julilili42/papers huggingface dataset:
Current sampling and sequencing biases of Lassa mammarenavirus limit inference from phylogeography and molecular epidemiology in Lassa Fever endemic regions
2023-06-22

Abstract Lassa fever (LF) is a potentially lethal viral haemorrhagic infection of humans caused by Lassa mammarenavirus (LASV). It is an important endemic zoonotic disease in West Africa with growing evidence for increasing frequency and sizes of outbreaks. Phylogeographic and molecular epidemiology methods have projected expansion of the Lassa fever endemic zone in the context of future global change. The Natal multimammate mouse ( Mastomys natalensis ) is the predominant LASV reservoir, with few studies investigating the role of other animal species. To explore host sequencing biases, all LASV nucleotide sequences and associated metadata available on GenBank (n = 2,298) were retrieved. Most data originated from Nigeria (54%), Guinea (20%) and Sierra Leone (14%). Data from non-human hosts (n = 703) were limited and only 69 sequences encompassed complete genes. We found a strong positive correlation between the number of confirmed human cases and sequences at the country level ( r = 0.93 (95% Confidence Interval = 0.71 - 0.98), p &lt; 0.001) but no correlation exists between confirmed cases and the number of available rodent sequences ( r = -0.019 (95% C.I. -0.71 - 0.69), p = 0.96). Spatial modelling of sequencing effort highlighted current biases in locations of available sequences, with increased effort observed in Southern Guinea and Southern Nigeria. Phylogenetic analyses showed geographic clustering of LASV lineages, suggestive of isolated events of human-to-rodent transmission and the emergence of currently circulating strains of LASV from the year 1498 in Nigeria. Overall, the current study highlights significant geographic limitations in LASV surveillance, particularly, in non-human hosts. Further investigation of the non-human reservoir of LASV, alongside expanded surveillance, are required for precise characterisation of the emergence and dispersal of LASV. Accurate surveillance of LASV circulation in non-human hosts is vital to guide early detection and initiation of public health interventions for future Lassa fever outbreaks.
Non-pollen palynomorph and palynofacies assemblages from the Lower Cretaceous of Iraq: A glimpse into palaeobiology and palaeoenvironment
2023-06-22

Atfy, Haytham El, Abeed, Qusay, Uhl, Dieter (2023): Non-pollen palynomorph and palynofacies assemblages from the Lower Cretaceous of Iraq: A glimpse into palaeobiology and palaeoenvironment. Geodiversitas 45 (11): 353-366, DOI: 10.5252/geodiversitas2023v45a11
Closing the loop: Autonomous experiments enabled by machine-learning-based online data analysis in synchrotron beamline environments
2023-06-22

Recently, there has been significant interest in applying machine learning (ML) techniques to X-ray scattering experiments, which proves to be a valuable tool for enhancing research that involves large or rapidly generated datasets. ML allows for the automated interpretation of experimental results, particularly those obtained from synchrotron or neutron facilities. The speed at which ML models can process data presents an important opportunity to establish a closed-loop feedback system, enabling real-time decision-making based on online data analysis. In this study, we describe the incorporation of ML into a closed-loop workflow for X-ray reflectometry (XRR), using the growth of organic thin films as an example. Our focus lies on the beamline integration of ML-based online data analysis and closed-loop feedback. We present solutions that provide an elementary data analysis in real time during the experiment without introducing the additional software dependencies in the beamline control software environment. Our data demonstrates the accuracy and robustness of ML methods for analyzing XRR curves and Bragg reflections and its autonomous control over a vacuum deposition setup.
Qualifying Mediterranean connectivity: Byzantium and the Franks during the seventh century
2023-06-22

