julilili42/papers huggingface dataset:
The lipidomics reporting checklist a framework for transparency of lipidomic experiments and repurposing resource data
2024-08-14

The rapid increase in lipidomic studies has led to a collaborative effort within the community to establish standards and criteria for producing, documenting, and disseminating data. Creating a dynamic easy-to-use checklist that condenses key information about lipidomic experiments into common terminology will enhance the field's consistency, comparability, and repeatability. Here, we describe the structure and rationale of the established Lipidomics Minimal Reporting Checklist to increase transparency in lipidomics research.
Targeting Cyclophilin A in the Cardiac Microenvironment Preserves Heart Function and Structure in Failing Hearts
2024-08-14

BACKGROUND: Cardiac hypertrophy is characterized by remodeling of the myocardium, which involves alterations in the ECM (extracellular matrix) and cardiomyocyte structure. These alterations critically contribute to impaired contractility and relaxation, ultimately leading to heart failure. Emerging evidence implicates that extracellular signaling molecules are critically involved in the pathogenesis of cardiac hypertrophy and remodeling. The immunophilin CyPA (cyclophilin A) has been identified as a potential culprit. In this study, we aimed to unravel the interplay between eCyPA (extracellular CyPA) and myocardial dysfunction and evaluate the therapeutic potential of inhibiting its extracellular accumulation to improve heart function. METHODS: Employing a multidisciplinary approach encompassing in silico, in vitro, in vivo, and ex vivo experiments we studied a mouse model of cardiac hypertrophy and human heart specimen to decipher the interaction of CyPA and the cardiac microenvironment in highly relevant pre-/clinical settings. Myocardial expression of CyPA (immunohistology) and the inflammatory transcriptome (NanoString) was analyzed in human cardiac tissue derived from patients with nonischemic, noninflammatory congestive heart failure (n=187). These analyses were paralleled by a mouse model of Ang (angiotensin) II–induced heart failure, which was assessed by functional (echocardiography), structural (immunohistology, atomic force microscopy), and biomolecular (Raman spectroscopy) analyses. The effect of inhibiting eCyPA in the cardiac microenvironment was evaluated using a newly developed neutralizing anti-eCyPA monoclonal antibody. RESULTS: We observed a significant accumulation of eCyPA in both human and murine-failing hearts. Importantly, higher eCyPA expression was associated with poor clinical outcomes in patients ( P =0.043) and contractile dysfunction in mice (Pearson correlation coefficient, −0.73). Further, myocardial expression of eCyPA was critically associated with an increase in myocardial hypertrophy, inflammation, fibrosis, stiffness, and cardiac dysfunction in vivo. Antibody-based inhibition of eCyPA prevented (Ang II)-induced myocardial remodeling and dysfunction in mice. CONCLUSIONS: Our study provides strong evidence of the pathogenic role of eCyPA in remodeling, myocardial stiffening, and dysfunction in heart failure. The findings suggest that antibody-based inhibition of eCyPA may offer a novel therapeutic strategy for nonischemic heart failure. Further research is needed to evaluate the translational potential of these interventions in human patients with cardiac hypertrophy.
Avalanche Terahertz Photon Detection in a Rydberg Tweezer Array
2024-08-14

We propose a protocol for the amplified detection of low-intensity terahertz radiation using Rydberg tweezer arrays. The protocol offers single photon sensitivity together with a low dark count rate. It is split into two phases: during a sensing phase, it harnesses strong terahertz-range transitions between highly excited Rydberg states to capture individual terahertz photons. During an amplification phase it exploits the Rydberg facilitation mechanism which converts a single terahertz photon into a substantial signal of Rydberg excitations. We discuss a concrete realization based on realistic atomic interaction parameters, develop a comprehensive theoretical model that incorporates the motion of trapped atoms and study the many-body dynamics using tensor network methods.
Mineral chemistry of the Geyer SW tin skarn deposit: understanding variable fluid/rock ratios and metal fluxes
2024-08-14

