julilili42/papers huggingface dataset:
Tripod Missions: Five Principles for Solving Society’s Most Pressing Challenges
2022-03-21

Abstract The COVID crisis has forced policymakers to design new and comprehensive rescue programmes under huge time pressure. This task has required innovative policy thinking and the pursuit of new kinds of collaboration. The handling of the pandemic, however, also provides valuable lessons on how to address some of society's other pressing challenges—above all climate change. ‘Tripod Missions’ provide a framework for turning the pandemic's lessons learned into a guide for tackling other major societal problems.
Assessment of Two Commonly used Dermal Regeneration Templates in a Swine Model without Skin Grafting
2022-03-21

In the medical care of partial and full-thickness wounds, autologous skin grafting is still the gold standard of dermal replacement. In contrast to spontaneous reepithelializing of superficial wounds, deep dermal wounds often lead to disturbing scarring, with cosmetically or functionally unsatisfactory results. However, modern wound dressings offer promising approaches to surface reconstruction. Against the background of our future aim to develop an innovative skin substitute, we investigated the behavior of two established dermal substitutes, a crosslinked and a non-crosslinked collagen biomatrix. The products were applied topically on a total of 18 full-thickness skin defects paravertebrally on the back of female Göttingen Minipigs—six control wounds remained untreated. The evaluation was carried out planimetrically (wound closure time) and histologically (neoepidermal cell number and epidermis thickness). Both treatment groups demonstrated significantly faster reepithelialization than the controls. The histologic examination verified the highest epidermal thickness in the crosslinked biomatrix-treated wounds, whereas the non-crosslinked biomatrix-treated wounds showed a higher cell density. Our data presented a positive influence on epidermal regeneration with the chosen dermis substitutes even without additional skin transplantation and, thus, without additional donor site morbidity. Therefore, it can be stated that the single biomatrix application might be used in a clinical routine with small wounds, which needs to be investigated further in a clinical setting to determine the size and depths of a suitable wound bed. Nevertheless, currently available products cannot solely achieve wound healing that is equal to or superior to autologous tissue. Thus, the overarching aim still is the development of an innovative skin substitute to manage surface reconstruction without additional skin grafting.
Vortex topology and the continuum limit of lattice gauge theories
2022-03-21

We study the stability of Z_2 topological vortex excitations in d+1 dimensional SU(2) Yang-Mills theory on the lattice at T=0. This is found to depend on d and on the coupling considered. We discuss the connection with lattice artifacts causing bulk transitions in the beta_A-beta_F plane and draw some conclusions regarding the continuum limit of the theory.
The Scalar Glueball in the Instanton Vacuum
2022-03-21

We study the contribution of instantons to the binding and the mass of the lightest scalar glueball, in gluondynamics. We show that the short-range correlations introduced by such non-perturbative vacuum fluctuations are sufficient to give raise to a scalar glueball bound-state, with mass in good agreement with the results of recent lattice calculations.
Future X-ray timing missions
2022-03-21

Thanks to the Rossi X-ray Timing Explorer (RXTE), it is now widely recognized that fast X-ray timing can be used to probe strong gravity fields around collapsed objects and constrain the equation of state of dense matter in neutron stars. We first discuss some of the outstanding issues which could be solved with an X-ray timing mission building on the great successes of RXTE and providing an order of magnitude better sensitivity. Then we briefly describe the 'Experiment for X-ray timing and Relativistic Astrophysics' (EXTRA) recently proposed to the European Space Agency as a follow-up to RXTE and the related US mission 'Relativistic Astrophysics Explorer' (RAE).
Research compendium for 'Bringing shape into focus: Assessing differences between blades and bladelets and their technological significance in 3D form'
2022-03-21

