julilili42/papers huggingface dataset:
Direct observation of structural heterogeneity and tautomerization of single hypericin molecules
2022-02-23

Tautomerization is a fast chemical reaction where structures of the reactants differ only in the position of a proton and a double bond. Tautomerization often occurs in natural substances and is a fundamental process in organic- and biochemistry. However, studying the optical properties of tautomeric species is challenging due to ensemble averaging. Many molecules, such as porphines, porphycenes or phenanthroperylene quinones, exhibit a reorientation of the transition dipole moment (TDM) during tautomerization, which can be directly observed in a single molecule experiment. A prominent phenanthroperylene quinone is hypericin showing antiviral, antidepressive, and photodynamical properties. Here, we study single hypericin molecules by using confocal microscopy combined with higher order laser modes. Observing abrupt flipping of the image pattern allows to draw conclusions about the coexistence of different tautomers and their conversion path. Time-dependent density functional theory calculations show that hypericin is cycling between the four most stable tautomers. This approach allows to unambiguously assign a TDM orientation to a specific tautomer and enables to determine the chemical structure in situ. Additionally, tautomerization can not only be observed by the image pattern orientation, but also as intermittency in the fluorescence emission of a single molecule. Time correlated single photon counting enables to determine the excited state lifetimes of the hypericin tautomers. Our approach is not only limited to hypericin, but can be applied to other molecules showing a TDM reorientation during tautomerization, helping to get a deeper understanding of this important process.
On proof theory in computer science
2022-02-23

The subject logic in computer science should entail proof theoretic applications. So the question arises whether open problems in computational complexity can be solved by advanced proof theoretic techniques. In particular, consider the complexity classes NP, coNP and PSPACE. It is well-known that NP and coNP are contained in PSPACE, but till recently precise characterization of these relationships remained open. Now [2], [3] (see also [4]) presented proofs of corresponding equalities NP = coNP = PSPACE. These results were obtained by appropriate proof theoretic tree-to-dag compressing techniques to be briefy explained below. [2] L. Gordeev, E. H. Haeusler, Proof Compression and NP Versus PSPACE, Studia Logica (107) (1): 55{83 (2019) [3] L. Gordeev, E. H. Haeusler, Proof Compression and NP Versus PSPACE II, Bulletin of the Section of Logic (49) (3): 213{230 (2020) http://dx.doi.org/10.18788/0138-0680.2020.16 [4] L. Gordeev, E. H. Haeusler, Proof Compression and NP Versus PSPACE II: Addendum, arXiv:2011.09262 (2020)
Gaussian Experts Selection using Graphical Models
2022-02-23

Local approximations are popular methods to scale Gaussian processes (GPs) to big data. Local approximations reduce time complexity by dividing the original dataset into subsets and training a local expert on each subset. Aggregating the experts' prediction is done assuming either conditional dependence or independence between the experts. Imposing the \\emph{conditional independence assumption} (CI) between the experts renders the aggregation of different expert predictions time efficient at the cost of poor uncertainty quantification. On the other hand, modeling dependent experts can provide precise predictions and uncertainty quantification at the expense of impractically high computational costs. By eliminating weak experts via a theory-guided expert selection step, we substantially reduce the computational cost of aggregating dependent experts while ensuring calibrated uncertainty quantification. We leverage techniques from the literature on undirected graphical models, using sparse precision matrices that encode conditional dependencies between experts to select the most important experts. Moreov
Mobility-Aware Routing and Caching: A Federated Learning Assisted Approach
2022-02-23

