Miracle-dz/UniFAR-FTUs huggingface dataset:
Do gradient models of primate vision perceive coherent motion in dynamic Glass patterns?

Dynamic Glass patterns are random image sequences whose local structure gives rise to an apparent global motion. They are of interest in the field of computational visual processing: previous papers predict that they should contain no low-level motion signals, conjecturing that the percept is due to a mechanism in the ventral pathway. In this essay, I summarise a number of motion perception models and describe processing a dynamic Glass pattern stimulus using a gradient model of motion perception. I found that, in the sequences I used, there was evidence for a coherent low-level motion for particular parameters but my analysis opposed the view that this was the sole factor inducing an apparent motion.
A review of machine learning and statistical approaches for detecting SNP interactions in high-dimensional genomic data.

In this era of genome-wide association studies (GWAS), the quest for understanding the genetic architecture of complex diseases is rapidly increasing more than ever before. The development of high throughput genotyping and next generation sequencing technologies enables genetic epidemiological analysis of large scale data. These advances have led to the identification of a number of single nucleotide polymorphisms (SNPs) responsible for disease susceptibility. The interactions between SNPs associated with complex diseases are increasingly being explored in the current literature. These interaction studies are mathematically challenging and computationally complex. These challenges have been addressed by a number of data mining and machine learning approaches. This paper reviews the current methods and the related software packages to detect the SNP interactions that contribute to diseases. The issues that need to be considered when developing these models are addressed in this review. The paper also reviews the achievements in data simulation to evaluate the performance of these models. Further, it discusses the future of SNP interaction analysis.
On the Security of Elliptic Curve Cryptosystems against Attacks with Special-Purpose Hardware

Since their invention in the mid 1980s, Elliptic Curve Cryptosystems (ECC) have become an alternative to common Public-Key (PK) cryptosystems such as, e.g., RSA. The utilization of Elliptic Curves (EC) in cryptography is very promising because of their resistance against powerful index-calculus attacks. For a similar level of security, ECC allows for efficient implementation due to a significantly smaller bit size of the operands. It is widely accepted that the only feasible way to attack actual cryptosystems is the application of dedicated hardware. In times of continuous technological improvements and increasing computing power, the question of the security of ECC against attacks based on special-purpose hardware arises. This work presents an architecture and the corresponding FPGA implementation of an attack against ECC over prime fields. We describe an FPGA-based multi-processing hardware architecture for the Pollard-Rho method which is, to our knowledge, currently the most efficient attack against ECC. The implementation is running on a contemporary lowcost FPGA which allows for a much better cost-performance ratio than conventional CPUs. With the implementation at hand, a fairly accurate estimate about the cost of an FPGAbased attack can be given. We will project the results on actual ECC key lengths (160 bit and above) and estimate the expected runtimes for a successful attack. Since FPGA-based attacks are out of reach for actual key lengths, we provide estimates for an ASIC design. As a result, we consider ECC over over prime fields to be far more secure than commonly believed. We show that the security of ECC-163 against hardware attacks is several orders of magnitude harder than that of RSA-1024. As a consequence, currently used elliptic curve cryptosystems are infeasible to break with available computational and financial resources.
Nonlinearity and the permanent effects of recessions

This paper presents a new nonlinear time series model that captures a post-recession 'bounce-back' in the level of aggregate output. While a number of studies have examined this type of business cycle asymmetry using recession-based dummy variables and threshold models, we relate the 'bounce-back' effect to an endogenously estimated unobservable Markov-switching state variable. When the model is applied to US real GDP, we find that the Markov-switching regimes are closely related to NBER-dated recessions and expansions. Also, the Markov-switching form of nonlinearity is statistically significant and the 'bounce-back' effect is large, implying that the permanent effects of recessions are small. Meanwhile, having accounted for the 'bounce-back' effect, we find little or no remaining serial correlation in the data, suggesting that our model is sufficient to capture the defining features of US business cycle dynamics. When the model is applied to other countries, we find larger permanent effects of recessions. Copyright © 2005 John Wiley & Sons, Ltd.
Timeliness in the German surveillance system for infectious diseases: Amendment of the infection protection act in 2013 decreased local reporting time to 1 day

