julilili42/papers huggingface dataset:
Radiation Dose Reduction in CT Torsion Measurement of the Lower Limb: Introduction of a New Ultra-Low Dose Protocol
2021-07-03

This study analyzed the radiation exposure of a new ultra-low dose (ULD) protocol compared to a high-quality (HQ) protocol for CT-torsion measurement of the lower limb. The analyzed patients (n = 60) were examined in the period March to October 2019. In total, 30 consecutive patients were examined with the HQ and 30 consecutive patients with the new ULD protocol comprising automatic tube voltage selection, automatic exposure control, and iterative image reconstruction algorithms. Radiation dose parameters as well as the contrast-to-noise ratio (CNR) and diagnostic confidence (DC; rated by two radiologists) were analyzed and potential predictor variables, such as body mass index and body volume, were assessed. The new ULD protocol resulted in significantly lower radiation dose parameters, with a reduction of the median total dose equivalent to 0.17 mSv in the ULD protocol compared to 4.37 mSv in the HQ protocol (p &lt; 0.001). Both groups showed no significant differences in regard to other parameters (p = 0.344–0.923). CNR was 12.2% lower using the new ULD protocol (p = 0.033). DC was rated best by both readers in every HQ CT and in every ULD CT. The new ULD protocol for CT-torsion measurement of the lower limb resulted in a 96% decrease of radiation exposure down to the level of a single pelvic radiograph while maintaining good image quality.
3D 31P MRSI of the human brain at 9.4 Tesla: Optimization and quantitative analysis of metabolic images
2021-07-04

Purpose To present 31 P whole brain MRSI with a high spatial resolution to probe quantitative tissue analysis of 31 P MRSI at an ultrahigh field strength of 9.4 Tesla. Methods The study protocol included a 31 P MRSI measurement with an effective resolution of 2.47 mL. For SNR optimization, the nuclear Overhauser enhancement at 9.4 Tesla was investigated. A sensitivity correction was achieved by applying a low rank approximation of the γ‐adenosine triphosphate signal. Group analysis and regression on individual volunteers were performed to investigate quantitative concentration differences between different tissue types. Results Differences in gray and white matter tissue 31 P concentrations could be investigated for 12 different 31 P resonances. In addition, the first highly resolved quantitative MRSI images measured at B 0 = 9.4 Tesla of 31 P detectable metabolites with high SNR could be presented. Conclusion With an ultrahigh field strength B 0 = 9.4 Tesla, 31 P MRSI moves further toward quantitative metabolic imaging, and subtle differences in concentrations between different tissue types can be detected.
Performance of the new FlashCam-based camera in the 28m telescope of H.E.S.S.
2021-07-04

In October 2019, the central 28 m telescope of the H.E.S.S. experiment has\\nbeen upgraded with a new camera. The camera is based on the FlashCam design\\nwhich has been developed in view of a possible future implementation in the\\nMedium-Sized Telescopes of the Cherenkov Telescope Array (CTA), with emphasis\\non cost and performance optimization and on reliability. The fully digital\\ndesign of the trigger and readout system makes it possible to operate the\\ncamera at high event rates and to precisely adjust and understand the trigger\\nsystem. The novel design of the front-end electronics achieves a dynamic range\\nof over 3,000 photoelectrons with only one electronics readout circuit per\\npixel. Here we report on the performance parameters of the camera obtained\\nduring the first year of operation in the field, including operational\\nstability and optimization of calibration algorithms.\\n
Food-Derived Bioactive Peptides: A Promising Substitute to Chemosynthetic Drugs Against the Dysregulated Renin-Angiotensin System in COVID-19 Patients
2021-07-04