We consider a service cost minimization problem for resource-constrained small-cell networks with caching, where the challenge mainly stems from (i) the insufficient backhaul capacity and limited network bandwidth and (ii) the limited storing capacity of small-cell base stations (SBSs). Besides, the optimization problem is NP-hard since both the users' mobility patterns and content preferences are unknown. In this paper, we develop a novel mobility-aware joint routing and caching strategy to address the challenges. The designed framework divides the entire geographical area into small sections containing one SBS and several MUs. Based on the concept of one-stop-shop (OSS), we propose a federated routing and popularity learning (FRPL) approach in which the SBSs cooperatively learn the routing and preference of their respective MUs and make a caching decision. The FRPL method completes multiple tasks in one shot, thus reducing the average processing time per global aggregation of learning. By exploiting the outcomes of FRPL together with the estimated service edge of SBSs, the proposed cache placement solution greedily approximates the minimizer of the challenging service cost optimization problem. Theoretical and numerical analyses show the effectiveness of our proposed approaches.
Bayesian Quadrature on Riemannian Data Manifolds
2022-02-23

Riemannian manifolds provide a principled way to model nonlinear geometric structure inherent in data. A Riemannian metric on said manifolds determines geometry-aware shortest paths and provides the means to define statistical models accordingly. However, these operations are typically computationally demanding. To ease this computational burden, we advocate probabilistic numerical methods for Riemannian statistics. In particular, we focus on Bayesian quadrature (BQ) to numerically compute integrals over normal laws on Riemannian manifolds learned from data. In this task, each function evaluation relies on the solution of an expensive initial value problem. We show that by leveraging both prior knowledge and an active exploration scheme, BQ significantly reduces the number of required evaluations and thus outperforms Monte Carlo methods on a wide range of integration problems. As a concrete application, we highlight the merits of adopting Riemannian geometry with our proposed framework on a nonlinear dataset from molecular dynamics.
Anytime Diagnosis for Reconfiguration
2022-02-23

Many domains require scalable algorithms that help to determine diagnoses efficiently and often within predefined time limits. Anytime diagnosis is able to determine solutions in such a way and thus is especially useful in real-time scenarios such as production scheduling, robot control, and communication networks management where diagnosis and corresponding reconfiguration capabilities play a major role. Anytime diagnosis in many cases comes along with a trade-off between diagnosis quality and the efficiency of diagnostic reasoning. In this paper we introduce and analyze FlexDiag which is an anytime direct diagnosis approach. We evaluate the algorithm with regard to performance and diagnosis quality using a configuration benchmark from the domain of feature models and an industrial configuration knowledge base from the automotive domain. Results show that FlexDiag helps to significantly increase the performance of direct diagnosis search with corresponding quality tradeoffs in terms of minimality and accuracy.
ESCAPED: Efficient Secure and Private Dot Product Framework for Kernel-based Machine Learning Algorithms with Applications in Healthcare
2022-02-23

To train sophisticated machine learning models one usually needs many training samples. Especially in healthcare settings these samples can be very expensive, meaning that one institution alone usually does not have enough on its own. Merging privacy-sensitive data from different sources is usually restricted by data security and data protection measures. This can lead to approaches that reduce data quality by putting noise onto the variables (e.g., in -differential privacy) or omitting certain values (e.g., for -anonymity). Other measures based on cryptographic methods can lead to very time-consuming computations, which is especially problematic for larger multi-omics data. We address this problem by introducing ESCAPED, which stands for Efficient SeCure And PrivatE Dot product framework, enabling the computation of the dot product of vectors from multiple sources on a third-party, which later trains kernel-based machine learning algorithms, while neither sacrificing privacy nor adding noise. We evaluated our framework on drug resistance prediction for HIV-infected people and multi-omics dimensionality reduction and clustering problems in precision medicine. In terms of execution time, our framework significantly outperforms the best-fitting existing approaches without sacrificing the performance of the algorithm. Even though we only show the benefit for kernel-based algorithms, our framework can open up new research opportunities for further machine learning models that require the dot product of vectors from multiple sources.
eROSITA detection of flares from the Be/X-ray binary A0538-66
2022-02-23