Time needed to report surveillance data within the public health service delays public health actions. The amendment to the infection protection act (IfSG) from 29 March 2013 requires local and state public health agencies to report surveillance data within one working day instead of one week. We analysed factors associated with reporting time and evaluated the IfSG amendment. Local reporting time is the time between date of notification and date of export to the state public health agency and state reporting time is time between date of arrival at the state public health agency and the date of export. We selected cases reported between 28 March 2012 and 28 March 2014. We calculated the median local and state reporting time, stratified by potentially influential factors, computed a negative binominal regression model and assessed quality and workload parameters. Before the IfSG amendment the median local reporting time was 4 days and 1 day afterwards. The state reporting time was 0 days before and after. Influential factors are the individual local public health agency, the notified disease, the notification software and the day of the week. Data quality and workload parameters did not change. The IfSG amendment has decreased local reporting time, no relevant loss of data quality or identifiable workload-increase could be detected. State reporting time is negligible. We recommend efforts to harmonise practices of local public health agencies including the exclusive use of software with fully compatible interfaces.
The Hayastan Shakarian cut: measuring the impact of network disconnections

In this article we present the Hayastan Shakarian (HS), a robustness index for complex networks. HS measures the impact of a network disconnection (edge) while comparing the sizes of the remaining connected components. Strictly speaking, the Hayastan Shakarian index is defined as edge removal that produces the maximal inverse of the size of the largest connected component divided by the sum of the sizes of the remaining ones. We tested our index in attack strategies where the nodes are disconnected in decreasing order of a specified metric. We considered using the Hayastan Shakarian cut (disconnecting the edge with max HS) and other well-known strategies as the higher betweenness centrality disconnection. All strategies were compared regarding the behavior of the robustness (R-index) during the attacks. In an attempt to simulate the internet backbone, the attacks were performed in complex networks with power-law degree distributions (scale-free networks). Preliminary results show that attacks based on disconnecting using the Hayastan Shakarian cut are more dangerous (decreasing the robustness) than the same attacks based on other centrality measures. We believe that the Hayastan Shakarian cut, as well as other measures based on the size of the largest connected component, provides a good addition to other robustness metrics for complex networks.
Individual Differences and Navigation in Hypermedia

This study derives from two important observations. First, that navigation in hypermedia is a difficult task, and second, that individual cognitive differences play a role in how well users are able to efficiently use computer systems. We found that of the cognitive abilities tested in our study, only spatial ability could be related to the time spent in completing a set of tasks in a large, hypermedia, information structure. We furthermore found that it was only certain aspects of spatial ability which were related to the ability navigate in hypermedia, namely those related to solving spatial problems mentally rather than solving spatial problems in the physical world.
Opportunities, Constraints, and Benefits of Relaying in the Presence of Interference

In this paper the interference channel is extended by additional relay nodes in order to investigate the influence of interference on the design and performance of relaying protocols. We introduce a framework in which the relay interference channel is decomposed into a cascade of individual interference channels with finite conference links at the transmitters. Each of these stages is able to implement interference cancellation and mitigation schemes such as dirty-paper and Han-Kobayashi coding. We discuss the dependencies between individual stages and propose specific approaches with reasonable complexity. Finally, we compare the performance of these protocols using a simplified model for the channel and network geometry of a mobile communications system. The results show that a reasonable choice is to coordinate the base-station to relay links using distributed dirty-paper coding and to mitigate interference on the relay to user link using Han-Kobayashi coding.
Personalised Recommendations for Context Aware Suggestions

Modern Information Retrieval has moved from standard text retrieval to novel applications of the same technology. Contextual suggestion is an example of this type of applications. The TREC Contextual Suggestion track addresses the problem of suggesting contextually relevant attractions to a user visiting a new city based on his/her recorded preferences from past visits to other cities. In this invited talk I will reframe the problem of representing and using context and briefly report our two past approaches to capturing the user profile to enable a system to provide more accurate and relevant recommendations. The results of our participation in the 2013 and 2015 TREC tracks, reporting how we can use such contextual information as geographical location, time, and friends’ interests, show that our system not only significantly outperforms the baselines method, but also performs better than most other participants to that track, managing to achieve the best results in nearly all test contexts.
Traffic engineering based on stochastic model predictive control for uncertain traffic change

Traffic engineering (TE) plays an essential role in deciding routes that effectively use network resources. This is particularly important when one considers the increasing time variation of Internet traffic such as streaming and cloud services. Traffic engineering with traffic prediction is one approach to stably accommodating time-varying traffic. This approach calculates routes from predicted traffic to avoid congestion, but predictions may include errors that instead cause congestion. We propose a prediction-based traffic engineering method that is robust to prediction errors by considering the probability distribution of predicted traffic. Our approach is based on a control-theoretic approach called stochastic model predictive control. Routes are calculated using a probability distribution of prediction errors so that the occurrence probability of congestion is lower than an operator-specified level. By considering the multi-step future dynamics of traffic, the routes are changed gradually to avoid route oscillation. We also show a relaxation method for unreliable far-future probabilistic constraints to avoid overly conservative route changes. Through simulations using backbone network traffic traces, we demonstrate that our method can accommodate most traffic variations under a given target link capacity without sudden large routes changes.
Evaluating the bioactivity and biocompatibility of nylon coated ultra-high molecular weight polyethylene (UHMWPE)

