julilili42/papers huggingface dataset:
I Prefer Not to Say: Protecting User Consent in Models with Optional Personal Data
2024-03-24

We examine machine learning models in a setup where individuals have the choice to share optional personal information with a decision-making system, as seen in modern insurance pricing models. Some users consent to their data being used whereas others object and keep their data undisclosed. In this work, we show that the decision not to share data can be considered as information in itself that should be protected to respect users' privacy. This observation raises the overlooked problem of how to ensure that users who protect their personal data do not suffer any disadvantages as a result. To address this problem, we formalize protection requirements for models which only use the information for which active user consent was obtained. This excludes implicit information contained in the decision to share data or not. We offer the first solution to this problem by proposing the notion of Protected User Consent (PUC), which we prove to be loss-optimal under our protection requirement. We observe that privacy and performance are not fundamentally at odds with each other and that it is possible for a decision maker to benefit from additional data while respecting users' consent. To learn PUC-compliant models, we devise a model-agnostic data augmentation strategy with finite sample convergence guarantees. Finally, we analyze the implications of PUC on challenging real datasets, tasks, and models.
Leverage the Explainability of Transformer Models to Improve the DNA 5-Methylcytosine Identification (Student Abstract)
2024-03-24

DNA methylation is an epigenetic mechanism for regulating gene expression, and it plays an important role in many biological processes. While methylation sites can be identified using laboratory techniques, much work is being done on developing computational approaches using machine learning. Here, we present a deep-learning algorithm for determining the 5-methylcytosine status of a DNA sequence. We propose an ensemble framework that treats the self-attention score as an explicit feature that is added to the encoder layer generated by fine-tuned language models. We evaluate the performance of the model under different data distribution scenarios.
Premorbid body weight predicts weight loss in both anorexia nervosa and atypical anorexia nervosa: Further support for a single underlying disorder
2024-03-25

Abstract Objective For adolescents, DSM‐5 differentiates anorexia nervosa (AN) and atypical AN with the 5th BMI‐centile‐for‐age. We hypothesized that the diagnostic weight cut‐off yields (i) lower weight loss in atypical AN and (ii) discrepant premorbid BMI distributions between the two disorders. Prior studies demonstrate that premorbid BMI predicts admission BMI and weight loss in patients with AN. We explore these relationships in atypical AN. Method Based on admission BMI‐centile &lt; or ≥5th, participants included 411 female adolescent inpatients with AN and 49 with atypical AN from our registry study. Regression analysis and t ‐tests statistically addressed our hypotheses and exploratory correlation analyses compared interrelationships between weight loss, admission BMI, and premorbid BMI in both disorders. Results Weight loss in atypical AN was 5.6 kg lower than in AN upon adjustment for admission age, admission height, premorbid weight and duration of illness. Premorbid BMI‐standard deviation scores differed by almost one between both disorders. Premorbid BMI and weight loss were strongly correlated in both AN and atypical AN. Discussion Whereas the weight cut‐off induces discrepancies in premorbid weight and adjusted weight loss, AN and atypical AN overall share strong weight‐specific interrelationships that merit etiological consideration. Epidemiological and genetic associations between AN and low body weight may reflect a skewed premorbid BMI distribution. In combination with prior findings for similar psychological and medical characteristics in AN and atypical AN, our findings support a homogenous illness conceptualization. We propose that diagnostic subcategorization based on premorbid BMI, rather than admission BMI, may improve clinical validity. Public significance Because body weights of patients with AN must drop below the 5th BMI‐centile per DSM‐5, they will inherently require greater weight loss than their counterparts with atypical AN of the same sex, age, height and premorbid weight. Indeed, patients with atypical AN had a 5.6 kg lower weight loss after controlling for these variables. In comparison to the reference population, we found a lower and higher mean premorbid weight in patients with AN and atypical AN, respectively. Considering previous psychological and medical comparisons showing little differences between AN and atypical AN, we view a single disorder as the most parsimonious explanation. Etiological models need to particularly account for the strong relationship between weight loss and premorbid body weight.
A paradigm shift?—On the ethics of medical large language models
2024-03-25