In the last two decades, historians researching the seventh century ce have increasingly emphasized mobility, communications and connectivity across the Mediterranean world that supposedly included close contacts between the Franks and Byzantium. These studies, however, rely often on optimistic, maximum interpretations of the comparatively sparse source base, and have not always precisely distinguished between different forms of mobility and connectivity. This article argues that a closer examination of the actual cultural and political consequences of mobility and contact between Byzantium and Gaul is required, and that the possibility of discontinuity and disintegration should not be disregarded. In our reading of the sources, we deliberately adopt a sceptical, methodologically cautious minimal position: the textual sources can be interpreted as showing that, while individual, sporadic contacts across the Mediterranean continued to exist, there was no established, continuous practice of communications between Byzantium and Gaul.
Results on sub-GeV dark matter from a 10 eV threshold CRESST-III silicon detector
2023-06-23

We present limits on the spin-independent interaction cross section of dark matter particles with silicon nuclei, derived from data taken with a cryogenic calorimeter with 0.35 g target mass operated in the CRESST-III experiment. A baseline nuclear recoil energy resolution of (1.36 ± 0.05) eVnr, currently the lowest reported for macroscopic particle detectors, and a corresponding energy thresh-old of (10.0 ± 0.2) eVnr have been achieved, improving the sensitivity to light dark matter particles with masses below 160 MeV/c2 by a factor of up to 20 compared to previous results. We characterize the observed low energy excess, and we exclude noise triggers and radioactive contaminations on the crystal surfaces as dominant contributions.
Barriers and facilitators affecting treatment uptake behaviours for patients with eating disorders: A systematic review synthesising patient, caregiver and clinician perspectives
2023-06-23

Abstract Objective A significant treatment gap exists between persons affected by eating disorders (ED), and those engaging with treatment services. This systematic review aims to provide a thorough understanding of the barriers and facilitators affecting eating disorder treatment engagement, including a synthesis of the perspectives of patients, caregivers and healthcare professionals. Method This systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses guidelines. Studies were retrieved from three databases (PubMed, PsycInfo, Web of Science) and were screened and assessed independently by two raters. A thematic analysis was completed to determine the key barriers and facilitators reported by the included studies. Results A total of 73 studies were included. From these studies, 12 barriers and 13 facilitators were identified. Patients reported stigma, shame and guilt as the most prominent barrier affecting their engagement with treatment services. Meanwhile, caregivers and healthcare professionals reported a lack of eating disorder knowledge of clinicians as the most important barrier. Positive social support was cited as the most prominent facilitator to promote help‐seeking. Discussion Patients, caregivers and healthcare professionals experience a variety of barriers and facilitators to treatment uptake for ED. Interventions addressing barriers and facilitators could increase treatment engagement, including anti‐stigma campaigns and positive peer‐support interventions.
There is an obstetrical dilemma: Misconceptions about the evolution of human childbirth and pelvic form
2023-06-23

Abstract Compared to other primates, modern humans face high rates of maternal and neonatal morbidity and mortality during childbirth. Since the early 20th century, this “difficulty” of human parturition has prompted numerous evolutionary explanations, typically assuming antagonistic selective forces acting on maternal and fetal traits, which has been termed the “obstetrical dilemma.” Recently, there has been a growing tendency among some anthropologists to question the difficulty of human childbirth and its evolutionary origin in an antagonistic selective regime. Partly, this stems from the motivation to combat increasing pathologization and overmedicalization of childbirth in industrialized countries. Some authors have argued that there is no obstetrical dilemma at all, and that the difficulty of childbirth mainly results from modern lifestyles and inappropriate and patriarchal obstetric practices. The failure of some studies to identify biomechanical and metabolic constraints on pelvic dimensions is sometimes interpreted as empirical support for discarding an obstetrical dilemma. Here we explain why these points are important but do not invalidate evolutionary explanations of human childbirth. We present robust empirical evidence and solid evolutionary theory supporting an obstetrical dilemma, yet one that is much more complex than originally conceived in the 20th century. We argue that evolutionary research does not hinder appropriate midwifery and obstetric care, nor does it promote negative views of female bodies. Understanding the evolutionary entanglement of biological and sociocultural factors underlying human childbirth can help us to understand individual variation in the risk factors of obstructed labor, and thus can contribute to more individualized maternal care.
Evidence for direct interaction between the oncogenic proteins E6 and E7 of high-risk human papillomavirus (HPV)
2023-06-23