AbstractCoronavirus disease-19 (COVID-19) pandemic is a global threat caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The viral infection dysregulates the functions of the renin-angiotensin system (RAS) through an interaction between SARS-CoV-2 spike protein and angiotensin-converting enzyme 2 (ACE2), leading to an upregulated level of Angiotensin II (Ang II) in blood plasma. The enhanced level of Ang II may contribute to various pathophysiological events, including vasoconstriction, oxidative stress, endothelial dysfunction, inflammation, beta-cell dysfunction, and many others. These phenomena are associated with developing multiple chronic diseases, including hypertension, cardiovascular disease, diabetes, lung disease, renal disease, and many other comorbidities in COVID-19 patients. Thus, the SARS-CoV-2 infection may contribute to severe conditions and higher mortality in COVID-19 patients with underlying comorbidities. Several synthetic drugs, especially RAS blockades, are currently prescribed to COVID-19 patients to minimize the severity of these comorbidities by limiting the deleterious effects of Ang II. However, these chemosynthetic drugs are limited by several side effects such as persistent cough, fetal abnormalities, hepatic disorder as well as promotion in the occurrence of new chronic diseases. These drawbacks raise an investigation to explore comparatively safe alternatives for COVID-19 patients. From this point of view, we have anticipated that applications of multifunctional food-derived bioactive peptides could be a promising approach through their preventive and therapeutic actions against underlying chronic complications in COVID-19 patients. This review enlightened the disease preventive and immunomodulatory effects of food-derived bioactive peptides that may enhance the survivability and vitality of COVID-19 patients with chronic complications.Keywords: Food-derived bioactive peptideschronic complicationsSARS-CoV-2renin-angiotensin system
Single-domain antibodies for targeting, detection andin vivoimaging of human CD4+cells
2021-07-04

Abstract The advancement of new immunotherapies necessitates appropriate probes to monitor the presence and distribution of distinct immune cell populations. Considering the key role of CD4 + T cells in regulating immunological processes, we generated novel single-domain antibodies (nanobodies, Nbs) that specifically recognize human CD4. After in depth analysis of their binding properties, recognized epitopes, and effects on T cell proliferation, activation and cytokine release, we selected CD4 Nbs that did not interfere with crucial T cell processes in vitro and converted them into immune tracers for non-invasive molecular imaging. By optical imaging, we demonstrate the ability of a high-affinity CD4-Nb to specifically visualize CD4 + cells in vivo using a xenograft model. Furthermore, time-resolved immune positron emission tomography (immunoPET) of a human CD4 knock-in mouse model showed rapid accumulation of 64 Cu-radiolabeled CD4-Nb in CD4 + T cell-rich tissues. We propose that the CD4 Nbs presented here could serve as versatile probes for stratifying patients and monitoring individual immune responses during personalized immunotherapy in both cancer and inflammatory diseases.
A 51,000-year-old engraved bone reveals Neanderthals’ capacity for symbolic behaviour
2021-07-05

While there is substantial evidence for art and symbolic behaviour in early Homo sapiens across Africa and Eurasia, similar evidence connected to Neanderthals is sparse and often contested in scientific debates. Each new discovery is thus crucial for our understanding of Neanderthals' cognitive capacity. Here we report on the discovery of an at least 51,000-year-old engraved giant deer phalanx found at the former cave entrance of Einhornhöhle, northern Germany. The find comes from an apparent Middle Palaeolithic context that is linked to Neanderthals. The engraved bone demonstrates that conceptual imagination, as a prerequisite to compose individual lines into a coherent design, was present in Neanderthals. Therefore, Neanderthal's awareness of symbolic meaning is very likely. Our findings show that Neanderthals were capable of creating symbolic expressions before H. sapiens arrived in Central Europe.
The Sedimentary Geochemistry and Paleoenvironments Project
2021-07-05

