Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Tears Contain a Chemosignal

Merely sniffing women's negative emotional tears reduces sexual arousal in men. Emotional tearing is a poorly understood behavior that is considered uniquely human. In mice, tears serve as a chemosignal. We therefore hypothesized that human tears may similarly serve a chemosignaling function. We found that merely sniffing negative-emotion–related odorless tears obtained from women donors induced reductions in sexual appeal attributed by men to pictures of women’s faces. Moreover, after sniffing such tears, men experienced reduced self-rated sexual arousal, reduced physiological measures of arousal, and reduced levels of testosterone. Finally, functional magnetic resonance imaging revealed that sniffing women’s tears selectively reduced activity in brain substrates of sexual arousal in men.
Disambiguating Entities Referred by Web Endpoints using Tree Ensembles

This paper describes system details and results of team “EOF” from the University of Melbourne in the shared task of ALTA 2016, which addresses the use of cross document coreference resolution to determine whether two URLs refer to the same underlying entity. In our submission, we develop a two stage system which ﬁrst identiﬁes the underlying entity for a given URL using entity-level features by ranking the entity mentions present in the crawled text with the help of logistic regression. This is followed by disambiguating entities present in the given pair of URLs using a tree ensemble model to classify if both URLs refer to the same underlying entity. Our system achieved a ﬁnal F1-score of 86.02% on the private leader-board 1 , which is the best score among all the participating systems.
Very low PSA concentrations and deletions of the KLK3 gene.

BACKGROUND Prostate-specific antigen (PSA), a widely used biomarker for prostate cancer (PCa), is encoded by a kallikrein gene (KLK3, kallikrein-related peptidase 3). Serum PSA concentrations vary in the population, with PCa patients generally showing higher PSA concentrations than control individuals, although a small proportion of individuals in the population display very low PSA concentrations. We hypothesized that very low PSA concentrations might reflect gene-inactivating mutations in KLK3 that lead to abnormally reduced gene expression. METHODS We have sequenced all KLK3 exons and the promoter and searched for gross deletions or duplications in KLK3 in the 30 individuals with the lowest observed PSA concentrations in a sample of approximately 85 000 men from the Prostate Testing for Cancer and Treatment (ProtecT) study. The ProtecT study examines a community-based population of men from across the UK with little prior PSA testing. RESULTS We observed no stop codons or frameshift mutations, but we did find 30 single-base genetic variants, including 3 variants not described previously. These variants included missense variants that could be functionally inactivating and splicing variants. At this stage, however, we cannot confidently conclude whether these variants markedly lower PSA concentration or activity. More importantly, we identified 3 individuals with different large heterozygous deletions that encompass all KLK3 exons. The absence of a functional copy of KLK3 in these individuals is consistent with their reduced serum PSA concentrations. CONCLUSIONS The clinical interpretation of the PSA test for individuals with KLK3 gene inactivation could lead to false-negative PSA findings used for screening, diagnosis, or monitoring of PCa.
Whole Genome Sequence of the Soybean Aphid Endosymbiont Buchnera aphidicola and Genetic Differentiation among Biotype-Specific Strains

Endosymbiosis with microorganisms is common in insects, with more than 10% of species requiring the metabolic capabilities of intracellular bacteria for their nutrient acquisition. Aphids harbor an obligate mutualism with the vertically transferred endosymbiont, Buchnera aphidicola, which produces key nutrients lacking in the aphid's phloem-based diet that are necessary for normal development and reproduction. It is thought that, in some groups of insects, bacterial symbionts may play key roles in biotype evolution against host-plant resistance. The genome of Buchnera has been sequenced in several aphid strains but little genomic data is currently available for the soybean aphid (Aphis glycines), one of the most important pests of soybean in North America. In this study, DNA sequencing was used to assemble and annotate the genome sequence of the Buchnera A. glycines strain and to reconstruct phylogenetic relationships among different strains. In addition, we identified several fixed Buchnera SNPs between Aphis glycines biotypes that were avirulent or virulent to a soybean aphid resistance gene (Rag1). The results of this study describe the genetic and evolutionary relationships of the Buchnera A. glycines strain, and begin to define the roles of an aphid symbiont in host-plant resistance.
logcondens: Computations Related to Univariate Log-Concave Density Estimation

Maximum likelihood estimation of a log-concave density has attracted considerable attention over the last few years. Several algorithms have been proposed to estimate such a density. Two of those algorithms, an iterative convex minorant and an active set algorithm, are implemented in the R package logcondens. While these algorithms are discussed elsewhere, we describe in this paper the use of the logcondens package and discuss functions and datasets related to log-concave density estimation contained in the package. In particular, we provide functions to (1) compute the maximum likelihood estimate (MLE) as well as a smoothed log-concave density estimator derived from the MLE, (2) evaluate the estimated density, distribution and quantile functions at arbitrary points, (3) compute the characterizing functions of the MLE, (4) sample from the estimated distribution, and finally (5) perform a two-sample permutation test using a modified Kolmogorov-Smirnov test statistic. In addition, logcondens makes two datasets available that have been used to illustrate log-concave density estimation.
Genital and body allometry in two species of noctuid moths (Lepidoptera: Noctuidae).