Abstract The Geyer tin skarn in the Erzgebirge, Germany, comprises an early skarnoid stage (stage I, ~ 320 Ma) and a younger metasomatic stage (stage II, ~ 305 Ma), but yet, the source and distribution of Sn and the physicochemical conditions of skarn alteration were not constrained. Our results illustrate that contact metamorphic skarnoids of stage I contain only little Sn. REE patterns and elevated concentrations of HFSE indicate that garnet, titanite and vesuvianite of stage I formed under rock-buffered conditions (low fluid/rock ratios). Prograde assemblages of stage II, in contrast, contain two generations of stanniferous garnet, titanite-malayaite and vesuvianite. Oscillation between rock-buffered and fluid-buffered conditions are marked by variable concentrations of HFSE, W, In, and Sn in metasomatic garnet. Trace and REE element signatures of minerals formed under high fluid/rock ratios appear to mimic the signature of the magmatic-hydrothermal fluid which gave rise to metasomatic skarn alteration. Concomitantly with lower fluid-rock ratio, tin was remobilized from Sn-rich silicates and re-precipitated as malayaite. Ingress of meteoric water and decreasing temperatures towards the end of stage II led to the formation of cassiterite, low-Sn amphibole, chlorite, and sulfide minerals. Minor and trace element compositions of cassiterite do not show much variation, even if host rock and gangue minerals vary significantly, suggesting a predominance of a magmatic-hydrothermal fluid and high fluid/rock ratios. The mineral chemistry of major skarn-forming minerals, hence, records the change in the fluid/rock ratio, and the arrival, distribution, and remobilization of tin by magmatic fluids in polyphase tin skarn systems.
Standards for conducting and reporting consensus and recommendation documents: European Society of Cardiovascular Radiology policy from the Guidelines Committee
2024-08-14

Abstract Cardiovascular imaging is exponentially increasing in the diagnosis, risk stratification, and therapeutic management of patients with cardiovascular disease. The European Society of Cardiovascular Radiology (ESCR) is a non-profit scientific medical society dedicated to promoting and coordinating activities in cardiovascular imaging. The purpose of this paper, written by ESCR committees and Executive board members and approved by the ESCR Executive Board and Guidelines committee, is to codify a standardized approach to creating ESCR scientific documents. Indeed, consensus development methods must be adopted to ensure transparent decision-making that optimizes national and global health and reaches a certain scientific credibility. ESCR consensus documents developed based on a rigorous methodology will improve their scientific impact on the management of patients with cardiac involvement. Critical relevance statement This document aims to codify the methodology for producing consensus documents of the ESCR. These ESCR indications will broaden the scientific quality and credibility of further publications and, consequently, the impact on the diagnostic management of patients with cardiac involvement. Key Points Cardiovascular imaging is exponentially increasing for diagnosis, risk stratification, and therapeutic management. The ESCR is committed to promoting cardiovascular imaging. A rigorous methodology for ESCR consensus documents will improve their scientific impact.
Chiral Electrokinetic Phenomena in Single Nanopores
2024-08-14

Abstract The arrangement of solvent molecules and ions at solid–liquid interfaces determines electrochemical properties that are important in separations platforms, sensing technologies, and energy‐storage systems. Here we show that single glass and polymer pores in contact with propylene carbonate (PC) solutions of LiClO 4 exhibit an effective surface potential that is modulated by the enantiomeric excess of the solvent. In particular, electrochemical and electrokinetic measurements of ionic transport through glass pipettes and polymer pores reveal that the effective surface potential is significantly lower in solutions prepared using enantiomerically pure PC than in solutions prepared using racemic PC. Both pore systems became positively charged in all racemic solutions examined in the range of LiClO 4 concentrations between 1 mM and 100 mM, whereas solutions in ( R )‐(+)‐PC induced a positive surface potential only at concentrations above ~5 mM. The effective surface potential is quantified through asymmetry in current–voltage curves and zeta‐potential measurements. Vibrational sum‐frequency‐generation experiments on LiClO 4 solutions in racemic and enantiomerically pure PC indicate that the surface lipid‐bilayer‐like region in the former is more strongly organized than in the latter, dictating the favorable positions for lithium and perchlorate ions in each case. The more ordered molecular packing in the racemic liquid leads to accumulation of lithium ions on the outside of the bilayer, creating a higher effective positive charge. Our results highlight the extreme sensitivity of the interfacial potential on molecular organization of the solvent, and the relatively unexplored role that chirality can play in electrokinetic phenomena.
Testing a Context-Enriched Model of Successful Aging in Multiple Large Data Infrastructures With Individuals in Advanced Old Age
2024-08-14

Abstract Background and Objectives Few people who are ages 80+ meet the criteria of successful aging (SA) proposed by Rowe and Kahn. Going beyond the individual-level conceptualization, we argue that SA always operates in multiple contexts and that context may become most critical in advanced old age. However, we are not aware of any previous study providing an empirical test of how contexts for SA unfold across persons 80 years and older, including those living in institutions. Research Design and Methods We estimated and compared prevalences of SA based on a classic versus context-enriched understanding of SA in multiple large surveys of older adults, that is, the D80+ study (N = 3.233) and the NRW80+ study (N [baseline] = 1.863). In addition to replication across independent samples, we investigated the stability of context-related SA across time. Results Prevalences of SA according to Rowe and Kahn were 9.1% in adults aged 80–84 and 0.7% in persons 90 years or older. However, prevalence rates for those with good contexts at their disposal even if not fulfilling Rowe and Kahn’s criteria were much higher across all age groups (80–84 years: 54.9%, 90 years and older: 44.4%). Greater 2-year stability was observed for contextual compared to individual criteria. Notably, positive effects of context on SA were stronger at onset compared to late fourth age. Discussion and Implications Our findings support a contextualized understanding of SA and inform policy that furthering SA in the fourth age requires the optimization of multiple contexts at the community level.
Basilar artery occlusion management: An international survey of gender influence on management
2024-08-14

