Miracle-dz/UniFAR-FTUs huggingface dataset:
A 25 Gb/s 3D-Integrated CMOS/Silicon-Photonic Receiver for Low-Power High-Sensitivity Optical Communication

Integrating optical receivers based on double-sampling architecture exhibit a low-power alternative to those designed around transimpedance amplifiers (TIA). In this paper, we present a 3D-integrated CMOS/silicon-photonic optical receiver. The receiver features a low-bandwidth TIA integrating front-end double-sampling technique and dynamic offset modulation. The copper-pillar-based 3D-integration technology used here enables ultralow parasitics and 40 μm pitch for interconnection. We study different tradeoffs in designing an optical receiver and how to choose between a full-bandwidth TIA front-end and integrating architecture using a resistive front-end or a low-bandwidth TIA front-end. The design methodology is supported by measurements of two 3D-integrated prototypes based on a conventional TIA and a double-sampling integrating receiver. The proposed receiver architecture achieves -14.9 dBm of sensitivity and energy efficiency of 170 fJ/b at 25 Gb/s, while the conventional receiver achieves a sensitivity of -10.4 dBm and energy efficiency of 260 fJ/b at 21.2 Gb/s.
Measuring the robustness of source program obfuscation: studying the impact of compiler optimizations on the obfuscation of C programs

Obfuscation is a commonly used technique to protect software from the reverse engineering process. Advanced obfuscations usually rely on semantic properties of programs and thus may be performed on source programs. This raises the question of how to be sure that the binary code (that is effectively running) is still obfuscated. This paper presents a data obfuscation of C programs and a methodology to evaluate how the obfuscation resists to the GCC compiler. Information generated by the compiler (including effects of relevant optimizations that could deobfuscate programs) and a study of the disassembled binary code, as well as a dynamic analysis of the performances of binary code show that our obfuscation is worthwhile.
Machined and plastic copings in three-element prostheses with different types of implantabutment joints: a strain gauge comparative analysis

Objective Using strain gauge (SG) analysis, the aim of this in vitro study was quantify the strain development during the fixation of three-unit screw implant-supported fixed partial dentures, varying the types of implant-abutment joints and the type of prosthetic coping. The hypotheses were that the type of hexagonal connection would generate different microstrains and the type of copings would produce similar microstrains after prosthetic screws had been tightened onto microunit abutments. Materials and methods Three dental implants with external (EH) and internal (IH) hexagonal configurations were inserted into two polyurethane blocks. Microunit abutments were screwed onto their respective implant groups, applying a torque of 20 Ncm. Machined Co-Cr copings (M) and plastic prosthetic copings (P) were screwed onto the abutments, which received standard wax patterns. The wax patterns were cast in Co-Cr alloy (n=5), forming four groups: G1) EH/M; G2) EH/P; G3) IH/M and G4) IH/P. Four SGs were bonded onto the surface of the block tangentially to the implants, SG 1 mesially to implant 1, SG 2 and SG 3 mesially and distally to implant 2, respectively, and SG 4 distally to implant 3. The superstructure’s occlusal screws were tightened onto microunit abutments with 10 Ncm torque using a manual torque driver. The magnitude of microstrain on each SG was recorded in units of microstrain (µε). The data were analyzed statistically by ANOVA and Tukey’s test (p<0.05). Results Microstrain values of each group were: G1= 338.1±223.0 µε; G2= 363.9±190.9 µε; G3= 415.1±53.5 µε; G4= 363.9±190.9 µε. No statistically significant difference was found between EH and IH, regardless of the type of copings (p>0.05). The hypotheses were partially accepted. Conclusions It was concluded that the type of hexagonal connection and coping presented similar mechanical behavior under tightening conditions.
A Compensatory Mutation Provides Resistance to Disparate HIV Fusion Inhibitor Peptides and Enhances Membrane Fusion

