Miracle-dz/UniFAR-FTUs huggingface dataset:
Intel Software Guard Extensions Applications: A Survey

Data confidentiality is a central concern in modern computer systems and services, as sensitive data from users and companies are being increasingly delegated to such systems. Several hardware-based mechanisms have been recently proposed to enforce security guarantees of sensitive information. Hardware-based isolated execution environments are a class of such mechanisms, in which the operating system and other low-level components are removed from the trusted computing base. One of such mechanisms is the Intel Software Guard Extensions (Intel SGX), which creates the concept of enclave to encapsulate sensitive components of applications and their data. Despite being largely applied in several computing areas, SGX has limitations and performance issues that must be addressed for the development of secure solutions. This text brings a categorized literature review of the ongoing research on the Intel SGX architecture, discussing its applications and providing a classification of the solutions that take advantage of SGX mechanisms. We analyze and categorize 293 papers that rely on SGX to provide integrity, confidentiality, and privacy to users and data, regarding different contexts and goals. We also discuss research challenges and provide future directions in the field of enclaved execution, particularly when using SGX.
Becoming an Online Wine Taster: An Ethnographic Study on the Digital Mediation of Taste

There has been a growing interest in taste research in the HCI and CSCW communities. However, the focus is more on stimulating the senses, while the socio-cultural aspects have received less attention. However, individual taste perception is mediated through social interaction and collective negotiation and is not only dependent on physical stimulation. Therefore, we study the digital mediation of taste by drawing on ethnographic research of four online wine tastings and one self-organized event. Hence, we investigated the materials, associated meanings, competences, procedures, and engagements that shaped the performative character of tasting practices. We illustrate how the tastings are built around the taste-making process and how online contexts differ in providing a more diverse and distributed environment. We then explore the implications of our findings for the further mediation of taste as a social and democratized phenomenon through online interaction.
Low-rank Representation with Adaptive Dimensionality Reduction via Manifold Optimization for Clustering

The dimensionality reduction techniques are often used to reduce data dimensionality for computational efficiency or other purposes in existing low-rank representation (LRR)-based methods. However, the two steps of dimensionality reduction and learning low-rank representation coefficients are implemented in an independent way; thus, the adaptability of representation coefficients to the original data space may not be guaranteed. This article proposes a novel model, i.e., low-rank representation with adaptive dimensionality reduction (LRRARD) via manifold optimization for clustering, where dimensionality reduction and learning low-rank representation coefficients are integrated into a unified framework. This model introduces a low-dimensional projection matrix to find the projection that best fits the original data space. And the low-dimensional projection matrix and the low-rank representation coefficients interact with each other to simultaneously obtain the best projection matrix and representation coefficients. In addition, a manifold optimization method is employed to obtain the optimal projection matrix, which is an unconstrained optimization method in a constrained search space. The experimental results on several real datasets demonstrate the superiority of our proposed method.
Values in Emotion Artificial Intelligence Hiring Services: Technosolutions to Organizational Problems

Despite debates about emotion artificial intelligence's (EAI) validity, legality, and social consequences, EAI is increasingly present in the high stakes context of hiring, with potential to shape the future of work and the workforce. The values laden in technology play a significant role in its societal impact.We conducted qualitative content analysis on the public-facing websites (N=229) of EAI hiring services. We identify the organizational problems that EAI hiring services claim to solve and reveal the values emerging in desired EAI uses as promoted by EAI hiring services to solve organizational problems. Our findings show that EAI hiring services market their technologies as technosolutions to three purported organizational hiring problems: 1) hiring (in)accuracy, 2) hiring (mis)fit, and 3) hiring (in)authenticity. We unpack these problems to expose how these desired uses of EAI are legitimized by the corporate ideals of data-driven decision making, continuous improvement, precision, loyalty, and stability. We identify the unfair and deceptive mechanisms by which EAI hiring services claim to solve the purported organizational hiring problems, suggesting that they unfairly exclude and exploit job candidates through EAI's creation, extraction, and affective commodification of a candidate's affective value through pseudoscientific approaches. Lastly, we interrogate EAI hiring service claims to reveal the core values that underpin their stated desired use: techno-omnipresence, techno-omnipotence, and techno-omniscience. We show how EAI hiring services position desired use of their technology as a moral imperative for hiring organizations with supreme capabilities to solve organizational hiring problems, then discuss implications for fairness, ethics, and policy in EAI-enabled hiring within the US policy landscape.
Understanding Platform Mediated Work-Life: A Diary Study with Gig Economy Freelancers

