or redox processes within the cell. The screening platform is simple and low cost and is broadly applicable to any bacterial genomic library or chemical collection. Indeed, this is a powerful tool in understanding the biology behind bacterial shape. IMPORTANCE Genetic perturbations of cellular functions are a prevailing approach to understanding cell systems, which are increasingly being practiced in very high throughput. Here, we report a high-content microscopy platform tailored to bacteria, which probes the impact of genetic mutation on cell morphology. This has particular utility in revealing elusive and subtle morphological phenotypes associated with blocks in nonessential cellular functions. We report 111 nonessential mutations impacting E. coli morphology, with nearly half of those genes being poorly annotated or uncharacterized. Further, these genes appear to be tightly linked to transport or redox processes within the cell. The screening platform is simple and low cost and is broadly applicable to any bacterial genomic library or chemical collection. Indeed, this is a powerful tool in understanding the biology behind bacterial shape.
On the impact of message packetization in networks of workstations with irregular topology

Networks of workstations (NOWs) are becoming an increasingly popular alternative to parallel computers for those applications with high needs of resources such as memory capacity and input/output storage space, and also for small scale parallel computing. Usually, the software messaging layers in these systems become a bottleneck due to the overhead they introduce. Some proposals like FM and BIP considerably reduce this overhead by splitting long messages into several packets. These proposals have been shown to improve communication performance. However, the effect of message packetization on the network interconnects has not been analyzed yet. In this paper we examine the effect of message packetization from the point of view of the interconnection network in the context of bimodal traffic. Two different routing algorithms have been considered: up*/down* and minimal adaptive routing. Our study shows that when the up */down* routing algorithm is used, message packetization dramatically increases latency and reduces throughput for both long and short messages. On the other hand, if minimal adaptive routing is used, short messages could benefit from message packetization, but at the cost of increasing latency for long messages. In any case, network throughput is considerably reduced.
Linear Ranking Analysis

We extend the classical linear discriminant analysis (LDA) technique to linear ranking analysis (LRA), by considering the ranking order of classes centroids on the projected subspace. Under the constrain on the ranking order of the classes, two criteria are proposed: 1) minimization of the classification error with the assumption that each class is homogenous Guassian distributed, 2) maximization of the sum (average) of the K minimum distances of all neighboring-class (centroid) pairs. Both criteria can be efficiently solved by the convex optimization for one-dimensional subspace. Greedy algorithm is applied to extend the results to the multi-dimensional subspace. Experimental results show that 1) LRA with both criteria achieve state-of-the-art performance on the tasks of ranking learning and zero-shot learning, and 2) the maximum margin criterion provides a discriminative subspace selection method, which can significantly remedy the class separation problem in comparing with several representative extensions of LDA.
Educate your avatar, educate your mind: motivating learning through play

Students, that are currently receiving an education have grown up not knowing a life without technology such as computers, the internet, mobile phones and online games. They use this technology to communicate with each other, connect with the world, research information, not only for the purpose of bettering themselves but to also establish themselves in the world. Much has been written about how technology can be an influence in todays adolescence and how it can, potentially, improve their way of life. A Massive Multiplayer Online Role Playing Game (MMORPG) is an example of such a technology that is being considered as an alternative means of teaching todays youth as being able to having them actively participating in their education instead of being bored and uninspired. Motivation is a key factor that propels us in life. It plays a major role in nearly everything we do. Without motivation, we would simply not care about outcomes in our lives resulting in failure in what we do in all walks of life, such as education and employment. This paper looks at how online gameplay might assist in developing engaging education resources.
On cooperative and efficient overlay network evolution based on a group selection pattern

In overlay networks, the interplay between network structure and dynamics remains largely unexplored. In this paper, we study dynamic coevolution between individual rational strategies (cooperative or defect) and the overlay network structure, that is, the interaction between peer's local rational behaviors and the emergence of the whole network structure. We propose an evolutionary game theory (EGT)-based overlay topology evolution scheme to drive a given overlay into the small-world structure (high global network efficiency and average clustering coefficient). Our contributions are the following threefold: From the viewpoint of peers' local interactions, we explicitly consider the peer's rational behavior and introduce a link-formation game to characterize the social dilemma of forming links in an overlay network. Furthermore, in the evolutionary link-formation phase, we adopt a simple economic process: Each peer keeps one link to a cooperative neighbor in its neighborhood, which can slightly speed up the convergence of cooperation and increase network efficiency; from the viewpoint of the whole network structure, our simulation results show that the EGT-based scheme can drive an arbitrary overlay network into a fully cooperative and efficient small-world structure. Moreover, we compare our scheme with a search-based economic model of network formation and illustrate that our scheme can achieve the experimental and analytical results in the latter model. In addition, we also graphically illustrate the final overlay network structure; finally, based on the group selection model and evolutionary set theory, we theoretically obtain the approximate threshold of cost and draw the conclusion that the small value of the average degree and the large number of the total peers in an overlay network facilitate the evolution of cooperation.
Steady-State Visual Evoked Potentials for EEG-Based Biometric Identification

