Miracle-dz/UniFAR-FTUs huggingface dataset:
"This is not a data problem": Algorithms and Power in Public Higher Education in Canada

Algorithmic decision-making is increasingly being adopted across public higher education. The expansion of data-driven practices by post-secondary institutions has occurred in parallel with the adoption of New Public Management approaches by neoliberal administrations. In this study, we conduct a qualitative analysis of an in-depth ethnographic case study of data and algorithms in use at a public college in Ontario, Canada. We identify the data, algorithms, and outcomes in use at the college. We assess how the college's processes and relationships support those outcomes and the different stakeholders' perceptions of the college's data-driven systems. In addition, we find that the growing reliance on algorithmic decisions leads to increased student surveillance, exacerbation of existing inequities, and the automation of the faculty-student relationship. Finally, we identify a cycle of increased institutional power perpetuated by algorithmic decision-making, and driven by a push towards financial sustainability.
The battle in the apoplast: further insights into the roles of proteases and their inhibitors in plant–pathogen interactions

Upon host penetration, fungal pathogens secrete a plethora of effectors to promote disease, including proteases that degrade plant antimicrobial proteins, and protease inhibitors (PIs) that inhibit plant proteases with antimicrobial activity. Conversely, plants secrete proteases and PIs to protect themselves against pathogens or to mediate recognition of pathogen proteases and PIs, which leads to induction of defense responses. Many examples of proteases and PIs mediating effector-triggered immunity in host plants have been reported in the literature, but little is known about their role in compromising basal defense responses induced by microbe-associated molecular patterns. Recently, several reports appeared in literature on secreted fungal proteases that modify or degrade pathogenesis-related proteins, including plant chitinases or PIs that compromise their activities. This prompted us to review the recent advances on proteases and PIs involved in fungal virulence and plant defense. Proteases and PIs from plants and their fungal pathogens play an important role in the arms race between plants and pathogens, which has resulted in co-evolutionary diversification and adaptation shaping pathogen lifestyles.
The normal natural troubles of driving with GPS

In-car GPS based satellite navigation systems are now a common part of driving, providing turn-by-turn navigation instructions on smartphones, portable units or in-car dashboard navigation systems. This paper uses interactional analysis of video data from fifteen naturalistically recorded journeys with GPS to understand the navigational practices deployed by drivers and passengers. The paper documents five types of 'trouble' where GPS systems cause issues and confusion for drivers around: destinations, routes, maps & sensors, timing and relevance and legality. The paper argues that to design GPS systems better we need to move beyond the notion of a docile driver who follows GPS command blindly, to a better understanding of how drivers, passengers and GPS systems work together. We develop this in discussing how technology might better support 'instructed action'.
Healing Regimes for Microscopic Wounds in the Vertex Model of Cell Tissues

Wounds in epithelial tissues compromise their vital role in homeostasis. A rapid and efficient wound healing encompasses different mechanisms, which includes the formation of a contractile actin-myosin cable around its edge, known as the purse-string mechanism. We combine mean-field calculations and numerical simulations of the Vertex model to study the interplay between tissue properties and the purse-string mechanism and its impact on the healing process. We find different regimes, where the wound opens, closes partially or completely. We also derive an analytic expression for the closure time which is validated by numerical simulations. This study establishes under which conditions the purse-string mechanism suffices for closure, providing an analytical mean-field expression for the respective thresholds.
HySim: An Efficient Hybrid Similarity Measure for Patch Matching in Image Inpainting

Inpainting, for filling missing image regions, is a crucial task in various applications, such as medical imaging and remote sensing. Trending data-driven approaches efficiency, for image inpainting, often requires extensive data preprocessing. In this sense, there is still a need for model-driven approaches in case of application constrained with data availability and quality, especially for those related for time series forecasting using image inpainting techniques. This paper proposes an improved modeldriven approach relying on patch-based techniques. Our approach deviates from the standard Sum of Squared Differences (SSD) similarity measure by introducing a Hybrid Similarity (HySim), which combines both strengths of Chebychev and Minkowski distances. This hybridization enhances patch selection, leading to high-quality inpainting results with reduced mismatch errors. Experimental results proved the effectiveness of our approach against other model-driven techniques, such as diffusion or patch-based approaches, showcasing its effectiveness in achieving visually pleasing restorations.
Asiatic Acid Attenuates the Progression of Left Ventricular Hypertrophy and Heart Failure Induced by Pressure Overload by Inhibiting Myocardial Remodeling in Mice

