julilili42/papers huggingface dataset:
Quantum reaction-limited reaction–diffusion dynamics of noninteracting Bose gases
2024-04-01

Abstract We investigate quantum reaction–diffusion (RD) systems in one-dimension with bosonic particles that coherently hop in a lattice, and when brought in range react dissipatively. Such reactions involve binary annihilation ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mrow> <mml:mi>A</mml:mi> <mml:mo>+</mml:mo> <mml:mi>A</mml:mi> <mml:mo accent="false" stretchy="false">→</mml:mo> <mml:mi mathvariant="normal">∅</mml:mi> </mml:mrow> </mml:math> ) and coagulation ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mrow> <mml:mi>A</mml:mi> <mml:mo>+</mml:mo> <mml:mi>A</mml:mi> <mml:mo accent="false" stretchy="false">→</mml:mo> <mml:mi>A</mml:mi> </mml:mrow> </mml:math> ) of particles at distance d . We consider the reaction-limited regime, where dissipative reactions take place at a rate that is small compared to that of coherent hopping. In classical RD systems, this regime is correctly captured by the mean-field approximation. In quantum RD systems, for noninteracting fermionic systems, the reaction-limited regime recently attracted considerable attention because it has been shown to give universal power law decay beyond mean field for the density of particles as a function of time. Here, we address the question whether such universal behavior is present also in the case of the noninteracting Bose gas. We show that beyond mean-field density decay for bosons is possible only for reactions that allow for destructive interference of different decay channels. Furthermore, we study an absorbing-state phase transition induced by the competition between branching <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mrow> <mml:mi>A</mml:mi> <mml:mo accent="false" stretchy="false">→</mml:mo> <mml:mi>A</mml:mi> <mml:mo>+</mml:mo> <mml:mi>A</mml:mi> </mml:mrow> </mml:math> , decay <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mrow> <mml:mi>A</mml:mi> <mml:mo accent="false" stretchy="false">→</mml:mo> <mml:mi mathvariant="normal">∅</mml:mi> </mml:mrow> </mml:math> and coagulation <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mrow> <mml:mi>A</mml:mi> <mml:mo>+</mml:mo> <mml:mi>A</mml:mi> <mml:mo accent="false" stretchy="false">→</mml:mo> <mml:mi>A</mml:mi> </mml:mrow> </mml:math> . We find a stationary phase-diagram, where a first and a second-order transition line meet at a bicritical point which is described by tricritical directed percolation. These results show that quantum statistics significantly impact on both the stationary and the dynamical universal behavior of quantum RD systems.
Toward More Accurate Synthetic Reflection Spectra: Improving the Calculations of Returning Radiation
2024-04-01

Abstract We present a new model to calculate reflection spectra of thin accretion disks in Kerr spacetimes. Our model includes the effect of returning radiation, which is the radiation that is emitted by the disk and returns to the disk because of the strong light bending near a black hole. The major improvement with respect to the existing models is that it calculates the reflection spectrum at every point on the disk by using the actual spectrum of the incident radiation. Assuming a lamppost coronal geometry, we simulate simultaneous observations of NICER and NuSTAR of bright Galactic black holes and we fit the simulated data with the latest version of relxill (modified to read the table of reflionx , which is the nonrelativistic reflection model used in our calculations). We find that relxill with returning radiation cannot fit well the simulated data when the black hole spin parameter is very high and the coronal height and disk’s ionization parameter are low, and some parameters can be significantly overestimated or underestimated. We can find better fits and recover the correct input parameters as the value of the black hole spin parameter decreases and the value of the coronal height increases.
Accelerated generation of gene‐engineered monoclonal CHO cell lines using FluidFM nanoinjection and CRISPR/Cas9
2024-04-01