Human papillomaviruses (HPVs) are DNA tumor viruses that infect mucosal and cutaneous epithelial cells of more than 20 vertebrates. High-risk HPV causes about 5% of human cancers worldwide, and the viral proteins E6 and E7 promote carcinogenesis by interacting with tumor suppressors and interfering with many cellular pathways. As a consequence, they immortalize cells more efficiently in concert than individually. So far, the networks of E6 and E7 with their respective cellular targets have been studied extensively but independently. However, we hypothesized that E6 and E7 might also interact directly with each other in a novel interaction affecting HPV-related carcinogenesis. Here, we report a direct interaction between E6 and E7 proteins from carcinogenic HPV types 16 and 31. We demonstrated this interaction via cellular assays using two orthogonal methods: coimmunoprecipitation and flow cytometry-based FRET assays. Analytical ultracentrifugation of the recombinant proteins revealed that the stoichiometry of the E6/E7 complex involves two E7 molecules and two E6 molecules. In addition, fluorescence polarization showed that (I) E6 binds to E7 with a similar affinity for HPV16 and HPV31 (in the same micromolar range) and (II) that the binding interface involves the unstructured N-terminal region of E7. The direct interaction of these highly conserved papillomaviral oncoproteins may provide a new perspective for studying HPV-associated carcinogenesis and the overall viral life cycle.
A puzzle about first-person imagination
2023-06-23

Abstract It is easy to imagine being someone else from the first-person point of view. Such imaginings give rise to a puzzle. In this paper I explain what the puzzle is and then consider several existing attempts of solving the puzzle. I argue that these attempts are unsuccessful. I propose a Lewisian account of first-person imagination and make the case that this account solves the puzzle
Analysis of accretion disc structure and stability using open code for vertical structure
2023-06-23

ABSTRACT Radial structure of accretion discs around compact objects is often described using analytic approximations which are derived from averaging or integrating vertical structure equations. For non-solar chemical composition, partial ionization, or for supermassive black holes, this approach is not accurate. Additionally, radial extension of ‘analytically-described’ disc zones is not evident in many cases. We calculate vertical structure of accretion discs around compact objects, with and without external irradiation, with radiative and convective energy transport taken into account. For this, we introduce a new open Python code, allowing different equations of state and opacity laws, including tabular values. As a result, radial structure and stability ‘S-curves’ are calculated for specific disc parameters and chemical composition. In particular, based on more accurate power-law approximations for opacity in the disc, we supply new analytic formulas for the farthest regions of the hot disc around stellar-mass object. On calculating vertical structure of a self-irradiated disc, we calculate a self-consistent value of the irradiation parameter Cirr for stationary α-disc. We find that, for a fixed shape of the X-ray spectrum, Cirr depends weakly on the accretion rate but changes with radius, and the dependence is driven by the conditions in the photosphere and disc opening angle. The hot zone extent depends on the ratio between irradiating and intrinsic flux: corresponding relation for is obtained.
Spectrum and Frequency of Germline FANCM Protein-Truncating Variants in 44,803 European Female Breast Cancer Cases
2023-06-23

FANCM germline protein truncating variants (PTVs) are moderate-risk factors for ER-negative breast cancer. We previously described the spectrum of FANCM PTVs in 114 European breast cancer cases. In the present, larger cohort, we report the spectrum and frequency of four common and 62 rare FANCM PTVs found in 274 carriers detected among 44,803 breast cancer cases. We confirmed that p.Gln1701* was the most common PTV in Northern Europe with lower frequencies in Southern Europe. In contrast, p.Gly1906Alafs*12 was the most common PTV in Southern Europe with decreasing frequencies in Central and Northern Europe. We verified that p.Arg658* was prevalent in Central Europe and had highest frequencies in Eastern Europe. We also confirmed that the fourth most common PTV, p.Gln498Thrfs*7, might be a founder variant from Lithuania. Based on the frequency distribution of the carriers of rare PTVs, we showed that the FANCM PTVs spectra in Southwestern and Central Europe were much more heterogeneous than those from Northeastern Europe. These findings will inform the development of more efficient FANCM genetic testing strategies for breast cancer cases from specific European populations.
Reimagining Violence in the Brontë Myth: "Tales of Positive Violence and Crime" in Neo-Victorian Brontë Afterlives
2023-06-23