Background The superiority of endovascular thrombectomy (EVT) over medical management was not established in two early basilar artery occlusion (BAO) randomized controlled trials. Despite this, many clinicians recommended EVT for acute BAO under certain circumstances. This paper aims to compare physicians’ diagnostic and management strategies of BAO according to gender. Methods From January to March 2022 an international survey was conducted regarding management strategies in acute BAO. We compared responses between clinicians by identifying gender. Questions were designed to examine clinical and imaging parameters influencing management of patients with BAO. Results Among the 1245 respondents from 73 countries, 311 (25.0%) identified as female. This figure was 13.6% amongst interventionists. Geographically, female respondents were lowest in Asia (14.5%) and North America (23.9%). The proportion of respondents identifying as female was consistent regardless of their years of experience. Female respondents were more likely to choose time of onset as time of first estimated stroke like symptom (48.0% vs. 38.5%, p &lt; .01), were less likely to favor thrombectomy in the V4 segment of vertebrobasilar artery occlusions (31.5% vs. 43.3%, p &lt; .01), and were less likely to find it acceptable to enroll all patients who met trial criteria in the standard medical treatment arm of a clinical trial (41.2% vs. 47.0%, p = .01). Male respondents were more likely to agree that thrombolysis would not alter their decision on proceeding with EVT (93.7% vs. 88.3%, p &lt; .01). Conclusions Female clinicians appear to be significantly underrepresented in stroke medicine. This is most pronounced amongst interventionists and in Asia. Although male and female opinions were closely aligned on many aspects of BAO management, differences in opinion were observed in a number of significant areas which influence decision making.
Proactive control adaptation in Stroop tasks reflects adjustments in the strength of distractor suppression
2024-08-14

Conflict tasks often yield smaller mean congruency effects when relevant (target) and irrelevant (distractor) information is mostly incongruent rather than mostly congruent. While this proportion congruency effect may reflect proactive control adaptation, only a few previous studies have provided convincing evidence for proactive control adaptation when ruling out contingency learning and reactive (item-specific) control adaptation. In this study, we present further evidence for proactive control adaptation (as reflected in proportion congruency effects and asymmetrical list-shifting effects in contingency-free transfer items) across three experiments (each N = 100 participants) using manual counting Stroop tasks (Experiment 1: number words as distractors; Experiment 2: Arabic numerals as distractors; Experiment 3: number words and Arabic numerals as inducer and transfer items, or vice versa). To better understand the processes underlying proactive control adaptation, we conducted fine-grained distributional analyses (delta functions) and model-based analyses (diffusion model for conflict tasks). These analyses suggest that proactive control adaptation in manual counting Stroop tasks mainly reflects adjustments in the strength of distractor suppression rather than in the timing of distractor suppression, the strength of target amplification, or response caution. Additional distributional and diffusion model re-analyses of the data by Spinelli and Lupker (2023, Experiments 1–3) revealed a similar pattern in vocal color Stroop tasks. In conclusion, the present study provides new evidence for proactive control adaptation in manual counting Stroop tasks, and indicates that proactive control adaptation mainly reflects adjustments in the strength of distractor suppression in both manual and vocal Stroop tasks.
Inflammatory plasma profile in genetic symptomatic and presymptomatic Frontotemporal Dementia − A GENFI study
2024-08-15

We showed that inflammatory proteins are upregulated in MAPT and GRN SMC, with some specific factors altered in GRN only, whereas no changes were seen in C9ORF72 carriers. Notably, only IL-1α levels were decreased in both SMC and PMC, independent of the type of causal mutation, suggesting common modifications occurring in the preclinical phase of the disease.
Grokking the Sequent Calculus (Functional Pearl)
2024-08-15

The sequent calculus is a proof system which was designed as a more symmetric alternative to natural deduction. The λμμ-calculus is a term assignment system for the sequent calculus and a great foundation for compiler intermediate languages due to its first-class representation of evaluation contexts. Unfortunately, only experts of the sequent calculus can appreciate its beauty. To remedy this, we present the first introduction to the λμμ-calculus which is not directed at type theorists or logicians but at compiler hackers and programming-language enthusiasts. We do this by writing a compiler from a small but interesting surface language to the λμμ-calculus as a compiler intermediate language.
Field conditions greatly modify a major growth-defense tradeoff inArabidopsis thaliana
2024-08-15

