Miracle-dz/UniFAR-FTUs huggingface dataset:
Navigating Expertise in Configurable Software Systems through the Maze of Variability

The understanding of source code in large-scale software systems poses a challenge for developers. The role of expertise in source code becomes critical for identifying developers accountable for substantial changes. However, in the context of configurable software systems (CSS) using pre-processing and conditional compilation, conventional expertise metrics may encounter limitations due to the non-alignment of variability implementation with the natural module structure. This early research study investigates the distribution of development efforts in CSS, specifically focusing on variable and mandatory code. It also examines the engagement of designated experts with variable code in their assigned files. The findings provide insights into task allocation dynamics and raise questions about the applicability of existing metrics, laying the groundwork for alternative approaches to assess developer expertise in handling variable code. This research aims to contribute to a comprehensive understanding of challenges within CSS, marking initial steps toward advancing the evaluation of expertise in this context.
Interventional Fairness on Partially Known Causal Graphs: A Constrained Optimization Approach

Fair machine learning aims to prevent discrimination against individuals or sub-populations based on sensitive attributes such as gender and race. In recent years, causal inference methods have been increasingly used in fair machine learning to measure unfairness by causal effects. However, current methods assume that the true causal graph is given, which is often not true in real-world applications. To address this limitation, this paper proposes a framework for achieving causal fairness based on the notion of interventions when the true causal graph is partially known. The proposed approach involves modeling fair prediction using a Partially Directed Acyclic Graph (PDAG), specifically, a class of causal DAGs that can be learned from observational data combined with domain knowledge. The PDAG is used to measure causal fairness, and a constrained optimization problem is formulated to balance between fairness and accuracy. Results on both simulated and real-world datasets demonstrate the effectiveness of this method.
Ultra-lightweight Neural Differential DSP Vocoder For High Quality Speech Synthesis

Neural vocoders model the raw audio waveform and synthesize high-quality audio, but even the highly efficient ones, like MB-MelGAN and LPCNet, fail to run real-time on a low-end device like a smartglass. A pure digital signal processing (DSP) based vocoder can be implemented via lightweight fast Fourier transforms (FFT), and therefore, is a magnitude faster than any neural vocoder. A DSP vocoder often gets a lower audio quality due to consuming over-smoothed acoustic model predictions of approximate representations for the vocal tract. In this paper, we propose an ultra-lightweight differential DSP (DDSP) vocoder that uses a jointly optimized acoustic model with a DSP vocoder, and learns without an extracted spectral feature for the vocal tract. The model achieves audio quality comparable to neural vocoders with a high average MOS of 4.36 while being efficient as a DSP vocoder. Our C++ implementation, without any hardware-specific optimization, is at 15 MFLOPS, surpasses MB-MelGAN by 340 times in terms of FLOPS, and achieves a vocoder-only RTF of 0.003 and overall RTF of 0.044 while running single-threaded on a 2GHz Intel Xeon CPU.
Understanding Learning through the Lens of Dynamical Invariants

This paper proposes a novel perspective on learning, positing it as the pursuit of dynamical invariants -- data combinations that remain constant or exhibit minimal change over time as a system evolves. This concept is underpinned by both informational and physical principles, rooted in the inherent properties of these invariants. Firstly, their stability makes them ideal for memorization and integration into associative networks, forming the basis of our knowledge structures. Secondly, the predictability of these stable invariants makes them valuable sources of usable energy, quantifiable as kTln2 per bit of accurately predicted information. This energy can be harnessed to explore new transformations, rendering learning systems energetically autonomous and increasingly effective. Such systems are driven to continuously seek new data invariants as energy sources. The paper further explores several meta-architectures of autonomous, self-propelled learning agents that utilize predictable information patterns as a source of usable energy.
On integer distance sets

We develop a new approach to address some classical questions concerning the size and structure of integer distance sets. Our main result is that any integer distance set in the Euclidean plane has all but a very small number of points lying on a single line or circle. From this, we deduce a near-optimal lower bound on the diameter of any non-collinear integer distance set of size $n$ and a strong upper bound on the size of any integer distance set in $[-N,N]^2$ with no three points on a line and no four points on a circle.
PhotoScout: Synthesis-Powered Multi-Modal Image Search

Due to the availability of increasingly large amounts of visual data, there is a growing need for tools that can help users find relevant images. While existing tools can perform image retrieval based on similarity or metadata, they fall short in scenarios that necessitate semantic reasoning about the content of the image. This paper explores a new multi-modal image search approach that allows users to conveniently specify and perform semantic image search tasks. With our tool, PhotoScout, the user interactively provides natural language descriptions, positive and negative examples, and object tags to specify their search tasks. Under the hood, PhotoScout is powered by a program synthesis engine that generates visual queries in a domain-specific language and executes the synthesized program to retrieve the desired images. In a study with 25 participants, we observed that PhotoScout allows users to perform image retrieval tasks more accurately and with less manual effort.
The complementary contributions of academia and industry to AI research

