Miracle-dz/UniFAR-FTUs huggingface dataset:
Cancer Stem Cell Markers in Head and Neck Squamous Cell Carcinoma

Head and neck squamous cell carcinoma (HNSCC) is one of the world's top ten most common cancers. Current survival rates are poor with only 50% of patients expected to survive five years after diagnosis. The poor survival rate of HNSCC is partly attributable to the tendency for diagnosis at the late stage of the disease. One of the reasons for treatment failure is thought to be related to the presence of a subpopulation of cells within the tumour called cancer stem cells (CSCs). CSCs display stem cell-like characteristics that impart resistance to conventional treatment modalities and promote tumour initiation, progression, and metastasis. Specific markers for this population have been investigated in the hope of developing a deeper understanding of their role in the pathogenesis of HNSCC and elucidating novel therapeutic strategies.
Understanding the training of infinitely deep and wide ResNets with Conditional Optimal Transport

We study the convergence of gradient flow for the training of deep neural networks. If Residual Neural Networks are a popular example of very deep architectures, their training constitutes a challenging optimization problem due notably to the non-convexity and the non-coercivity of the objective. Yet, in applications, those tasks are successfully solved by simple optimization algorithms such as gradient descent. To better understand this phenomenon, we focus here on a ``mean-field'' model of infinitely deep and arbitrarily wide ResNet, parameterized by probability measures over the product set of layers and parameters and with constant marginal on the set of layers. Indeed, in the case of shallow neural networks, mean field models have proven to benefit from simplified loss-landscapes and good theoretical guarantees when trained with gradient flow for the Wasserstein metric on the set of probability measures. Motivated by this approach, we propose to train our model with gradient flow w.r. t. the conditional Optimal Transport distance: a restriction of the classical Wasserstein distance which enforces our marginal condition. Relying on the theory of gradient flows in metric spaces we first show the well-posedness of the gradient flow equation and its consistency with the training of ResNets at finite width. Performing a local Polyak-\L{}ojasiewicz analysis, we then show convergence of the gradient flow for well-chosen initializations: if the number of features is finite but sufficiently large and the risk is sufficiently small at initialization, the gradient flow converges towards a global minimizer. This is the first result of this type for infinitely deep and arbitrarily wide ResNets.
On Safety in Safe Bayesian Optimization

Optimizing an unknown function under safety constraints is a central task in robotics, biomedical engineering, and many other disciplines, and increasingly safe Bayesian Optimization (BO) is used for this. Due to the safety critical nature of these applications, it is of utmost importance that theoretical safety guarantees for these algorithms translate into the real world. In this work, we investigate three safety-related issues of the popular class of SafeOpt-type algorithms. First, these algorithms critically rely on frequentist uncertainty bounds for Gaussian Process (GP) regression, but concrete implementations typically utilize heuristics that invalidate all safety guarantees. We provide a detailed analysis of this problem and introduce Real-\b{eta}-SafeOpt, a variant of the SafeOpt algorithm that leverages recent GP bounds and thus retains all theoretical guarantees. Second, we identify assuming an upper bound on the reproducing kernel Hilbert space (RKHS) norm of the target function, a key technical assumption in SafeOpt-like algorithms, as a central obstacle to real-world usage. To overcome this challenge, we introduce the Lipschitz-only Safe Bayesian Optimization (LoSBO) algorithm, which guarantees safety without an assumption on the RKHS bound, and empirically show that this algorithm is not only safe, but also exhibits superior performance compared to the state-of-the-art on several function classes. Third, SafeOpt and derived algorithms rely on a discrete search space, making them difficult to apply to higher-dimensional problems. To widen the applicability of these algorithms, we introduce Lipschitz-only GP-UCB (LoS-GP-UCB), a variant of LoSBO applicable to moderately high-dimensional problems, while retaining safety.
Evidence in duck for supporting alteration of incubation temperature may have influence on methylation of genomic DNA

