julilili42/papers huggingface dataset:
Differential metabolism of choline supplements in adult volunteers
2021-07-21

Abstract Background Adequate intake of choline is essential for growth and homeostasis, but its supply does often not meet requirements. Choline deficiency decreases phosphatidylcholine (PC) and betaine synthesis, resulting in organ pathology, especially of liver, lung, and brain. This is of particular clinical importance in preterm infants and cystic fibrosis patients. We compared four different choline supplements for their impact on plasma concentration and kinetics of choline, betaine as a methyl donor and trimethylamine oxide (TMAO) as a marker of bacterial degradation prior to absorption. Methods Prospective randomized cross-over study (1/2020–4/2020) in six healthy adult men. Participants received a single dose of 550 mg/d choline equivalent in the form of choline chloride, choline bitartrate, α-glycerophosphocholine (GPC), and egg-PC in randomized sequence at least 1 week apart. Blood was taken from t = − 0.1–6 h after supplement intake. Choline, betaine, TMAO, and total PC concentrations were analyzed by tandem mass spectrometry. Results are shown as medians and interquartile range. Results There was no difference in the AUC of choline plasma concentrations after intake of the different supplements. Individual plasma kinetics of choline and betaine differed and concentrations peaked latest for PC (at ≈3 h). All supplements similarly increased plasma betaine. All water-soluble supplements rapidly increased TMAO, whereas egg-PC did not. Conclusion All supplements tested rapidly increased choline and betaine levels to a similar extent, with egg-PC showing the latest peak. Assuming that TMAO may have undesirable effects, egg-PC might be best suited for choline supplementation in adults. Study registration This study was registered at “Deutsches Register Klinischer Studien” (DRKS) (German Register for Clinical Studies), 17.01.2020, DRKS00020454.
Late Anisian microbe‐metazoan build‐ups in the Germanic Basin: aftermath of the Permian–Triassic crisis
2021-07-21

The so-called Permian–Triassic mass extinction was followed by a prolonged period of ecological recovery that lasted until the Middle Triassic. Triassic stromatolites from the Germanic Basin seem to be an important part of the puzzle but have barely been investigated so far. Here, we analysed late Anisian (upper Middle Muschelkalk) stromatolites from across the Germanic Basin by combining petrographic approaches (optical microscopy, micro X-ray fluorescence, Raman imaging) and geochemical analyses (sedimentary hydrocarbons, stable carbon and oxygen isotopes). Palaeontological and sedimentological evidence, such as Placunopsis bivalves, intraclasts and disrupted laminated fabrics, indicate that the stromatolites formed in subtidal, shallow marine settings. This interpretation is consistent with δ13Ccarb of about −2.1‰ to −0.4‰. Occurrences of calcite pseudomorphs after gypsum possibly suggest occasionally elevated salinities, which is well in line with the relative rarity of fossils in the host strata. Remarkably, the stromatolites are composed of microbes (perhaps cyanobacteria and sulphate-reducing bacteria) and metazoans such as non-spicular demosponges, Placunopsis bivalves and/or microconchids. Therefore, these ‘stromatolites’ should more correctly be referred to as microbe-metazoan build-ups. They are characterized by diverse lamination types, including planar, wavy, domal and conical ones. Microbial mats likely played an important role in forming the planar and wavy laminations. Domal and conical laminations commonly show clotted to peloidal features and mesh-like fabrics, attributed to fossilized non-spicular demosponges. Our observations not only point up that non-spicular demosponges are easily overlooked and might be mistakenly interpreted as stromatolites, but also demonstrate that microbe-metazoan build-ups were widespread in the Germanic Basin during Early to Middle Triassic times. In the light of our findings, it appears plausible that the involved organisms benefited from elevated salinities. Another (not necessarily contradictory) possibility is that the mutualistic relationship between microbes and non-spicular demosponges enabled these organisms to fill ecological niches cleared by the Permian–Triassic crisis. If that is to be the case, it means that such microbe-metazoan associations maintained their advantage until the Middle Triassic.
Short term morphological rescue of the fovea after gene therapy with voretigene neparvovec
2021-07-21