Artificial intelligence (AI) has seen tremendous development in industry and academia. However, striking recent advances by industry have stunned the world, inviting a fresh perspective on the role of academic research in this field. Here, we characterize the impact and type of AI produced by both environments over the last 25 years and establish several patterns. We find that articles published by teams consisting exclusively of industry researchers tend to get greater attention, with a higher chance of being highly cited and citation-disruptive, and several times more likely to produce state-of-the-art models. In contrast, we find that exclusively academic teams publish the bulk of AI research and tend to produce higher novelty work, with single papers having several times higher likelihood of being unconventional and atypical. The respective impact-novelty advantages of industry and academia are robust to controls for subfield, team size, seniority, and prestige. We find that academic-industry collaborations struggle to replicate the novelty of academic teams and tend to look similar to industry teams. Together, our findings identify the unique and nearly irreplaceable contributions that both academia and industry make toward the healthy progress of AI.
Distributed Genetic Algorithm for Feature Selection

We empirically show that process-based Parallelism speeds up the Genetic Algorithm (GA) for Feature Selection (FS) 2x to 25x, while additionally increasing the Machine Learning (ML) model performance on metrics such as F1-score, Accuracy, and Receiver Operating Characteristic Area Under the Curve (ROC-AUC).
ERLIN1/2 scaffolds bridge TMUB1 and RNF170 and restrict cholesterol esterification to regulate the secretory pathway

Complexes of ERLIN1 and ERLIN2 form large ring-like cup-shaped structures on the endoplasmic reticulum (ER) membrane and serve as platforms to bind cholesterol and E3-ubiquitin ligases, potentially defining functional nanodomains. Here, we show that ERLIN scaffolds mediate the interaction between the full-length isoform of TMUB1 and RNF170. We identify a luminal N-terminal conserved region in TMUB1 and RNF170 required for this interaction. Three-dimensional modelling shows that this conserved motif binds the SPFH domain of two adjacent ERLIN subunits at different interfaces. Protein variants that preclude these interactions have been previously linked to hereditary spastic paraplegia (HSP). By using omics approaches in combination with phenotypic characterisation of cells lacking both ERLINs, we demonstrate a role for ERLIN scaffolds in maintaining cholesterol levels in the ER by favouring transport to the Golgi over esterification, thereby regulating Golgi morphology and the secretory pathway.
Characterisation of anhydro-sialic acid transporters from mucosa-associated bacteria

Sialic acid (Sia) transporters are critical to the capacity of host-associated bacteria to utilise sialic acid for growth and/or cell-surface modification. While N-acetyl-neuraminic acid (Neu5Ac)-specific transporters have been studied extensively, little is known on transporters dedicated to anhydro-sialic acid forms such as 2,7-anhydro-Neu5Ac (2,7-AN) or 2,3-dehydro-2-deoxy-Neu5Ac (Neu5Ac2en). Here, we used a Sia-transport-null strain of Escherichia coli to investigate the function of members of anhydro-Sia transporter families previously identified by computational studies. First, we showed that the transporter NanG, from the Glycoside-Pentoside-Hexuronide:cation symporter family, is a specific 2,7-AN transporter, and identified by mutagenesis a crucial functional residue within the putative substrate-binding site. We then demonstrated that NanX transporters, of the Major Facilitator Superfamily, also only transport 2,7-AN and not Neu5Ac2en nor Neu5Ac. Finally, we provided evidence that SiaX transporters, of the Sodium-Solute Symporter superfamily, are promiscuous Neu5Ac/Neu5Ac2en transporters able to acquire either substrate equally well. The characterisation of anhydro-Sia transporters expands our current understanding of prokaryotic Sia metabolism within host-associated microbial communities.
Sunpheno: a deep neural network for phenological classification of sunflower images

Leaf senescence is a complex mechanism governed by multiple genetic and environmental variables that affect crop yield. It is the last stage of leaf development and is characterized by an active decline in the photosynthetic rate, nutrient recycling, and cell death. Leaf senescence begins in the lower leaves, and photoassimilates are translocated to the younger tissues. During early anthesis, leaf senescence becomes crucial for grain filling, because photoassimilates are translocated to the seeds. Therefore, a correct sync between leaf senescence and phenological stages is necessary to obtain the required yields. Furthermore, genotypes with early senescence were correlated with poor yield and low seed quality. Like all the crops growing in the field, studying phenology and its correlation with the senescence process is a laborious task where most of the parameters depend on highly trained people who conduct sampling and measurements. Several high-throughput phenotyping techniques have been developed in recent years. In this study, we evaluated the performance of five deep machine-learning methods for the evaluation of the phenological stages of sunflowers using images taken with cell phones in the field. From the analysis, we found that the method based on the pre-trained network resnet50 outperformed the other methods, both in terms of accuracy and velocity. Finally, the model generated, Sunpheno, was used to evaluate the phenological stages of two contrasting lines, B481_6 and R453, during senescence. We observed clear differences in phenological stages, confirming the results obtained in previous studies.
Biodiversity shows unique responses to land-use change across regional biomes