Geobiology explores how Earth's system has changed over the course of geologic history and how living organisms on this planet are impacted by or are indeed causing these changes. For decades, geologists, paleontologists, and geochemists have generated data to investigate these topics. Foundational efforts in sedimentary geochemistry utilized spreadsheets for data storage and analysis, suitable for several thousand samples, but not practical or scalable for larger, more complex datasets. As results have accumulated, researchers have increasingly gravitated toward larger compilations and statistical tools. New data frameworks have become necessary to handle larger sample sets and encourage more sophisticated or even standardized statistical analyses.&#13;\\n&#13;\\nIn this paper, we describe the Sedimentary Geochemistry and Paleoenvironments Project (SGP; Figure 1), which is an open, community-oriented, database-driven research consortium. The goals of SGP are to (1) create a relational database tailored to the needs of the deep-time (millions to billions of years) sedimentary geochemical research community, including assembling and curating published and associated unpublished data; (2) create a website where data can be retrieved in a flexible way; and (3) build a collaborative consortium where researchers are incentivized to contribute data by giving them priority access and the opportunity to work on exciting questions in group papers. Finally, and more idealistically, the goal was to establish a culture of modern data management and data analysis in sedimentary geochemistry. Relative to many other fields, the main emphasis in our field has been on instrument measurement of sedimentary geochemical data rather than data analysis (compared with fields like ecology, for instance, where the post-experiment ANOVA (analysis of variance) is customary). Thus, the longer-term goal was to build a collaborative environment where geobiologists and geologists can work and learn together to assess changes in geochemical signatures through Earth history.
Tetrahedra of varying density and their applications
2021-07-05

Abstract We propose concepts to utilize basic mathematical principles for computing the exact mass properties of objects with varying densities. For objects given as 3D triangle meshes, the method is analytically accurate and at the same time faster than any established approximation method. Our concept is based on tetrahedra as underlying primitives, which allows for the object’s actual mesh surface to be incorporated in the computation. The density within a tetrahedron is allowed to vary linearly, i.e., arbitrary density fields can be approximated by specifying the density at all vertices of a tetrahedral mesh. Involved integrals are formulated in closed form and can be evaluated by simple, easily parallelized, vector-matrix multiplications. The ability to compute exact masses and centroids for objects of varying density enables novel or more exact solutions to several interesting problems: besides the accurate analysis of objects under given density fields, this includes the synthesis of parameterized density functions for the make-it-stand challenge or manufacturing of objects with controlled rotational inertia. In addition, based on the tetrahedralization of Voronoi cells we introduce a precise method to solve <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mi>L</mml:mi><mml:mrow><mml:mn>2</mml:mn><mml:mo>|</mml:mo><mml:mi>∞</mml:mi></mml:mrow></mml:msub></mml:math> Lloyd relaxations by exact integration of the Chebyshev norm. In the context of additive manufacturing research, objects of varying density are a prominent topic. However, current state-of-the-art algorithms are still based on voxelizations, which produce rather crude approximations of masses and mass centers of 3D objects. Many existing frameworks will benefit by replacing approximations with fast and exact calculations. Graphic abstract
Genetic Overlap Between Alzheimer’s Disease and Depression Mapped Onto the Brain
2021-07-05

Background: Alzheimer’s disease (AD) and depression are debilitating brain disorders that are often comorbid. Shared brain mechanisms have been implicated, yet findings are inconsistent, reflecting the complexity of the underlying pathophysiology. As both disorders are (partly) heritable, characterising their genetic overlap may provide aetiological clues. While previous studies have indicated negligible genetic correlations, this study aims to expose the genetic overlap that may remain hidden due to mixed directions of effects. Methods: We applied Gaussian mixture modelling, through MiXeR, and conjunctional false discovery rate (cFDR) analysis, through pleioFDR, to genome-wide association study (GWAS) summary statistics of AD ( n = 79,145) and depression ( n = 450,619). The effects of identified overlapping loci on AD and depression were tested in 403,029 participants of the UK Biobank (UKB) (mean age 57.21, 52.0% female), and mapped onto brain morphology in 30,699 individuals with brain MRI data. Results: MiXer estimated 98 causal genetic variants overlapping between the 2 disorders, with 0.44 concordant directions of effects. Through pleioFDR, we identified a SNP in the TMEM106B gene, which was significantly associated with AD ( B = −0.002, p = 9.1 × 10 –4 ) and depression ( B = 0.007, p = 3.2 × 10 –9 ) in the UKB. This SNP was also associated with several regions of the corpus callosum volume anterior ( B &amp;gt; 0.024, p &amp;lt; 8.6 × 10 –4 ), third ventricle volume ventricle ( B = −0.025, p = 5.0 × 10 –6 ), and inferior temporal gyrus surface area ( B = 0.017, p = 5.3 × 10 –4 ). Discussion: Our results indicate there is substantial genetic overlap, with mixed directions of effects, between AD and depression. These findings illustrate the value of biostatistical tools that capture such overlap, providing insight into the genetic architectures of these disorders.
Transcriptional response of mushrooms to artificial sun exposure
2021-07-05