Abstract Purpose Leber congenital amaurosis type 2 (LCA2) and early‐onset severe retinal dystrophy (EOSRD) are linked to visual impairment with nyctalopia and visual acuity reduction in early childhood. In 2017, the first gene therapy voretigene neparvovec (LuxturnaTM) for patients with LCA and EOSRD cause by bi‐allelic mutations in the RPE65 gene has been approved. Here we report on an example of short‐term change in the foveal morphology after functionally successful gene therapy with voretigene neparvovec in a 15‐year old patient. Methods The clinical examinations included best corrected visual acuity (BCVA), spectral domain optical coherence tomography (OCT) and adaptive optics retinal imaging. Results During follow‐up over a period of 3 months after the treatment, an improvement of the central foveal morphology could be observed in OCT, with a clear demarcation of the external limiting membrane and changes in the photoreceptor mosaic on adaptive optics retinal imaging. These morphological rescue parameters correlated in part with the improvement in foveal‐mediated vision after the treatment and adaptive optics imaging. Although the visual acuity improved only slightly at month 3, objective central cone evaluation with chromatic pupil campimetry showed an increase in the central sensitivity. In daily life, the patient reported her visional experience after the treatment as ‘brighter’. Conclusion Rapid changes in the correlates of photoreceptor morphology after successful gene therapy in patients with LCA/EORD can be quantifiable on individual level.
The MpsAB Bicarbonate Transporter Is Superior to Carbonic Anhydrase in Biofilm-Forming Bacteria with Limited CO 2 Diffusion
2021-07-21

CO 2 and bicarbonate are required for carboxylation reactions in central metabolism and biosynthesis of small molecules in all bacteria. This is achieved by two different systems for dissolved inorganic carbon supply (DICS): these are the membrane potential-generating system (MpsAB) and the carbonic anhydrase (CA), but both rarely coexist in a given species.
Longitudinal Changes of Fixation Stability and Location Within 24 Months in Stargardt Disease: ProgStar Report No. 16
2021-07-21

Fixation parameters are unlikely to be sensitive outcome measures for clinical trials in STGD1 but may provide useful ancillary information in selected cases to longitudinally describe and understand an eye's visual function.
From Center-Vortex Ensembles to the Confining Flux Tube
2021-07-21

In this review, we discuss the present status of the description of confining flux tubes in SU(N) pure Yang–Mills theory in terms of ensembles of percolating center vortices. This is based on three main pillars: modeling in the continuum the ensemble components detected in the lattice, the derivation of effective field representations, and contrasting the associated properties with Monte Carlo lattice results. The integration of the present knowledge about these points is essential to get closer to a unified physical picture for confinement. Here, we shall emphasize the last advances, which point to the importance of including the non-oriented center-vortex component and non-Abelian degrees of freedom when modeling the center-vortex ensemble measure. These inputs are responsible for the emergence of topological solitons and the possibility of accommodating the asymptotic scaling properties of the confining string tension.
Predictors of COVID-19 in an outpatient fever clinic
2021-07-21

Background The objective of this study was to identify clinical risk factors for COVID-19 in a German outpatient fever clinic that allow distinction of SARS-CoV-2 infected patients from other patients with flu-like symptoms. Methods This is a retrospective, single-centre cohort study. Patients were included visiting the fever clinic from 4 th of April 2020 to 15 th of May 2020. Symptoms, comorbidities, and socio-demographic factors were recorded in a standardized fashion. Multivariate logistic regression was used to identify risk factors of COVID-19, on the bases of those a model discrimination was assessed using area under the receiver operation curves (AUROC). Results The final analysis included 930 patients, of which 74 (8%) had COVID-19. Anosmia (OR 10.71; CI 6.07–18.9) and ageusia (OR 9.3; CI 5.36–16.12) were strongly associated with COVID-19. High-risk exposure (OR 12.20; CI 6.80–21.90), especially in the same household (OR 4.14; CI 1.28–13.33), was also correlated; the more household members, especially with flu-like symptoms, the higher the risk of COVID-19. Working in an essential workplace was also associated with COVID-19 (OR 2.35; CI 1.40–3.96), whereas smoking was inversely correlated (OR 0.19; CI 0.08–0.44). A model that considered risk factors like anosmia, ageusia, concomitant of symptomatic household members and smoking well discriminated COVID-19 patients from other patients with flu-like symptoms (AUROC 0.84). Conclusions We report a set of four readily available clinical parameters that allow the identification of high-risk individuals of COVID-19. Our study will not replace molecular testing but will help guide containment efforts while waiting for test results.
The effect of fertility-sparing surgery on sexuality and global quality of life in women with malignant ovarian germ cell and sex cord stromal tumors: an analysis of the CORSETT database of the AGO study group
2021-07-21

