julilili42/papers huggingface dataset:
An Automated Real-Time PCR Assay versus Next-Generation Sequencing in the Detection of BRAF V600 Mutations in Melanoma Tissue Samples
2024-07-30

Background: Next-generation sequencing (NGS) is the most commonly used method for determining BRAF mutational status in patients with advanced melanoma. Automated PCR-based methods, such as the IdyllaTM system, are increasingly used for mutation diagnostics, but it is unclear what impact the choice of diagnostic method has on the management of melanoma. Objectives: To compare the concordance rate of BRAF V600 mutational analysis using IdyllaTM and NGS and to analyze the technical and clinical turnaround time. The clinical relevance is compared by analyzing the impact on the treatment decision. Methods: In this monocentric prospective cohort study, the BRAF mutation status of 51 patients was determined using both methods in parallel. Results: BRAF V600 mutation was detected in 23/51 cases (45%). IdyllaTM showed a 100% concordant result with a faster turnaround time (0.2 days) compared to NGS (12.2 days). In general, less tumor material was required for IdyllaTM than for NGS. Most patients received immunotherapy as a first-line therapy regardless of the BRAF V600 status. Conclusions: IdyllaTM testing proved to be a reliable and rapid alternative to NGS in the determination of BRAF V600 mutation. Although BRAF. status was available earlier, this had no influence on the treatment decision in most cases.
Sharing Electricity over Money: Third-Person Perspectives on Human-Robot Dictator Game Outcomes
2024-07-30

With the increasing integration of robots into various facets of human life, understanding prosociality towards robots emerges as a crucial research endeavour. Across two studies (N = 117 and N = 310), we adopt a third-person perspective to investigate different outcomes of the Dictator Game paradigm. Participants were tasked with evaluating the shared allocation of distinct resources (Study 1: money, access to electricity; Study 2: money, access to electricity, food, and electronic tools). Results reveal that only ~24% of responses, as averaged for the two studies, indicated a preference for non-sharing across all resource types and shared amounts. For Study 1 and 2, we find that people tend to agree to the sharing of access to electricity over money. Additionally, for Study 2 findings suggest a tendency towards greater sharing of electronic tools and lesser sharing of food, compared to access to electricity. Moreover, perceptions of robot trustworthiness corresponded to a preference for sharing higher resource quantities. This relationship was mediated by participant gender as well as robot related risk and opportunity perception. These findings provide valuable insights into the socio-cognitive mechanisms underlying human perceptions of sharing behaviors with robots. Our studies indicate an emerging societal expectation regarding the types and extent of resources to be shared with robots, thus contributing to the delineation of evolving social norms towards robots. Furthermore, the results shed light on the nuanced dynamics of human-robot interaction, enriching our comprehension of how humans navigate social exchanges with artificial agents.
Learned Insignificance of Credibility Signs
2024-07-30

A large part of how people learn about their shared world is via social information. However, in complex modern information ecosystems, it can be challenging to identify deception or filter out misinformation. This challenge is exacerbated by the existence of a dual-learning problem whereby: (1) People draw inferences about the world, given new social information; and simultaneously (2), they draw inferences about how credible various sources of information are, given social cues and previous knowledge. In this context, we investigate how social influence and individual cognitive processing interact to explain how one might loose the ability to reliably assess information. Crucially, we show how this happens even when individuals engage in rational belief updating and have access to objective cues of deception. Using an agent based model, the Reputation Game Simulation, we show that mere misinformation is not the problem: The dual-learning problem can be solved successfully with limited Bayesian reasoning, even in the presence of deceit. However, when some agents pursue additional non-epistemic strategies (e.g., flattering others or promoting themselves), other agents in their network may learn to discount objective cues of credibility. This is an emergent delusion-like state, wherein false beliefs resist correction by true incoming information. Further, we show how such delusion-like states can be rehabilitated when agents who had previously lost the ability to discern cues of credibility are put into new, healthy---though not necessarily honest---environments.Altogether, this suggests that correcting misinformation is not the optimal solution to epistemically toxic environments. Though difficult, socially-induced cognitive biases can be repaired in healthy environments, ones where cues of credibility can be re-learned in the absence of non-epistemic communication motives.
Lay Theories About Artificial Versus Artificial Intelligence: Rethinking Theory of Machine
2024-07-30

