julilili42/papers huggingface dataset:
Analysis of diagnostic test outcomes in a large loiasis cohort from an endemic region: Serological tests are often false negative in hyper-microfilaremic infections
2024-03-14

Background The parasitic disease loiasis is associated with significant morbidity and mortality. Individuals with hyper-microfilaremia (greater than 20,000 microfilariae per mL of blood) may suffer from serious treatment-related or spontaneous adverse events. Diagnosing loiasis remains complex and primarily relies on direct parasite detection. In this study, we analyzed the performance of various diagnostic tests and the influence of parasitological and clinical factors on test outcomes in samples from individuals living in an endemic region. Methods Data and samples were collected from rural Gabon. Loiasis was defined as either detectable microfilaremia, or a positive history of eyeworm as assessed by the RAPLOA questionnaire. Diagnostic testing included a quantitative PCR (qPCR) for detection of Loa loa DNA in blood samples, an in-house crude L . loa antigen IgG ELISA, and a rapid test for antibodies against the Ll-SXP-1 antigen (RDT). Sensitivity and specificity were determined for each test and factors potentially influencing outcomes were evaluated in an exploratory analysis. Results ELISA, RDT and qPCR results were available for 99.8%, 78.5%, and 100% of the 1,232 participants, respectively. The ELISA and RDT had only modest diagnostic accuracy. qPCR was specific for L . loa microfilaremia and Cycle threshold values correlated with microfilarial density. Anti- L . loa IgG levels were highest in occult loiasis, and antibody levels correlated inversely with L . loa microfilarial density as did RDT line intensities. Only 84.6% and 16.7% of hyper-microfilaremic individuals tested positive by ELISA (11/13) and RDT (2/12), respectively. Conclusion None of the tests demonstrated high sensitivity and specificity for loiasis. Indirect diagnostic assays were characterized by low specificity. Additionally, hyper-microfilaremic individuals often tested negative by RDT and ELISA, indicating that these tests are not suitable for individual case management in endemic populations.
Identifying Dynamic Shifts to Careless and Insufficient Effort Behavior in Questionnaire Responses; a Novel Approach and Experimental Validation
2024-03-14

Careless and insufficient effort responding (C/IER) is a situation where participants respond to survey instruments without considering the item content. This phenomena adds noise to data leading to erroneous inference. There are multiple approaches to identifying and accounting for C/IER in survey settings, of these approaches the best performing are model based classification techniques. Classic approaches to accounting for C/IER treat it as a person level phenomena. They first use some method to identify participants who exhibit C/IER, then use list-wise deletion to remove them prior to analysis. We argue that C/IER is actually a state that participants may exhibit for a portion of a survey instrument. In other words, participants start a survey with the intention to follow instructions, but at some point transition to a C/IER state and no longer respond in line with item contents. Accounting for C/IER at the item level, as opposed to the person level preserves data resulting in increased power. In this article we present a Bayesian Dynamic Latent Class Structural Equation Modeling (DLCSEM) approach for simultaneously accounting for C/IER at the item level and estimating a model of interest. We use a simulation study to establish the approaches performance under empirically relevant conditions and to compare it to other methods. We then conducted an experimental validation in which we induce C/IER like responses from human subjects and investigate the approaches ability to identify the point in which participants transition to a C/IER state. We also compare the model to existing approaches. In both the simulation and experimental validation the DLCSEM outperforms the alternative approaches. We conclude that the approach should be used by applied researchers for the pragmatic benefits of the method. Conclusions, limitations, and future directions are discussed.
Differing industrial relations: The public and the private sector in Germany
2024-03-14

Abstract This article argues that industrial relations (IR) in the German public sector are not just a replica of private sector IR. It suggests that neither the structures, nor the outcomes can be sufficiently explained by derivation from private sector IR processes. Primarily, the specifics and developments of the public sector explain public sector IR. It is of fundamental importance whether trade unions operate in a profit‐driven market environment or a publicly financed environment that is under public control. Differences between the public and the private sector result not least in the distinct relevance and meanings of trade union power resources. This influences the ways in which industrial action in the private and the public sector works and is relevant for trade union strategies.
The Base-Rate and Longer-Term Relevance of Year-to-Year Change in Personality Traits
2024-03-14