Abstract: Laminar technologies were adopted by Paleolithic foragers to produce a variable range of stone implements. Archaeologists have reconstructed the different reduction procedures involved in the production of laminar stone tools, often underlying a separation between the bigger blanks (i.e., blades) and smaller bladelets. However, these two blank types are in most cases poorly defined, as their classification typically relies on arbitrary size thresholds that do not consider blank shape, which is a fundamental component of tool production and function. In this study, we investigate whether traditional classifications of blades and bladelets are morphologically and technologically meaningful. For this purpose, we employ a three-dimensional geometric morphometric approach on a large sample of complete blanks retrieved from one of the earliest laminar industries assigned to modern humans in southern Europe: the Protoaurignacian from Fumane Cave. We rely on a cutting-edge protocol for acquiring virtual 3D meshes of stone tools using micro-computed tomography. This novel approach allows us to scan large quantities of small lithics in a short period of time and without the typical technical problems associated with scanning small objects. After calculating the principal components of shape variation, we explore differences and similarities across the dataset using linear discriminant analysis and analysis of variance. Our multivariate study highlights distinct morphological tendencies across blades and bladelets that are however better framed when the technological organization of Protoaurignacian stone knapping is taken into consideration. Overall, our results demonstrate that virtual analysis of stone tool shape can help elucidate aspects of lithic technology and its implications for past human behavior. Overview of contents: 1. Raw landmark data. All landmark coordinates for each blank analyzed in this study and digitized in AGMT3-D; 2. R project with all steps performed to import the Cartesian coordinates of each artifact to R and run GPA, PCA, and Shape ANOVA in geomorph. Furthermore, we include the steps to visualize the shape changes in both geomorph and Morpho (after performing a GPA and PCA in that package too); 3. PC scores of the PCA performed in geomorph and .csv dataset with all attributes used in this study; 4. Datasets in .sav and .dat formats used to run statistical analyses in SPSS and Past; 5. Results of the LDA analyses conducted in the study; 6. R script used to design the bivariate plot of the PCA; Extra: All 3D meshes of blades and bladelets are available on Zenodo following this link: https://doi.org/10.5281/zenodo.6362150
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes
2022-03-21

Bacterial specialized metabolites are a proven source of antibiotics and cancer therapeutics, but whether we have sampled all the secondary metabolite chemical diversity of cultivated bacteria is not known. We analysed ~ 170,000 bacterial genomes and ~ 47,000 metagenome assembled genomes (MAGs) using a modified BiG-SLiCE and the new clust-o-matic algorithm. We found that only 3% of the natural products potentially encoded in bacterial genomes have been experimentally characterized. We show that the variation of secondary metabolite biosynthetic diversity drops significantly on a genus level, identifying it as an appropriate taxonomic rank for comparison. Equal comparison of genera based on Relative Evolutionary Distance revealed that <em>Streptomyces</em> bacteria encode the largest biosynthetic diversity by far, with <em>Amycolatopsis</em>, <em>Kutzneria</em> and <em>Micromonospora</em> also encoding substantial chemical diversity. Finally we find that several less-well-studied taxa such as Weeksellaceae (Bacteroidota), Myxococcaceae (Myxococcota), <em>Pleurocapsa</em> and Nostocaceae (Cyanobacteria) have potential to produce highly diverse secondary metabolites that warrant further investigation.
Recent results in the center vortex model for the infrared sector of Yang-Mills theory
2022-03-21

A model for the infrared sector of SU(2) Yang-Mills theory, based on magnetic vortices represented by (closed) random surfaces, is presented. The model quantitatively describes both confinement and the topological aspects of Yang-Mills theory. Details (including an adequate list of references) can be found in hep-lat/9912003 and hep-lat/0004013, both to appear in Nucl. Phys. B.
FUV Spectroscopy of the sdOB Primary of the Eclipsing Binary System AA Dor
2022-03-21

AA Dor is an eclipsing, close, post common-envelope binary (PCEB). We present a detailed spectral analysis of its sdOB primary star based on observations obtained with the Far Ultraviolet Spectroscopic Explorer (FUSE). Due to a strong contamination by interstellar absorption, we had to model both, the stellar spectrum as well as the interstellar line absorption in order to reproduce the FUV observation well and to determine the photospheric parameters precisely.
Short-Term Radio-X-ray Correlations of Cygnus X-1
2022-03-21