Incubation temperature has an immediate and long-term influence on the embryonic development in birds. DNA methylation as an important environment-induced mechanism could serve as a potential link between embryos’ phenotypic variability and temperature variation, which reprogrammed by DNA (cytosine-5)-methyltransferases (DNMTS) and Methyl-CpG binding domain proteins (MBPS) 3&5 (MBD3&5). Five genes in DNMTS and MBPS gene families were selected as target genes, given their important role in epigenetic modification. In this study, we aimed to test whether raising incubation temperature from 37.8°C to 38.8°C between embryonic days (ED) 1–10, ED10–20 and ED20–27 have effect on DNA methylation and whether DNMTS, MBPS play roles in thermal epigenetic regulation of early development in duck. Real-time quantitative PCR analysis showed that increased incubation temperature by 1°C has remarkably dynamic effect on gene expression levels of DNMTS and MBPS. Slight changes in incubation temperature significantly increased mRNA levels of target genes in breast muscle tissue during ED1–10, especially for DNMT1, DNMT3A and MBD5. In addition, higher temperature significantly increased enzyme activities of DNMT1 in leg muscle during ED10–20, liver tissue during ED1–10, ED20–27 and DNMT3A in leg muscle and breast muscle tissue during ED10–20. These results suggest that incubation temperature has an extended effect on gene expression levels and enzyme activities of DNMTS and MBPS, which provides evidence that incubation temperature may influence DNA methylation in duck during early developmental stages. Our data indicated that DNMTS and MBPS may involved in thermal epigenetice regulation of embryos during the early development in duck. The potential links between embryonic temperature and epigenetic modification need further investigation
HOIDiffusion: Generating Realistic 3D Hand-Object Interaction Data

3D hand-object interaction data is scarce due to the hardware constraints in scaling up the data collection process. In this paper, we propose HOIDiffusion for generating realistic and diverse 3D hand-object interaction data. Our model is a conditional diffusion model that takes both the 3D hand-object geometric structure and text description as inputs for image synthesis. This offers a more controllable and realistic synthesis as we can specify the structure and style inputs in a disentangled manner. HOIDiffusion is trained by leveraging a diffusion model pre-trained on large-scale natural images and a few 3D human demonstrations. Beyond controllable image synthesis, we adopt the generated 3D data for learning 6D object pose estimation and show its effectiveness in improving perception systems. Project page: https://mq-zhang1.github. io/HOIDiffusion
Evaluating Hydroperiod Response in Restored Carolina Bay Wetlands Using Soil Physicochemical Properties

Carolina bays are shallow depression wetlands found in the southeastern United States that have been severely altered by human activity. The need to restore these complex and diverse systems is well established, but our limited understanding of wetland hydrologic processes in these systems hinders our ability to assess the effectiveness of bay restoration efforts. Carolina bays exhibit a wide range of moisture regimes from seasonally saturated to semipermanently inundated. Differing physicochemical properties of soils within bay interiors may control bay hydrology. However, previous efforts to establish relationships between soil characteristics and bay hydrology have been inconclusive. An assessment of soil and hydroperiod was initiated in 16 bays designated to be restored and 6 bays that were not restored (reference). Soil morphology was described, and permanent monitoring wells were installed at each site. Multiple regression analysis was used to determine relationships between the soil physicochemical characteristics and the bay hydroperiod for restored and reference bays in both pre‐ and postrestoration periods. A significant relationship (r2= 0.75, p= 0.02) between prerestoration hydroperiod and clay content in the argillic horizon (Bt) of the reference bays was observed. This relationship was then used to evaluate hydroperiod change in the restored bays from the postrestoration period. The relationship accurately identified sites that exhibited high prerestoration hydroperiods and did not need hydrologic restoration (n= 4) and effectively showed sites that exhibited substantial increases in hydroperiod due to the restoration activities (n= 7).
SC-Diff: 3D Shape Completion with Latent Diffusion Models