Fusion inhibitors are a class of antiretroviral drugs used to prevent entry of HIV into host cells. Many of the fusion inhibitors being developed, including the drug enfuvirtide, are peptides designed to competitively inhibit the viral fusion protein gp41. With the emergence of drug resistance, there is an increased need for effective and unique alternatives within this class of antivirals. One such alternative is a class of cyclic, cationic, antimicrobial peptides known as θ-defensins, which are produced by many non-human primates and exhibit broad-spectrum antiviral and antibacterial activity. Currently, the θ-defensin analog RC-101 is being developed as a microbicide due to its specific antiviral activity, lack of toxicity to cells and tissues, and safety in animals. Understanding potential RC-101 resistance, and how resistance to other fusion inhibitors affects RC-101 susceptibility, is critical for future development. In previous studies, we identified a mutant, R5-tropic virus that had evolved partial resistance to RC-101 during in vitro selection. Here, we report that a secondary mutation in gp41 was found to restore replicative fitness, membrane fusion, and the rate of viral entry, which were compromised by an initial mutation providing partial RC-101 resistance. Interestingly, we show that RC-101 is effective against two enfuvirtide-resistant mutants, demonstrating the clinical importance of RC-101 as a unique fusion inhibitor. These findings both expand our understanding of HIV drug-resistance to diverse peptide fusion inhibitors and emphasize the significance of compensatory gp41 mutations.
Code fragment summarization

Current research in software engineering has mostly focused on the retrieval accuracy aspect but little on the presentation aspect of code examples, e.g., how code examples are presented in a result page. We investigate the feasibility of summarizing code examples for better presenting a code example. Our algorithm based on machine learning could approximate summaries in an oracle manually generated by humans with a precision of 0.71. This result is promising as summaries with this level of precision achieved the same level of agreement as human annotators with each other.
Nefclass | a Neuro{fuzzy Approach for the Classification of Data

In this paper we present NEFCLASS, a neuro{fuzzy system for the classiication of data. This approach is based on our generic model of a fuzzy perceptron which can be used to derive fuzzy neural networks or neural fuzzy systems for spe-ciic domains. The presented model derives fuzzy rules from data to classify patterns into a number of (crisp) classes. NEFCLASS uses a supervised learning algorithm based on fuzzy error backpropagation that is used in other derivations of the fuzzy perceptron.
Transient Electric Birefringence Study of Intermediate Filament Formation from Vimentin and Glial Fibrillary Acidic Protein*

Mg2+-induced polymerization of type III intermediate filament proteins vimentin and glial fibrillary acidic protein was studied by transient electric birefringence. In the absence of MgCl2 we found a net permanent dipole moment, ∼45-nm-long dimers for vimentin, ∼65-nm-long tetramers, hexamers, and possibly octamers for both proteins, and 100-nm aggregates for glial fibrillary acidic protein. Controlled oligomerization occurred after the addition of MgCl2. Although the solutions contained (small) aggregates of different sizes, more or less discrete steps in polymer formation were observed, and it was possible to discriminate between an increase in width and length. At the first stage of polymerization (in 0.3 mm MgCl2 for vimentin and 0.2 mm MgCl2 for glial fibrillary acidic protein), the permanent dipole moment disappeared without a change in length of the particles. At higher MgCl2concentrations, structures of approximately 100 nm were formed, which strongly tended to laterally assemble into full-width intermediate filament structures consisting of about 32 monomers. This contrasts with previous models where first full-width (∼10-nm) aggregates are formed, which then increase in length. Subsequently, two discrete elongation steps of 35 nm are observed that increase the length to 135 and 170 nm, respectively. Possible structural models are suggested for the polymerization.
Gendered Multilingualism in highland Daghestan: story of a loss

ABSTRACT The paper traces the level of bilingualism in several highland villages of Daghestan (Northeast Caucasus) through the twentieth century. We show that historically, men were more multilingual than women, but this was not true to the same extent for all languages. Highlanders’ repertoires suggest a correlation between the social function of the second language and the degree to which its command was gendered. We also explore the dynamics of multilingualism from the generation born at the end of the nineteenth century to the generation born in the 1990s. We show that during the twentieth century local L2s were gradually displaced by Russian, and Daghestanian multilingualism lost its gendered character. We argue that these changes were caused by the introduction of Soviet schooling.
NuSTAR OBSERVATIONS OF MAGNETAR 1E 1841−045