We analyze simultaneous radio-X-ray data of Cygnus X-1 from the Ryle telescope (RT) and RXTE over more than 4 a. We show that apparent correlations on short time scales in the lightcurves of Cyg X-1 are probably the coincidental outcome of white noise statistics.
The iron abundance in hot central stars of planetary nebulae derived from IUE spectra
2022-03-21

We present the first attempt to determine the iron abundance in hot central stars of planetary nebulae. We perform an analysis with fully metal-line blanketed NLTE model atmospheres for a sample of ten stars (T_eff &gt;= 70.000 K) for which high-resolution UV spectra are available from the IUE archive. In all cases lines of Fe VI or Fe VII can be identified. As a general trend, the iron abundance appears to be subsolar by 0.5-1 dex, however, the S/N of the IUE spectra is not sufficient to exclude a solar abundance in any specific case. Improved spectroscopy by either FUSE or HST is necessary to verify the possibility of a general iron deficiency in central stars. The suspected deficiency may be the result of gravitational settling in the case of three high-gravity objects. For the other stars with low gravity and high luminosity dust fractionation during the previous AGB phase is a conceivable origin.
ORFEUS II echelle spectra: On the influence of iron-group line blanketing in the Far-UV spectral range of hot subdwarfs
2022-03-21

We present an analysis of the subdwarf O star Feige 67 with a fully metal-line blanketed NLTE model atmosphere based on high-resolution Far-UV (912-2000 A) and Near-UV (2000-3400 A) spectra from new ORFEUS II echelle observations and the IUE final archive. The Far-UV spectra are heavily blanketed by iron and nickel lines, preventing the detection of the stellar continuum and complicating the abundance analysis. Important points concerning the account for blanketing by millions of iron-group lines and for an accurate determination of iron and nickel abundances are discussed: The usage of all theoretically and experimentally known line opacities of the iron-group elements, the consideration of a broad wavelength range for a reliable determination of the stellar continuum flux, and the role of interstellar reddening. This paper outlines a basic approach for spectral analysis of future high-resolution Far-UV spectra of hot compact stars. During this study we re-analyzed the iron and nickel abundance of our exemplary object Feige 67 and confirm their extraordinarily amount.
Electromagnetic properties of nucleons and hyperons in a Lorentz covariant quark model
2022-03-21

We calculate magnetic moments of nucleons and hyperons and N -&gt; Delta + gamma transition characteristics using a manifestly Lorentz covariant chiral quark approach for the study of baryons as bound states of constituent quarks dressed by a cloud of pseudoscalar mesons.
Anatomy of Gossamer Superconductivity
2022-03-21

There are many systems in which two order parameters compete with each other. Of particular interest are systems in which these order parameters are both unconventional. In this contribution, we examine the representative example of a d-wave superconductor in the presence of a d-wave density wave, which has been suggested as a model for the pseudogap phase in the high- T_c superconductors. The physical properties of unconventional superconductivity in the presence of an anisotropic charge density wave are investigated within mean field theory. This model describes many features that were anticipated by an earlier phenomenological treatment of Tallon and Loram. In addition, the quasiparticle density of states in the presence of these two order parameters is calculated, which should be accessible by scanning tunneling microscopy.
On the multiplication map of a multigraded algebra
2022-03-21

Given a multigraded algebra , it is a natural question whether or not for two homogeneous components and , the product is the whole component for big enough. We give combinatorial and geometric answers to this question.
Cygnus X-1: A Case for a Magnetic Accretion Disk?
2022-03-21

With the advent of RXTE, which is capable of broad spectral coverage and fast timing, as well as other instruments which are increasingly being used in multi-wavelength campaigns (via both space-based and ground-based observations), we must demand more of our theoretical models. No current model mimics all facets of a system as complex as an x-ray binary. However, a modern theory should qualitatively reproduce -- or at the very least not fundamentally disagree with - all of Cygnus X-1's most basic average properties: energy spectrum (viewed within a broader framework of black hole candidate spectral behavior), power spectrum (PSD), and time delays and coherence between variability in different energy bands. Below we discuss each of these basic properties in turn, and we assess the health of one of the currently popular theories: Comptonization of photons from a cold disk. We find that the data pose substantial challenges for this theory, as well as all other currently discussed models.
Functional connectivity of the reward circuit predicts changes in appetite in depression
2022-03-21

