Miracle-dz/UniFAR-FTUs huggingface dataset:
The social and ecological costs of an ‘over-extended' phenotype

Extended phenotypes offer a unique opportunity to experimentally manipulate and identify sources of selection acting on traits under natural conditions. The social cichlid fish Neolamprologus multifasciatus builds nests by digging up aquatic snail shells, creating an extended sexual phenotype that is highly amenable to experimental manipulation through addition of extra shells. Here, we find sources of both positive sexual selection and opposing natural selection acting on this trait; augmenting shell nests increases access to mates, but also increases social aggression and predation risk. Increasing the attractiveness of one male also changed social interactions throughout the social network and altered the entire community structure. Manipulated males produced and received more displays from neighbouring females, who also joined augmented male territories at higher rates than unmanipulated groups. However, males in more attractive territories received more aggression from neighbouring males, potentially as a form of social policing. We also detected a significant ecological cost of the ‘over-extended' phenotype; heterospecific predators usurped augmented nests at higher rates, using them as breeding sites and displacing residents. Using these natural experiments, we find that both social and ecological interactions generate clear sources of selection mediating the expression of an extended phenotype in the wild.
Is There Skill-Biased Technological Change in Italian Manufacturing ? Evidence from Firm-Level Data

The bulk of literature finding support for the Skill-Biased Technological Change (SBTC) hypothesis has focused on the US and the UK, while evidence on other countries is ‘mixed’. We use firm-level data to test for the presence of SBTC in Italian manufacturing. This is interesting since, as well known, Italy is a ‘late comer’ country and stands as a follower in the realm of new technologies. We estimate employment-share equations and find evidence that the impact of R&D on the skill-ratio (the ratio between white collars and blue collars) varies across Pavitt sectors and according to destination of R&D. However, whenever evidence supporting SBTC (i.e. a positive impact on the skill-ratio) is found, it mainly operates through the reduction of unskilled workers. This can be easily reconciled with the structural features of Italian manufacturing where traditional sectors and small and medium sized firms prevail, innovative activity is scarce and mainly labour-saving and the capacity to absorb skilled labour rather limited. JEL Class. : J210 L600 O330
Proof-Checking, Theorem Proving, and Program Verification.

Abstract : This article consists of three parts: a tutorial introduction to a computer program that proves theorems by induction; a brief description of recent applications of that theorem-prover; and a discussion of several nontechnical aspects of the problem of building automatic theorem-provers. The theorem-prover described has proved such theorems as the uniqueness of prime factorizations, Fermat's theorem, and the recursive unsolvability of the halting problem. The article is aimed at those who know nothing about automatic theorem-proving but would like a glimpse of one such system. The authors' in opinion, the limiting factor in progress in automatic theorem-proving is the quality of the mathematicians who are attempting to build such systems. They encourage good mathematicians to work in the field.
A novel role for transcription-coupled nucleotide excision repair for the in vivo repair of 3,N4-ethenocytosine

Abstract Etheno (ε) DNA base adducts are highly mutagenic lesions produced endogenously via reactions with lipid peroxidation (LPO) products. Cancer-promoting conditions, such as inflammation, can induce persistent oxidative stress and increased LPO, resulting in the accumulation of ε-adducts in different tissues. Using a recently described fluorescence multiplexed host cell reactivation assay, we show that a plasmid reporter bearing a site-specific 3,N4-ethenocytosine (εC) causes transcriptional blockage. Notably, this blockage is exacerbated in Cockayne Syndrome and xeroderma pigmentosum patient-derived lymphoblastoid and fibroblast cells. Parallel RNA-Seq expression analysis of the plasmid reporter identifies novel transcriptional mutagenesis properties of εC. Our studies reveal that beyond the known pathways, such as base excision repair, the process of transcription-coupled nucleotide excision repair plays a role in the removal of εC from the genome, and thus in the protection of cells and tissues from collateral damage induced by inflammatory responses.
Vasoactive Intestinal Peptide and Its Receptors in Human Ovarian Cortical Follicles