Abstract Chinese hamster ovary (CHO) cells are the commonly used mammalian host system to manufacture recombinant proteins including monoclonal antibodies. However unfavorable non‐human glycoprofile displayed on CHO‐produced monoclonal antibodies have negative impacts on product quality, pharmacokinetics, and therapeutic efficiency. Glycoengineering such as genetic elimination of genes involved in glycosylation pathway in CHO cells is a viable solution but constrained due to longer timeline and laborious workflow. Here, in this proof‐of‐concept (PoC) study, we present a novel approach coined CellEDIT to engineer CHO cells by intranuclear delivery of the CRISPR components to single cells using the FluidFM technology. Co‐injection of CRISPR system targeting BAX, DHFR, and FUT8 directly into the nucleus of single cells, enabled us to generate triple knockout CHO‐K1 cell lines within a short time frame. The proposed technique assures the origin of monoclonality without the requirement of limiting dilution, cell sorting or positive selection. Furthermore, the approach is compatible to develop both single and multiple knockout clones ( FUT8 , BAX , and DHFR ) in CHO cells. Further analyses on single and multiple knockout clones confirmed the targeted genetic disruption and altered protein expression. The knockout CHO‐K1 clones showed the persistence of gene editing during the subsequent passages, compatible with serum free chemically defined media and showed equivalent transgene expression like parental clone.
On the role of variation in measures, the worth of underpowered studies, and the need for tolerance among researchers: Some more reflections on Leising et al. from a methodological, statistical, and social-psychological perspective
2024-04-01

We point out potential drawbacks of some of Leising et al.’s (2022a) proposed ways how personality science can be improved. We argue that it is ill-advised to use only one measure for a concept. Also, we argue that researchers should not refrain from conducting a study when a high level of statistical power is precluded. Then, we go one step further and formulate additional ideas of how to improve research. Specifically, we argue that it is a good thing to use different methods rather than only one when attempting to generalize across these methods. Moreover, we argue for a more theory-driven strategy for specifying factor analytic models, and we emphasize that high-quality research is often interdisciplinary. Finally, we point to a particular risk associated with any formal reward system.
Towards engineering a portable platform for laparoscopic pre-training in virtual reality with haptic feedback
2024-04-01

Background: Laparoscopic surgery is a surgical technique in which special instruments are inserted through small incision holes inside the body. For some time, efforts have been made to improve surgical pre-training through practical exercises on abstracted and reduced models. Methods: The authors strive for a portable, easy to use and cost-effective Virtual Reality-based (VR) laparoscopic pre-training platform and therefore address the question of how such a system has to be designed to achieve the quality of today's gold standard using real tissue specimens. Current VR controllers are limited regarding haptic feedback. Since haptic feedback is necessary or at least beneficial for laparoscopic surgery training, the platform to be developed consists of a newly designed prototype laparoscopic VR controller with haptic feedback, a commercially available head-mounted display, a VR environment for simulating a laparoscopic surgery, and a training concept. Results: To take full advantage of benefits such as repeatability and cost-effectiveness of VR-based training, the system shall not require a tissue sample for haptic feedback. It is currently calculated and visually displayed to the user in the VR environment. On the prototype controller, a first axis was provided with perceptible feedback for test purposes. Two of the prototype VR controllers can be combined to simulate a typical both-handed use case, e.g., laparoscopic suturing. A Unity-based VR prototype allows the execution of simple standard pre-trainings. Conclusions: The first prototype enables full operation of a virtual laparoscopic instrument in VR. In addition, the simulation can compute simple interaction forces. Major challenges lie in a realistic real-time tissue simulation and calculation of forces for the haptic feedback. Mechanical weaknesses were identified in the first hardware prototype, which will be improved in subsequent versions. All degrees of freedom of the controller are to be provided with haptic feedback. To make forces tangible in the simulation, characteristic values need to be determined using real tissue samples. The system has yet to be validated by cross-comparing real and VR haptics with surgeons.
Extending the phenotypic spectrum assessed by the CDR plus NACC FTLD in genetic frontotemporal dementia
2024-04-01