Biogeography has a critical influence on how ecological communities respond to threats and how effective conservation interventions are designed. For example, the resilience of ecological communities is linked to environmental and climatic features, and the nature of threats impacting ecosystems also varies geographically. Understanding community-level threat responses may be most accurate at fine spatial scales, however collecting detailed ecological data at such a high resolution would be prohibitively resource intensive. In this study, we aim to find the spatial scale that could best capture variation in community-level threat responses whilst keeping data collection requirements feasible. Using a database of biodiversity records with extensive global coverage, we modelled species richness and total abundance (the responses) across land-use types (reflecting threats), considering three different spatial scales: biomes, biogeographical realms, and regional biomes (the interaction between realm and biome). We then modelled data from three highly sampled biomes separately to ask how responses to threat differ between regional biomes and taxonomic group. We found strong support for regional biomes in explaining variation in species richness and total abundance compared to biomes or realms alone. Our biome case studies demonstrate that there is a high variation in magnitude and direction of threat responses across both regional biomes and taxonomic group, but all groups in tropical forest showed a consistently negative response, whilst many taxon-regional biome groups showed no clear response to threat in temperate forest and tropical grassland. Our results suggest that the taxon-regional biome unit has potential as a reasonable spatial and ecological scale for understanding how ecological communities respond to threats and designing effective conservation interventions to bend the curve on biodiversity loss.
COMPARATIVE STUDY ON THE PLANT LIFE OF TWO MEDITERRANEAN DELTAIC LAKES IN EGYPT

The terrestrial and aquatic flora of the two largest natural lakes of Egypt (Lake Manzala and Lake Burollos) were studied. Lake Manzala is located on the eastern side of Damietta branch of the Nile, whereas, Lake Burollos lies on the eastern side of Rosetta branch of the Nile, occupying the central position along the Mediterranean coast of the Nile delta . Despite the two times larger area of Lake Manzala compared with Lake Burollos and physiographic similarity, Lake Burollos is floristically rich (135 species, 41 families) as compared with Lake Manzala (102 species, 36 families). Both lakes have many floristic differences. Lake Burollos is characterized with lower number of euhydrophytes (7 species) compared to 16 species recorded in Lake Manzala. The highest number of species are belonging to Gramineae and Chenopodiaceae, respectively in both lakes. The life form spectrum of both lakes showed that therophytes are highly represented followed by geophytes . The islands in both lakes are floristically rich. However, islands of Lake Burollos seem to be suitable habitat for some plant species absent from the islands of Lake Manzala e.g. Lycium schweinfurthii, Pancratium maritimum, Allium roseum, Silene succulenta, Asparagus stipularis and several annuals, some plant species recorded in one site in Lake Burollos, are considered as rare species such as Ipomoea imperati and Limonium narbonense which are threatened and need protection . In the present paper, the authors compared the floristic composition of the different habitats of both lakes.
Évolution Des Extrêmes Pluviométriques Dans La Région Du Gôh (Centre-Ouest De La Côte d’Ivoire)

The Goh region located in western-central Ivory Coast is a region whose economy depends mainly on agriculture, which itself is dependent on the climate. Thus, variation and climate change has a significant impact on crop yields. The objective of this work is to study the evolution of extreme rainfall on rainfall station in the region (Gagnoa station). The calculation of rainfall indices was performed with the software RclimDex. It appears from this study has the Gagnoa station, five (5) of the seven indices calculated namely, the maximum rainfall of one day height (Rx1day), the maximum total rainfall of 5 days (Rx5daiy), the days very rainy (R95) extremely rainy days (R99p) and consecutive dry days (CDD) experienced an increase. While the total annual rainfall (PRCPTOT) and consecutive wet days (CWD) declined. In general, the GOH region is experiencing a decline in rainfall and therefore an increase in dry spells during the rainy seasons.
Assessing body burden of persistent organic pollutants (POPs) in infants/toddlers through analysis of faeces