Abstract After a wave of breakthroughs in image‐based medical diagnostics and risk prediction models, machine learning (ML) has turned into a normal science. However, prominent researchers are claiming that another paradigm shift in medical ML is imminent—due to most recent staggering successes of large language models—from single‐purpose applications toward generalist models, driven by natural language. This article investigates the implications of this paradigm shift for the ethical debate. Focusing on issues like trust, transparency, threats of patient autonomy, responsibility issues in the collaboration of clinicians and ML models, fairness, and privacy, it will be argued that the main problems will be continuous with the current debate. However, due to functioning of large language models, the complexity of all these problems increases. In addition, the article discusses some profound challenges for the clinical evaluation of large language models and threats to the reproducibility and replicability of studies about large language models in medicine due to corporate interests.
The role of phonology in non-native word learning: Evidence from cross-situational statistical learning
2024-03-25

Abstract Adults often encounter difficulty perceiving and processing sounds of a second language (L2). In order to acquire word-meaning mappings, learners need to determine what the language-relevant phonological contrasts are in the language. In this study, we examined the influence of phonology on non-native word learning, determining whether the language-relevant phonological contrasts could be acquired by abstracting over multiple experiences, and whether awareness of these contrasts could be related to learning. We trained English- and Mandarin-native speakers with pseudowords via a cross-situational statistical learning task (CSL). Learners were able to acquire the phonological contrasts across multiple situations, but similar-sounding words (i.e., minimal pairs) were harder to acquire, and words that contrast in a non-native suprasegmental feature (i.e., Mandarin lexical tone) were even harder for English-speakers, even with extended exposure. Furthermore, awareness of the non-native phonology was not found to relate to learning.
Rel Family Transcription Factor NFAT5 Upregulates COX2 via HIF-1α Activity in Ishikawa and HEC1a Cells
2024-03-25

Nuclear factor of activated T cells 5 (NFAT5) and cyclooxygenase 2 (COX2; PTGS2) both participate in diverse pathologies including cancer progression. However, the biological role of the NFAT5-COX2 signaling pathway in human endometrial cancer has remained elusive. The present study explored whether NFAT5 is expressed in endometrial tumors and if NFAT5 participates in cancer progression. To gain insights into the underlying mechanisms, NFAT5 protein abundance in endometrial cancer tissue was visualized by immunohistochemistry and endometrial cancer cells (Ishikawa and HEC1a) were transfected with NFAT5 or with an empty plasmid. As a result, NFAT5 expression is more abundant in high-grade than in low-grade endometrial cancer tissue. RNA sequencing analysis of NFAT5 overexpression in Ishikawa cells upregulated 37 genes and downregulated 20 genes. Genes affected included cyclooxygenase 2 and hypoxia inducible factor 1α (HIF1A). NFAT5 transfection and/or treatment with HIF-1α stabilizer exerted a strong stimulating effect on HIF-1α promoter activity as well as COX2 expression level and prostaglandin E2 receptor (PGE2) levels. Our findings suggest that activation of NFAT5—HIF-1α—COX2 axis could promote endometrial cancer progression.
Lithospheric- and crustal-scale controls on variations in foreland basin development in the Northern Alpine Foreland Basin
2024-03-25