This paper introduces a 3D shape completion approach using a 3D latent diffusion model optimized for completing shapes, represented as Truncated Signed Distance Functions (TSDFs), from partial 3D scans. Our method combines image-based conditioning through cross-attention and spatial conditioning through the integration of 3D features from captured partial scans. This dual guidance enables high-fidelity, realistic shape completions at superior resolutions. At the core of our approach is the compression of 3D data into a low-dimensional latent space using an auto-encoder inspired by 2D latent diffusion models. This compression facilitates the processing of higher-resolution shapes and allows us to apply our model across multiple object classes, a significant improvement over other existing diffusion-based shape completion methods, which often require a separate diffusion model for each class. We validated our approach against two common benchmarks in the field of shape completion, demonstrating competitive performance in terms of accuracy and realism and performing on par with state-of-the-art methods despite operating at a higher resolution with a single model for all object classes. We present a comprehensive evaluation of our model, showcasing its efficacy in handling diverse shape completion challenges, even on unseen object classes. The code will be released upon acceptance.
Towards automated formal security analysis of SAML V2.0 Web Browser SSO standard -- the POST/Artifact use case

Single Sign-On (SSO) protocols streamline user authentication with a unified login for multiple online services, improving usability and security. One of the most common SSO protocol frameworks - the Security Assertion Markup Language V2.0 (SAML) Web SSO Profile - has been in use for more than two decades, primarily in government, education and enterprise environments. Despite its mission-critical nature, only certain deployments and configurations of the Web SSO Profile have been formally analyzed. This paper attempts to bridge this gap by performing a comprehensive formal security analysis of the SAML V2.0 SP-initiated SSO with POST/Artifact Bindings use case. Rather than focusing on a specific deployment and configuration, we closely follow the specification with the goal of capturing many different deployments allowed by the standard. Modeling and analysis is performed using Tamarin prover - state-of-the-art tool for automated verification of security protocols in the symbolic model of cryptography. Technically, we build a meta-model of the use case that we instantiate to eight different protocol variants. Using the Tamarin prover, we formally verify a number of critical security properties for those protocol variants, while identifying certain drawbacks and potential vulnerabilities.
Pseudospark Discharge Behavior at a Low Charging Voltage

Evolution maps of the sputtered copper vapor in the hollow cathode and the main gap areas of two experimental pseudospark switches operating with several buffer gases are obtained with laser-induced fluorescence. The measurements aim to understand the pseudospark breakdown formation and are deliberately made at low charging voltages (1 kV) at which the interval between the trigger pulse and the pseudospark breakdown is characterized with a low current (~10 A) and a long (1-5 mus) randomly variable shot-to-shot duration. Reported are the results for prebreakdown intervals with different lengths. On the other hand, the unfavorable statistical behavior is utilized with the method of the Laue diagrams, which allow phenomenological investigation of the breakdown. In addition, spectrally integrated plasma-emission images taken with an intensified charge-coupled-device camera are represented
Cytomegalovirus-Specific T Cells Persist at Very High Levels during Long-Term Antiretroviral Treatment of HIV Disease

Background In healthy, HIV seronegative, CMV seropositive adults, a large proportion of T cells are CMV-specific. High-level CMV-specific T cell responses are associated with accelerated immunologic aging (“immunosenesence”) in the elderly population. The impact of untreated and treated HIV infection on the frequency of these cells remains undefined. Methodology/Principal Findings We measured the proportion of CD4+ and CD8+ T cells responding to CMV pp65 and IE proteins was measured using flow cytometry in 685 unique HIV seronegative and seropositive individuals. The proportion of CMV-specific CD8+ T cells was consistently higher in the HIV-seropositive subjects compared to the HIV-seronegative subjects. This HIV effect was observed even in patients who lacked measurable immunodeficiency. Among the HIV-seropositive subjects, CMV-specific CD8+ T cell responses were proportionately lower during recent infection, higher during chronic untreated infection and higher still during long-term antiretroviral treated infection. The CD8+ T cell response to just two CMV proteins (pp65 and IE) was approximately 6% during long-term therapy, which was over twice that seen in HIV-seronegative persons. CMV-specific CD4+ T cell responses followed the same trends, but the magnitude of the effect was smaller. Conclusions/Significance Long-term successfully treated HIV infected patients have remarkably high levels of CMV-specific effector cells. These levels are similar to that observed in the elderly, but occur at much younger ages. Future studies should focus on defining the potential role of the CMV-specific inflammatory response in non-AIDS morbidity and mortality, including immunosenescence.
Aging, Health, and Quality of Life for Older People Living With HIV in Sub-Saharan Africa: A Review and Proposed Conceptual Framework