Personality traits are assumed to change slowly and incrementally. Recent intervention studies apparently challenge this assumption, showing that personality traits can also change quickly and substantially. However, how frequently do such quick changes manifest in the general population? This study sought to determine (1) a base rate of year-to-year changes in the general population and (2) the extent to which these shifts are related to longer-term change patterns. We examined year-to-year change in Big Five traits with nationally representative data from 7,005 German participants, annually tracked for up to 6 years. Year-to-year patterns exhibited stability and change (e.g., ≥ 1 SD year-to-year change in ≈ 20%). Across participants, year-to-year trait score increases and decreases occurred in equal proportions, suggesting that in a given sample, year-to-year changes in different directions average out. Within participants, however, in all domains but agreeableness, year-to-year changes reliably propagated to longer-term trajectories. While much of the year-to-year change faded away in subsequent years, lasting shifts in individuals’ trait levels remained, particularly upon pronounced year-to-year decreases. Overall, (pronounced) year-to-year changes were relatively common, largely reversible, and yet predictive of individuals’ longer-term trajectories. We discuss how the results bridge set-point assumptions with assumptions of incremental trait change.
Embodied magnitude processing: On the relation between the SNARC effect and perceived reachability
2024-03-14

Magnitude information, for instance, regarding weight, distance, or velocity, is crucial for planning goal-directed interactions. Accordingly, magnitude information, including numerical magnitude, can affect actions: Responses to small numbers are faster with the left hand than the right and vice versa (hand-based SNARC effect). Previous experiments found an influence of effector placements on the SNARC effect but also an influence of the mere distance between effectors and numbers. This indicates a sensorimotor grounding of space-number processing. In the current study, we investigated this grounding by probing the SNARC effect close to and far from the hands. We used a magnitude comparison task with a fixed standard of 5 (smaller numbers 1, 2, 3, 4; larger numbers 6, 7, 8, 9) and a sagittal response arrangement to measure hand-based and sagittal SNARC effects for digits presented at different sagittal distances to the hands, i.e., in peripersonal and extrapersonal space. A significant sagittal SNARC effect was found, with the largest effect size in extrapersonal space. Meanwhile, the hand-based SNARC effect appeared only descriptively, with the largest effect size between the hands, i.e., in peripersonal space. Additionally, a purely spatial congruency effect surfaced, prioritizing responses with the hand closer to the number. Together, these results emphasize that responses in simple decision-making tasks can be influenced interactively by a multitude of task-relevant axes and relative spatial locations, including effector placement and stimulus placement, as well as number magnitude.
The T4bSS ofLegionellafeatures a two-step secretion pathway with an inner membrane intermediate for secretion of transmembrane effectors
2024-03-14

Abstract To promote intracellular survival and infection, Legionella spp. translocate hundreds of effector proteins into eukaryotic host cells using a type IV b protein secretion system (T4bSS). T4bSS are well known to translocate soluble as well as transmembrane domain-containing effector proteins (TMD-effectors) but the mechanisms of secretion are still poorly understood. Herein we investigated the secretion of hydrophobic TMD-effectors, of which about 80 were previously reported to be encoded by L. pneumophila . A proteomic analysis of fractionated membranes revealed that TMD-effectors are targeted to and inserted into the bacterial inner membranes of L. pneumophila independent of the presence of a functional T4bSS. While the T4bSS chaperones IcmS and IcmW were critical for secretion of all tested TMD-effectors, they did not influence inner membrane targeting of these proteins. As for soluble effector proteins, translocation of TMD-effectors into host cells depended on a C-terminal secretion signal and this signal needed to be presented towards the cytoplasmic side of the inner membrane. A different secretion behavior of TMD- and soluble effectors and the need for small periplasmic loops within TMD-effectors provided strong evidence that TMD-effectors are secreted in a two-step secretion process: Initially, an inner membrane intermediate is formed, that is extracted towards the cytoplasmic side, possibly by the help of the type IV coupling protein complex and subsequently secreted into eukaryotic host cells by the T4bSS core complex. Overall, our study highlights the amazing versatility of T4bSS to secrete soluble and TMD-effectors from different subcellular locations of the bacterial cell.
Most discriminative stimuli for functional cell type clustering.
2024-03-14