Importance: Major depressive disorder (MDD) is characterized by a substantial burden on health including changes in appetite and body weight. Heterogeneity of depressive symptoms has hampered the identification of robust biomarkers thus limiting the potential for personalized treatment. Objective: To define the functional architecture of the reward circuit subserving increases versus decreases in appetite and body weight in MDD by specifying their respective contributions and their influence on disease biomarkers using resting-state functional connectivity (FC).Design, Setting, &amp;amp; Participants: Functional magnetic resonance imaging (fMRI) data were from the Marburg-Münster FOR 2107 Affective Disorder Cohort (MACS) study, collected between September 2014 and November 2016. Cross-sectional data of patients with MDD (NMDD=407) and healthy control participants (NHC=400) were analyzed.Main outcomes and measures: We examined dimensional changes in appetite during the depressive episode and their association with functional connectivity of the reward circuit at rest using fMRI. By taking the nucleus accumbens (NAcc) as seed, we mapped associations with opposing changes in appetite and build a sparse symptom-specific prediction model using elastic net with tenfold cross-validation.Results: Among 407 MDD patients (mean [SD] age, 36.79 [13.4] years; 249 women [61%]), reduced NAcc-based FC to the ventromedial prefrontal cortex (vmPFC) and the hippocampus was associated with reduced appetite (bootstrap r [95% CI], vmPFC: r = .13 [.02, .23]; hippocampus r = .15 [.05, .26]). In contrast, reduced NAcc-based FC to the insular ingestive cortex was associated with increased appetite (bootstrap r [95% CI], r = -.14 [-.24, -.04]). Critically, the cross-validated elastic net model predicted changes in appetite based on NAcc FC and explained variance increased with increasing symptom severity (bootstrap mean [95% CI], all patients r = .24 [.16, .31, BDI ≥ 28 r = .42 [.25, .58]). In contrast, NAcc FC did not predict diagnosis (MDD vs. HC).Conclusions and relevance: Our results show that the FC of the reward circuit reflects important individual differences in appetite and body weight in depression that can be leveraged for personalized prediction. However, classification of diagnosis based on FC of the reward circuit did not exceed chance levels. Such symptom-specific associations emphasize the need to map biomarkers onto more confined facets of psychopathology to improve the classification and treatment of patients with MDD.
Transposable element dynamics in a wild population collection of the Brassicaceae Thlaspi arvense.
2022-03-21

This repository contains molecular phenotype data of transposable element (TE) activity within individuals of the species <em>Thlaspi arvense</em>. The raw genomic data used in this study proceeds from 2 different studies: Y. Geng et al. (2021). Genomic Analysis of Field Pennycress (<em>Thlaspi Arvense</em>) Provides Insights into Mechanisms of Adaptation to High Elevation (https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01079-0). D. Galanti et al. (2022). Genetic and environmental drivers of large-scale epigenetic variation in <em>Thlaspi arvense </em>(https://doi.org/10.1101/2022.03.16.484610). Transposon insertion polymorphisms (TIPS) were detected using SPLITREADER (https://github.com/LeanQ/SPLITREADER) and the initial calls were curated following the steps described in P. Baduel et al. (2021). Efficient Detection of Transposable Element Insertion Polymorphisms Between Genomes Using Short-Read Sequencing Data. J. Cho. Plant Transposable Elements: Methods and Protocols. Springer US. (https://link.springer.com/book/10.1007/978-1-0716-1134-0). We also screen the samples searching for transposon absence polymorphisms (TAPS) using a custom pipeline deposited at https://github.com/weigelworld/popTAP. All TE polymorphisms were detected using as reference genome published by A. Nunn et al. (2021). Chromosome-level <em>Thlaspi arvense</em> genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates. (https://pubmed.ncbi.nlm.nih.gov/34990041/). Both datasets and their corresponding metadata are included in this repository.
GLA/DRST real-world outcome analysis of CAR-T cell therapies for large B-cell lymphoma in Germany
2022-03-22