Abstract: Cardiac structural remodeling, including cardiomyocyte apoptosis, interstitial fibrosis, and inflammation, appears to be a key event associated with the progression of left ventricular hypertrophy and heart failure. Asiatic acid (AA) is a triterpenoid compound extracted from Centella asiatica that exhibits antiapoptotic, antifibrotic, and anti-inflammatory activities. In the present study, a transverse aortic constriction (TAC) model was created in mice to mimic the progression of hypertrophy (2 weeks post-TAC) and heart failure (4 weeks post-TAC) to investigate whether the potential therapeutic drug AA ameliorates hypertrophy progression and which mechanisms are involved in this amelioration. Our results demonstrated that AA markedly inhibited the process of progression induced by pressure overload. The increases cardiomyocyte apoptosis and interstitial fibrosis, and inflammatory responses were significantly suppressed by AA. Our investigation revealed that this inhibitory effect was mediated by blocking the activation of both mitochondrial and death receptor-dependent apoptotic signaling pathways. Additional experiments demonstrated that AA attenuated fibrosis by blocking both transforming growth factor-&bgr;1/Smad and interleukin-6, signaling activation. Consequently, these findings indicated that AA attenuated pathological cardiac structural remodeling and preserved cardiac function via multiple intracellular signaling pathways in response to cardiac stimuli.
A SIMULATION-BASED ANALYSIS OF THE CYCLE TIME OF CLUSTER TOOLS IN SEMICONDUCTOR MANUFACTURING

Cluster tools are widely used in modern semiconductor manufacturing facilities. In parallel mode they offer high throughput at the cost of a complex behaviour with regard to lot cycle times. The reason is that cluster tools are behave like small factories themselves. We analyze the slow-down of the processing of a lot that is caused by other lots in the tool and examine how the slowdown factor can be used for scheduling and for predicting lot cycle times. This cycle time analysis is mandatory for production planning and can only be done by simulation so far.
(S,s) Pricing: Does the Heterogeneity Wipe Out the Asymmetry on Micro Level?

This paper presents a model of asymmetric (S,s) pricing. We investigate whether the asymmetry on micro level is carried over on macro level and what is the role of agent heterogeneity in the process. We look at two kinds of asymmetries: (i) asymmetric output responses monetary shocks and (ii) asymmetric responses to shocks during different phases of business cycle. We conclude that the first type of asymmetry can be attributed to the differences in adjustment bands and that heterogeneity softens this effect. The second type of asymmetry is the result of pricing behavior, thus of agent heterogeneity itself.
Exploring the Role of Enterprise Architecture in IS-enabled Ot: An EA Principles Perspective

Although EA principles have received considerable attention in recent years, there is still little known about how EA principles can be used to govern the transformation of the Information Systems enabled organization. In this research-in- progress paper, we communicate our initial step towards answering the sub-question: how do enforcing EA principles contribute to IS-enabled OT? Based on a comprehensive literature review, we initially propose five testable hypotheses and a research model, which is a pre-requisite to developing a data-driven theory for this important area of research. It is anticipated that the ensuing theory will provide a basis for further research studying the impact of EA on IS-enabled OT. The tested research model will also provide guidance to practitioners on how to effectively design and use EA principles in managing transformative changes caused by IS within their organizations and overall industry sectors.
Molecular Characterization of Vaginal Microbiota Using a New 22-Species qRT-PCR Test to Achieve a Relative-abundance and Species-based Diagnosis of Bacterial Vaginosis