Online freelancing platforms, such as Upwork, hold great promise in enabling flexible work opportunities where freelancers can combine their work with other life responsibilities, hereafter work-life. However, prior research suggests that platform features and self-managing demands of freelance work can jeopardise this apparent flexibility. In this paper, we report findings from a qualitative study, combining a 14-diary and semi-structured interview with 15 Upwork freelancers. We explored online freelancers' work practices, challenges, and the impact of platform features on their everyday lives. Our qualitative data suggest that platform features and individual context shape online freelancers' work-life practices. Freelancers develop strategies to mitigate platforms' constraints and balance their individual preferences and responsibilities. Further, our findings illustrate how platform features challenge freelancers' availability expectations, work autonomy, and work detachment. This paper contributes an empirical understanding of the factors influencing online freelancers' work-life practices by drawing upon Wanda J. Orlikowski's Structuration Model of Technology. This theoretical lens renders the interplay of freelancers, platforms, and instituted norms of freelance work.
On variational problems and gradient flows in image

This thesis treats different methods and theoretical aspects of the calculus of variations and their applications in image processing, especially those in which gradient flows for the minimization of the variational problems are used. The focus lies on geometrical methods for image registration, as well as numerical methods for computing the solution for an implicit variant of Willmore flow (level set method). The problem of image registration aims at finding a suitable correspondence map by means of a deformation of one image domain to the other, such that significant structures are overlaid correctly. In practical applications, these images are often aquired by different sensors and hence yield different image modalities. Image registration plays an important role in the clinical evaluation of medical data as for example from computed tomography or magnetic resonance imaging, as well as diagnosis and surgery planning. The proposed method aims at an alignment of geometrical descriptors instead of merely comparing image intensities. In particular, the approach is morphological (contrast invariant). Registration methods are in general ill-posed inverse problems, hence regularization methods are necessary. In order to ensure a robust and stable minimization process, three complementary regularization strategies are incorporated and linked to each other, namely multiscale methods, Tikhonov-regularization and regularized gradient flows. The latter are based on the definition of a regularizing metric, that is used to define the representation of the regularized gradient of the energy functional. Furthermore, a nonlinear polyconvex and hyperelastic energy functional that takes the role of the Tikhonov-regularization functional allows to devise an existence proof of the geometric registration approach. The theoretical justification of the multiscale approach is given by the study of the variational convergence of the regularized functionals by means of Gamma-convergence. In order to further stabilize the registration process, a new Mumford-Shah-based method to align significant edges is proposed. It aims the simultaneous process of registration, segmentation (feature detection) and image restoration, since these processes typically interdepend on each other. Here, two different approaches are proposed, numerically incorporated and compared: a phase-field approach, that is based on the Ambrosio-Tortorelli approximation of the Mumford-Shah functional and a corresponding level set approach. The minimization of the Willmore functional via a semi-implicit numerical scheme is applied to the recontruction of destroyed regions of surfaces that are given by a level set representation. The introduction of an implicit narrow band method allows a significant acceleration of the geometrical evolution.
Decision Making Strategies and Team Efficacy in Human-AI Teams

Human-AI teams are increasingly prevalent in various domains. We investigate how the decision-making of a team member in a human-AI team impacts the outcome of the collaboration and perceived team-efficacy. In a large scale study on Mechanical Turk (n=125), we find significant differences across different decision making styles and disclosed AI identity disclosure in an AI-driven collaborative game. We find that autocratic decision-making negatively impacts team-efficacy in Human-AI teams, similar to its effects on human-only teams. We find that decision making style and AI-identity disclosure impacts how individuals make decisions in a collaborative context. We discuss our findings of the differences of collaborative behavior in human-human-AI teams and human-AI-AI teams.
All square chiliagonal numbers