We report new spectral and temporal observations of the magnetar 1E 1841−045 in the Kes 73 supernova remnant obtained with the Nuclear Spectroscopic Telescope Array. Combined with new Swift and archival XMM-Newton and Chandra observations, the phase-averaged spectrum is well characterized by a blackbody plus double power law, in agreement with previous multimission X-ray results. However, we are unable to reproduce the spectral results reported based on Suzaku observations. The pulsed fraction of the source is found to increase with photon energy. The measured rms pulsed fractions are ∼12% and ∼17% at ∼20 and ∼50 keV, respectively. We detect a new feature in the 24–35 keV band pulse profile that is uniquely double peaked. This feature may be associated with a possible absorption or emission feature in the phase-resolved spectrum. We fit the X-ray data using the recently developed electron–positron outflow model by Beloborodov for the hard X-ray emission from magnetars. This produces a satisfactory fit, allowing a constraint on the angle between the rotation and magnetic axes of the neutron star of ∼20° and on the angle between the rotation axis and line of sight of ∼50°. In this model, the soft X-ray component is inconsistent with a single blackbody; adding a second blackbody or a power-law component fits the data. The two-blackbody interpretation suggests a hot spot of temperature kT ≈ 0.9 keV occupying ∼1% of the stellar surface.
Deletion of the Basement Membrane Heparan Sulfate Proteoglycan Type XVIII Collagen Causes Hypertriglyceridemia in Mice and Humans

Background Lipoprotein lipase (Lpl) acts on triglyceride-rich lipoproteins in the peripheral circulation, liberating free fatty acids for energy metabolism or storage. This essential enzyme is synthesized in parenchymal cells of adipose tissue, heart, and skeletal muscle and migrates to the luminal side of the vascular endothelium where it acts upon circulating lipoproteins. Prior studies suggested that Lpl is immobilized by way of heparan sulfate proteoglycans on the endothelium, but genetically altering endothelial cell heparan sulfate had no effect on Lpl localization or lipolysis. The objective of this study was to determine if extracellular matrix proteoglycans affect Lpl distribution and triglyceride metabolism. Methods and Findings We examined mutant mice defective in collagen XVIII (Col18), a heparan sulfate proteoglycan present in vascular basement membranes. Loss of Col18 reduces plasma levels of Lpl enzyme and activity, which results in mild fasting hypertriglyceridemia and diet-induced hyperchylomicronemia. Humans with Knobloch Syndrome caused by a null mutation in the vascular form of Col18 also present lower than normal plasma Lpl mass and activity and exhibit fasting hypertriglyceridemia. Conclusions This is the first report demonstrating that Lpl presentation on the lumenal side of the endothelium depends on a basement membrane proteoglycan and demonstrates a previously unrecognized phenotype in patients lacking Col18.
One and two dimensional LiNbO3 photonic crystals

In this report, we present an investigation of the optical properties and band structure calculations for the photonic crystal structures (PCs) based on one-dimensional (1D) and two-dimensional (2D) ferroelectric LiNbO3 crystal. Here we use 1D and 2D periodic crystal structure of dielectric rods and layers in air background. We have theoretically calculated photonic band structure and optical properties of 1D and 2D LiNbO3 PCs. Beside, we have calculated affect PBG properties of different parameters such as filling fraction and the shape. In order to get photonic gap map, we have calculated the gaps as a function of radius of the rods. We have also investigated the nature of guided modes in line defect waveguide. In our simulation, we employed the finite-difference time domain (FDTD) technique which implies the solution of Maxwell equations with centered finite-difference expressions for the space and time derivatives.
Poisson multi-Bernoulli conjugate prior for multiple extended object estimation