Most research on augmented judgment and decision-making is human-centered. Specifically, Theory of Machine is a conceptual framework for describing and analyzing people’s lay theories about how human and algorithmic judgment differ. Reminiscent of the Theory of Mind, it conceptualizes the idea of ascribing thought processes or mental states to algorithms. However, based on their own perceptions, past personal experiences, and shaped by public media, people may conceive of humans and algorithms as functionally distinct ontological entities. Therefore, research on augmented judgment and decision-making should also focus on the differences between various algorithms in terms of (cognitive) abilities and behavior. In this article, several agendas for future research are proposed that explicitly consider people’s diverse interactions with various decision-support and artificial intelligence systems in their daily lives. Such primarily algorithm-centric research will help to gain insights into a more fine-grained Theory of Machine that also distinguishes between different levels of algorithmic fairness, transparency, and explainability. Ideally, a better understanding of how people mentalize about algorithmic behavior can also be used to improve algorithmic augmentations of human judgment and decision-making.
Health economic evaluation of an electronic mindfulness-based intervention (eMBI) to improve maternal mental health during pregnancy – a randomized controlled trial (RCT)
2024-07-30

Abstract Background Anxiety and depression are the most prevalent psychiatric diseases in the peripartum period. They can lead to relevant health consequences for mother and child as well as increased health care resource utilization (HCRU) and related costs. Due to the promising results of mindfulness-based interventions (MBI) and digital health applications in mental health, an electronic MBI on maternal mental health during pregnancy was implemented and assessed in terms of transferability to standard care in Germany. The present study focused the health economic outcomes of the randomized controlled trial (RCT). Methods The analysis, adopting a payer’s and a societal perspective, included women of increased emotional distress at &lt; 29 weeks of gestation. We applied inferential statistics (α = 0.05 significance level) to compare the intervention group (IG) and control group (CG) in terms of HCRU and costs. The analysis was primarily based on statutory health insurance claims data which covered the individual observational period of 40 weeks. Results Overall, 258 women (IG: 117, CG: 141) were included in the health economic analysis. The results on total health care costs from a payer’s perspective indicated higher costs for the IGi compared to the CG (Exp(ß) = 1.096, 95% CI: 1.006–1.194, p = 0.037). However, the estimation was not significant after Bonferroni correction ( p &lt; 0.006). Even the analysis from a societal perspective as well as sensitivity analyses did not show significant results. Conclusions In the present study, the eMBI did neither reduced nor significantly increased health care costs. Further research is needed to generate robust evidence on eMBIs for women suffering from peripartum depression and anxiety. Trial registration German Clinical Trials Register: DRKS00017210. Registered on 13 January 2020. Retrospectively registered.
Role of Carbon, Nitrogen, Phosphate and Sulfur Metabolism in Secondary Metabolism Precursor Supply in Streptomyces spp.
2024-07-31

The natural soil environment of Streptomyces is characterized by variations in the availability of nitrogen, carbon, phosphate and sulfur, leading to complex primary and secondary metabolisms. Their remarkable ability to adapt to fluctuating nutrient conditions is possible through the utilization of a large amount of substrates by diverse intracellular and extracellular enzymes. Thus, Streptomyces fulfill an important ecological role in soil environments, metabolizing the remains of other organisms. In order to survive under changing conditions in their natural habitats, they have the possibility to fall back on specialized enzymes to utilize diverse nutrients and supply compounds from primary metabolism as precursors for secondary metabolite production. We aimed to summarize the knowledge on the C-, N-, P- and S-metabolisms in the genus Streptomyces as a source of building blocks for the production of antibiotics and other relevant compounds.
Swirls and scoops: Ice base melt revealed by multibeam imagery of an Antarctic ice shelf
2024-07-31