Abstract Climate change causes increased tree mortality leading to canopy loss and thus sun‐exposed forest floors. Sun exposure creates extreme temperatures and radiation, with potentially more drastic effects on forest organisms than the current increase in mean temperature. Such conditions might potentially negatively affect the maturation of mushrooms of forest fungi. A failure of reaching maturation would mean no sexual spore release and, thus, entail a loss of genetic diversity. However, we currently have a limited understanding of the quality and quantity of mushroom‐specific molecular responses caused by sun exposure. Thus, to understand the short‐term responses toward enhanced sun exposure, we exposed mushrooms of the wood‐inhabiting forest species Lentinula edodes, while still attached to their mycelium and substrate, to artificial solar light (ca. 30°C and 100,000 lux) for 5, 30, and 60 min. We found significant differentially expressed genes at 30 and 60 min. Eukaryotic Orthologous Groups (KOG) class enrichment pointed to defense mechanisms. The 20 most significant differentially expressed genes showed the expression of heat‐shock proteins, an important family of proteins under heat stress. Although preliminary, our results suggest mushroom‐specific molecular responses to tolerate enhanced sun exposure as expected under climate change. Whether mushroom‐specific molecular responses are able to maintain fungal fitness under opening forest canopies remains to be tested.
Metabolic Screening of Cytotoxic T-cell Effector Function Reveals the Role of CRAC Channels in Regulating Lethal Hit Delivery
2021-07-05

Abstract Cytotoxic T lymphocytes (CTL) mediate cytotoxicity toward tumor cells by multistep cell–cell interactions. However, the tumor microenvironment can metabolically perturb local CTL effector function. CTL activity is typically studied in two-dimensional (2D) liquid coculture, which is limited in recapitulating the mechanisms and efficacy of the multistep CTL effector response. We here developed a microscopy-based, automated three-dimensional (3D) interface coculture model suitable for medium-throughput screening to delineate the steps and CTL effector mechanisms affected by microenvironmental perturbation. CTL effector function was compromised by deregulated redox homeostasis, deficient mitochondrial respiration, as well as dysfunctional Ca2+ release-activated Ca2+ (CRAC) channels. Perturbation of CRAC channel function dampened calcium influx into CTLs, delayed CTL degranulation, and lowered the frequency of sublethal hits (i.e., additive cytotoxicity) delivered to the target cell. Thus, CRAC channel activity controls both individual contact efficacy and CTL cooperativity required for serial killing of target cells. The multistep analysis of CTL effector responses in 3D coculture will facilitate the identification of immune-suppressive mechanisms and guide the rational design of targeted intervention strategies to restore CTL effector function.
Making the Invisible Stratigraphy Visible: A Grid-Based, Multi-Proxy Geoarchaeological Study of Umhlatuzana Rockshelter, South Africa
2021-07-05

Umhlatuzana rockshelter is an archaeological site with an occupational record covering the Middle Stone Age, Later Stone Age, and Iron Age. The presence of both Middle and Later Stone Age assemblages makes Umhlatuzana the ideal location for the study of the MSA–LSA transition (20–40 ka) in southern Africa. This transitional period is characterized by important modifications in stone tool technology, from prepared core technology to a toolkit based on microlith production. These changes are argued to have occurred in response to changes in climate and environment leading up to the Last Glacial Maximum. The deposits bearing the transitional assemblages at Umhlatuzana rockshelter appear homogeneous with no visible stratigraphic boundaries. This study integrates geoarchaeological techniques in order to explore fine-resolution geochemical differentiations of the sediments that are macroscopically invisible, and that will provide insight into (post-)depositional processes over time. Samples were systematically retrieved from the western profile of the site following a grid-based sampling strategy and analyzed for pH, elemental composition (XRF), and Magnetic Susceptibility. Additionally, the results were integrated with preliminary micromorphological observations. Our study reveals a steady, gradual change in the geochemistry of the deposits throughout the Pleistocene, related to a combination of environmental change and occupation intensity. We suggest that the part of the sequence reported to bear Middle to Later Stone Age transitional industries is characterized by wetter environmental conditions compared to the underlying deposits. Additionally, we support results from previous studies that excluded large scale post-depositional movement of the sedimentary sequence. Our study offers a successful multi-proxy approach to systematically sample and study archaeological deposits at the macro and micro scale, integrating a variety of geoarchaeological techniques. The approach provides insight into the depositional and post-depositional history of the site, and allows for questions of stratigraphic integrity, anthropogenic input, preservation, and environmental change to be addressed.
Work between Obligation and Right in Muslim Culture: Is There a Paradigm Shift?
2021-07-05