Identifying cell types and understanding their functional properties is crucial for unraveling the mechanisms underlying perception and cognition. In the retina, functional types can be identified by carefully selected stimuli, but this requires expert domain knowledge and biases the procedure towards previously known cell types. In the visual cortex, it is still unknown what functional types exist and how to identify them. Thus, for unbiased identification of the functional cell types in retina and visual cortex, new approaches are needed. Here we propose an optimization-based clustering approach using deep predictive models to obtain functional clusters of neurons using Most Discriminative Stimuli (MDS). Our approach alternates between stimulus optimization with cluster reassignment akin to an expectation-maximization algorithm. The algorithm recovers functional clusters in mouse retina, marmoset retina and macaque visual area V4. This demonstrates that our approach can successfully find discriminative stimuli across species, stages of the visual system and recording techniques. The resulting most discriminative stimuli can be used to assign functional cell types fast and on the fly, without the need to train complex predictive models or show a large natural scene dataset, paving the way for experiments that were previously limited by experimental time. Crucially, MDS are interpretable: they visualize the distinctive stimulus patterns that most unambiguously identify a specific type of neuron.
Semaphorin 7A coordinates neutrophil response during pulmonary inflammation and sepsis
2024-03-15

Abstract Pulmonary defense mechanisms are critical for host integrity during pneumonia and sepsis. This defense is fundamentally dependent on the activation of neutrophils during the innate immune response. Recent work has shown that semaphorin 7A (Sema7A) holds significant impact on platelet function, yet its role on neutrophil function within the lung is not well understood. This study aimed to identify the role of Sema7A during pulmonary inflammation and sepsis. In patients with acute respiratory distress syndrome (ARDS), we were able to show a correlation between Sema7A and oxygenation levels. During subsequent workup, we found that Sema7A binds to the neutrophil PlexinC1 receptor, increasing integrins, and L-selectin on neutrophils. Sema7A prompted neutrophil chemotaxis in vitro and the formation of platelet-neutrophil complexes in vivo. We also observed altered adhesion and transmigration of neutrophils in Sema7A−/−animals in the lung during pulmonary inflammation. This effect resulted in increased number of neutrophils in the interstitial space of Sema7A−/− animals but reduced numbers of neutrophils in the alveolar space during pulmonary sepsis. This finding was associated with significantly worse outcome of Sema7A−/− animals in a model of pulmonary sepsis. Sema7A has an immunomodulatory effect in the lung, affecting pulmonary sepsis and ARDS. This effect influences the response of neutrophils to external aggression and might influence patient outcome. This trial was registered at www.ClinicalTrials.gov as #NCT02692118.
Application of immersive virtual reality for assessing chronic neglect in individuals with stroke: the immersive virtual road-crossing task
2024-03-15

Our findings suggest that a virtual road crossing task, such as iVRoad, has the potential to identify subtle symptoms of neglect by providing virtual scenarios that more closely resemble the demands and challenges of everyday life. iVRoad is an immersive, naturalistic virtual reality task that can measure clinically relevant behavioral variance and identify discrete neglect symptoms.
Phototrophic Fe( II ) oxidation benefits from light/dark cycles
2024-03-15