Abstract INTRODUCTION We aimed to expand the range of the frontotemporal dementia (FTD) phenotypes assessed by the Clinical Dementia Rating Dementia Staging Instrument plus National Alzheimer's Coordinating Center Behavior and Language Domains (CDR plus NACC FTLD). METHODS Neuropsychiatric and motor domains were added to the standard CDR plus NACC FTLD generating a new CDR plus NACC FTLD‐NM scale. This was assessed in 522 mutation carriers and 310 mutation‐negative controls from the Genetic Frontotemporal dementia Initiative (GENFI). RESULTS The new scale led to higher global severity scores than the CDR plus NACC FTLD: 1.4% of participants were now considered prodromal rather than asymptomatic, while 1.3% were now considered symptomatic rather than asymptomatic or prodromal. No participants with a clinical diagnosis of an FTD spectrum disorder were classified as asymptomatic using the new scales. DISCUSSION Adding new domains to the CDR plus NACC FTLD leads to a scale that encompasses the wider phenotypic spectrum of FTD with further work needed to validate its use more widely. Highlights The new Clinical Dementia Rating Dementia Staging Instrument plus National Alzheimer's Coordinating Center Behavior and Language Domains neuropsychiatric and motor (CDR plus NACC FTLD‐NM) rating scale was significantly positively correlated with the original CDR plus NACC FTLD and negatively correlated with the FTD Rating Scale (FRS). No participants with a clinical diagnosis in the frontotemporal dementia spectrum were classified as asymptomatic with the new CDR plus NACC FTLD‐NM rating scale. Individuals had higher global severity scores with the addition of the neuropsychiatric and motor domains. A receiver operating characteristic analysis of symptomatic diagnosis showed nominally higher areas under the curve for the new scales.
A multi-institutional comparison of retrospective deformable dose accumulation for online adaptive magnetic resonance-guided radiotherapy
2024-04-01

BACKGROUND AND PURPOSE: Application of different deformable dose accumulation (DDA) solutions makes institutional comparisons after online-adaptive magnetic resonance-guided radiotherapy (OA-MRgRT) challenging. The aim of this multi-institutional study was to analyze accuracy and agreement of DDA-implementations in OA-MRgRT.\\nMATERIAL AND METHODS: One gold standard (GS) case deformed with a biomechanical-model and five clinical cases consisting of prostate (2x), cervix, liver, and lymph node cancer, treated with OA-MRgRT, were analyzed. Six centers conducted DDA using institutional implementations. Deformable image registration (DIR) and DDA results were compared using the contour metrics Dice Similarity Coefficient (DSC), surface-DSC, Hausdorff-distance (HD95%), and accumulated dose-volume histograms (DVHs) analyzed via intraclass correlation coefficient (ICC) and clinical dosimetric criteria (CDC).\\nRESULTS: For the GS, median DDA errors ranged from 0.0 to 2.8 Gy across contours and implementations. DIR of clinical cases resulted in DSC &gt; 0.8 for up to 81.3% of contours and a variability of surface-DSC values depending on the implementation. Maximum HD95%=73.3 mm was found for duodenum in the liver case. Although DVH ICC &gt; 0.90 was found after DDA for all but two contours, relevant absolute CDC differences were observed in clinical cases: Prostate I/II showed maximum differences in bladder V28Gy (10.2/7.6%), while for cervix, liver, and lymph node the highest differences were found for rectum D2cm\\nCONCLUSION: Overall, high agreement was found between the different DIR and DDA implementations. Case- and algorithm-dependent differences were observed, leading to potentially clinically relevant results. Larger studies are needed to define future DDA-guidelines.
ParlaMint II: Advancing Comparable Parliamentary Corpora Across Europe
2024-04-01