CD19-directed chimeric antigen receptor (CAR) T cells have evolved as new standard-of-care (SOC) treatment in patients with relapsed/refractory large B-cell lymphoma (LBCL). Here, we report the first German real-world data on SOC CAR-T cell therapies with the aim to explore risk factors associated with outcome. Patients who received SOC axicabtagene ciloleucel (axi-cel) or tisagenlecleucel (tisa-cel) for LBCL and were registered with the German Registry for Stem Cell Transplantation (DRST) were eligible. Main outcomes analyzed were toxicities, response, overall survival (OS), and progression-free survival (PFS). We report 356 patients who received axi-cel (n=173) or tisa-cel (n=183) between November 2018 and April 2021 at 21 German centers. Whereas the axi-cel and tisa-cel cohorts were comparable for age, sex, LDH, IPI, and pretreatment, the tisa-cel group comprised significantly more patients with poor performance status, ineligibility for ZUMA-1, and need for bridging, respectively. With a median follow-up alive of 11 months, Kaplan-Meier estimates of OS, PFS, and non-relapse mortality (NRM) 12 months after dosing were 52%, 30%, and 6%, respectively. While NRM was largely driven by infections subsequent to prolonged neutropenia and/or severe neurotoxicity and significantly higher with axi-cel, significant risk factors for PFS on multivariate analysis included bridging failure, elevated LDH, age, and tisa-cel use. In conclusion, this study suggests that important outcome determinants of CD19-directed CAR-T cell treatment of LBCL in the real-world setting are bridging success, CAR-T product selection, LDH, and the absence of prolonged neutropenia and/or severe neurotoxicity. These findings may have implications for designing risk-adapted CAR-T cell therapy strategies.
Molnupiravir: A lethal mutagenic drug against rapidly mutating severe acute respiratory syndrome coronavirus 2—A narrative review
2022-03-22

Abstract Broad‐spectrum antiviral agents targeting viral RNA‐dependent RNA polymerase (RdRp) are expected to be a key therapeutic strategy in the ongoing coronavirus disease 2019 (COVID‐19) pandemic and its future variants of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), the virus that causes COVID‐19. Molnupiravir is a nucleoside analog that in vivo experiments have been reported to inhibit the replication of SARS‐CoV‐2, the virus that causes COVID‐19. Clinical trials of molnupiravir as a therapy for patients with mild‐to‐moderate COVID‐19 also suggest its significant therapeutic efficacy in comparison to placebo. Molnupiravir is lethally mutagenic against viral RNA, but its effect on host cell DNA is being questioned. Herein, the safety concerns of molnupiravir are discussed with recent findings from published reports and clinical trials. The unchanged efficacy of molnupiravir against mutated SARS‐CoV‐2 variants is also highlighted. With its administration via the oral route, molnupiravir is expected to turn the tide of the COVID‐19 pandemic.
The role of intracellular calcium‐store‐mediated calcium signals in in vivo sensor and effector functions of microglia
2022-03-22

Abstract Under physiological conditions microglia, the immune sentinels of the brain, constantly monitor their microenvironment. In the case of danger, damage or cell/tissue dyshomeostasis, they react with changes in process motility, polarization, directed process movement, morphology and gene expression profile; release pro‐ and anti‐inflammatory mediators; proliferate; and clean brain parenchyma by means of phagocytosis. Based on recent transcriptomic and in vivo Ca 2+ imaging data, we argue that the local cell/tissue dyshomeostasis is sensed by microglia via intracellular Ca 2+ signals, many of which are mediated by Ca 2+ release from the intracellular Ca 2+ stores. These signals encode the strength, duration and spatiotemporal pattern of the stimulus and, at the same time, relay this information further to trigger the respective Ca 2+ ‐dependent effector pathways. We also point to the fact that microglial Ca 2+ signalling is sexually dimorphic and undergoes profound changes across the organism's lifespan. Interestingly, the first changes in microglial Ca 2+ signalling are visible already in 9‐ to 11‐month‐old mice, roughly corresponding to 40‐year‐old humans. image