The Northern Alpine Foreland Basin (i.e., Molasse Basin) developed due to flexural subsidence from slab- and topographic loading during continental collision between the Adriatic and European plates. Previous studies highlight a diachronous transition from underfilled- to overfilled conditions in the Molasse Basin in response to orogen-parallel variations in flexural subsidence and sediment supply. In this contribution, we investigate the lithospheric- and crustal-scale orogenic process(es) that generated this diachronous transition. For this, we conducted a tectonostratigraphic analysis of the Molasse Basin. Firstly, we constructed a 3D geological model to derive the architecture of the European margin during the Eocene onset of flexure. Second, 2D/3D reflection seismic- and borehole data were used to characterise the spatiotemporal development of depositional environments and syn-flexural normal fault kinematics in the German Molasse. Our data show a stepwise rather than continuous eastward migration of the underfilled- to overfilled transition. Furthermore, syn-flexural fault kinematics document a Rupelian to early Burdigalian northward younging trend and higher cumulative Cenozoic offsets in the Eastern German Molasse (< 230 m) compared to the Western German Molasse (< 150 m). This implies a west-to-east increase in the curvature of bending of the European plate, induced by along-strike variations in the magnitude of applied loads and/or European lithospheric strength variations. These variations drove lateral variations in accommodation space and sediment supply. Subsequently, this led to the diachronous underfill-to-overfilled transition in the Molasse Basin. Taken together, we suggest that the diachronous transition was driven by spatiotemporal variations in the thickening of the orogenic wedge supported by slab detachment, promoted by subduction- and collision of the irregular European margin.
Coherent Spin-Phonon Scattering in Facilitated Rydberg Lattices
2024-03-25

We investigate the dynamics of a one-dimensional spin system with facilitation constraint that can be studied using Rydberg atoms in arrays of optical tweezer traps. The elementary degrees of freedom of the system are domains of Rydberg excitations that expand ballistically through the lattice. Because of mechanical forces, Rydberg excited atoms are coupled to vibrations within their traps. At zero temperature and large trap depth, it is known that virtually excited lattice vibrations only renormalize the timescale of the ballistic propagation. However, when vibrational excitations are initially present-i.e., when the external motion of the atoms is prepared in an excited Fock state, coherent state or thermal state-resonant scattering between spin domain walls and phonons takes place. This coherent and deterministic process, which is free from disorder, leads to a reduction of the power-law exponent characterizing the expansion of spin domains. Furthermore, the spin domain dynamics is sensitive to the coherence properties of the atoms' vibrational state, such as the relative phase of coherently superimposed Fock states. Even for a translationally invariant initial state the latter manifests macroscopically in a phase-sensitive asymmetric expansion.
Quantum parameter estimation with many-body fermionic systems and application to the Hall effect
2024-03-25

We calculate the quantum Fisher information for a generic many-body fermionic system in a pure state depending on a parameter. We discuss the situations where the parameter is imprinted in the basis states, in the state coefficients, or both. In the case where the parameter dependence of coefficients results from a Hamiltonian evolution, we derive a particularly simple expression for the quantum Fisher information. We apply our findings to the quantum Hall effect, and evaluate the quantum Fisher information associated with the optimal measurement of the magnetic field for a system in the ground state of the effective Hamiltonian. The occupation of electron states with high momentum enforced by the Pauli principle leads to a ``super-Heisenberg’’ scaling of the sensitivity with a power law that depends on the geometry of the sensor.
New Light on the Land of Sūḫu
2024-03-25

Abstract In this review article, Philippe Clancier’s recent monograph on the history of the overlooked Late Bronze and Early Iron-age polity of Sūḫu lying on the Middle Euphrates is examined. It is demonstrated that the central contention of two identically named polities of Sūḫu (“Eastern” and “Western Sūḫu” respectively), ruled by two competing dynasties with differing political relationships to Assyria, is not supported by the textual record. As a corrective, a new comprehensive political history of Sūḫu in the early first millennium BC is presented here, as a basis for future research.
Development of Highly Potent and Selective Covalent FGFR4 Inhibitors Based on SNAr Electrophiles
2024-03-25