Abstract Phototrophic Fe(II)‐oxidizers use Fe(II) as electron donor for CO 2 fixation thus linking Fe(II) oxidation, ATP formation, and growth directly to the availability of sunlight. We compared the effect of short (10 h light/14 h dark) and long (2–3 days light/2–3 days dark) light/dark cycles to constant light conditions for the phototrophic Fe(II)‐oxidizer Chlorobium ferrooxidans KoFox. Fe(II) oxidation was completed first in the setup with constant light (9 mM Fe(II) oxidised within 8.9 days) compared to the light/dark cycles but both short and long light/dark cycles showed faster maximum Fe(II) oxidation rates. In the short and long cycle, Fe(II) oxidation rates reached 3.5 ± 1.0 and 2.6 ± 0.3 mM/d, respectively, compared to 2.1 ± 0.3 mM/d in the constant light setup. Maximum Fe(II) oxidation was significantly faster in the short cycle compared to the constant light setup. Cell growth reached roughly equivalent cell numbers across all three light conditions (from 0.2–2.0 × 10 6 cells/mL to 1.1–1.4 × 10 8 cells/mL) and took place in both the light and dark phases of incubation. SEM images showed different mineral structures independent of the light setup and 57 Fe Mössbauer spectroscopy confirmed the formation of poorly crystalline Fe(III) oxyhydroxides (such as ferrihydrite) in all three setups. Our results suggest that periods of darkness have a significant impact on phototrophic Fe(II)‐oxidizers and significantly influence rates of Fe(II) oxidation.
Reliability and Accuracy of the Outerbridge Classification in Staging of Cartilage Defects
2024-03-15

Objective The decision on whether or not and how to treat a local cartilage defect is still made intraoperatively based on the visual presentation of the cartilage and findings from indentations with an arthroscopic probe. The treatment decision is then usually based on grading according to established classifications systems, which, therefore, need to have high reliability and accuracy. The aim of the present study was to evaluate the reliability and accuracy of the Outerbridge classification in staging cartilage defects. Methods We performed an observer arthroscopic study using the Outerbridge classification on seven fresh‐frozen human cadaveric knees, which collectively exhibited nine cartilage defects. To evaluate accuracy, defect severity was verified through histological examination. Interrater and intrarater reliabilites were calculated using Cohen's kappa and the intra‐class correlation coefficient (ICC 3.1). Results The interrater and intrarater reliability for the Outerbridge classification ranged from poor to substantial, with 0.24 ≤ κ ≤ 0.70 and κ = 0.55 to κ = 0.66, respectively. The accuracy evaluated by comparison with the histological examination was 63% overall. The erroneous evaluations were, however, still often at the discrimination of grade 2 and 3. We did not find any relationship between higher experience and accuracy or intraobserver reliability. Taken together, these results encourage surgeons to further use diagnostic arthroscopy for evaluating cartilage lesions. Nevertheless, especially in grade 2 and 3, deviations from the histology were observed. This is, however, the point where a decision is made on whether to surgically address the defect or not. Conclusion Diagnostic arthroscopy is the standard for cartilage lesion assessment, yet interobserver reliability is fair to substantial. Caution is warranted in interpreting varied observer results. The accuracy of the “simpler” Outerbridge classification is insufficient compared to histological examinations, highlighting the need for improved techniques in guideline‐based intraoperative decision‐making.
Gaze-based attention network analysis in a virtual reality classroom
2024-03-15

This article provides a step-by-step guideline for measuring and analyzing visual attention in 3D virtual reality (VR) environments based on eye-tracking data. We propose a solution to the challenges of obtaining relevant eye-tracking information in a dynamic 3D virtual environment and calculating interpretable indicators of learning and social behavior. With a method called "gaze-ray casting," we simulated 3D-gaze movements to obtain information about the gazed objects. This information was used to create graphical models of visual attention, establishing attention networks. These networks represented participants' gaze transitions between different entities in the VR environment over time. Measures of centrality, distribution, and interconnectedness of the networks were calculated to describe the network structure. The measures, derived from graph theory, allowed for statistical inference testing and the interpretation of participants' visual attention in 3D VR environments. Our method provides useful insights when analyzing students' learning in a VR classroom, as reported in a corresponding evaluation article with <i>N</i> = 274 participants. •Guidelines on implementing gaze-ray casting in VR using the Unreal Engine and the HTC VIVE Pro Eye.•Creating gaze-based attention networks and analyzing their network structure.•Implementation tutorials and the Open Source software code are provided via OSF: https://osf.io/pxjrc/?view_only=1b6da45eb93e4f9eb7a138697b941198.
A compositional and technological reassessment of the function of potters’ marks on Early Bronze Age sherds from Tell el-‘Abd, Syria
2024-03-15