Knowledge gaps about how the ocean melts Antarctica’s ice shelves, borne from a lack of observations, lead to large uncertainties in sea level predictions. Using high-resolution maps of the underside of Dotson Ice Shelf, West Antarctica, we reveal the imprint that ice shelf basal melting leaves on the ice. Convection and intermittent warm water intrusions form widespread terraced features through slow melting in quiescent areas, while shear-driven turbulence rapidly melts smooth, eroded topographies in outflow areas, as well as enigmatic teardrop-shaped indentations that result from boundary-layer flow rotation. Full-thickness ice fractures, with bases modified by basal melting and convective processes, are observed throughout the area. This new wealth of processes, all active under a single ice shelf, must be considered to accurately predict future Antarctic ice shelf melt.
Drug-induced hepatotoxicity and association with slow acetylation variants NAT2*5 and NAT2*6 in Cameroonian patients with tuberculosis and HIV co-infection
2024-07-31

Abstract Background Human immunodeficiency virus (HIV) and tuberculosis (TB) are major contributors to morbidity and mortality in sub-Saharan Africa including Cameroon. Pharmacogenetic variants could serve as predictors of drug-induced hepatotoxicity (DIH), in patients with TB co-infected with HIV. We evaluated the occurrence of DIH and pharmacogenetic variants in Cameroonian patients. Methods Treatment-naïve patients with HIV, TB or TB/HIV co-infection were recruited at three hospitals in Cameroon, between September 2018 and November 2019. Appropriate treatment was initiated, and patients followed up for 12 weeks to assess DIH. Pharmacogenetic variants were assessed by allele discrimination TaqMan SNP assays. Results Of the 141 treatment naïve patients, the overall incidence of DIH was 38% (53/141). The highest incidence of DIH, 52% (32/61), was observed among HIV patients. Of 32 pharmacogenetic variants, the slow acetylation variants NAT2 *5 was associated with a decreased risk of DIH (OR: 0.4; 95%CI: 0.17–0.96; p = 0.038), while NAT2 *6 was found to be associated with an increased risk of DIH (OR: 4.2; 95%CI: 1.1–15.2; p = 0.017) among patients treated for TB. Up to 15 SNPs differed in ≥ 5% of allele frequencies among African populations, while 25 SNPs differed in ≥ 5% of the allele frequencies among non-African populations, respectively. Conclusions DIH is an important clinical problem in African patients with TB and HIV. The NAT2 *5 and NAT2 *6 variants were found to be associated with DIH in the Cameroonian population. Prior screening for the slow acetylation variants NAT2*5 and NAT2*6 may prevent DIH in TB and HIV-coinfected patients.
tessilator: a one-stop shop for measuring TESS rotation periods
2024-07-31

ABSTRACT We present a software package designed to produce photometric light curves and measure rotation periods from full-frame images taken by the Transiting Exoplanet Survey Satellite (TESS), which we name ‘tessilator’. tessilator is the only publicly available code that will run a full light curve and rotation period ( ) analysis based on just a (list of) target identifier(s) or sky position(s) via a simple command-line prompt. This paper sets out to introduce the rationale for developing tessilator, and then describes the methods, considerations, and assumptions for: extracting photometry; dealing with potential contamination; accounting for natural and instrumental systematic effects; light-curve normalization and detrending; removing outliers and unreliable data; and finally, measuring the value and several periodogram attributes. Our methods have been tuned specifically to optimize TESS light curves and are independent from the pipelines developed by the TESS Science Processing Operations Center (SPOC), meaning tessilator can, in principle, analyse any target across the entire celestial sphere. We compare tessilator measurements with TESS-SPOC-derived light curves of 1560 (mainly solar-type and low-mass) stars across four benchmark open clusters (Pisces–Eridanus, the Pleiades, the Hyades, and Praesepe) and a sample of nearby field M-dwarfs. From a vetted subsample of 864 targets we find an excellent return of matches for the first three open clusters ( per cent) and a moderate ( per cent) match for the 700 Myr Praesepe and MEarth sample, which validates tessilator as a tool for measuring . The tessilator code is available at https://github.com/alexbinks/tessilator.
Paleobiological implications of chevron pathology in the sauropodomorph Plateosaurus trossingensis from the Upper Triassic of SW Germany
2024-07-31