ABSTRACT A square chiliagonal number is a number which is simultaneously a chiliagonal number and a perfect square (just as the well-known square triangular number is both triangular and square). In this work, we determine which of the chiliagonal numbers are perfect squares and provide the indices of the corresponding chiliagonal numbers and square numbers. The study revealed that the determination of square chiliagonal numbers naturally leads to a generalized Pell equation x2 − Dy2 = N with D = 1996 and N = 9962, and has six fundamental solutions out of which only three yielded integer values for use as indices of chiliagonal numbers. The crossing/independent recurrence relations satisfied by each class of indices of the corresponding chiliagonal numbers and square numbers are obtained. Finally, the generating functions serve as a clothesline to hang up the indices of the corresponding chiliagonal numbers and square numbers for easy display and this was used to obtain the first few sequence of square chiliagonal numbers.
Redefining rock doves, Columba livia, using historical whole genome sequences

The domestic pigeon’s exceptional phenotypic diversity was key in developing Darwin’s Theory of Evolution and establishing the concept of artificial selection in domestic species. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia, has received considerably less attention. Therefore, questions regarding their domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock dove samples representing all currently recognised subspecies and spanning the species’ original geographic distribution. Our dataset includes three specimens from Darwin’s collection and the type specimens of five different taxa. We characterised rock doves’ population structure, genomic diversity and gene-flow patterns. We show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons. Our results show gene-flow signals between the rock dove’s sister species C. rupestris and all rock doves except the West African populations. Our results led us to propose an evolutionary model for the rock dove considering the Pleistocene refugia theory. We propose that today’s rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least one domestication event in the Levant region that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.
Structures of Langya Virus Fusion Protein Ectodomain in Pre- and Postfusion Conformation

The Henipavirus genus is quickly expanding into new animal hosts and geographic locations. This study compares the structure and antigenicity of the Langya virus fusion protein to other henipaviruses, which have important vaccine and therapeutic development implications. Furthermore, the study proposes a new mechanism to explain the early steps of the fusion initiation process that can be more broadly applied to the Paramyxoviridae family. ABSTRACT Langya virus (LayV) is a paramyxovirus in the Henipavirus genus, closely related to the deadly Nipah (NiV) and Hendra (HeV) viruses, that was identified in August 2022 through disease surveillance following animal exposure in eastern China. Paramyxoviruses present two glycoproteins on their surface, known as attachment and fusion proteins, that mediate entry into cells and constitute the primary antigenic targets for immune response. Here, we determine cryo-electron microscopy (cryo-EM) structures of the uncleaved LayV fusion protein (F) ectodomain in pre- and postfusion conformations. The LayV-F protein exhibits pre- and postfusion architectures that, despite being highly conserved across paramyxoviruses, show differences in their surface properties, in particular at the apex of the prefusion trimer, that may contribute to antigenic variability. While dramatic conformational changes were visualized between the pre- and postfusion forms of the LayV-F protein, several domains remained invariant, held together by highly conserved disulfides. The LayV-F fusion peptide (FP) is buried within a highly conserved, hydrophobic interprotomer pocket in the prefusion state and is notably less flexible than the rest of the protein, highlighting its “spring-loaded” state and suggesting that the mechanism of pre-to-post transition must involve perturbations to the pocket and release of the fusion peptide. Together, these results offer a structural basis for how the Langya virus fusion protein compares to its Henipavirus relatives and propose a mechanism for the initial step of pre- to postfusion conversion that may apply more broadly to paramyxoviruses. IMPORTANCE The Henipavirus genus is quickly expanding into new animal hosts and geographic locations. This study compares the structure and antigenicity of the Langya virus fusion protein to other henipaviruses, which have important vaccine and therapeutic development implications. Furthermore, the study proposes a new mechanism to explain the early steps of the fusion initiation process that can be more broadly applied to the Paramyxoviridae family.
Cell-based optimization and characterization of genetically encoded location-based biosensors for Cdc42 or Rac activity