APA Citation Hassanein, N. (2019). Evaluating the bioactivity and biocompatibility of nylon coated ultra-high molecular weight polyethylene (UHMWPE) [Master's Thesis, the American University in Cairo]. AUC Knowledge Fountain. https://fount.aucegypt. edu/etds/1568 MLA Citation Hassanein, Nancy. Evaluating the bioactivity and biocompatibility of nylon coated ultra-high molecular weight polyethylene (UHMWPE). 2019. American University in Cairo, Master's Thesis. AUC Knowledge Fountain. https://fount.aucegypt. edu/etds/1568
Nano-QSAR modeling for ecosafe design of heterogeneous TiO2-based nano-photocatalysts

The human health and environmental risk assessment of engineered nanomaterials (NPs) is nowadays of high interest. It is important to assess and predict the biological activity, toxicity, physicochemical properties, fate and transport of NPs. In this work, a combined experimental and computational study is performed in order to estimate the toxicity and develop a predictive model for heterogeneous NPs (i.e. modified NPs, created from more than one type of NPs). Quantitative structure–activity relationship (QSAR) methods have not been yet adopted for predicting the toxicity/physicochemical properties of modified heterogeneous nanoparticles (so-called heterogeneous NPs). Since the main problem for nano-QSAR/nano-QSPR modeling of heterogeneous NPs was a lack of appropriate descriptors that are able to express the specific characteristics of 2nd generation NPs, we developed here a novel approach. The novel approach to encode heterogeneous NPs is based on the idea of additive descriptors for mixture systems previously applied only to mixtures of organic/inorganic compounds. Thus, based on the proposed novel approach, we have performed experimental and theoretical studies to develop nano-QSAR models describing the cytotoxicity of 34 TiO2-based NPs modified by (poly)metallic clusters (Au, Ag, Pt) to the Chinese hamster ovary cell line. The models showed a good predictive ability and robustness. This approach can be used as an efficient tool for assessing the toxicity as well as physicochemical properties of unexplored heterogeneous NPs.
Combined compressive sampling and distribution discontinuities detection approach to wideband spectrum sensing for cognitive radios

This paper1 presents a new sensing technique for cognitive radio systems which combines algebraic tools and com-pressive sampling techniques. The proposed approach consists of the detection of spectrum holes using spectrum distribution discontinuities detector fed by a compressed measurements. The compressed sensing algorithm is designed to take advantage from the primary signals sparsity and to keep the linearity and properties of the original signal in order to be able to apply algebraic detector on the compressed measurements. The complexity of the proposed detector is also discussed and compared with the energy detector as reference algorithm. The comparison shows that the proposed technique outperforms energy detector in addition to its low complexity.
Appearance of Males in a Thelytokous Strain of Milnesium cf. tardigradum (Tardigrada)

Abstract Tardigrades are generally gonochoristic. Many moss-dwelling species propagate by parthenogenesis, but heterogony has not yet been found. Milnesium tardigradum, a carnivorous tardigrade, also has both sexes, but males are usually rare and many populations appear to have only parthenogenetic reproduction. Since 2000, I have maintained a thelytokous strain of Milnesium cf. tardigradum that originated from one female. Individuals of this strain were thought to be all females, but here I report that males have emerged in this strain at a very low frequency. This is the first report of the appearance of males in parthenogenetic tardigrades. On the first pair of legs of some individuals, I observed the modified claws characteristic of males of this species. It is unknown whether these males can actually function in sexual reproduction; however, they might allow some possibility of genetic exchange among clonal populations. No environmental factors that generate males were determined.
Limb chondrogenesis of the seepage salamander, Desmognathus aeneus (Amphibia: Plethodontidae)