Paleopathology, the study of diseases and injuries from the fossil record, allows for a unique view into the life of prehistoric animals. Pathologies have nowadays been described in nearly all groups of fossil vertebrates, especially dinosaurs. Despite the large number of skeletons, pathologies had never been reported in the sauropodomorph Plateosaurus trossingensis . Here we describe the first pathologies of Plateosaurus using two individuals with pathologies in the chevrons of the tail, from the Upper Triassic of Trossingen, SW Germany. The two specimens each contain three consecutive pathological chevrons. Our results show that the pathologies were caused by external trauma in one individual and potentially tendinous trauma in the other. Healing of the lesions allowed survival of both animals. Using additional pathological specimens found in other collections and from multiple localities, we observe that 14.8% of all individuals of Plateosaurus contain pathologies within their chevrons, suggesting it was a vulnerable bone.
Generation of lysolipin derivatives by genetic engineering
2024-07-31

Lysolipin I is a halogenated, polycyclic xanthone natural product belonging to the polyketide class of antibiotics, naturally produced by Streptomyces violaceoniger TÜ96 and Streptomyces tendae TÜ4042. The biosynthesis is encoded on a 43 kb-spanning biosynthetic gene cluster. Heterologous expression of the gene cluster has been established in previous work by using the cosmid 4H04, which was transferred to Streptomyces albus . In the current study, we demonstrate the optimization of production yields of therapeutically interesting lysolipin derivatives with extended activity against Gram-negatives and less cytotoxic bioactivities, respectively, by using mutated heterologous S. albus producer strains. Production yields were significantly increased by adapting cultivation conditions as well as by inactivating the transcriptional repressor gene llpRI , which lead to increased and consistent lysolipin (derivatives) production. Furthermore, cultivation of a S. albus 4H04 ∆llpOI mutant strain in bromide-containing fermentation medium resulted in the production of a new brominated lysolipin derivative (C 28 H 20 BrNO 9 ).
Bridging the divide: addressing discrepancies between clinical guidelines, policy guidelines, and biomarker utilization
2024-07-31

Abstract Objectives This paper aims to identify and address gaps in cancer treatment and diagnosis within European health services, focusing specifically on discrepancies between clinical guidelines and policy guidelines. It seeks to highlight how the underutilization of advanced diagnostic techniques recommended by medical societies contributes to missed opportunities for improving patient outcomes. Methods A comprehensive analysis was conducted across multiple European countries to assess the compliance and integration of clinical guidelines with the availability of advanced diagnostic technologies. Secondary data related to clinical and policy guidelines in cancer care were collected and analyzed. Key indicators of adoption and utilization of next-generation sequencing and liquid biopsy were examined to evaluate their impact on health service efficiency and patient care. Results The analysis revealed significant discrepancies between the recommendations of medical societies regarding advanced diagnostic techniques and their adoption in health policy decisions across Europe. Country-specific assessments indicated varying levels of alignment between clinical guidelines and the availability of advanced diagnostics. These findings underscored missed opportunities for optimizing patient care and health service efficiency through better alignment and integration of clinical guidelines with policy decisions. Conclusions This study concludes that there is a critical need for health policy decision-makers to prioritize the adoption of clinical guidelines in resource allocation and health service organization. Greater attention to the recommendations of medical societies regarding advanced diagnostic techniques could significantly enhance diagnostic accuracy, treatment efficacy, and overall patient outcomes in cancer care. The paper advocates for policy reforms that acknowledge and leverage the potential benefits of advanced diagnostics in improving health service performance and patient-centered care across Europe.
Structural disconnections caused by white matter hyperintensities in post-stroke spatial neglect
2024-07-31