A highly distinctive feature of the Early Bronze Age ceramic assemblage of the site of Tell el-‘Abd in northern Syria is the presence of large numbers of pots that were incised with a diverse range of symbols prior to firing. Several hypotheses have been proposed to explain the function of such ceramic “potters’ marks”. One is that they functioned as a signature or trademark used by potters or workshops to identify their work. Another possibility is that they were used for quality control or accounting purposes during manufacture. Alternatively, they may have signified vessels intended for specific customers, or the size or contents of the vessels. In the case of the Tell el-‘Abd potters’ marks, distinguishing between these possibilities has proven difficult based upon their macroscopic examination and archaeological context alone. The present research, therefore, attempts to shed further light on the function of the potters’ marks by studying the clay paste recipes of 33 ceramic samples using scientific methods. Thin section petrography, instrumental geochemistry and scanning electron microscopy have been used to characterise and classify sherds according to their raw materials and manufacturing technology. This has been compared to the type of potters’ mark and other archaeological information in order to test the hypotheses that the distinctive ceramic markings signified ceramics made at different production centres or distinguished between different artisans operating at the same workshop.
Effect of Breastfeeding Duration on Coagulation in Women With and Without History of Gestational Diabetes Mellitus
2024-03-15

Abstract Context Breastfeeding is associated with a reduced maternal risk for cardiovascular diseases (CVDs). Objective Since the underlying mechanisms are still poorly understood, we here examined the effect of breastfeeding on the plasmatic coagulation system in women with and without history of gestational diabetes mellitus (GDM). Methods A total of 76 participants of the German Gestational Diabetes Study (PREG; NCT04270578) were examined 14 months (interquartile range [IQR], 12-26 months) after delivery with a 5-point oral glucose tolerance test. Global coagulation tests, prothrombotic coagulation proteins (FII/FVII/FVIII/FIX), antithrombotic proteins (antithrombin, protein C/S), and endothelial markers (von Willebrand factor and plasminogen activator inhibitor 1) were determined. The Framingham risk score was used to estimate the 10-year CV risk. The effect of breastfeeding duration on coagulation was analyzed using multivariable linear models. Results The mean duration of breastfeeding was 11 months (IQR, 7-14 months). Overall, longer duration of breastfeeding was associated with lower CV risk (Framingham risk score; P = .05) and was negatively associated with FIX (P = .018). We detected an interaction between previous GDM and breastfeeding duration for FIX (PInteraction = .017): Only in women with GDM history was the duration of breastfeeding negatively associated with FIX activity (P = .016). This association persisted in statistical models adjusted for age, body mass index, insulin sensitivity, and C-reactive protein. The duration of breastfeeding was not associated with anticoagulant proteins and endothelial markers. Conclusion Longer duration of breastfeeding is associated with lower CV risk and an improved coagulation profile. Women with GDM history appear to benefit particularly from prolonged breastfeeding.
Understanding monogenic Parkinson's disease at a global scale
2024-03-15

Until recently, about three-quarters of all monogenic Parkinson's disease (PD) studies were performed in European/White ancestry, thereby severely limiting our insights into genotype-phenotype relationships at global scale. The first systematic approach to embrace monogenic PD worldwide, The Michael J. Fox Foundation Global Monogenic PD (MJFF GMPD) Project, contacted authors of publications reporting individuals carrying pathogenic variants in known PD-causing genes. In contrast, the Global Parkinson's Genetics Program's (GP2) Monogenic Network took a different approach by targeting PD centers not yet represented in the medical literature. Here, we describe combining both efforts in a "merger project" resulting in a global monogenic PD cohort with build-up of a sustainable infrastructure to identify the multi-ancestry spectrum of monogenic PD and enable studies of factors modifying penetrance and expression of monogenic PD. This effort demonstrates the value of future research based on team science approaches to generate comprehensive and globally relevant results.