Background Ovarian cryopreservation is one option for fertility preservation in patients with cancer. The danger of reseeding malignancies could be eliminated by in vitro maturation of primordial follicles from the frozen-thawed tissue. However, the development of this system is hindered by uncertainties regarding factors that activate primordial follicles. Neuronal growth factors such as vasoactive intestinal peptide (VIP) play important roles in early mammalian folliculogenesis. There are no data on the expression of VIP and its vasoactive intestinal peptide pituitary adenylate cyclase 1 and 2 receptors (VPAC1-R and VPAC2-R) in human preantral follicles. Methodology/Principal Findings Tissue samples from 14 human fetal ovaries and 40 ovaries from girls/women were prepared to test for the expression of VIP, VPAC1-R, and VPAC2-R on the protein (immunohistochemisty) and mRNA (reverse transcription polymerase chain reaction) levels. Immunohistochemistry staining was mostly weak, especially in fetal samples. The VIP protein was identified in oocytes and granulosa cells (GCs) in the fetal samples from 22 gestational weeks (GW) onwards. In girls/women, VIP follicular staining (oocytes and GCs) was identified in 45% of samples. VPAC1-R protein was identified in follicles in all fetal samples from 22GW onwards and in 63% of the samples from girls/women (GC staining only in 40%). VPAC2-R protein was identified in follicles in 33% of fetal samples and 47% of the samples from girls/women. The mRNA transcripts for VIP, VPAC1-R, and VPAC2-R were identified in ovarian extracts from fetuses and women. Conclusions VIP and its two receptors are expressed in human ovarian preantral follicles. However, their weak staining suggests they have limited roles in early follicular growth. To elucidate if VIP activates human primordial follicles, it should be added to the culture medium.
A Generic Parameter Optimization Workflow for Camera Control Algorithms

Cameras are often controlled by algorithms adapting the image capturing process parameters (like exposure or gain) to the present scene. In most cases these algorithms have to be parametrized by a parameter set in order to define the behavior of the control. The issue of selecting the best parameter set for a specific application or environment arises. The parameter selection is not a simple task since the internal structure of the control algorithm is often not sufficiently known by the user. Only the inputs (parameter sets) can be specified and the outputs (images) can be analyzed. This paper presents a generic workflow for the determination of a parameter set which achieves good image quality for a chosen application with specific light conditions. The developed workflow is able to deal with any control algorithm and any chosen application. In general, the four main steps of the developed workflow are: 1. Build a database of images with their related parameter sets, 2. Evaluate which image criteria are best to assess the image quality for the particular application, 3. Choose an optimization method, 4. Optimize the parameter sets. The presented workflow is developed and examined based on the example of real-world automotive scenarios. At the end of the paper experimental results confirm that the optimized camera parameters achieve a meaningful and useful optimization result regarding the images captured by the camera.
Object Partitioning Using Local Convexity

The problem of how to arrive at an appropriate 3D-segmentation of a scene remains difficult. While current state-of-the-art methods continue to gradually improve in benchmark performance, they also grow more and more complex, for example by incorporating chains of classifiers, which require training on large manually annotated data-sets. As an alternative to this, we present a new, efficient learning- and model-free approach for the segmentation of 3D point clouds into object parts. The algorithm begins by decomposing the scene into an adjacency-graph of surface patches based on a voxel grid. Edges in the graph are then classified as either convex or concave using a novel combination of simple criteria which operate on the local geometry of these patches. This way the graph is divided into locally convex connected subgraphs, which -- with high accuracy -- represent object parts. Additionally, we propose a novel depth dependent voxel grid to deal with the decreasing point-density at far distances in the point clouds. This improves segmentation, allowing the use of fixed parameters for vastly different scenes. The algorithm is straightforward to implement and requires no training data, while nevertheless producing results that are comparable to state-of-the-art methods which incorporate high-level concepts involving classification, learning and model fitting.
Adherence to wearing therapeutic shoes among people with diabetes: a systematic review and reflections

Introduction Therapeutic shoes are prescribed to prevent diabetic foot ulcers, but adherence to wearing the shoes is often poor. Aim The aim of this study was to review the literature on factors that are associated with adherence to wearing therapeutic shoes and construct a model of adherence to aid future research and development in the field. Methods We conducted a systematic search in PubMed, CINAHL, and PsycINFO for quantitative studies on factors associated with adherence to wearing therapeutic shoes among people with diabetes. Results Six studies were included in the review. The studies focused mainly on patient-, therapy-, and condition-related adherence factors. There is some evidence (three to five studies) that sex, diabetes duration, and ulcer history are not associated with adherence. The evidence for or against the other factors was weak (only one or two studies) or conflicting. Conclusion There is no conclusive evidence for using any factor to predict adherence to wearing therapeutic shoes, but there is some evidence against using certain factors for predicting adherence. Future studies should include a broader range of factors, including health system and social/economic factors, and they should investigate perceived costs and benefits of wearing therapeutic shoes in comparison with other shoes or no shoes. A seesaw model is presented illustrating the complex phenomenon of adherence. Further research is needed to identify factors associated with adherence to wearing therapeutic shoes, to enable the development of interventions to improve adherence and thereby reduce ulceration rates among people with diabetic foot complications.
Mining Structured Data