Abstract White matter hyperintensities (WMH), a common feature of cerebral small vessel disease, affect a wide range of cognitive dysfunctions, including spatial neglect. The latter is a disorder of spatial attention and exploration typically after right hemisphere brain damage. To explore the impact of WMH on neglect-related structural disconnections, the present study investigated the indirectly quantified structural disconnectome induced by either stroke lesion alone, WMH alone, or their combination. Further, we compared different measures of structural disconnections – voxel-wise, pairwise, tract-wise, and parcel-wise – to identify neural correlates and predict acute neglect severity. We observed that WMH-derived disconnections alone were not associated to neglect behavior. However, when combined with disconnections derived from individual stroke lesions, pre-stroke WMH contributed to post-stroke neglect severity by affecting right frontal and subcortical substrates, like the middle frontal gyrus, basal ganglia, thalamus, and the fronto-pontine tract. Predictive modeling demonstrated that voxel-wise disconnection data outperformed other measures of structural disconnection, explaining 42% of the total variance. Compared to using stroke lesion anatomy, prediction performance can be improved by either estimating stroke-based structural disconnections or delineating the combined anatomy of stroke lesion and WMH. We conclude that pre-stroke alterations in the white matter microstructure due to WMH contribute to post-stroke deficits in spatial attention, likely by impairing the integrity of human attention networks.
Prognostic Significance of Disseminated Tumor Cells in Bone Marrow for Endometrial Carcinoma Patients
2024-07-31

Background: Until now, limited clinical significance had been reported for disseminated tumor cells (DTCs) in gynecologic malignancies. DTCs were previously reported not to be associated with established risk factors, L1CAM immunoreactivity, and outcome in endometrial carcinoma (EC). This study’s primary objective was to investigate potential correlations of DTCs in the bone marrow (BM) of EC patients with disease-related survival, and a secondary objective was to evaluate associations between molecular classification of EC and DTCs. Methods: Patients treated for primary EC at Tuebingen University women’s hospital between 2003 and 2016 were identified. A total of 402 patients with a complete set of BM cytology, molecular, and clinical data were evaluable. Results: DTC occurrence was distributed equally among all four molecular groups (p = 0.651). DTC positivity was associated with a less favorable disease-free survival (HR: 1.86, 95% CI: 1.03–3.36, p = 0.036) and progression-free survival (HR: 1.86, 95% CI: 1.01–3.44, p = 0.045). Presence of DTCs was associated with a higher frequency of distant disease recurrence (p = 0.017). Conclusions: In line with our previous findings, tumor cell dissemination is not associated with molecular features in our large cohort of primary EC patients. Since DTCs seem to be associated with survival and location of disease recurrence, further studies are needed to decisively define their role in EC survival.
La botanique d’Aristote
2024-07-31

Abstract Whereas several zoological Aristotelian works have been preserved, Aristotle is reported to have written only one short botanical treatise. Such reports seem to conflict with his self-described ambition to study plants as well as animals. Even though this treatise is now lost, the available evidence suggests that Aristotle had valid reasons to find the subject-matter of plants much less interesting, as their activities amount to a subset of what animals do. When studying attributes common to both plants and animals in the transmitted corpus, Aristotle systematically focuses on the case of the most complex animals and, once an explanatory model has been found, proceeds to apply it to the remaining cases with less details. I argue that this procedure, although it runs counters to the intuition that one ought to start with the most simple case, corresponds to a general scientific method. Consequently, most of Aristotle’s botany is found to be already encapsulated in the main results of his study of animals.
On the Bayes risk of a sequential design for estimating a mean difference
2024-07-31

The problem addressed is that of sequentially estimating the difference between the means of two populations with respect to the squared error loss, where each population distribution is a member of the one-parameter exponential family.A Bayesian approach is adopted in which the population means are estimated by the posterior means at each stage of the sampling process and the prior distributions are not specified but have twice continuously differentiable density functions.The main result determines an asymptotic second-order lower bound, as t → ∞, for the Bayes risk of a sequential procedure that takes M observations from the first population and t -M from the second population, where M is determined according to a sequential design, and t denotes the total number of observations sampled from both populations.