In this paper we propose a biometric recognition system based on steady-state visual evoked potentials (SSVEPs), exploiting brain signals elicited by repetitive stimuli having a constant frequency as identifiers. EEG responses to SSVEP stimuli flickering at different frequencies are recorded, and both mel-frequency cepstral coefficients (MFCCs) and autoregressive (AR) reflection coefficients are used as discriminative features of the enrolled users. An analysis of the permanence across time of the brain response to SSVEP stimuli is also performed, by exploiting EEG data acquired in sessions disjoint in time. The employed database is composed by EEG recordings taken from 25 healthy subjects during two different sessions with 15 day average distance between them. The results show that good recognition performance and a high level of permanence can be reached exploiting the proposed method.
Parameterized Constraint Satisfaction Problems: a Survey

We consider constraint satisfaction problems parameterized above or below guaranteed values. One example is MaxSat parameterized above m/2: given a CNF formula F with m clauses, decide whether there is a truth assignment that satisfies at least m/2 + k clauses, where k is the parameter. Among other problems we deal with are MaxLin2-AA (given a system of linear equations over F2 in which each equation has a positive integral weight, decide whether there is an assignment to the variables that satisfies equations of total weight at leastW/2+k, whereW is the total weight of all equations), Max-r-Lin2-AA (the same as MaxLin2-AA, but each equation has at most r variables, where r is a constant) and Max-r-Sat-AA (given a CNF formula F with m clauses in which each clause has at most r literals, decide whether there is a truth assignment satisfying at least ∑m i=1(1 − 2 ri ) + k clauses, where k is the parameter, ri is the number of literals in clause i, and r is a constant). We also consider Max-r-CSP-AA, a natural generalization of both Max-r-Lin2-AA and Max-r-Sat-AA, order (or, permutation) constraint satisfaction problems parameterized above the average value and some other problems related to MaxSat. We discuss results, both polynomial kernels and parameterized algorithms, obtained for the problems mainly in the last few years as well as some open questions. 1998 ACM Subject Classification F.2. 2 Nonnumerical Algorithms and Problems
Allozyme Variation in the Camaenid Tree Snails Amphidromus atricallosus (Gould, 1843) and A. inversus (Müller, 1774)

Abstract We examined allozyme variation in two camaenid tree snails, Amphidromus atricallosus and A. inversus, across two principal regions of Thailand and from Singapore, plus for A. inversus, one site in peninsular Malaysia. Using horizontal starch gel electrophoresis, 13 allozyme loci (11 polymorphic) were screened for A. atricallosus and 18 (5 polymorphic) for A. inversus. Heterozygosity was higher in A. atricallosus (Hexp=0.018–0.201, mean=0.085) than in A. inversus (Hexp=0–0.023, mean= 0.002). Genetic heterogeneity among samples was higher in A. inversus (Fst=0.965) than in A. atricallosus (Fst=0.781). Within A. atricallosus, populations were more differentiated in southern Thailand (Fst=0.551) than in eastern Thailand (Fst=0.144). The high Fst and low Hexp in populations of A. inversus suggest that this species is likely to have experienced a series of strong bottlenecks, perhaps occurring chiefly on offshore continental-shelf islands. The low Fst values of A. atricallosus in eastern Thailand suggest frequent gene flows among populations in this region. The southern and eastern samples of A. atricallosus exhibited fixed allele differences at four loci and great genetic distance (Nei's D=0.485–0.946), suggesting that these two samples may actually represent, or else be evolving into, separate species.
Detecting Android application malicious behaviors based on the analysis of control flows and data flows

This paper explores the problem of identifying malicious code sections in applications for the Android. A method for analyzing Android applications is proposed, based on applying of static analysis using control flow graphs and data flow graphs. The paper formally describes the dependency relationships that are used to construct graphs, and also describes an algorithm that allows to identify malicious sections of code using the received graphs. The results of an experimental evaluation of the effectiveness of the proposed method are presented, demonstrated a high probability of detecting malicious portions of the code of Android applications.
Ultra Fast In Situ X-Ray Micro-Tomography: Application to Solidification of Aluminium Alloys