Objective: The number of people living with HIV (PLWH) over 50 years old in sub-Saharan Africa is predicted to triple in the coming decades, to 6-10 million. Yet, there is a paucity of data on the determinants of health and quality of life for older PLWH in the region. Methods: A review was undertaken to describe the impact of HIV infection on aging for PLWH in sub-Saharan Africa. Results: We (a) summarize the pathophysiology and epidemiology of aging with HIV in resource-rich settings, and (b) describe how these relationships might differ in sub-Saharan Africa, (c) propose a conceptual framework to describe determinants of quality of life for older PLWH, and (d) suggest priority research areas needed to ensure long-term gains in quality of life for PLWH in the region. Conclusions: Differences in traditional, lifestyle, and envirnomental risk factors, as well as unique features of HIV epidemiology and care delivery appear to substantially alter the contribution of HIV to aging in sub-Saharan Africa. Meanwhile, unique preferences and conceptualizations of quality of life will require novel measurement and intervention tools. An expanded research and public health infrastructure is needed to ensure that gains made in HIV prevention and treamtent are translated into long-term benefits in this region.
Comparing forward and inverse models to estimate the seasonal variation of hemisphere-integrated fluxes of carbonyl sulfide

Comparing forward and inverse models to estimate the seasonal variation of hemisphere-integrated fluxes of carbonyl sulfide A. J. Kettle, U. Kuhn, M. von Hobe, J. Kesselmeier, P. S. Liss, and M. O. Andreae School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom Biogeochemistry Department, Max Planck Institute for Chemistry, Mainz, Germany Received: 16 April 2002 – Accepted: 8 May 2002 – Published: 12 June 2002 Correspondence to: A. J. Kettle (anthony.kettle@uea.ac.uk)
Interprofessional teamwork innovations for primary health care practices and practitioners: evidence from a comparison of reform in three countries

Context A key aim of reforms to primary health care (PHC) in many countries has been to enhance interprofessional teamwork. However, the impact of these changes on practitioners has not been well understood. Objective To assess the impact of reform policies and interventions that have aimed to create or enhance teamwork on professional communication relationships, roles, and work satisfaction in PHC practices. Design Collaborative synthesis of 12 mixed methods studies. Setting Primary care practices undergoing transformational change in three countries: Australia, Canada, and the USA, including three Canadian provinces (Alberta, Ontario, and Quebec). Methods We conducted a synthesis and secondary analysis of 12 qualitative and quantitative studies conducted by the authors in order to understand the impacts and how they were influenced by local context. Results There was a diverse range of complex reforms seeking to foster interprofessional teamwork in the care of patients with chronic disease. The impact on communication and relationships between different professional groups, the roles of nursing and allied health services, and the expressed satisfaction of PHC providers with their work varied more within than between jurisdictions. These variations were associated with local contextual factors such as the size, power dynamics, leadership, and physical environment of the practice. Unintended consequences included deterioration of the work satisfaction of some team members and conflict between medical and nonmedical professional groups. Conclusion The variation in impacts can be understood to have arisen from the complexity of interprofessional dynamics at the practice level. The same characteristic could have both positive and negative influence on different aspects (eg, larger practice may have less capacity for adoption but more capacity to support interprofessional practice). Thus, the impacts are not entirely predictable and need to be monitored, and so that interventions can be adapted at the local level.
An Empirical Study of Speech Language Models for Prompt-Conditioned Speech Synthesis