In many application domains, the amount of available data increased so much that humans need help from automatic computerized methods for extracting relevant information. Moreover, it is becoming more and more common to store data that possess inherently structural or relational characteristics. These types of data are best represented by graphs, which can very naturally represent entities, their attributes, and their relationships to other entities. In this article, we review the state of the art in graph mining, and we present advances in processing trees and graphs by two computational intelligence classes of methods, namely neural networks and kernel methods.
Dynamic Time Slot Partitioning for Multimedia Transmission in Two-Hop Cellular Networks

In recent years, there has been an exponential increase in the number of mobile phone users. In addition, a significant growth in the demand for high-rate multimedia services over wireless networks, such as video conferencing, multimedia streaming, etc., was noted. Different solutions were proposed to support high-quality high data rate delivery to mobile users, including resource allocation techniques for packet-radio-based next generation cellular networks. In this paper, an efficient time slot allocation method-Dynamic Time Slot Partitioning (DTSP) algorithm based on statistical multiplexing is proposed for a two-hop cellular architecture. In DTSP, the available bandwidth resources are increased by partitioning each time slot into several minislots wherein different numbers of minislots are allocated to different users. The DTSP algorithm is based on asynchronous time-division multiplexing, wherein users with variable number of packets in their buffers can transmit data sequentially without any loss in the overall available resources. The key advantage of DTSP is that it can flexibly adapt to different quality of service requirements, especially when combined with adaptive modulation. It has been observed that the system capacity achieved by the DTSP algorithm in the downlink mode using adaptive modulation is up to 41 percent higher than when existing solutions are employed. In addition, DTSP results in significantly lower time for data transmission than the state-of-the-art region and time partitioning techniques.
Total Phenolic, Flavonoid, Tomatine, and Tomatidine Contents and Antioxidant and Antimicrobial Activities of Extracts of Tomato Plant

The purpose of this study was to evaluate the antioxidant and antimicrobial properties of extracts of different fractions of two tomato plant cultivars. The stems, roots, leaves, and whole-plant fractions were evaluated. Tomatine and tomatidine were identified by HPLC-DAD. The leaf extracts from the two varieties showed the highest flavonoids, chlorophyll, carotenoids, and total phenolics contents and the highest antioxidant activity determined by DPPH, ABTS, and ORAC. A positive correlation was observed between the antioxidant capacities of the extracts and the total phenolic, flavonoid, and chlorophyll contents. The Pitenza variety extracts inhibited the growth of pathogens such as E. coli O157:H7, Salmonella Typhimurium, Staphylococcus aureus, and Listeria ivanovii, yielding inhibition halos of 8.0 to 12.9 mm in diameter and MIC values of 12.5 to 3.125 mg/mL. These results suggest that tomato plant shows well potential as sources of various bioactive compounds, antioxidants, and antimicrobials.
Helminth-Associated Systemic Immune Activation and HIV Co-receptor Expression: Response to Albendazole/Praziquantel Treatment

Background It has been hypothesized that helminth infections increase HIV susceptibility by enhancing systemic immune activation and hence contribute to elevated HIV-1 transmission in sub-Saharan Africa. Objective To study systemic immune activation and HIV-1 co-receptor expression in relation to different helminth infections and in response to helminth treatment. Methods HIV-negative adults with (n = 189) or without (n = 57) different helminth infections, as diagnosed by Kato-Katz, were enrolled in Mbeya, Tanzania. Blinded to helminth infection status, T cell differentiation (CD45RO, CD27), activation (HLA-DR, CD38) and CCR5 expression was determined at baseline and 3 months after Albendazole/Praziquantel treatment. Plasma cytokine levels were compared using a cytometric bead array. Results Trichuris and Ascaris infections were linked to increased frequencies of “activated” CD4 and/or CD8 T cells (p<0.05), whereas Hookworm infection was associated with a trend towards decreased HLA-DR+ CD8 T cell frequencies (p = 0.222). In Trichuris infected subjects, there was a linear correlation between HLA-DR+ CD4 T cell frequencies and the cytokines IL-1β and IL-10 (p<0.05). Helminth treatment with Albendazole and Praziquantel significantly decreased eosinophilia for S. mansoni and Hookworm infections (p<0.005) but not for Trichuris infection and only moderately modulated T cell activation. CCR5 surface density on memory CD4 T cells was increased by 1.2-fold during Trichuris infection (p-value: 0.053) and reduced after treatment (p = 0.003). Conclusions Increased expression of T cell activation markers was associated with Trichuris and Ascaris infections with relatively little effect of helminth treatment.
COGNITION MODEL IN CONCEPTUAL DESIGNING Case studies of architecture students ’ designs