In 2018, XMM-Newton observed the awakening in X-rays of the Be/X-ray binary (Be/XRB) A0538-66. It showed bright and fast flares close to periastron with properties that had never been observed in other Be/XRBs before. We report the results from the observations of A0538-66 collected during the first all-sky survey of eROSITA, an X-ray telescope (0.2-10 keV) on board the Spektrum-Roentgen-Gamma (SRG) satellite. eROSITA caught two flares within one orbital cycle at orbital phases and (where corresponds to periastron), with peak luminosities of erg/s (0.2-10 keV) and durations of s. The flare observed at shows that the neutron star can accrete considerably far from periastron, although it is expected to be outside of the circumstellar disk, thus providing important new information about the plasma environment surrounding the binary system. We also report the results from the photometric monitoring of A0538-66 carried out with the REM, OGLE, and MACHO telescopes from January 1993 until March 2020. We found that the two sharp peaks that characterize the orbital modulation in the optical occur asymmetrically in the orbit, relative to the position of the donor star.
Assessment of neutralizing antibody responses after natural SARS-CoV-2 infection and vaccination in Congolese individuals
2022-02-23

Abstract Background Assessing immune responses after vaccination is part of the evaluation package of vaccine effectiveness in the real world. With regard to SARS-CoV-2, neutralizing antibody levels has been shown to be a good indicator of antibody immune response boosting. So far, limited data have been reported from Africa including in Central Africa. The objective of this study was to provide data on anti-S1 spike total IgG and neutralizing antibodies in vaccinated and non-vaccinated including naturally infected Congolese population during B.1.214.1 and B.1.617.2 variant waves. Methods Recruited patients were divided into 4 groups: (1) Naturally infected by the B.1.214.1 variant on January 2021 and followed up until September 2021. These patients have been vaccinated at month 07 and then followed up for 2 months post vaccination; (2) Naturally infected by the B.1.617.2 variant from June 2021; (3) unvaccinated SARS-CoV-2 individuals with no history of prior SARS-CoV-2 infection; (3) fully vaccinated individuals with Sinopharm/BBIP-CorV or Janssen/Ad26.COV2.S. SARS-CoV-2 was detected by qRT-PCR and sequenced using Next-Generation Sequencing. ELISA method was used for detecting IgG, and neutralizing Antibody against SARS-CoV-2 antigens using commercial neutralizing assay. Results Individuals infected by the B.1214.1 variant elicited consistently high IgG titers at 02, 03 and 06 months. Two months post vaccination with BBIP-CorV, participants showed a significant increase by x2.5 fold (p&lt;0.0001) of total IgG and X1.5 fold for neutralizing antibody capacity. This study showed that natural infection with B1.617.2 (delta) variant was more immunogenic compared to those being infected with B1.214.2 variant at the same period. We found a significantly higher concentration in anti-SARS-CoV-2 IgG (p&lt;0.0002) and antibodies neutralization capacity (P&lt;0.0001) in fully vaccinated compared to unvaccinated participants. Two months post vaccination, individuals who received Janssen/Ad26.COV2.S presented higher (p= 0.01) total IgG to spike protein compared to BBIP-CorV. Conclusion Both natural infection and vaccination with BBIP-CorV and Janssen/Ad26.COV2.S induced antibody response in Congolese population. In addition, Janssen/Ad26.COV2.S was more immunogenic than Sinopharm/BBIP-CorV. There is a need to investigate the duration of these antibodies both in previously infected and naive vaccinated Congolese to allow public heath stakeholders to make evidence-based decision on vaccine schedule for the Congolese population.
Energy in Fourth Order Gravity
2022-02-23

In this paper we make a detailed analysis of conservation principles in the context of a family of fourth-order gravitational theories generated via a quadratic Lagrangian. In particular, we focus on the associated notion of energy and start a program related to its study. We also exhibit examples of solutions which provide intuitions about this notion of energy which allows us to interpret it, and introduce several study cases where its analysis seems tractable. Finally, positive energy theorems are presented in restricted situations.
Circ_0020123 promotes NSCLC tumorigenesis via up-regulating KIAA1522 expression through miR-940
2022-02-23