Background Numerous bacteria are involved in the etiology of bacterial vaginosis (BV). Yet, current tests only focus on a select few. We therefore designed a new test targeting 22 BV-relevant species. Methods Using 946 stored vaginal samples, a new qPCR test that quantitatively identifies 22 bacterial species was designed. The distribution and relative abundance of each species, α- and β-diversities, correlation and species co-existence were determined per sample. A diagnostic index was modeled from the data, trained, and tested to classify samples into BV-positive, BV-negative, or transitional BV. Results The qPCR test identified all 22 targeted species with 95 – 100% sensitivity and specificity within 8 hours (from sample reception). Across most samples, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensenii, Gardnerella vaginalis, Fannyhessea (Atopobium) vaginae, Prevotella bivia, and Megasphaera sp. type 1 were relatively abundant. BVAB-1 was more abundant and distributed than BVAB-2 and BVAB-3. No Mycoplasma genitalium was found. Inter-sample similarity was very low, and correlations existed between key species, which were used to model, train, and test a diagnostic index: MDL-BV index. The MDL-BV index, using both species and relative abundance markers, classified samples into three vaginal microbiome states. Testing this index on our samples, 491 were BV-positive, 318 were BV-negative, and 137 were transitional BV. Although important differences in BV status were observed between different age groups, races, and pregnancy status, they were statistically insignificant. Conclusion Using a diverse and large number of vaginal samples from different races and age groups, including pregnant women, the new qRT-PCR test and MDL-BV index efficiently diagnosed BV within 8 hours (from sample reception), using 22 BV-associated species. Lay summary/Importance/Significance Bacterial vaginosis (BV) affects nearly 30% of women between 14 – 49 years old, increasing the risk and complications of endometriosis, pelvic inflammatory disease, pre-term births and low-birth weights, STIs, and cervicitis. Notwithstanding, BV’s diagnosis and etiology remain elusive. Not all BV-causing bacteria can be seen under a microscope or grown in a laboratory, making detection difficult. Moreover, current molecular BV diagnostic tests focus on a few signature species and thereby do not characterize the true state of the vaginal microbiome. Therefore, we designed a new Real-Time PCR test that identifies and quantifies 22 bacteria important in the prevention and development of BV. The data obtained from this test were further used to design and test a model that can easily use the relative abundance of the 22 species in any given vaginal sample to diagnose its BV status: all within 8 hours (from sample reception). The expansion of the bacterial spectrum in our new test enhances its resolution and broadens its diagnostic capacity to reduce false diagnoses and improve therapy.
Efficiently preconditioned inexact Newton methods for large symmetric eigenvalue problems

In this paper, we propose an efficiently preconditioned Newton method for the computation of the leftmost eigenpairs of large and sparse symmetric positive definite matrices. A sequence of preconditioners based on the BFGS update formula is proposed, for the preconditioned conjugate gradient solution of the linearized Newton system to solve Au=q(u) u, q(u) being the Rayleigh quotient. We give theoretical evidence that the sequence of preconditioned Jacobians remains close to the identity matrix if the initial preconditioned Jacobian is so. Numerical results onto matrices arising from various realistic problems with size up to one million unknowns account for the efficiency of the proposed algorithm which reveals competitive with the Jacobi–Davidson method on all the test problems.
An improved procedure for pre-drill calculation of fracture pressure

Abstract Pre-drill modelling of fracture pressure (FP) is an essential part of well planning, reserve estimation and evaluation of the potential for inducing seismicity as the result of fluid injection. Estimation of stress ratio or Poisson's ratio values or compaction state with depth is required in frequently used FP models. A new method to estimate FP is proposed which is based on Leak Off (LOT) and pore fluid pressure (Pp) data from offset wells and vertical stress (Sv)–depth relationships. LOT/Sv ratios observed in intervals of offset wells that are normally pressured (hydrostatic) are used to define an expected FP/Sv ratio for hydrostatic Pp conditions for all depths. Typical FP/Sv ratios for hydrostatic conditions derived using LOT data range from 0.81 to 0.89. Observed LOT values associated with Pp greater than hydrostatic (overpressured) in offset wells are used to quantify the rate of increase in FP with increasing overpressure (OP). The expected FP for hydrostatic conditions is compared with observed LOT values from depths where the pore fluid is overpressured and a relationship of increased FP, relative to the expected FP for hydrostatic conditions (residual FP (FPr)) with increasing OP is defined. The FPr:OP ratio typically ranges from 0.24 to 0.43. Fracture pressure models developed by this procedure may be used to predict FP for wells in different water depths and with Pp conditions different from those in the offset wells. The use of the model is demonstrated in three case studies taken from different geological settings: the Scotian shelf (offshore Nova Scotia), offshore Central Gulf of Mexico and the chalk interval from the Central North Sea.
The onset and cross-temporal patterning of sexual intercourse in middle adolescence: prospective relations with behavioral and emotional problems.