Speech language models (LMs) are promising for high-quality speech synthesis through in-context learning. A typical speech LM takes discrete semantic units as content and a short utterance as prompt, and synthesizes speech which preserves the content's semantics but mimics the prompt's style. However, there is no systematic understanding on how the synthesized audio is controlled by the prompt and content. In this work, we conduct an empirical study of the widely used autoregressive (AR) and non-autoregressive (NAR) speech LMs and provide insights into the prompt design and content semantic units. Our analysis reveals that heterogeneous and nonstationary prompts hurt the audio quality in contrast to the previous finding that longer prompts always lead to better synthesis. Moreover, we find that the speaker style of the synthesized audio is also affected by the content in addition to the prompt. We further show that semantic units carry rich acoustic information such as pitch, tempo, volume and speech emphasis, which might be leaked from the content to the synthesized audio.
Optimal estimate of electromagnetic field concentration between two nearly-touching inclusions in the quasi-static regime

We investigate the electromagnetic field concentration between two nearly-touching inclusions that possess high-contrast electric permittivities in the quasi-static regime. By using layer potential techniques and asymptotic analysis in the low-frequency regime, we derive low-frequency expansions that provide integral representations for the solutions of the Maxwell equations. For the leading-order term $\bE_0$ of the asymptotic expansion of the electric field, we prove that it has the blow up order of $\epsilon^{-1} |\ln \epsilon|^{-1}$ within the radial geometry, where $\epsilon$ signifies the asymptotic distance between the inclusions. By delicate analysis of the integral operators involved, we further prove the boundedness of the first-order term $\bE_1$. We also conduct extensive numerical experiments which not only corroborate the theoretical findings but also provide more discoveries on the field concentration in the general geometric setup. Our study provides the first treatment in the literature on field concentration between nearly-touching material inclusions for the full Maxwell system.
Impaired cerebral vasoreactivity and risk of stroke in patients with asymptomatic carotid artery stenosis.

CONTEXT Standards for treating patients with asymptomatic carotid artery stenosis have been difficult to establish because of the lack of evidence for factors influencing these patients' prognoses. However, preliminary evidence suggests that an alteration in cerebral hemodynamic function may play a relevant role in the occurrence of stroke in patients with carotid artery disease. OBJECTIVE To investigate the relationship between cerebrovascular reactivity to hypercapnia and cerebrovascular events in patients with severe unilateral asymptomatic carotid artery stenosis. DESIGN AND SETTING Prospective, blinded longitudinal study conducted in an outpatient neurovascular department in Italy between June 1996 and April 1998, with a median follow-up of 28.5 months. PATIENTS Ninety-four patients with asymptomatic carotid artery stenosis of at least 70% (74 men; mean age, 71 years). MAIN OUTCOME MEASURES Subsequent occurrence of cerebral ischemic events (transient ischemic attack or stroke) or death, analyzed by cerebrovascular reactivity to hypercapnia (measured by transcranial Doppler ultrasonography and calculated by the breath-holding index values in the middle cerebral arteries). RESULTS The overall annual rate for all ischemic events was 7.9%. Seventeen patients (18%) had ischemic events, all but 1 of which were ipsilateral to the carotid artery stenosis. Among factors considered, only lower breath-holding index values in the middle cerebral artery ipsilateral to carotid artery stenosis were significantly associated with the risk of an event (hazard ratio, 0.09; 95% confidence interval, 0.02-0.38; P=.001, by multivariate analysis). Based on data from previously studied healthy subjects, the cutoff of the breath-holding index for distinguishing between impaired and normal cerebrovascular reactivity was determined to be 0.69. Using this cutoff, the annual ipsilateral ischemic event risk was 4.1% in patients with normal and 13.9% in those with impaired breath-holding index values. CONCLUSIONS These results suggest a link between impaired cerebrovascular reactivity and the risk of ischemic events ipsilateral to severe asymptomatic carotid stenosis.