Rac and Cdc42 are Rho GTPases which regulate the formation of lamellipoda and filopodia and are therefore crucial in processes such as cell migration. Relocation-based biosensors for Rac and Cdc42 have not been characterized well in terms of their specificity or affinity. In this study, we identify relocation sensor candidates for either Rac or Cdc42. We compared their (i) ability to bind the constitutively active Rho GTPases, (ii) specificity for Rac and Cdc42 and (iii) relocation efficiency in cell-based assays. Subsequently, the relocation efficiency was improved by a multi-domain approach. For Rac1 we found a sensor candidate with low relocation efficiency. For Cdc42 we found several sensors with sufficient relocation efficiency and specificity. These optimized sensors enable the wider application of Rho GTPase relocation sensors, which was showcased by the detection of local endogenous Cdc42 activity at assembling invadopodia. Moreover, we tested several fluorescent proteins and HaloTag for their influence on the recruitment efficiency of the Rho location sensor, to find optimal conditions for a multiplexing experiment. The characterization and optimization of relocation sensors will broaden their application and acceptance.
Genome-wide gene birth-death dynamics are associated with diet breadth variation in Lepidoptera

Comparative analyses of gene birth-death dynamics (GBDD) have the potential to reveal gene families that played an important role in the evolution of morphological, behavioral, or physiological variation. Here, we used whole genomes of 30 species of butterflies and moths to identify GBDD among the Lepidoptera that are associated with specialist or generalist feeding strategies. Our work advances this field by using a uniform set of annotated proteins for all genomes, investigating associations while correcting for phylogeny, and assessing all gene familes rather than a priori subsets. We discovered that the sizes of several important gene families (e.g., those associated with pesticide resistance, xenobiotic detoxification, and/or protein digestion) are significantly correlated with diet breadth. We also found 12 gene families showing significant shifts in GBDD at the butterfly (Papilionoidea) crown node, the most notable of which was a family of pheromone receptors that underwent a contraction potentially linked with a shift to visual-based mate recognition. Our findings highlight the importance of uniform annotations, phylogenetic corrections and unbiased gene family analyses in generating a list of candidate genes that warrant further exploration. Significance Statement Gene duplications and gene deaths are important for the development of novel traits, but their study is often complicated by methodological issues, such as input data coming from different sources with different biases. Here, we address many of these issues in an analysis of gene duplication and death across 30 species of moths by using standardized, genome-wide input data. Importantly, our analysis uses a model that can correlate gene family sizes with any quantitative trait, while also accounting for relatedness between species. Using this model, we provide novel evolutionary insights by showing that the sizes of several important gene families are correlated with increases or decreases in the number of host plant orders that Lepidoptera eat.
Annotation of the non-canonical translatome reveals that CHO cell microproteins are a new class of mAb drug product impurity

Chinese hamster ovary (CHO) cells are used to produce almost 90% of therapeutic monoclonal antibodies (mAbs). The annotation of non-canonical translation events in these cellular factories remains incomplete, limiting not only our ability to study CHO cell biology but also detect host cell protein (HCP) contaminants in the final mAb drug product. We utilised ribosome footprint profiling (Ribo-seq) to identify novel open reading frames (ORFs) including N-terminal extensions and thousands of short ORFs (sORFs) predicted to encode microproteins. Mass spectrometry-based HCP analysis of four commercial mAb drug products using the extended protein sequence database revealed the presence of microprotein impurities for the first time. We also show that microprotein abundance varies with growth phase and can be affected by the cell culture environment. In addition, our work provides a vital resource to facilitate future studies of non-canonical translation as well as the regulation of protein synthesis in CHO cell lines.
In depth amino acid mutational analysis of the key interspecific incompatibility transmembrane factor Stigmatic Privacy 1

In plants, there is an active prezygotic interspecific-incompatibility mechanism to prevent unfavorable hybrids between two species. We previously reported that an uncharacterized protein with four-transmembrane domains, named as Stigmatic Privacy 1 (SPRI1), is responsible for rejecting hetero-specific pollen grains in Arabidopsis thaliana. We have conducted a functional study of the SPRI1 protein, via point-mutational experiments and biochemical analysis. We studied the molecular regulatory mechanisms of SPRI1 and the relationships with its function. The alanine- and glycine-scanning experiments together with the evolutional analysis showed that the structural integrity of the C-terminal regions of the extracellular domain of this protein is important for its function. In addition, we found two cysteines (C67 and C80) within the extracellular domain that may be involved in the formation of intermolecular disulfide bonds. SPRI1 may form homo-multimers and is present as part of a ca. 300 kDa complex. Our present study indicates that molecular complex formation ability of SPRI1 may be important to maintain its stability and interspecific incompatibility functions in cells.