2 List of Figures . 15 List of Tables . 16 List of Abbreviations . 17 Chapter 1: Introduction and objectives . 19 Early-life exposure to POPs may influence people’s health over a life-time . 20 Challenges in exposure-response analysis of POPs . 24 Assessing concentrations of POPs in the blood (Cb) of infants/toddlers is an issue . 30 Potential biomarker for concentrations of POPs . 32 Uncertainty of using faeces as a biomarker of POPs . 32 Objectives of thesis . 35 Chapter References . 37 Chapter 2: A preliminary study on assessing body burden of persistent organic pollutants (POPs) in infants/toddlers through analysis of faeces . 49 Abstract . 50 Introduction . 51 Materials and methods . 52 Results and Discussion . 53 Acknowledgements . 55 Chapter References . 56 Chapter 3: Persistent organic pollutants (POPs) in matched breast milk and infant faeces samples . 57 Abstract . 58 Introduction . 59 Materials and methods . 60 Results and discussion . 63 Acknowledgements . 69 Chapter Reference . 70 Chapter 4: Monthly variation in faeces:blood concentration ratio of persistent organic pollutants (POPs) over the first year of life: a case study of one infant . 73 Abstract . 74 Introduction . 75 Experiment . 76 Results . 81 Discussion . 87 Acknowledgements . 90 Chapter References . 91
Evolution of genes and genomes on the Drosophila phylogeny Drosophila 12 Genomes

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species. As one might expect from a genus with species living in deserts, in the tropics, on chains of volcanic islands and, often, commensally with humans, Drosophila species vary considerably in their morphology, ecology and behaviour 1. Species in this genus span a wide range of global distributions: the 12 sequenced species originate from Africa, Asia, the Americas and the Pacific Islands, and also include cosmopolitan species that have colonized the planet (D. melanogaster and D. simulans) as well as closely related species that live on single islands (D. sechellia) 2. A variety of behavioural strategies is also encompassed by the sequenced species, ranging in feeding habit from generalist, such as D. ananassae, to specialist, such as D. sechellia, which feeds on the fruit of a single plant species. Despite this wealth of phenotypic diversity, Drosophila species share a distinctive body plan and life cycle. Although only D. mela-nogaster has been extensively characterized, it seems that the most important aspects of the cellular, molecular and developmental biology of these species are well conserved. Thus, in addition to providing an extensive resource for the study of the relationship between sequence and phenotypic diversity, the genomes of these species provide an excellent model for studying how conserved functions are maintained in the face of sequence divergence. These genome sequences provide an unprecedented dataset to contrast genome structure, genome content, and evolutionary dynamics across the well-defined phylogeny of the sequenced species (Fig. 1). Genome assembly, annotation and alignment Genome sequencing and assembly. We used the previously published …
Aspectos da biologia reprodutiva de Eretmochelys imbricata (testudines, cheloniidae) no litoral sul do Rio Grande do Norte, Brasil

Os dados que compoem esta dissertacao, estao organizados em dois capitulos que correspondem a dois artigos cientificos a serem submetidos a publicacao. O primeiro, Body weight and energy budget of gravid hawksbill turtles (Eretmochelys imbricata) during the nest season esta sendo submetido ao Journal of Herpetology e o segundo intitulado Preferencias individuais por local de desova em Eretmochelys imbricata (LINNAEUS, 1756), na Praia de Pipa, Tibau do Sul, RN
Beta-blockers use in patients with chronic obstructive pulmonary disease and concomitant cardiovascular conditions

The mortality and incidence of chronic obstructive pulmonary disease (COPD) and coronary heart disease increase with age. Despite the clear evidence of beta blockers (BBs) effectiveness, there is a general reluctance to use them in patients with COPD due to a perceived contraindication and fear of inducing adverse reactions and bronchspasm. BBs are well tolerated in patients with cardiac disease and concomitant COPD with no evidence of worsening of respiratory symptoms or FEV1, and the safety of BBs in patients with COPD has been demonstrated, but their use in this group of patients remains low. The cumulative evidence from trials and meta-analysis indicates that cardioselective BBs should not be withheld in patients with reactive airway disease or COPD. Patients with COPD have a high incidence of cardiac events necessitating careful consideration of prophylactic treatment. The benefits of beta blockade in this group appear to outweigh any potential risk of side effects according to the available evidence. In this article, we will discuss the use of BBs in patients with COPD and review the evidence for their use and safety in this group of patients.
Caribbean sea surface temperatures and El Niño : a new outlook

Mass coral bleaching in recent years has become a recurring event and was suspected to have a relationship with El Niño events. Changes in the understanding of what constitutes an El Niño event prompted further research into the relationship with Caribbean sea surface temperatures due to their impact on corals. Multiple statistical tests were employed to profile the relationship between the individual event types and the Caribbean. Ultimately, a bootstrapping technique determined that Central Pacific El Niño events bear a relationship, while Eastern Pacific event types do not. An attempt to hindcast El Niño events in order to comment on the history of impacts upon the Caribbean was unsuccessful due to a lack of sufficient input data, but a model determining potential locations of data is presented.