Abstract Purpose Malignant ovarian germ cell (MOGCT) and sex cord stromal tumors (SCST) are ovarian neoplasms that affect disproportionally young women. Little is known about the impact of surgical and adjuvant management of these patient’s sexual life. This study investigated the effect of fertility-sparing surgery on sexual activity and global quality of life (gQoL) in women with MOGCT and SCST. Methods CORSETT was an observational, multicenter, mixed retrospective/prospective cohort study of the AGO study group. Women of any age who had been diagnosed with MOGCTs and SCSTs between 2001 and 2011 were asked to complete the Sexual Activity Questionnaire (SAQ) and the EORTC QLQ-C30. Results In total, 355 patients were included. Of these, 152 patients with confirmed histological diagnosis had completed the questionnaires. A total of 106 patients were diagnosed with SCST and 46 with MOGCT. Totally, 83 women (55%) were sexually active. After fertility-sparing surgery, patients had a 2.6 fold higher probability for being sexually active than after non-fertility-conserving treatment (unadjusted odds ratio (OR) 2.6, p = 0.01). After adjustment for age, time since diagnosis, FIGO stage, histology and phase of disease, the OR dropped to 1.8 ( p = 0.22). Of the sexually active patients, 35 (42%) reported high levels of discomfort during intercourse; 38% after fertility-sparing; and 58% after non-fertility-sparing surgery (adjusted OR 2.8, p = 0.18). Women with fertility-conserving treatment reported a significantly better global QoL ( F adj 2.1, 6.2 points difference, p = 0.03) but not more pleasure during intercourse than women without fertility-sparing surgery ( F adj 0.4, p = 0.52). Conclusion Fertility preserving approaches should be offered to every patient, when oncologically acceptable.
Platform Generation for Edge AI Devices with Custom Hardware Accelerators
2021-07-21

In recent years artificial neural networks (NNs) have been at the center of research on data processing. However, their high computational demand often prohibits deployment on resource-constrained Industrial IoT Systems. Custom hardware accelerators can enable real-time NN processing on small-scale edge devices but are generally hard to develop and integrate. In this paper we present a hardware generation approach to rapidly create, test, and deploy entire SoC platforms with application-specific NN hardware accelerators. The feasibility of the approach is demonstrated by the generation of a condition monitoring system for high-speed valves.
Two circadian oscillators in one cyanobacterium
2021-07-21

Abstract Organisms from all kingdoms of life have evolved diverse mechanisms to address the predictable environmental changes resulting from the Earth’s rotation. The circadian clock of cyanobacteria is a particularly simple and elegant example of a biological timing mechanism for predicting daily changes in the light environment. The three proteins KaiA, KaiB, and KaiC constitute the central timing mechanism that drives circadian oscillations in the cyanobacterium Synechococcus elongatus PCC 7942. In addition to the standard oscillator, Synechocystis sp. PCC 6803, another model organism for cyanobacterial research, harbors several divergent clock homologs. Here, we describe a potential new chimeric KaiA homolog that we named KaiA3. At the N-terminus, KaiA3 is similar to the NarL-type response regulator receiver domain. However, its similarity to canonical NarL transcription factors drastically decreases in the C-terminal domain, which resembles the circadian clock protein, KaiA. In line with this, we detected KaiA3-mediated stimulation of KaiC3 phosphorylation. Phosphorylation of KaiC3 was rhythmic over 48 h in vitro in the presence of KaiA3 and KaiB3 as well as in Synechocystis cells under free-running conditions after light/dark entrainment. This results in the presence of two different oscillators in a single-celled prokaryotic organism. Deletion of the kaiA3 gene leads to KaiC3 dephosphorylation and results in growth defects during mixotrophic growth and in the dark. In summary, we suggest that KaiA3 is a nonstandard KaiA homolog, thereby extending the KaiB3-KaiC3 system in Cyanobacteria and potentially other prokaryotes.
Should I Stay or Should I Go? The Impact of Social Networks on the Choice to Play for a National Team in Football
2021-07-21