Abstract When plants defend themselves from pathogens, this often comes with a trade-off: the same genes that protect a plant from disease can also reduce its growth and fecundity in the absence of pathogens. One protein implicated in a major growth-defense trade-off in the plant Arabidopsis thaliana is ACCELERATED CELL DEATH 6 (ACD6), an ion channel that modulates salicylic acid (SA) synthesis to potentiate a wide range of defenses. Wild plant populations maintain significant functional variation in the ACD6 gene, with some alleles making the protein hyperactive. In the greenhouse, plants with hyperactive ACD6 alleles are resistant to diverse pathogens, yet are of smaller stature, their leaves senesce earlier, and they set fewer seeds. We hypothesized that such hyperactive alleles would not only affect the growth of microbial pathogens, but also more generally leaf microbiome assembly in the wild. To test this, we grew plants with hyperactive, standard, and defective ACD6 alleles in the same field-collected soil, both in climate-controlled conditions and outdoors. We surveyed visual phenotypes, gene expression, hormone levels, seed production, and the microbiome in each environment. To our surprise, we discovered that mature field plants, in stark contrast to greenhouse plants, were unaffected by their ACD6 genotype, suggesting that additional abiotic and/or microbial signals present outdoors – but not in the greenhouse – greatly modulate ACD6 activity.
Correlations between local geoclimatic variables and hatchling body size in the sea turtles Caretta caretta and Chelonia mydas
2024-08-15

Abstract It has been widely demonstrated that air and sand temperatures influence the anatomy of sea turtle hatchlings. We examined the impact of precipitation during the nesting season on the hatchling body size of loggerhead and green turtles from 37 beaches worldwide. Longitudinal data collected between 2012 and 2018 from Florida (US) and from a sample on Bõa Vista Island (Cabo Verde) carried out in 2019 showed that loggerhead body size at hatching was negatively correlated with precipitation, while precipitation was not correlated with hatchling body size in green turtles. A meta-analysis revealed that precipitation is positively correlated with hatchling mass in loggerhead turtles, while it is positively correlated with straight carapace length and width in green turtle hatchlings. The strongest influence of precipitation was found in the middle of the incubation period of loggerhead turtles in Cabo Verde, and we posit that this is due to an increase in the uptake of water for embryonic growth. These findings highlight the great importance of understanding the correlated effects of regional environmental variables, such as precipitation, on the development of sea turtle hatchlings and will have an impact on the evaluation of ongoing conservation and climate change discussions.
Sensing multi-directional forces at superresolution using taxel value isoline theory
2024-08-15

<title>Abstract</title> Robots can benefit from a good sense of touch to perceive their interaction with the world. However, contacts are complex phenomena that involve tactile sensing devices, contact objects, and the complex directional (normal and shear) force motions in-between. To advance tactile sensor research, we propose a comprehensive theory that unites these components, providing insights for sensor designs, explaining performance drops due to shear forces, and suggesting application scenarios with various contact objects. Our theory, based on sensor isolines, achieves superresolution sensing performance using only a few sensing units, avoiding the need for dense layouts. Through analysis of the sensor perception field and force sensitivity from a structural perspective, along with the influences of contact object sizes, we also explore the effects of different force directions: normal, tangential shear, and radial shear forces. The theoretical model covers all these aspects and predicts a system-level inherent accuracy loss introduced by shear forces compared to pure normal forces. To validate our theory, we developed Barodome, a 3D sensor capable of predicting contact locations and decoupling shear forces from normal forces. The sensor's performance confirms the significant impact of shear forces on performance, alongside normal forces. The observed 0.5 mm drop in the real sensor's performance (normal and shear forces) closely matches the theoretical prediction of 0.33 mm. Overall, our theory offers valuable guidance for future tactile sensor designs, informing various design choices and enhancing the development of advanced robotic touch systems.
Human population dynamics in Upper Paleolithic Europe inferred from fossil dental phenotypes
2024-08-16

Despite extensive archaeological research, our knowledge of the human population history of Upper Paleolithic Europe remains limited, primarily due to the scarce availability and poor molecular preservation of fossil remains. As teeth dominate the fossil record and preserve genetic signatures in their morphology, we compiled a large dataset of 450 dentitions dating between ~47 and 7 thousand years ago (ka), outnumbering existing skeletal and paleogenetic datasets. We tested a range of competing demographic scenarios using a coalescent-based machine learning Approximate Bayesian Computation (ABC) framework that we modified for use with phenotypic data. Mostly in agreement with but also challenging some of the hitherto available evidence, we identified a population turnover in western Europe at ~28 ka, isolates in western and eastern refugia between ~28 and 14.7 ka, and bottlenecks during the Last Glacial Maximum. Methodologically, this study marks the pioneering application of ABC to skeletal phenotypes, paving the way for exciting future research avenues.