One-size-fits-all and related hypotheses predict that static allometry slopes for male genitalia will be consistently lower than 1.0 and lower than the slopes for most other body parts (somatic traits). We examined the allometry of genitalic and somatic morphological traits in males and females of two species of noctuid moths, Spodoptera exigua (Hubner, [1808]) and Helicoverpa armigera (Hubner, [1808]). The relationship between genitalic traits and body size was generally strongly negative-allometric in males but with no significant differences from 1.00 in females of the two species examined. However, in females, the slope of genital traits was also lower than the slopes for somatic traits. The relationship between somatic traits and the body size indicator was approximately isometric in most cases in males, except in four traits in S. exigua, in which the slopes showed slight negative allometry, and the hind tibia in H. armigera, in which the slope had positive allometry. However, in females, some somatic traits showed isometric and some other showed negative allometry in both species. The coefficients of variation (CV) for all structures in the males were low, not exceeding 10%. Genitalic traits showed significantly lower CV than somatic traits in males. In females, somatic traits showed lower CV than genitalic traits but with no significant difference in the H. armigera. Our observations of strongly negative allometry for genitalic traits in males are consistent with stabilizing selection on genital size and we suggest that male performance in interactions with females is the source of selection on male genital allometry. The difference in the degree of phenotypic variation between genitalic and somatic traits in the two studied species is attributed to the different developmental-genetic architectures of these traits. Female genitalia showed a similar trend to the males, although the difference between genital and somatic traits was not significant in females. This finding suggests that selection is acting differently on male and female genitalia. Positive allometry of hind tibia in H. armigera may be a result of secondary sexual function.
Deflection Routing in Hierarchical Mesh NoCs

Deflection routing has benefits that may make it attractive especially when inexpensive network-on-chip (NoC) implementations are considered. In this letter, we present a proposal of deflection routing in hierarchical mesh NoCs. An evaluation of performance and power, obtained with a cycle accurate simulator and using both synthetic and application benchmarks, is reported. We introduce interleaving and shifting, two techniques that reduce the number of routers with a high radix crossbar without reducing network performance.
Natural Language Access to Relational Databases through STEP

This paper introduces the STEP system for natural language access to relational databases. In STEP the administrator couples phrasal patterns to elementary expressions within a decidable fragment of tuple relational calculus. This phrasal lexicon serves as a bi-directional grammar, enabling the generation of natural language from tuple relational calculus and the inverse parsing of natural language to tuple calculus expressions. This ability to both understand and generate natural language enables STEP to engage the user in clarification dialogs when the parse of their query is of questionable quality. The STEP system is implemented and is currently being evaluated over a geography database. Additional evaluations are planned and will also be available on STEP’s website (http://www.cs.umu.se/ ̃mjm/step).
An Integrative Approach Revealing the Landscape of Long Noncoding RNAs in Human Brain

Long noncoding RNAs (lncRNAs) function as regulators and play critical roles in diverse biological processes, however, the majority of lncRNAs are not characterized, and their roles in regulation remain to be elucidated. Present RNA-seq assembly approaches are insufficient to identify complete full-length transcripts and often reveal excessive amount of single-exon lncRNAs, many of them tend to be the fragments of transcripts. Here we developed an integrated approach that combined the results from reference-guided and de novo assembly to systematically identify lncRNAs. Experiments on simulated data and real RNA-seq data showed that our method effectively yielded a more comprehensive set of lncRNAs. We applied the method on 299 human brain RNA-seq samples with a total of 4.5 billion raw reads. The results yield a comprehensive lncRNAs mapping in human brain, allowing discovery of novel lncRNAs and further function annotation.
Random intersection graphs and their applications in security, wireless communication, and social networks

Random intersection graphs have received much interest and been used in diverse applications. They are naturally induced in modeling secure sensor networks under random key predistribution schemes, as well as in modeling the topologies of social networks including common-interest networks, collaboration networks, and actor networks. Simply put, a random intersection graph is constructed by assigning each node a set of items in some random manner and then putting an edge between any two nodes that share a certain number of items. Broadly speaking, our work is about analyzing random intersection graphs, and models generated by composing it with other random graph models including random geometric graphs and Erd\H{o}s-R\'enyi graphs. These compositional models are introduced to capture the characteristics of various complex natural or man-made networks more accurately than the existing models in the literature. For random intersection graphs and their compositions with other random graphs, we study properties such as ($k$-)connectivity, ($k$-)robustness, and containment of perfect matchings and Hamilton cycles. Our results are typically given in the form of asymptotically exact probabilities or zero-one laws specifying critical scalings, and provide key insights into the design and analysis of various real-world networks.
Intrusion Free Monitoring : An Observation Engine For Message Server Based Applications