This study examined precursors and correlates of sexual intercourse patterns (e.g., earlier/later onset, persistence across time) among tenth and eleventh graders. Data regarding intercourse were collected for lifetime and for 6-month periods at 4 occasions of measurement over a 2-year span. Significant differences in behavioral (e.g., delinquency) and emotional (e.g., depression) problems were indicated via repeated-measures MANOVA analyses. Significant interactions among intercourse patterns, gender, and time on emotional and behavioral problems indicated synergistic relations. Planned comparisons indicated that the transition to the onset of sexual intercourse was associated with increases in delinquency and a slower rate of increase for school grades. Earlier onset and a more persistent pattern of sexual intercourse were associated with more childhood problem behaviors, earlier alcohol use, and higher levels of preadolescent antisocial behavior.
Sexual dimorphism and allometry in human scapular morphology

Scapular morphology is highly variable across the human population and appears to be sexually dimorphic – differing significantly between males and females. However, previous investigations of sexual dimorphism in scapula shape have not considered the effects of allometry (the relationship between size and shape). Disentangling allometry from sexual dimorphism is necessary because apparent sex-based differences in morphology could be due to inherent differences in body size. This study aimed to investigate sexual dimorphism in scapula shape and examine the role of allometry in sex-based variation. We used three-dimensional geometric morphometrics with Procrustes ANOVA to quantify scapula shape variation associated with sex and size in 125 scapulae. Scapular morphology significantly differed between males and females, and males tended to have larger scapulae than females for the same body height. We found that males and females exhibited distinct allometric relationships, and sexually dimorphic shape changes did not align with male- or female-specific allometry. A secondary test revealed that sexual dimorphism in scapula shape persisted between males and females of similar body heights. Overall, our findings indicate that sex-based differences in scapular shape are independent of size-shape relationships. Our results shed light on the potential role of sexual selection in human shoulder evolution, present new hypotheses for biomechanical differences in shoulder function between sexes, and identify relevant traits for improving sex classification accuracy in forensic analyses.
NONEXPRESSOR OF PATHOGENESIS-RELATED GENES control Huanglongbing tolerance by regulating immune balance in citrus plants

Huanglongbing (HLB) is a devastating citrus disease caused by the phloem-resident bacterial pathogen Candidatus liberibacter asiaticus (CLas). CLas infection of susceptible varieties triggers unbalanced immune responses, leading to overaccumulation of callose and reactive oxygen species (ROS), which in turn causes phloem plugging and HLB symptom development. Interestingly, some citrus relatives exhibit little or no symptoms in the presence of CLas, a phenomenon termed HLB tolerance. Moreover, overexpression of the Arabidopsis thaliana NPR1 (AtNPR1) gene in susceptible varieties has been shown to confer robust HLB tolerance. However, the mechanisms underlying HLB tolerance remain enigmatic. Here, we show that overexpression of AtNPR1 suppresses CLas- and Pseudomonas syringae pv. maculicola ES4326 (Psm)-induced overaccumulation of callose and ROS in citrus and Arabidopsis, respectively. Importantly, we found that knocking out of the Arabidopsis negative immune regulators, AtNPR3 and AtNPR4, and silencing of their Citrus sinensis ortholog CsNPR3, similarly suppress Psm- and CLas-induced callose and ROS overaccumulation, respectively, and that silencing of CsNPR3 also enhances HLB tolerance. These results reveal a conserved role of the NPR1/NPR3/NPR4-mediated signaling pathway in regulating plant immune balances and provide mechanistic support for overexpression of AtNPR1 or silencing of AtNPR3/AtNPR4 orthologs in citrus as a long-term solution to the HLB disease.
Transfer and Capture of Envelope Protein Receptor-Binding Domains in the Retroviruses