<title>Abstract</title> The paper presents the results of the ParlaMint II project, which comprise comparable corpora of parliamentary debates of 29 European countries and autonomous regions, covering at least the period from 2015 to 2022, and containing over 1 billion words. The corpora are uniformly encoded, contain rich metadata about their 24 thousand speakers, and are linguistically annotated up to the level of Universal Dependencies syntax and named entities. The paper focuses on the enhancement made since the ParlaMint I project and presents the compilation of the corpora, including the encoding infrastructure, use of GitHub, the production of individual corpora, the common pipeline for producing their distribution, and use of CLARIN services for dissemination. It then gives a quantitative overview of the produced corpora, followed by the qualitative additions made within the ParlaMint II project, namely metadata localisation, the addition of new metadata, such as the political orientation of political parties, the machine translation of the corpora to English and its tagging with semantic classes, and the production of pilot speech corpora. Finally, outreach activities and further work are discussed.
National and International Comparisons of Gynecological Research in Germany Based on a Bibliometric Analysis of Publications
2024-04-01

Abstract Recent years have seen a considerable shift from male doctors to female doctors in the field of gynecology. Female doctors are traditionally more involved with planning and maintaining their family. For gynecology, this could be associated with a risk that research activities will decrease, particularly if results are published in scientific journals. In view of this shift, a comparative observational study was carried for 2022 in which 1306 publications were matched to 1786 female and male doctors reported on the websites of the 44 locations of university gynecology departments in Germany. In addition, the volume of publications issued between 2014 and 2022 was compared for Germany, France, the United Kingdom, and the United States. In Germany, the volume of publications in Gynecology was additionally compared with the publication outputs of the specialties Urology and Trauma Surgery. Since 2014, the increase in the numbers of publications in the field of Gynecology in Germany was lower (225%) than that of the countries with which it was compared (238%/252%/260% for F/UK/USA). When Gynecology was compared with other medical specialties in Germany, the number of publications in Urology were found to have increased at a lower rate (196%) while the number of publications in the field of Trauma Surgery increased by more (286%) than that of Gynecology. At the start of 2023, the percentage of women who were working as doctors at the lowest hierarchical level (junior doctor) was 81%. The publication output per capita of female doctors working at lower levels in the medical hierarchy, i.e., working as junior doctors and senior physicians, was between 40% and 80% lower than that of male doctors working at the same level. However, female directors published as much as male directors did. In the lower hierarchy levels, men were up to 14% more likely to be without an academic title. Predictors for more extensive publication activities by young female and male doctors include the extent and quality of publications by doctors in senior positions, the presence of a comprehensive cancer center or an institute for human genetics at the location where the young doctors were working, and joint publications with foreign authors. For the German Society of Gynecology and Obstetrics, the results suggest a number of approaches to promote young researchers. The support provided to young female doctors is especially important as this should help to retain them as junior researchers over the long term.
A Context-based Teaching Concept on Electric Circuits - Development and First Results
2024-04-01

Abstract Despite the importance of electricity for today’s industrial society, students often perceive the abstract topic of electric circuits as uninteresting. In order to foster students’ interest, we developed a context-based teaching concept on simple circuits. Building on research findings on students’ interests, the concept covers the topic at the example of contexts like bumper cars, the electric eel, or the electric fence. While previous studies suggest that such a context-based approach can improve affective factors such as student interest, the evidence on the impact on students’ conceptual understanding is inconclusive. Therefore, we empirically evaluated the teaching concept in a field study with 7 th and 8 th graders to investigate the effects of context-based teaching on students’ conceptual understanding, while also assessing their interest and self-concept. By comparing our concept with conventional teaching in a pre-post-follow-up design, we aim to improve the current state of research regarding the effects of context-based teaching in authentic teaching environments. First analyses did not reveal significant differences between the context-based concept and conventional approaches, neither regarding the affective factors interest and self-concept nor conceptual understanding.
Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links
2024-04-01

Abstract In protein‐RNA cross‐linking mass spectrometry, UV or chemical cross‐linking introduces stable bonds between amino acids and nucleic acids in protein‐RNA complexes that are then analyzed and detected in mass spectra. This analytical tool delivers valuable information about RNA‐protein interactions and RNA docking sites in proteins, both in vitro and in vivo. The identification of cross‐linked peptides with oligonucleotides of different length leads to a combinatorial increase in search space. We demonstrate that the peptide retention time prediction tasks can be transferred to the task of cross‐linked peptide retention time prediction using a simple amino acid composition encoding, yielding improved identification rates when the prediction error is included in rescoring. For the more challenging task of including fragment intensity prediction of cross‐linked peptides in the rescoring, we obtain, on average, a similar improvement. Further improvement in the encoding and fine‐tuning of retention time and intensity prediction models might lead to further gains, and merit further research.
How to Quantify Heavy Mineral Fertility From Point‐Counting Data
2024-04-01