X-ray micro-tomography has been applied recently in a wide range of research fields (damage in materials, solidification …). Thanks to the high flux of synchrotrons and specific cameras the total time to acquire a scan was considerably reduced. The use of a specific camera based on CMOS technology allows dividing the acquisition time for a complete scan by a factor of 100. Therefore we have been able to perform in situ solidification of aluminium-copper alloys at high cooling rates (between 1 and 10°C/s) and we will show results concerning the evolution of the microstructure in 3D in the early stage of solidification, in particular the morphology of the solid phase and the kinetics of growth.
Rat hippocampal CA3 neuronal injury induced by limb ischemia/reperfusion: A possible restorative effect of alpha lipoic acid

ABSTRACT Limb ischemia reperfusion (I/R) injury is associated with serious local and systemic effects. Reperfusion may augment tissue injury in excess of that produced by ischemia alone. The hippocampus has been reported to be vulnerable to I/R injury. Alpha lipoic acid (ALA) is an endogenous antioxidant with a powerful antioxidative, anti-inflammatory, and antiapoptotic properties. We studied the probable restorative effect of ALA on limb I/R-induced structural damage of rat hippocampus. Forty adult male albino rats were divided equally into four groups: group I (sham); group II (I/R-1 day) has undergone bilateral femoral arteries occlusion (3 h), then reperfusion for 1 day; group III (I/R-7 days) has undergone reperfusion for seven days; group IV (I/R-ALA) has undergone I/R as group III and received an intraperitoneal injection of ALA (100 mg/kg) for 7 days. I/R groups revealed degenerative changes in the pyramidal neuronal perikarya of CA3 field in the form of dark-stained cytoplasm, dilated RER cisternae, mitochondrial alterations, and dense bodies’ accumulation. Their dendrites showed disorganized microtubules. Astrogliosis is featured by an increased number and increased immunoreactivity of astrocytes for glial fibrillary acid protein. Morphometric data revealed significant reduction of light neurons, surface area of neurons, and thickness of the CA3 layer. Most blood capillaries exhibited narrow lumen and irregular basal lamina. ALA ameliorated the neuronal damage. Pyramidal neurons revealed preservation of normal structure. Significant increase in the thickness of pyramidal layer in CA3 field and surface area and number of light neurons was observed but astrogliosis persisted. Limb I/R had a deleterious remote effect on the hippocampus aggravated with longer period of reperfusion. This work may encourage the use of ALA in the critical clinical settings with I/R injury.
Neural architecture for tibetan word segmentation

Tibetan word segmentation (TWS) is a primary task for Tibetan language processing. In this paper, a novel hybrid neural architecture is proposed to solve TWS which is considered as a sequence tagging task. Due to the high frequency of the contracted words in Tibetan sentences, we firstly use conditional random field (CRF) to deal with this problem. Then we use the character embedding method to obtain basic character representation as input. Most importantly, we apply bi-directional Long short-term memory and CRF (BiLSTM-CRF) to our system. Experimental result shows that our approach obtained state-of-art performance compared with previous approaches used in TWS.
Structural Health Monitoring of Composites Using Integrated and Flexible Piezoelectric Ultrasonic Transducers

Two types of ultrasonic sensors are presented for structural health monitoring (SHM) and non-destructive testing (NDT) of graphite/epoxy (Gr/Ep) composites of thickness ranging from 1 mm to 12.7 mm. These piezoelectric film-based sensors are fabricated using a sol-gel spray technique. The center operation frequency of these sensors ranges from 1.3 MHz to 14.5 MHz. For the first sensor type, piezoelectric films of thickness ≥30 μm were deposited directly onto planar and curved Gr/Ep composites surfaces as integrated sensors. Ultrasonic signals propagating in a distance of more than 300 mm have been obtained. Anisotropy of 08 and 908 cross ply Gr/Ep composite is measured and delamination detected. For the second sensor type, piezoelectric films are coated onto a 50 μm thick polyimide membrane as flexible sensors that may be attached to a host composite structure with planar or curved surfaces. An induction type non-contact method for the interrogation of the Gr/Ep composites using integrated sensors is also presented.
A simple optical system to optimize a high depth to width aspect ratio applied to a positive photoresist lithography process

The fabrication of micro electro mechanical systems by electrodeposition inside resist moulds has provided much interest in recent years. In this paper, we propose a method to optimize the lithography process of a thick positive photoresist. This technique is based on the variation of transparency of the photoresist during exposure. During exposure the absorption of the light-sensitive compound decreases due to its conversion into indene carboxylic acid. A very good aspect ratio (height:width) of up to 10:1 and high edge steepness has been obtained from one coat and one UV exposure.
Efficacy of folic acid therapy in primary prevention of stroke among adults with hypertension in China: the CSPPT randomized clinical trial.