In the course of their careers, elite athletes are faced with crucial decisions. This applies particularly to adolescent athletes who additionally have to cope with a variety of age-related developmental tasks. For young top football players with a migrant background, this can be even more challenging as they often attract the interest of national associations. From a network-theoretical perspective, it can be considered likely that the decision to join a top national association is not taken independently of the players’ networks. This article addresses the role of network actors within the players’ decision-making process. Our analysis is guided by constructivist network theory and based on a qualitative research approach that used guided expert interviews as its core research tool. Ten interviews with German-born youth internationals with a migrant background were conducted. The present analysis reveals several network actors such as family, coaches and players’ agents involved in the ‘national team question’. Evidently, most relevant networks of players with a migrant background are sports-related. These networks turned out to be highly functionalized and leave only limited room for manoeuvring. At the same time, the interviews reveal ‘structural holes’ within the players’ networks and indicate a considerable need for the optimization of talent counselling.
Inference of time series components by online co-evolution
2021-07-21

Abstract Time series data is often composed of a multitude of individual, superimposed dynamics. We propose a novel algorithm for inferring time series compositions through evolutionary synchronization of modular networks (ESMoN). ESMoN orchestrates a set of trained dynamic modules, assuming that some of those modules’ dynamics, suitably parameterized, will be present in the targeted time series. With the help of iterative co-evolution techniques, ESMoN optimizes the activities of its modules dynamically, which effectively synchronizes the system with the unfolding time series signal and distributes the dynamic subcomponents present in the time series over the respective modules. We show that ESMoN can adapt modules of different types. Moreover, it is able to precisely identify the signal components of various time series dynamics. We thus expect that ESMoN will be useful also in other domains—including, for example, medical, physical, and behavioral data domains—where the data is composed of known signal sources.
Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition
2021-07-22

The ratio of microbial population size relative to the amount of host tissue, or ‘microbial load’, is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because existing methods to determine load, such as serial dilution plating, quantitative PCR, and whole metagenome sequencing add substantial cost and/or experimental burden, they are only rarely paired with amplicon sequencing. We introduce host-associated microbe PCR (hamPCR), a robust strategy to both quantify microbial load and describe interkingdom microbial community composition in a single amplicon library. We demonstrate its accuracy across multiple study systems, including nematodes and major crops, and further present a cost-saving technique to reduce host overrepresentation in the library prior to sequencing. Because hamPCR provides an accessible experimental solution to the well-known limitations and statistical challenges of compositional data, it has far-reaching potential in culture-independent microbiology.
Phosphine‐Stabilized Pnictinidenes
2021-07-22

Abstract The reaction of the intramolecular germylene‐phosphine Lewis pair (o‐PPh 2 )C 6 H 4 GeAr* ( 1 ) with Group 15 element trichlorides ECl 3 (E=P, As, Sb) was investigated. After oxidative addition, the resulting compounds ( o ‐PPh 2 )C 6 H 4 (Ar*)Ge(Cl)ECl 2 ( 2 : E=P, 3 : E=As, 4 : E=Sb) were reduced by using sodium metal or LiHBEt 3 . The molecular structures of the phosphine‐stabilized phosphinidene ( o ‐PPh 2 )C 6 H 4 (Ar*)Ge(Cl)P ( 5 ), arsinidene ( o ‐PPh 2 )C 6 H 4 (Ar*)Ge(Cl)As ( 6 ) and stibinidene ( o ‐PPh 2 )C 6 H 4 (Ar*)Ge(Cl)Sb ( 7 ) are presented; they feature a two‐coordinate low‐valent Group 15 element. After chloride abstraction, a cyclic germaphosphene [( o ‐PPh 2 )C 6 H 4 (Ar*)GeP] [B(C 6 H 3 (CF 3 ) 2 ) 4 ] ( 8 ) was isolated. The 31 P NMR data of the germaphosphene were compared with literature examples and analyzed by quantum chemical calculations. The phosphinidene was treated with [ i Bu 2 AlH] 2 , and the product of an Al−H addition to the low‐valent phosphorus atom ( o ‐PPh 2 )C 6 H 4 (Ar*)Ge(H)P(H)Al(C 4 H 9 ) 2 ( 9 ) was characterized.
Typically asymptomatic but with robust antibody formation: Children’s unique humoral immune response to SARS-CoV-2
2021-07-22