Circ_0020123 was highly expressed in NSCLC tissues and cell lines, and knockdown of circ_0020123 abolished cell growth, migration and invasion <i>in vitro</i> and hindered tumor growth in nude mice. Mechanically, circ_0020123 directly targeted miR-940, and KIAA1522 was a target of miR-940. Thereafter, a series of rescue experiments showed that circ_0020123 served its biological functions by miR-940/KIAA1522 axis. In all, circ_0020123 acted as an oncogene to promote the tumorigenesis of NSCLC via miR-940/KIAA1522 axis, suggesting a potential therapeutic target for NSCLC treatment.
PharmVar GeneFocus: CYP3A5
2022-02-24

The Pharmacogene Variation Consortium (PharmVar) catalogs star (*) allele nomenclature for the polymorphic human CYP3A5 gene. Genetic variation within the CYP3A5 gene locus impacts the metabolism of several clinically important drugs, including the immunosuppressants tacrolimus, sirolimus, cyclosporine, and the benzodiazepine midazolam. Variable CYP3A5 activity is of clinical importance regarding tacrolimus metabolism. This GeneFocus provides a CYP3A5 gene summary with a focus on aspects regarding standardized nomenclature. In addition, this review also summarizes recent changes and updates, including the retirement of several allelic variants and provides an overview of how PharmVar CYP3A5 star allele nomenclature is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
Using the WWF Water Risk Filter to Screen Existing and Projected Hydropower Projects for Climate and Biodiversity Risks
2022-02-24

Climate change is predicted to drive various changes in hydrology that can translate into risks for river ecosystems and for those who manage rivers, such as for hydropower. Here we use the WWF Water Risk Filter (WRF) and geospatial analysis to screen hydropower projects, both existing (2488 dams) and projected (3700 dams), for a variety of risks at a global scale, focusing on biodiversity risks, hydrological risks (water scarcity and flooding), and how those hydrological risks may shift with climate change, based on three scenarios. Approximately 26% of existing hydropower dams and 23% of projected dams are within river basins that currently have medium to very high risk of water scarcity; 32% and 20% of the existing and projected dams, respectively, are projected to have increased risk by 2050 due to climate change. For flood risk, 75% of existing dams and 83% of projected dams are within river basins with medium to very high risk, and the proportion of hydropower dams in basins with the highest levels of flood risk is projected to increase by nearly twenty times (e.g., from 2% to 36% of dams). In addition, a large proportion of existing (76%) and projected hydropower dams (93%) are located in river basins with high or very high freshwater biodiversity importance. This is a high-level screening, intended to elucidate broad patterns of risk to increase awareness, highlight trends, and guide more detailed studies.
Quantitative Metabolomics of Tissue, Perfusate, and Bile from Rat Livers Subjected to Normothermic Machine Perfusion
2022-02-24

Machine perfusion (MP) allows the maintenance of liver cells in a metabolically active state ex vivo and can potentially revert metabolic perturbations caused by donor warm ischemia, procurement, and static cold storage (SCS). The present preclinical research investigated the metabolic outcome of the MP procedure by analyzing rat liver tissue, bile, and perfusate samples by means of high-field (600 MHz) nuclear magnetic resonance (NMR) spectroscopy. An established rat model of normothermic MP (NMP) was used. Experiments were carried out with the addition of an oxygen carrier (OxC) to the perfusion fluid (OxC-NMP, n = 5) or without (h-NMP, n = 5). Bile and perfusate samples were collected throughout the procedure, while biopsies were only taken at the end of NMP. Two additional groups were: (1) Native, in which tissue or bile specimens were collected from rats in resting conditions; and (2) SCS, in which biopsies were taken from cold-stored livers. Generally, NMP groups showed a distinctive metabolomic signature in all the analyzed biological matrices. In particular, many of the differentially expressed metabolites were involved in mitochondrial biochemical pathways. Succinate, acetate, 3-hydroxybutyrate, creatine, and O-phosphocholine were deeply modulated in ex vivo perfused livers compared to both the Native and SCS groups. These novel results demonstrate a broad modulation of mitochondrial metabolism during NMP that exceeds energy production and redox balance maintenance.
Higher Work-Privacy Conflict and Lower Job Satisfaction in GP Leaders and Practice Assistants Working Full-Time Compared to Part-Time: Results of the IMPROVEjob Study
2022-02-24