This paper presents a Poisson multi-Bernoulli mixture (PMBM) conjugate prior for multiple extended object estimation. A Poisson point process is used to describe the existence of yet undetected targets, while a multi-Bernoulli mixture describes the distribution of the targets that have been detected. The prediction and update equations are presented for the standard transition density and measurement likelihood. Both the prediction and the update preserve the PMBM form of the density, and in this sense the PMBM density is a conjugate prior. However, the unknown data associations lead to an intractably large number of terms in the PMBM density, and approximations are necessary for tractability. A gamma Gaussian inverse Wishart implementation is presented, along with methods to handle the data association problem. A simulation study shows that the extended target PMBM filter outperforms the extended target PHD, CPHD and LMB filters. An experiment with Lidar data illustrates the benefit of tracking both detected and undetected targets.
Illustrative Context-Preserving Exploration of Volume Data

In volume rendering, it is very difficult to simultaneously visualize interior and exterior structures while preserving clear shape cues. Highly transparent transfer functions produce cluttered images with many overlapping structures, while clipping techniques completely remove possibly important context information. In this paper, we present a new model for volume rendering, inspired by techniques from illustration. It provides a means of interactively inspecting the interior of a volumetric data set in a feature-driven way which retains context information. The context-preserving volume rendering model uses a function of shading intensity, gradient magnitude, distance to the eye point, and previously accumulated opacity to selectively reduce the opacity in less important data regions. It is controlled by two user-specified parameters. This new method represents an alternative to conventional clipping techniques, sharing their easy and intuitive user control, but does not suffer from the drawback of missing context information
Les modèles de régression angulaire

For the analysis of directional data, there are three types of regression models: angular-linear, linear-angular and angular-angular. The type of regression depends on the nature of the data. Hence, if the explanatory variable and the response variable are angles, the angular-angular regression model can explain the relationship between these variables. Several models have been developed for this purpose and in this paper, three of these directional models are discussed: the decentred predictor of Rivest (1997), the Mobius model Downs & Mardia (2002) and the nonparametric regression of Di Marzio et al. (2012). Estimation procedures are highlighted for the parameters of each of these models. We compare the models together with simulations and examples using real data.
Meta-Type Analysis of Dopaminergic Effects on Gene Expression in the Neuroendocrine Brain of Female Goldfish

Dopamine (DA) is a major neurotransmitter important for neuroendocrine control and recent studies have described genomic signaling pathways activated and inhibited by DA agonists and antagonists in the goldfish brain. Here we perform a meta-type analysis using microarray datasets from experiments conducted with female goldfish to characterize the gene expression responses that underlie dopaminergic signaling. Sexually mature, pre-spawning [gonadosomatic index (GSI) = 4.5 ± 1.3%] or sexually regressing (GSI = 3 ± 0.4%) female goldfish (15–40 g) injected intraperitoneally with either SKF 38393, LY 171555, SCH 23390, sulpiride, or a combination of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine and α-methyl-p-tyrosine. Microarray meta-type analysis identified 268 genes in the telencephalon and hypothalamus as having reciprocal (i.e., opposite between agonism and antagonism/depletion) fold change responses, suggesting that these transcripts are likely targets for DA-mediated regulation. Noteworthy genes included ependymin, vimentin, and aromatase, genes that support the significance of DA in neuronal plasticity and tissue remodeling. Sub-network enrichment analysis (SNEA) was used to identify common gene regulators and binding proteins associated with the differentially expressed genes mediated by DA. SNEA analysis identified gene expression targets that were related to three major categories that included cell signaling (STAT3, SP1, SMAD, Jun/Fos), immune response (IL-6, IL-1β, TNFs, cytokine, NF-κB), and cell proliferation and growth (IGF1, TGFβ1). These gene networks are also known to be associated with neurodegenerative disorders such as Parkinsons’ disease, well-known to be associated with loss of dopaminergic neurons. This study identifies genes and networks that underlie DA signaling in the vertebrate CNS and provides targets that may be key neuroendocrine regulators. The results provide a foundation for future work on dopaminergic regulation of gene expression in fish model systems.
Evolution of Fitnesses in Structured Populations With Correlated Environments