Both design researchers and cognitive scientists have developed various process models to study human creative behaviour in design. The models developed are often based on observations of design processes and analysis of design protocols. This research paper reports the-stateof-the-art in the area of cognition models that present design activities in conceptual designing. The research paper investigates the approaches of these cognition models. A new approach of a cognition activity model in conceptual designing is proposed. The new approach used in the introduced model takes into the account factors and activities that are related to the external environment of design (design medium). The external environment has an important role in the cognition activities and the evaluation process in a way that can hardly be ignored or neglected. The presented model of cognition activities in conceptual designing highlights two main factors employed in all the iteration loops of the model, namely: media use and representation. Case studies of architecture students’ designs have been analyzed. The analysis of these case studies helped in forming the proposed model. Various results have been concluded and reported.
Partitioned Sampling of Public Opinions Based on Their Social Dynamics

Public opinion polling is usually done by random sampling from the entire population, treating individual opinions as independent. In the real world, individuals' opinions are often correlated, e.g., among friends in a social network. In this paper, we explore the idea of partitioned sampling, which partitions individuals with high opinion similarities into groups and then samples every group separately to obtain an accurate estimate of the population opinion. We rigorously formulate the above idea as an optimization problem. We then show that the simple partitions which contain only one sample in each group are always better, and reduce finding the optimal simple partition to a well-studied Min-r-Partition problem. We adapt an approximation algorithm and a heuristic algorithm to solve the optimization problem. Moreover, to obtain opinion similarity efficiently, we adapt a well-known opinion evolution model to characterize social interactions, and provide an exact computation of opinion similarities based on the model. We use both synthetic and real-world datasets to demonstrate that the partitioned sampling method results in significant improvement in sampling quality and it is robust when some opinion similarities are inaccurate or even missing.
Mechanistic differences between phenotypes of chronic lung allograft dysfunction after lung transplantation

Distinct phenotypes of chronic lung allograft dysfunction (CLAD) after lung transplantation are emerging with lymphocytic bronchiolitis (LB)/azithromycin reversible allograft dysfunction (ARAD), classical or fibrotic bronchiolitis obliterans syndrome (BOS), and restrictive allograft syndrome (RAS) proposed as separate entities. We have additionally identified lung transplant recipients with prior LB, demonstrating persistent airway neutrophilia (PAN) despite azithromycin treatment. The aim of this study was to evaluate differences in the airway microenvironment in different phenotypes of CLAD. Bronchoalveolar lavage (BAL) from recipients identified as stable (control), LB/ARAD, PAN, BOS, and RAS were evaluated for differential cell counts and concentrations of IL‐1α, IL‐1β, IL‐6, IL‐8, and TNF‐α. Primary human bronchial epithelial cells were exposed to BAL supernatants from different phenotypes and their viability measured. BOS and RAS showed increased BAL neutrophilia but no change in cytokine concentrations compared with prediagnosis. In both LB/ARAD and PAN, significant increases in IL‐1α, IL‐1β, and IL‐8 were present. BAL IL‐6 and TNF‐α concentrations were increased in PAN and only this phenotype demonstrated decreased epithelial cell viability after exposure to BAL fluid. This study demonstrates clear differences in the airway microenvironment between different CLAD phenotypes. Systematic phenotyping of CLAD may help the development of more personalized approaches to treatment.
Massive Star Formation and Tidal Structures in HCG 31

We present new broadband optical and near-infrared CCD imaging together with deep optical intermediate-resolution spectroscopy of the Hickson Compact Group 31. We analyze the morphology and colors of the stellar populations of the galaxies, as well as the kinematics, physical conditions, and chemical composition of the ionized gas in order to get a more complete view on the origin and evolution of the system. We estimate the ages of the most recent star formation bursts of the system, finding an excellent consistency among the values obtained with different indicators and starburst models. We find that member F hosts the youngest starburst of the group, showing a substantial population of Wolf-Rayet stars. The chemical abundances are fairly similar in all the members of the group despite their very different absolute magnitudes. We argue that the use of traditional metallicity-luminosity relations based on the absolute B-magnitude is not appropriate for dwarf starburst galaxies, because their luminosity is dominated by the transient contribution of the starburst to the blue luminosity. We think that members E and F of the group are candidate tidal dwarf galaxies because of their high metallicity, their kinematics, and the absence of underlying old stellar populations. Finally, we propose that HCG 31 is suffering several almost simultaneous interaction processes. The most relevant of these processes are (1) the merging of members A and C, which would have produced two optical tidal tails, and (2) a fly-by encounter between G and the A+C complex, which would have produced an H I tidal tail from the stripping of the external gas of A+C, from which members F and E have originated.