Background: Work-privacy conflict (WPC) has become an important issue for medical professionals. The cluster-randomized controlled IMPROVEjob study aimed at improving job satisfaction (primary outcome), with additional outcomes such as examining the work-privacy conflict in German general practice personnel. Using baseline data of this study, the relationship between work-privacy conflict and job satisfaction (JS) was analyzed. In addition, factors associated with higher WPC were identified. Methods: At baseline, 366 participants (general practitioners (GPs) in leadership positions, employed general practitioners, and practice assistants) from 60 German practices completed a questionnaire addressing socio-demographic data and job characteristics. Standardized scales from the German version of the COPSOQ III requested data concerning job satisfaction and work-privacy conflict. Both scores range from 0 (lowest) to 100 (highest). Multilevel analysis accounted for the clustered data. Statistical analyses were performed using IBM SPSS and RStudio software, with a significance level set at p &lt; 0.05. Results: Job satisfaction was 77.16 (mean value; SD = 14.30) among GPs in leadership positions (n = 84), 79.61 (SD = 12.85) in employed GPs (n = 28), and 72.58 (SD = 14.42) in practice assistants (n = 254). Mean values for the WPC-scale were higher for professionals with more responsibilities: GPs in leadership positions scored highest with 64.03 (SD = 29.96), followed by employed physicians (M = 45.54, SD =30.28), and practice assistants (M = 32.67, SD = 27.41). General practitioners and practice assistants working full-time reported significantly higher work-privacy conflict than those working part-time (p &lt; 0.05). In a multilevel analysis, work-privacy conflict was significantly associated with job satisfaction (p &lt; 0.001). A multiple regression analysis identified working hours, as well as and being a practice owner or an employed physician as factors significantly influencing WPC. Discussion: WPC was high among general practice leaders and practice personnel working full-time. Future interventions to support practice personnel should focus on reducing WPC, as there is good evidence of its effects on job satisfaction.
Work-related psychosocial demands related to work organization in small sized companies (SMEs) providing health-oriented services in Germany – a qualitative analysis
2022-02-24

Abstract Background Micro, small and medium-sized enterprises (SMEs) represent the majority of businesses in the EU. Little is known about psychosocial demands faced by company owners, managers, and employees in SMEs, especially in the health and service sector. The current study aimed to identify which psychosocial demands related to work organization are reported by managers and employees in the health and service sector, and if managers and employees differ in their perspective on these psychosocial demands. Methods We conducted nine single interviews and two focus group discussions with seven company owners and managers as well as eleven employees from six different German companies between January and February 2020. The psychosocial factors of the psychosocial risk assessment of the Joint German Occupational Safety and Health Strategy (GDA) served as a framework for data collection and analysis. The interview material was analysed using Mayring’s method of qualitative content analysis. Results We identified four prevailing work-related psychosocial demands related to work organization among managers and employees: (1) possibilities and time for recovery after work, (2) communication and cooperation, (3) work intensity, and (4) interruptions, and prioritization. According to the managers, they were confronted with a lack of possibilities and time for recovery after work. They report issues related to inadequate communication and cooperation affecting the entire company team, and also face high work intensity and frequent interruptions and prioritization. Employees reported a clearer division between work and private life. However, they also face periods of high work intensity, frequent interruptions and the need for prioritization. Conclusion Managers and employees in SMEs in the health and service sector would benefit from evidence-based and evaluated tailored interventions and approaches for improved work organization. Further studies are needed to support managers and employees in SMEs in the health and service sector in facing and handling work-related psychosocial demands like lack of possibilities and time for recovery after work, high work intensity or frequent interruptions.