Abstract Background Long-term persistence of antibodies against SARS-CoV-2, particularly the SARS-CoV-2 Spike Trimer, determines individual protection against infection and potentially viral spread. The quality of children’s natural humoral immune response following SARS-CoV-2 infection is yet incompletely understood but crucial to guide pediatric SARS-CoV-2 vaccination programs. Methods In this prospective observational multi-center cohort study, we followed 328 households, consisting of 548 children and 717 adults, with at least one member with a previous laboratory-confirmed SARS-CoV-2 infection. The serological response was assessed at 3-4 months and 11-12 months after infection using a bead-based multiplex immunoassay for 23 human coronavirus antigens including SARS-CoV-2 and its Variants of Concern (VOC) and endemic human coronaviruses (HCoVs), and additionally by three commercial SARS-CoV-2 antibody assays. Results Overall, 33.76% of SARS-CoV-2 exposed children and 57.88% adults were seropositive. Children were five times more likely to have seroconverted without symptoms compared to adults. Despite the frequently asymptomatic course of infection, children had higher specific antibody levels, and their antibodies persisted longer than in adults (96.22% versus 82.89% still seropositive 11-12 months post infection). Of note, symptomatic and asymptomatic infections induced similar humoral responses in all age groups. In symptomatic children, only dysgeusia was found as diagnostic indicator of COVID-19. SARS-CoV-2 infections occurred independent of HCoV serostatus. Antibody binding responses to VOCs were similar in children and adults, with reduced binding for the Beta variant in both groups. Conclusions The long-term humoral immune response to SARS-CoV-2 infection in children is robust and may provide long-term protection even after asymptomatic infection. (Study ID at German Clinical Trials Register: 00021521)
Interplay between Kinetics and Dynamics of Liquid–Liquid Phase Separation in a Protein Solution Revealed by Coherent X-ray Spectroscopy
2021-07-22

Microscopic dynamics of complex fluids in the early stage of spinodal decomposition (SD) is strongly intertwined with the kinetics of structural evolution, which makes a quantitative characterization challenging. In this work, we use X-ray photon correlation spectroscopy to study the dynamics and kinetics of a protein solution undergoing liquid–liquid phase separation (LLPS). We demonstrate that in the early stage of SD, the kinetics relaxation is up to 40 times slower than the dynamics and thus can be decoupled. The microscopic dynamics can be well described by hyper-diffusive ballistic motions with a relaxation time exponentially growing with time in the early stage followed by a power-law increase with fluctuations. These experimental results are further supported by simulations based on the Cahn–Hilliard equation. The established framework is applicable to other condensed matter and biological systems undergoing phase transitions and may also inspire further theoretical work.
Interplay between Kinetics and Dynamics of Liquid–Liquid\\nPhase Separation in a Protein Solution Revealed by Coherent X‑ray\\nSpectroscopy
2021-07-22

Microscopic dynamics\\nof complex fluids in the early stage of spinodal\\ndecomposition (SD) is strongly intertwined with the kinetics of structural\\nevolution, which makes a quantitative characterization challenging.\\nIn this work, we use X-ray photon correlation spectroscopy to study\\nthe dynamics and kinetics of a protein solution undergoing liquid–liquid\\nphase separation (LLPS). We demonstrate that in the early stage of\\nSD, the kinetics relaxation is up to 40 times slower than the dynamics\\nand thus can be decoupled. The microscopic dynamics can be well described\\nby hyper-diffusive ballistic motions with a relaxation time exponentially\\ngrowing with time in the early stage followed by a power-law increase\\nwith fluctuations. These experimental results are further supported\\nby simulations based on the Cahn–Hilliard equation. The established\\nframework is applicable to other condensed matter and biological systems\\nundergoing phase transitions and may also inspire further theoretical\\nwork.