Salamanders are infrequently mentioned in analyses of tetrapod limb formation, as their development varies considerably from that of amniotes. However, urodeles provide an opportunity to study how limb ontogeny varies with major differences in life history. Here we assess limb development in Desmognathus aeneus, a direct‐developing salamander, and compare it to patterns seen in salamanders with larval stages (e.g., Ambystoma mexicanum). Both modes of development result in a limb that is morphologically indistinct from an amniote limb. Developmental series of A. mexicanum and D. aeneus were investigated using Type II collagen immunochemistry, Alcian Blue staining, and whole‐mount TUNEL staining. In A. mexicanum, as each digit bud extends from the limb palette Type II collagen and proteoglycan secretion occur almost simultaneously with mesenchyme condensation. Conversely, collagen and proteoglycan secretion in digits of D. aeneus occur only after the formation of an amniote‐like paddle. Within each species, Type II collagen expression patterns resemble those of proteoglycans. In both, distal structures form before more proximal structures. This observation is contrary to the proximodistal developmental pattern of other tetrapods and may be unique to urodeles. In support of previous findings, no cell death was observed during limb development in A. mexicanum. However, apoptotic cells that may play a role in digit ontogeny occur in the limbs of D. aeneus, thereby suggesting that programmed cell death has evolved as a developmental mechanism at least twice in tetrapod limb evolution. J. Morphol. © 2005 Wiley‐Liss, Inc.
Development and Validation of Two Enzyme-Linked Immunosorbent Assay (ELISA) Methods for Recombinant Hirudin

Recombinant hirudin is currently being developed as a potential prophylactic and therapeutic antithrombotic drug in various clinical indications such as angina and deep venous thrombosis. In this report, we have discussed the production of specific polyclonal antibodies to recombinant hirudin (rH) and the development of two ELISA methods to measure rH concentrations in biological fluids: a sandwich and a competitive ELISA method. Intra- and inter-assay variations in the two methods are extremely low (3-7%). The competitive ELISA method is rapid, simple and highly reproducible. Saturation binding curves, selection of appropriate incubation times, recovery of different hirudin variants and reactivity in the presence of thrombin are discussed. The methods can be easily adapted to monitor hirudin concentrations in the clinical laboratory for diagnostic purposes as well as for performing pharmacokinetic studies.
EEG Abnormalities Are Associated With Poorer Depressive Symptom Outcomes With Escitalopram and Venlafaxine-XR, but Not Sertraline

Rationale. Limited research is available on electrophysiological abnormalities such as epileptiform EEG or EEG slowing in depression and its association with antidepressant treatment response. Objectives. We investigated the association between EEG abnormalities and antidepressant treatment response in the international Study to Predict Optimized Treatment in Depression (iSPOT-D). Methods. Of 1008 participants with major depressive disorder randomized to escitalopram, sertraline, or venlafaxine-XR, 622 completed 8 weeks of treatment per protocol. The study also recruited 336 healthy controls. Treatment response was established after 8 weeks using the 17-item Hamilton Rating Scale for Depression (HRSD17). The resting-state EEG was assessed at baseline with eyes closed. EEG abnormalities including epileptiform activity, EEG slowing, and alpha peak frequency (APF) were scored for all subjects, blind to treatment outcome. Results. Patients and controls did not differ in the occurrence of EEG abnormalities. Furthermore, in the per protocol sample the occurrence of epileptiform EEG and EEG slowing (as a combined marker) were associated with a reduced likelihood of responding to escitalopram (P = .019; odds ratio [OR] = 3.56) and venlafaxine-XR (P = .043; OR = 2.76), but not sertraline (OR = 0.73). The response rates for this “any EEG abnormality” groups versus the “no-abnormality” group were 33% and 64% for escitalopram and 41% and 66% for venlafaxine-XR, respectively. A slow APF was associated with treatment response only in the sertraline group (P = .21; d = .027). Conclusions. EEG abnormalities are associated with nonresponse to escitalopram and venlafaxine-XR, but not sertraline, whereas a slow APF is associated to response for sertraline only.
Replication slippage of the thermophilic DNA polymerases B and D from the Euryarchaeota Pyrococcus abyssi

Replication slippage or slipped-strand mispairing involves the misalignment of DNA strands during the replication of repeated DNA sequences, and can lead to genetic rearrangements such as microsatellite instability. Here, we show that PolB and PolD replicative DNA polymerases from the archaeal model Pyrococcus abyssi (Pab) slip in vitro during replication of a single-stranded DNA template carrying a hairpin structure and short direct repeats. We find that this occurs in both their wild-type (exo+) and exonuclease deficient (exo-) forms. The slippage behavior of PabPolB and PabPolD, probably due to limited strand displacement activity, resembles that observed for the high fidelity P. furiosus (Pfu) DNA polymerase. The presence of PabPCNA inhibited PabPolB and PabPolD slippage. We propose a model whereby PabPCNA stimulates strand displacement activity and polymerase progression through the hairpin, thus permitting the error-free replication of repetitive sequences.