The surface subunit (SU) of the envelope protein (Env) or retroviruses is highly variable due to adaptation to different hosts during their long evolutionary history. Several exogenous and endogenous retroviral gamma-like Env have a receptor-binding domain (RBD) in the amino-terminal region of SU that folds independently from the carboxyterminal SU C-domain. Two structurally distinct RBD classes have been described, one that adopts a modified immunoglobulin (Ig)-like domain fold and a second, in the Env of RDR interference group retroviruses, with a distinct β-sheet fold. Here, the distribution of different RBD classes among exogenous and endogenous gammatype Env was determined by phylogenetic analyses of Env and structural modeling of retroviral SU with AlphaFold2. The patterns of RBD distribution indicate multiple RBD transfer events in the retroviruses. In addition, SU structural modeling identified an endogenous alpharetroviral-like Env in mammalian species with an amino-terminal RBD. This RDB has a typical IgV domain fold closely related both structurally and in sequence to the mammalian signal regulatory proteins (SIRP) α, β and γ, indicating, for the first time, acquisition of an RBD from a mammalian gene by the retroviruses. The results described herein indicate intragenic env recombination between retroviruses and between retroviruses and their hosts as a major factor in the evolution of retroviral Env.
Connexin 43 Regulates Intercellular Mitochondrial Transfer from Human Mesenchymal Stromal Cells to Chondrocytes

Background The phenomenon of intercellular mitochondrial transfer from mesenchymal stromal cells (MSCs) has shown promise for improving tissue healing after injury and has potential for treating degenerative diseases like osteoarthritis (OA). Recently MSC to chondrocyte mitochondrial transfer has been documented, but the mechanism of transfer is unknown. Full-length connexin43 (Cx43, encoded by GJA1) and the truncated internally translated isoform GJA1-20k have been implicated in mitochondrial transfer between highly oxidative cells, but have not been explored in orthopaedic tissues. Here, our goal was to investigate the role of Cx43 in MSC to chondrocyte mitochondrial transfer. In this study, we tested the hypotheses that (a) mitochondrial transfer from MSCs to chondrocytes is increased when chondrocytes are under oxidative stress and (b) MSC Cx43 expression mediates mitochondrial transfer to chondrocytes. Methods Oxidative stress was induced in immortalized human chondrocytes using tert-Butyl hydroperoxide (t-BHP) and cells were evaluated for mitochondrial membrane depolarization and reactive oxygen species (ROS) production. Human bone-marrow derived MSCs were transduced for mitochondrial fluorescence using lentiviral vectors. MSC Cx43 expression was knocked down using siRNA or overexpressed (GJA1+ and GJA1-20k+) using lentiviral transduction. Chondrocytes and MSCs were co-cultured for 24 hrs in direct contact or separated using transwells. Mitochondrial transfer was quantified using flow cytometry. Co-cultures were fixed and stained for actin and Cx43 to visualize cell-cell interactions during transfer. Results Mitochondrial transfer was significantly higher in t-BHP-stressed chondrocytes. Contact co-cultures had significantly higher mitochondrial transfer compared to transwell co-cultures. Confocal images showed direct cell contacts between MSCs and chondrocytes where Cx43 staining was enriched at the terminal ends of actin cellular extensions containing mitochondria in MSCs. MSC Cx43 expression was associated with the magnitude of mitochondrial transfer to chondrocytes; knocking down Cx43 significantly decreased transfer while Cx43 overexpression significantly increased transfer. Interestingly, GJA1-20k expression was highly correlated with incidence of mitochondrial transfer from MSCs to chondrocytes. Conclusions Overexpression of GJA1-20k in MSCs increases mitochondrial transfer to chondrocytes, highlighting GJA1-20k as a potential target for promoting mitochondrial transfer from MSCs as a regenerative therapy for cartilage tissue repair in OA.