Abstract: In the area of distributed applications communicating using message exchange, debugging is inherently difficult. Underlying distributed architecture, lack of global state expression, unpredictable communication delays and various speeds of multiple machines are typical difficulties and imply to pick up pertinent information. In this paper, we propose a monitoring technique to help in debugging message server based applications. We propose to collect monitoring information at the application level by introducing an Observation Engine. This Engine is a standard application which is only able to listen all exchanged messages. To plug such an application on the message server without modifying existing ones is possible by the use of a registration mechanism. The Observation Engine can register itself to all emitted messages, without any limitation. The use of this Observation Engine does not require to modify the debugged applications nor to stop their execution. Moreover, our technique does not change the behavior of the observed applications. Side effects only appear in communication delays and are due to additional messages routed to the Observation Engine by the message server.
Eating from a salad bowl: Examining the cognitive demands and levels of difficulty in the Setswana NSC examination question papers

The aim of this article is to address the apparent lack of confidence in the quality assurance processes in the teaching and assessment of African languages, including Setswana. The article looks at whether the Setswana Grade 12 question papers accommodate and maintain a balance between the lower, middle and higher order cognitive demands and levels of difficulty. The importance of assessing cognitive demands, levels of difficulty and principles of high-quality assessment practices in the Setswana question papers, in relation to subject content knowledge, as processes to assure quality, cannot be overemphasised. One hundred and twenty-six Grade 12 Setswana examination question papers were analysed. The analysis was underpinned by Vygotsky’s theory of constructivism for assessment as it puts more emphasis on the learner as an active ‘maker of meaning’ of the content that is taught. A desktop approach was used, and the examination question papers were analysed through Bloom’s taxonomy as a framework or a key tool used in standardised assessment. The results of the research done prove that, although there are challenges in terms of resources, whether human or material, the Setswana Grade 12 examination question papers are of an appropriate standard and are fit for the purpose they are designed for.
Characteristics of E. coli K12 strains carrying both an F prime and an R factor.

The interrelationship between an F prime and an F-like or I-like R factor was studied in Escherichia coli K 12 strains carrying both. The donorability of such strains suggested that these plasmids were transferred independently by their own transfer systems. Plaque formation by several male- and female-specific phage was tested; the inhibition by F lac of several female-specific phage was not affected by an F-like R factor. Neither did an R factor affect the incompatibility between F lac and F his . However, the surface exclusion characteristic of F lac was lost in the presence of an F-like R factor. This is probably closely related to the simultaneous loss of donorability, the F-pilus, and the f + antigen: all may be the result of the inhibition by an R product of the formation or activity of a single F product.
What prones adolescents to act assertively:the social information processing in assertiveness

Dissertacao de mestrado em Psicologia Clinica (Intervencoes Cognitivo-Comportamentais nas Perturbacoes Psicologicas e Saude) apresentada a Faculdade de Psicologia e Ciencias da Educacao da Universidade de Coimbra
Altered rate of fibronectin matrix assembly by deletion of the first type III repeats

The assembly of fibronectin (FN) into a fibrillar matrix is a complex stepwise process that involves binding to integrin receptors as well as interactions between FN molecules. To follow the progression of matrix formation and determine the stages during which specific domains function, we have developed cell lines that lack an endogenous FN matrix but will form fibrils when provided with exogenous FN. Recombinant FNs (recFN) containing deletions of either the RGD cell- binding sequence (RGD-) or the first type III repeats (FN delta III1-7) including the III1 FN binding site were generated with the baculovirus insect cell expression system. After addition to cells, recFN matrix assembly was monitored by indirect immunofluorescence and by insolubility in the detergent deoxycholate (DOC). In the absence of any native FN, FN delta III1-7 was assembled into fibrils and was converted into DOC-insoluble matrix. This process could be inhibited by the amino- terminal 70 kD fragment of FN, showing that FN delta III1-7 follows an assembly pathway similar to FN. The progression of FN delta III1-7 assembly differed from native FN in that the recFN became DOC-insoluble more quickly. In contrast, RGD- recFNs were not formed into fibrils except when added in combination with native FN. These results show that the RGD sequence is essential for the initiation step but fibrils can form independently of the III1-7 modules. The altered rate of FN delta III1-7 assembly suggests that one function of the missing repeats might be to modulate an early stage of matrix formation.
Square root update acceleration of the EM algorithm in Gaussian mixture processes