IMPORTANCE Uncertainty remains about the efficacy of folic acid therapy for the primary prevention of stroke because of limited and inconsistent data. OBJECTIVE To test the primary hypothesis that therapy with enalapril and folic acid is more effective in reducing first stroke than enalapril alone among Chinese adults with hypertension. DESIGN, SETTING, AND PARTICIPANTS The China Stroke Primary Prevention Trial, a randomized, double-blind clinical trial conducted from May 19, 2008, to August 24, 2013, in 32 communities in Jiangsu and Anhui provinces in China. A total of 20,702 adults with hypertension without history of stroke or myocardial infarction (MI) participated in the study. INTERVENTIONS Eligible participants, stratified by MTHFR C677T genotypes (CC, CT, and TT), were randomly assigned to receive double-blind daily treatment with a single-pill combination containing enalapril, 10 mg, and folic acid, 0.8 mg (n = 10,348) or a tablet containing enalapril, 10 mg, alone (n = 10,354). MAIN OUTCOMES AND MEASURES The primary outcome was first stroke. Secondary outcomes included first ischemic stroke; first hemorrhagic stroke; MI; a composite of cardiovascular events consisting of cardiovascular death, MI, and stroke; and all-cause death. RESULTS During a median treatment duration of 4.5 years, compared with the enalapril alone group, the enalapril-folic acid group had a significant risk reduction in first stroke (2.7% of participants in the enalapril-folic acid group vs 3.4% in the enalapril alone group; hazard ratio [HR], 0.79; 95% CI, 0.68-0.93), first ischemic stroke (2.2% with enalapril-folic acid vs 2.8% with enalapril alone; HR, 0.76; 95% CI, 0.64-0.91), and composite cardiovascular events consisting of cardiovascular death, MI, and stroke (3.1% with enalapril-folic acid vs 3.9% with enalapril alone; HR, 0.80; 95% CI, 0.69-0.92). The risks of hemorrhagic stroke (HR, 0.93; 95% CI, 0.65-1.34), MI (HR, 1.04; 95% CI, 0.60-1.82), and all-cause deaths (HR, 0.94; 95% CI, 0.81-1.10) did not differ significantly between the 2 treatment groups. There were no significant differences between the 2 treatment groups in the frequencies of adverse events. CONCLUSIONS AND RELEVANCE Among adults with hypertension in China without a history of stroke or MI, the combined use of enalapril and folic acid, compared with enalapril alone, significantly reduced the risk of first stroke. These findings are consistent with benefits from folate use among adults with hypertension and low baseline folate levels. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00794885.
Association between germline homeobox B13 (HOXB13) G84E allele and prostate cancer susceptibility: a meta-analysis and trial sequential analysis

Germline HOXB13 G84E mutation (rs138213197) has been described associated with prostate cancer (PCa) susceptibility but results of different studies are inconsistent. We conducted this meta-analysis to evaluate the specific role of this mutation. Relevant available studies were identified by searching the databases Pubmed, Embase and Web of Science. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to measure the strength of the association. Subgroup analysis were performed to evaluate the specific role of rs138213197 in disease aggressiveness, diagnostic age and family history. Furthermore, trial sequential analysis (TSA) was conducted for the first time to estimate whether the evidence of the results is sufficient. Our results indicated that significant increased PCa susceptibility was associated with rs138213197 compared with non-carriers (OR = 3.38, 95% CI: 2.45–4.66). Besides, in subgroup analysis, HOXB13 G84E variant was obviously associated with early onset (OR = 2.90, 95% CI: 2.24–3.75), affected relatives (OR = 2.60, 95% CI 2.19–3.10) and highly aggressive disease (OR = 2.38, 95% CI 1.84–3.08). By TSA, the findings in the current study were based on sufficient evidence. Therefore, our results indicated that the G84E mutation in HOXB13 gene might increase susceptibility to PCa.