&amp;lt;p&amp;gt;This article argues that narratives of violence are fundamental to both the creation and dismantling of the Bront&amp;euml; myth. Perceptions of violence in the Bront&amp;euml; legacy have undergone a shift. Nineteenth-century responses initially deemed violence a coarse and unfeminine aspect of Anne, Charlotte, and Emily Bront&amp;euml;&amp;rsquo;s novels, but also one integral to the creation of their fictions and to visions of Haworth. Meanwhile, more recent neo-Victorian reimaginings of the Bront&amp;euml;s&amp;rsquo; works and lives often seek to reinstate and accentuate violence, partly to offer an apparently more &amp;lsquo;authentic&amp;rsquo; depiction of the books and their authors. This essay considers how current narratives of violence connected to the Bront&amp;euml;s can be contextualised through a focus on Elizabeth Gaskell&amp;rsquo;s &amp;lt;em&amp;gt;The Life of Charlotte Bront&amp;euml; &amp;lt;/em&amp;gt;(1857) and early sources central to the Bront&amp;euml; myth, arguing that, rather than demythologising the Bront&amp;euml;s, neo-Victorian representations of violence often revert to earlier myths in a process of &amp;lt;em&amp;gt;re&amp;lt;/em&amp;gt;-romanticisation.&amp;lt;/p&amp;gt;
Overexpression of the receptor-like kinase BIR1 gene causes SOBIR1- and EDS1-dependent cell death phenotypes in Arabidopsis
2023-06-23

Abstract The receptor-like kinase BAK1-INTERACTING RECEPTOR-LIKE KINASE 1 ( BIR1 ) functions as a negative regulator of multiple resistance signaling pathways in Arabidopsis thaliana . Previous studies showed that loss of BIR1 function leads to extensive cell death and activation of constitutive immune responses. Here, we use a dexamethasone (DEX)-inducible expression system to investigate the impact of BIR1 overexpression on plant growth and development and immune regulation. We show that, in the absence of microbes or microbe-derived elicitors/effectors, plants that overexpress BIR1 displayed cell death phenotypes that concur with the transcriptomic up-regulation of multiple immune pathways involved in pathogen perception and defense signal transduction. BIR1 overexpression has similar loss-of-function effects to BIR1 depletion in knockout plants, which suggests that proper BIR1 homeostasis requires a tight regulation of BIR1 expression within a functional threshold. We show that ENHANCED DISEASE SUSCEPTIBILITY 1 ( EDS1 ) and SUPPRESSOR OF BIR1-1 ( SOBIR1 ) are required for the effector-triggered immunity (ETI)-type cell death phenotypes associated with overexpression of BIR1 . Our data is then consistent with the current hypothesis by which loss of BIR1 regulation and/or integrity is sensed by one or several guarding resistance (NLR) proteins to initiate a cell death response, in which SOBIR1 cooperates with EDS1 to transduce signals downstream of R proteins. Summary Statement Regulation of the receptor-like kinase BIR1 has a strong impact on plant growth and development and immune homeostasis in Arabidopsis. BIR1 overexpression causes cell death-and senescence-like phenotypes that require EDS1 and SOBIR1 signaling pathways, and that resemble to those observed by BIR1 depletion.
A Novel Approach to Visualizing Olfactory Landscapes
2023-06-24

Abstract This article focuses on the exploration and mapping of olfactory landscapes. For this purpose, a brief introduction to the social and cultural significance of odors in the 'Western world', especially in the sciences and philosophy, is first given and the visuality paradigm of these societies is highlighted. Subsequently, olfactory landscapes are integrated into a basic social constructivist-phenomenological concept to create a theoretical basis for the discussion of these special landscapes. This is accompanied by a brief discussion of current approaches to smellscape survey and the particular mapping approach of Kate McLean (in comparison with the here used approach), which forms the basis for the mapping and presentation presented here. This presented approach was developed and tested in a master's thesis on the smellscape of Christmas and Christmas markets. An extended signature system and the detailed procedure for a smellwalk are presented.
Comparison of Resting-State EEG Network Analyses With and Without Parallel MRI in Genetic Generalized Epilepsy
2023-06-24