This paper presents a new expectation maximization (EM) algorithm, which employees Square-root Update method combined by conventional Gaussian mixture EM algorithm, to accelerate the parameter learning of Gaussian mixture models. The algorithm enables us to improve poor convergence, avoids us unstable implementation and removes unnecessary iterations by employing inexact searches during the maximization processes. The convergence is faster compared to conventional EM algorithm. Furthermore, our proposal algorithm can be applied to autoregressive Gaussian mixture stationary processes.
Surface stresses on a thin shell surrounding a traversable wormhole

We match an interior solution of a spherically symmetric traversable wormhole to a unique exterior vacuum solution, with a generic cosmological constant, at a junction interface, and the surface stresses on the thin shell are deduced. In the spirit of minimizing the usage of exotic matter we determine regions in which the weak and null energy conditions are satisfied on the junction surface. The characteristics and several physical properties of the surface stresses are explored, namely, regions where the sign of the tangential surface pressure is positive and negative (surface tension) are determined. This is done by expressing the tangential surface pressure as a function of several parameters, namely, that of the matching radius, the redshift parameter, the surface energy density and of the generic cosmological constant. An equation governing the behaviour of the radial pressure across the junction surface is also deduced.
Accelerating Gene Regulatory Network Modeling Using Grid-Based Simulation

Modeling gene regulatory networks has, in some cases, enabled biologists to predict cellular behavior long before such behavior can be experimentally validated. Unfortunately, the extent to which biologists can take advantage of these modeling techniques is limited by the computational complexity of gene regulatory network simulation algorithms. This study presents a new platform-independent, grid-based distributed computing environment that accelerates biological model simulation and, ultimately, development. Applying this environment to gene regulatory network simulation shows a significant reduction in execution time versus running simulation jobs locally. To analyze this improvement, a performance model of the distributed computing environment is built. Although this grid-based system was specifically developed for biological simulation, the techniques discussed are applicable to a variety of simulation performance problems.
Uplink resource allocation for interworking of WLAN and OFDMA-based femtocell systems

Efficiency of the wireless local area network (WLAN)/femtocell interworking system essentially relies on the efficiency of the resource allocation protocol employed in the system. Efficiency of the resource allocation protocol depends on whether it has been designed considering physical layer and medium access control layer technologies of different networks in the interworking system. Therefore, in this paper, we formulate a resource (user, subcarrier, and power) allocation problem for maximizing the sum of weighted rates of the interworking system considering multi-homing capable users and the main features of IEEE 802.11 distributed coordination function (DCF) and orthogonal frequency division multiple access (OFDMA) based femtocell networks. Solving this problem optimally is prohibitively complex as it is a non-convex problem. Thus, the problem is sub-optimally solved by dividing it to two sub-problems. A heuristic algorithm is proposed for user and subcarrier allocation while an optimal and fast converging power allocation algorithm is derived based on dual decomposition and the characteristics of Lagrangian. Simulation results have shown that the proposed resource allocation protocol achieves results close to the optimum.
Toward the modeling of mucus draining from human lung: role of airways deformation on air-mucus interaction

Chest physiotherapy is an empirical technique used to help secretions to get out of the lung whenever stagnation occurs. Although commonly used, little is known about the inner mechanisms of chest physiotherapy and controversies about its use are coming out regularly. Thus, a scientific validation of chest physiotherapy is needed to evaluate its effects on secretions. We setup a quasi-static numerical model of chest physiotherapy based on thorax and lung physiology and on their respective biophysics. We modeled the lung with an idealized deformable symmetric bifurcating tree. Bronchi and their inner fluids mechanics are assumed axisymmetric. Static data from the literature is used to build a model for the lung's mechanics. Secretions motion is the consequence of the shear constraints apply by the air flow. The input of the model is the pressure on the chest wall at each time, and the output is the bronchi geometry and air and secretions properties. In the limit of our model, we mimicked manual and mechanical chest physiotherapy techniques. We show that for secretions to move, air flow has to be high enough to overcome secretion resistance to motion. Moreover, the higher the pressure or the quicker it is applied, the higher is the air flow and thus the mobilization of secretions. However, pressures too high are efficient up to a point where airways compressions prevents air flow to increase any further. Generally, the first effects of manipulations is a decrease of the airway tree hydrodynamic resistance, thus improving ventilation even if secretions do not get out of the lungs. Also, some secretions might be pushed deeper into the lungs; this effect is stronger for high pressures and for mechanical chest physiotherapy. Finally, we propose and tested two a dimensional numbers that depend on lung properties and that allow to measure the efficiency and comfort of a manipulation.