The outcome of selection in structured populations with spatially varying selection pressures depends on the interaction of two factors: the level of gene flow and the amount of heterogeneity among the demes. Here we investigate the effect of three different levels of spatial heterogeneity on the levels of genetic polymorphisms for different levels of gene flow, using a construction approach in which a population is constantly bombarded with new mutations. We further compare the relative importance of two kinds of balancing selection (heterozygote advantage and selection arising from spatial heterogeneity), the level of adaptation and the stability of the resulting polymorphic equilibria. The different levels of environmental heterogeneity and gene flow have a large influence on the final level of polymorphism. Both factors also influence the relative importance of the two kinds of balancing selection in the maintenance of variation. In particular, selection arising from spatial heterogeneity does not appear to be an important form of balancing selection for the most homogeneous scenario. The level of adaptation is highest for low levels of gene flow and, at those levels, remarkably similar for the different levels of spatial heterogeneity, whereas for higher levels of gene flow the level of adaptation is substantially reduced.
An analysis of XML binary formats and compression

XML simplifies data exchange amongst disparate computers, but is notoriously verbose and has spawned development of a variety of XML compressors and binary formats. Some formats allow streaming access to the data without complete decompression. We present an XML test file corpus, akin to corpora such as the Canterbury corpus and a combined efficiency metric integrating compression ratio and speed. We then use the test corpus to assess 14 general-purpose and XML-specific compressors against the efficiency and other metrics. After constructing linear regression models, we identify the factors influencing compressor selection and then rank the best-performing compressors.
Evolution Model of Spatial Interaction Network in Online Social Networking Services

The development of online social networking services provides a rich source of data of social networks including geospatial information. More and more research has shown that geographical space is an important factor in the interactions of users in social networks. In this paper, we construct the spatial interaction network from the city level, which is called the city interaction network, and study the evolution mechanism of the city interaction network formed in the process of information dissemination in social networks. A network evolution model for interactions among cities is established. The evolution model consists of two core processes: the edge arrival and the preferential attachment of the edge. The edge arrival model arranges the arrival time of each edge; the model of preferential attachment of the edge determines the source node and the target node of each arriving edge. Six preferential attachment models (Random-Random, Random-Degree, Degree-Random, Geographical distance, Degree-Degree, Degree-Degree-Geographical distance) are built, and the maximum likelihood approach is used to do the comparison. We find that the degree of the node and the geographic distance of the edge are the key factors affecting the evolution of the city interaction network. Finally, the evolution experiments using the optimal model DDG are conducted, and the experiment results are compared with the real city interaction network extracted from the information dissemination data of the WeChat web page. The results indicate that the model can not only capture the attributes of the real city interaction network, but also reflect the actual characteristics of the interactions among cities.
Lightweight Component Models for Embedded Systems ∗

Components are receiving attention as a means of advancing the state of software distribution beyond the traditional choices of source code, compiled binary executable, and compiled libraries. In this paper, we examine lightweight component models for embedded real-time software systems, and propose two different component models based on the concepts of actors and models of computation.
Prediction of Postoperative Pain: A Systematic Review of Predictive Experimental Pain Studies

Quantitative testing of a patient's basal pain perception before surgery has the potential to be of clinical value if it can accurately predict the magnitude of pain and requirement of analgesics after surgery. This review includes 14 studies that have investigated the correlation between preoperative responses to experimental pain stimuli and clinical postoperative pain and demonstrates that the preoperative pain tests may predict 4–54% of the variance in postoperative pain experience depending on the stimulation methods and the test paradigm used. The predictive strength is much higher than previously reported for single factor analyses of demographics and psychologic factors. In addition, some of these studies indicate that an increase in preoperative pain sensitivity is associated with a high probability of development of sustained postsurgical pain.