Abstract Heavy minerals (HM) are widely used in provenance studies, for example, for reconstructing source areas and quantifying sediment budgets. Source rock mineral fertility influences the composition and concentration of HM in sediments. The resulting bias is of particular interest when interpreting single‐grain data such as detrital age distributions. However, the quantification of fertility is complex and there are no robust data for most HM, which prevents the routine implementation of fertility in many studies. In this study, we test whether mineral fertility can be assessed by quantifying mineral concentrations in detrital samples through point counting and quantitative evaluation of minerals by scanning electron microscopy (QEMSCAN). The challenge is to transform the resulting area percentage into mass percentage, which is a prerequisite for comparing those data with grain size or geochemical data. We suggest overcoming this problem by recording grain‐size and shape metrics of minerals using image analysis, and applying several transformation steps. We test our method by (a) using a series of detrital grain mixtures of known density and mass, and (b) applying it to a natural sediment from the European Alps. Our results agree with existing methods developed for apatite and zircon, that is, the quantification of fertility through geochemistry (with P 2 O 5 and Zr concentrations as proxies for apatite and zircon) and the separation of pure apatite and zircon concentrates using additional separation steps. The advantage of our method is its applicability to all HM (not only apatite and zircon) and the redundancy of additional separation steps, which might create bias.
Porous Se@SiO2 nanocomposites play a potential inhibition role in hyperoxaluria associated kidney stone by exerting antioxidant effects
2024-04-01

Se@SiO<sub>2</sub> nanocomposites appear to protect renal TECs from hyperoxaluria by reducing reactive oxygen species production, suggesting the potential role of preventing kidney stone formation and recurrence.
Sulfur Implantation into Water Ice with Propane: Implications for Organic Chemistry on the Surface of Europa
2024-04-01

Abstract We performed experiments of implantation of energetic sulfur ions (105 keV) into 2:1 water:propane ices at 80 K and analyzed the resulting refractory organic matter with ultrahigh-resolution mass spectrometry. Our goal was to characterize the organic matter processed in the surface conditions of Europa, where it would receive a heavy flux of energetic particles, including sulfur ions, and determine whether organosulfurs could be formed in these conditions, using the simplest alkane that can exist in solid form on Europa’s surface. We find that the produced organic matter contains a large variety of both aliphatic and aromatic compounds (several thousand unique formulae), including polycyclic aromatic hydrocarbons (PAHs), with masses up to 900 amu. A large number of aromatic hydrocarbons is found along with oxygenated, mostly aliphatic, compounds. Organosulfurs are found in both CHS and CHOS form, demonstrating they can be formed from any organic compound through sulfur implantation. These organosulfurs’ properties (aromaticity, mass) appear similar to the rest of the organic matter, albeit their low quantity does not allow for a thorough comparison. Our results have implications for the type of refractory organic matter that could be observed by the JUICE and Europa Clipper space missions and how the surface of Europa could generate complex organics, including PAHs and organosulfurs, that could then enrich the subsurface ocean. In particular, they indicate that a large diversity of organic matter, including organosulfurs, can be formed from simple precursors in a geologically short time frame under the ion flux that reaches Europa.
Kalba: research on trade networks of a prehistoric coastal community on the Gulf of Oman, United Arab Emirates
2024-04-01

Abstract This project investigates the prehistoric coastal site of Kalba on the Gulf of Oman in the context of exchange networks between maritime waterways and land-based caravan routes on the south-eastern Arabian Peninsula. In addition to favourable environmental conditions, raw-material procurement strategies were important for the economy of this multi-crafting community.