Fibroblast Growth Factor Receptor 4 (FGFR4) is thought to be a driver in several cancer types, most notably in hepatocellular carcinoma. One way to achieve high potency and isoform-selectivity for FGFR4 is covalently targeting a rare cysteine (C552) in the hinge region of its kinase domain that is not present in other FGFR family members (FGFR1-3). Typically, this cysteine is addressed via classical acrylamide electrophiles. We demonstrate that non-canonical covalent “warheads” based on nucleophilic aromatic substitution (SNAr) chemistry can be employed in a rational manner to generate highly potent and (isoform )selective FGFR4 inhibitors with a low intrinsic reactivity. Key compounds showed low- to subnanomolar potency, efficient covalent inactivation, and excellent selectivity over other FGFRs, kinases with an equivalent cysteine and a representative subset of the kinome. Moreover, these compounds achieved nanomolar potencies in cellular assays and demonstrated good microsomal stability highlighting the potential of SNAr-based approaches in covalent inhibitor design.
Association among childhood adversity and susceptibility to interference during varying salience: two studies in healthy males
2024-03-25

Abstract Childhood adversity, a prevalent experience, is related to a higher risk for externalizing and internalizing psychopathology. Alterations in the development of cognitive processes, for example in the attention-interference domain may link childhood adversity and psychopathology. Interfering stimuli can vary in their salience, i.e. ability to capture attentional focus, and valence. However, it is not known if interference by salience or valence is associated with self-reported adversity. In two independent study samples of healthy men (Study 1: n = 44; mean age [standard deviation (SD)] = 25.9 [3.4] years; Study 2: n = 37; 43.5 [9.7] years) we used the attention modulation task (AMT) that probed interference by two attention-modulating conditions, salience and valence separately across repeated target stimuli. The AMT measures the effects of visual distractors (pictures) on the performance of auditory discrimination tasks (target stimuli). We hypothesized that participants reporting higher levels of childhood adversity, measured with the childhood trauma questionnaire, would show sustained interference in trials with lower salience. Due to conflicting reports on the valence-modulation, we tested the valence condition in an exploratory manner. Linear mixed models revealed an interaction between reported childhood adversity and the salience condition across tone presentations in both study samples (Sample 1: p = .03; Sample 2: p = .04), while there were no effects for the valence condition across both studies. Our study suggests that higher self-reported childhood adversity is related to faster processing of target cues during high salience, but slower during low salience conditions. These results hint to the mechanisms linking childhood adversity and psychopathological symptoms in the attentional domain.
Triclosan alters biofilm structures and confers antibiotic tolerance in Staphylococcus aureus using multiple regulatory pathways
2024-03-25

Abstract The biocide triclosan is used extensively in both household and hospital settings. The chronic exposure to the biocide occurring in individuals that use triclosan-containing products results in low levels of triclosan present in the human body that has been linked to induction of antibiotic tolerance and altered biofilm formation. Here we aimed to unravel the molecular mechanisms involved in triclosan-induced antibiotic tolerance and biofilm formation in Staphylococcus aureus . Triclosan treatment prior to planktonic exposure to bactericidal antibiotics resulted in 1,000 fold higher viable cell counts compared to non-pretreated cultures. Triclosan pretreatment also protected S. aureus biofilms against otherwise lethal doses of antibiotics as shown by live/dead cell staining and viable cell counting. Triclosan mediated antibiotic tolerance in S. aureus biofilms required an active stringent response because biofilms of a pppGpp 0 strain were not protected from antibiotic killing. Incubation of S. aureus with triclosan also altered biofilm structure due to SarA-mediated overproduction of the polysaccharide intercellular adhesin (PIA) in the biofilm matrix. Thus, physiologically relevant concentrations of triclosan can trigger (p)ppGpp dependent antibiotic tolerance as well as SarA dependent biofilm formation.
Wearing face masks as a potential source for inhalation and oral uptake of inanimate toxins – A scoping review
2024-03-26

Undoubtedly, mask mandates during the SARS-CoV-2 pandemic have been generating an additional source of potentially harmful exposition to toxins with health threatening and carcinogenic properties at population level with almost zero distance to the airways.
Rapid Phenotypic Antibiotics Susceptibility Analysis by a 3D Printed Prototype
2024-03-26