Abstract The paper starts from the premise that the revolutions in the countries of the so-called Arab Spring (2011 and onwards) brought about an important shift in the understanding of right and duty. This trend is related to the transformation of the relationship of the ruler and the ruled in those countries as well as in the perception of work ethics. Whereas the systems of these countries have consistently considered work as a duty of citizens and encouraged them to work hard for the development and prospering of the state, these popular movements have transformed work from a duty and responsibility on the shoulders of the individual into a right of the individual that can be claimed from the state, which is trying to evade its responsibilities – including the duty to provide job opportunities for its citizens. The researcher does not claim to present a comprehensive outline of the topic; this is rather a preliminary approach that deserves further study and analysis. What happened is not necessarily caused by direct contact with the “West” or being influenced by “Western” political philosophy, as we can find hints and origins for this transformation in both classical and modern Islamic moral thought. This paper presents examples of the relationship of right and duty from different historical periods.
Establishing a controlled hookworm human infection (CHHI) model for Africa: A report from the stakeholders meeting held in Lambaréné, Gabon, November 10–11, 2019
2021-07-05

Abstract Background Hookworm is a major contributor to worldwide disease burden with over 230 million people infected. It has been identified as one of the Neglected Tropical Diseases that can be controlled and even eliminated through mass drug administration and other effective interventions. Mathematical models have shown that hookworm can only be eliminated via a vaccine. Controlled Hookworm Human Infection (CHHI) models can facilitate rapid development of vaccines and drugs. Methods As a first step towards the establishment of CHHI in Africa, we held a stakeholders meeting in Lamberene, Gabon from 10 to 11 November 2019. Results Discussions revolved around the roles of the different regulatory institutions concerned; the need to strengthen existing regulatory capacity and the role of legislation; creating Gabon-specific ethical guidelines to govern Controlled Human Infection (CHI) studies; development of a study protocol; consideration of cultural and social peculiarities; the need for regular joint review meetings between interested parties throughout the process of protocol implementation; and participant compensation. Moreover, operational considerations concerning the introduction of CHHI in Gabon include the use of the local strain of hookworm for the challenge infections, capacity building for the local production of challenge material, and the establishment of adequate quality assurance procedures. Conclusion The workshop addressed several of the anticipated hurdles to the successful implementation of CHHI in Gabon. It is our aim that this report will stimulate interest in the implementation of this model in the sub-Saharan African setting.
Symmetric multiqudit states: Stars, entanglement, and rotosensors
2021-07-06

A constellation of Majorana stars represents an arbitrary pure quantum state of dimension or a permutation-symmetric state of a system consisting of qubits. We generalize the latter construction to represent in a similar way an arbitrary symmetric pure state of subsystems with levels each. For , such states are equivalent, as far as rotations are concerned, to a collection of various spin states, with definite relative complex weights. Following Majorana's lead, we introduce a multiconstellation, consisting of the Majorana constellations of the above spin states, augmented by an auxiliary, "spectator" constellation, encoding the complex weights. Examples of stellar representations of symmetric states of four qutrits, and two spin- systems, are presented. We revisit the Hermite and Murnaghan isomorphisms, which relate multipartite states of various spins, number of parties, and even symmetries. We show how the tools introduced can be used to analyze multipartite entanglement and to identify optimal quantum rotosensors, i.e., pure states which are maximally sensitive to rotations around a specified axis, or averaged over all axes.