Abstract Genetic generalized epilepsy (GGE) is conceptualized as a brain disorder involving distributed bilateral networks. To study these networks, simultaneous EEG-fMRI measurements can be used. However, inside-MRI EEG suffers from strong MR-related artifacts; it is not established whether EEG-based metrics in EEG-fMRI resting-state measurements are suitable for the analysis of group differences at source-level. We evaluated the impact of the inside-MR measurement condition on statistical group comparisons of EEG on source-level power and functional connectivity in patients with GGE versus healthy controls. We studied the cross-modal spatial relation of statistical group differences in seed-based FC derived from EEG and parallel fMRI. We found a significant increase in power and a frequency-specific change in functional connectivity for the inside MR-scanner compared to the outside MR-scanner condition. For power, we found reduced group difference between GGE and controls both in terms of statistical significance as well as effect size. Group differences for ImCoh remained similar both in terms of statistical significance as well as effect size. We found increased seed-based FC for GGE patients from the thalamus to the precuneus cortex region in fMRI, and in the theta band of simultaneous EEG. Our findings suggest that the analysis of EEG functional connectivity based on ImCoh is suitable for MR-EEG, and that relative group difference in a comparison of patients with GGE against controls are preserved. Spatial correspondence of seed-based FC group differences between the two modalities was found for the thalamus.
Homo sapiens expanded into the Northern European Plains by 45,000 years ago
2023-06-24

&amp;lt;p&amp;gt;1,322 morphologically unidentified fragmentary bone specimens were analyzed using MALDI-TOF and a subset of 341 bone specimens with LC-MS/MS in order to characterize their proteome for species identification and potential hominin specimens related to the LRJ transitional period derived from the site Ilsenh&amp;ouml;hle&amp;nbsp;Ranis, Germany (50&amp;deg;39.7563&amp;rsquo;N, 11&amp;deg;33.9139&amp;rsquo;E).&amp;lt;/p&amp;gt;
Homo sapiens expanded into the Northern European Plains by 45,000 years ago
2023-06-24

1,322 morphologically unidentified fragmentary bone specimens were analyzed using MALDI-TOF and a subset of 341 bone specimens with LC-MS/MS in order to characterize their proteome for species identification and potential hominin specimens related to the LRJ transitional period derived from the site Ilsenhöhle Ranis, Germany (50°39.7563’N, 11°33.9139’E).
MR‐zero meets RARE MRI: Joint optimization of refocusing flip angles and neural networks to minimize T2‐induced blurring in spin echo sequences
2023-06-25

Purpose An end‐to‐end differentiable 2D Bloch simulation is used to reduce T 2 induced blurring in single‐shot turbo spin echo sequences, also called rapid imaging with refocused echoes (RARE) sequences, by using a joint optimization of refocusing flip angles and a convolutional neural network. Methods Simulation and optimization were performed in the MR‐zero framework. Variable flip angle train and DenseNet parameters were optimized jointly using the instantaneous transverse magnetization, available in our simulation, at a certain echo time, which serves as ideal blurring‐free target. Final optimized sequences were exported for in vivo measurements at a real system (3 T Siemens, PRISMA) using the Pulseq standard. Results The optimized RARE was able to successfully lower T 2 ‐induced blurring for single‐shot RARE sequences in proton density‐weighted and T 2 ‐weighted images. In addition to an increased sharpness, the neural network allowed correction of the contrast changes to match the theoretical transversal magnetization. The optimization found flip angle design strategies similar to existing literature, however, visual inspection of the images and evaluation of the respective point spread function demonstrated an improved performance. Conclusions This work demonstrates that when variable flip angles and a convolutional neural network are optimized jointly in an end‐to‐end approach, sequences with more efficient minimization of T 2 ‐induced blurring can be found. This allows faster single‐ or multi‐shot RARE MRI with longer echo trains.