Abstract One of the most important public health concerns is the increase in antibiotic‐resistant pathogens and corresponding treatment of associated infections. Addressing this challenge requires more efficient use of antibiotics, achievable by the use of evidence‐based, effective antibiotics identified by antibiotic susceptibility testing (AST). However, the current standard method of phenotypic AST used for this purpose requires 48 h or more from sample collection to result. Until results are available, broad‐spectrum antibiotics are used to avoid delaying treatment. The turnaround time must therefore be shortened in order for the results to be available before the second administration of antibiotics. The phenotypic electrochemical AST method presented here identifies effective antibiotics within 5–10 h after sampling. Spiked serum samples, including polymicrobial samples, with clinically relevant pathogens and respective concentrations commonly found in bloodstream infections ( Escherichia coli , Staphylococcus aureus , Klebsiella pneumoniae , and Pseudomonas aeruginosa ) are used. Direct loading of the test with diluted serum eliminates the need for a pre‐culture, as required by existing methods. Furthermore, by combining several electrochemical measurement procedures with computational analysis, allowing the method to be used both online and offline, the AST achieves a sensitivity of 94.44% and a specificity of 95.83% considering each replicate individually.
Sedimentological and sequence-stratigraphic analyses of the Tithonian Hith Anhydrite Formation in the Dahal Hit outcrop, Saudi Arabia
2024-03-26

Abstract The Dahal Hit cavern in Central Saudi Arabia is the only locality where the Tithonian Hith Anhydrite Formation is exposed in the Middle East. In 2010, a 28.5-m interval in the 90-m-thick Hith Formation was logged and described in the cavern as part of a study to evaluate its sedimentological and sequence-stratigraphic architecture and to identify potential high-permeability layers within the seal of the world’s most prolific petroleum system. Seven facies types were interpreted as reflecting sabkha (subaerial) or salina (subaqueous) settings, and their vertical stacking patterns revealed that the logged interval consists of three transgressive–regressive cycles and part of a fourth cycle. The cavern was revisited in 2016 but only to find that the water level had risen by about 50 m rendering further geological studies impossible. The higher level of the water suggests that the cavern was flooded by the flow in the subsurface of treated sewage water released into a former quarry. The quarry is situated about 10 km southeast of the cavern, and the storage of water in it started in 2008. The flow pathways to the Dahal Hit cavern are apparently well-connected karsts, caverns, and high-permeability flow zones present in dolomite layers.
Locally Produced Sedimentary Biomarkers in High-Altitude Catchments Outweigh Upstream River Transport in Sedimentary Archives
2024-03-26

Abstract. Sedimentary records of lipid biomarkers such as leaf wax n-alkanes are not only influenced by ecosystem turnover and physiological changes in plants, they are also influenced by earth surface processes integrating these signals. The integration of biomarkers into the sedimentary record and the effects of integration processes on recorded environmental signals are complex and not fully understood. To determine the depositional constraints on biomarker records in a high-altitude small catchment system, we collected both soil and stream sediments along a 1000 m altitude transect (1500 – 2500 masl) in the Areguni Mountains, a subrange of the Lesser Caucasus Mountains in Armenia. We utilize the existence of a treeline at ~ 2000 masl, which separates alpine meadow above from deciduous forest below, to assess the relative contribution of upstream biomarker transport to local vegetation input in the stream. We find that average chain length (ACL), hydrogen isotope (δD) and carbon isotope (δ13C) values of n-alkanes are significantly different in soils collected above and below the treeline. However, samples collected from the stream sediments do not integrate these signals quantitively. As the stream drops below the treeline, the ACL, δD and δ13C values of n-alkanes preserved in streambed sediments reflect a bias toward n-alkanes sourced from trees. This suggests that there is either 1) minimal transportation of organic matter from the more open vegetation in higher elevations, or 2) greater production of target biomarkers by trees and shurbs found at lower elevations results in overprinting of stream signals by local vegetation. Though this latter observation may preclude using n-alkanes to measure past treeline movement in these mountains, δD values of biomarkers in fluvial deposits in these settings are more likely to record local hydrological changes rather than changes in upstream fractionation differences associated with vegetation turnover.