bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capillary flow experiments for thermodynamic and kinetic characterization of protein liquid-liquid phase separation
Authors: Stender Emil G. P. , Ray Soumik , Norrild Rasmus K. , Larsen Jacob Aunstrup , Petersen Daniel , Farzadfard Azad , Galvagnion Céline , Jensen Henrik , Buell Alexander K. 
Published: December 2021

AbstractLiquid-liquid phase separation or LLPS of proteins is a field of mounting importance and the value of quantitative kinetic and thermodynamic characterization of LLPS is increasingly recognized. We present a method, Capflex, which allows rapid and accurate quantification of key parameters for LLPS: Dilute phase concentration, relative droplet size distributions, and the kinetics of droplet formation and maturation into amyloid fibrils. The binding affinity between the polypeptide undergoing LLPS and LLPS-modulating compounds can also be determined. We apply Capflex to characterize the LLPS of Human DEAD-box helicase-4 and the coacervate system ssDNA/RP3. Furthermore, we study LLPS and the aberrant liquid-to-solid phase transition of α-synuclein. We quantitatively measure the decrease in dilute phase concentration as the LLPS of α-synuclein is followed by the formation of Thioflavin-T positive amyloid aggregates. The high information content, throughput and the versatility of Capflex makes it a valuable tool for characterizing biomolecular LLPS.
Piezoelectricity in hafnia
Authors: Dutta Sangita , Buragohain Pratyush , Glinsek Sebastjan , Richter Claudia , Aramberri Hugo , Lu Haidong , Schroeder Uwe , Defay Emmanuel , Gruverman Alexei , Íñiguez Jorge 
Published: December 2021

AbstractBecause of its compatibility with semiconductor-based technologies, hafnia (HfO2) is today’s most promising ferroelectric material for applications in electronics. Yet, knowledge on the ferroic and electromechanical response properties of this all-important compound is still lacking. Interestingly, HfO2 has recently been predicted to display a negative longitudinal piezoelectric effect, which sets it apart from classic ferroelectrics (e.g., perovskite oxides like PbTiO3) and is reminiscent of the behavior of some organic compounds. The present work corroborates this behavior, by first-principles calculations and an experimental investigation of HfO2 thin films using piezoresponse force microscopy. Further, the simulations show how the chemical coordination of the active oxygen atoms is responsible for the negative longitudinal piezoelectric effect. Building on these insights, it is predicted that, by controlling the environment of such active oxygens (e.g., by means of an epitaxial strain), it is possible to change the sign of the piezoelectric response of the material.
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
Authors: Van Den Bossche Tim , Kunath Benoit J. , Schallert Kay , Schäpe Stephanie S. , Abraham Paul E. , Armengaud Jean , Arntzen Magnus Ø. , Bassignani Ariane , Benndorf Dirk , Fuchs Stephan , Giannone Richard J. , Griffin Timothy J. , Hagen Live H. , Halder Rashi , Henry Céline , Hettich Robert L. , Heyer Robert , Jagtap Pratik , Jehmlich Nico , Jensen Marlene , Juste Catherine , Kleiner Manuel , Langella Olivier , Lehmann Theresa , Leith Emma , May Patrick , Mesuere Bart , Miotello Guylaine , Peters Samantha L. , Pible Olivier , Queiros Pedro T. , Reichl Udo , Renard Bernhard Y. , Schiebenhoefer Henning , Sczyrba Alexander , Tanca Alessandro , Trappe Kathrin , Trezzi Jean-Pierre , Uzzau Sergio , Verschaffelt Pieter , von Bergen Martin , Wilmes Paul , Wolf Maximilian , Martens Lennart , Muth Thilo 
Published: December 2021

AbstractMetaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
Directly recruited GATA6 + peritoneal cavity macrophages contribute to the repair of intestinal serosal injury
Authors: Honda Masaki , Kadohisa Masashi , Yoshii Daiki , Komohara Yoshihiro , Hibi Taizo 
Published: December 2021

AbstractRecruitment of bone marrow derived monocytes via bloodstream and their subsequent conversion to CX3CR1+ macrophages in response to intestinal injury is dependent on CCR2, Nr4a1, and the microbiome. This process is critical for proper tissue repair; however, GATA6+ peritoneal cavity macrophages might represent an alternative, more readily available source of mature and functional myeloid cells at the damaged intestinal locations. Here we show, using spinning-disk confocal microscopy, that large F4/80hiGATA6+ peritoneal cavity macrophages promptly accumulate at damaged intestinal sites upon intestinal thermal injury and upon dextran sodium sulfate induced colitis in mice via a direct route from the peritoneal cavity. In contrast to bloodstream derived monocytes/macrophages, cavity macrophages do not depend on CCR2, Nr4a1 or the microbiome for recruitment, but rather on the ATP-release and exposed hyaluronan at the site of injury. They participate in the removal of necrotic cells, revascularization and collagen deposition and thus resolution of tissue damage. In summary, peritoneal cavity macrophages represent a rapid alternative route of intestinal tissue repair to traditional monocyte-derived macrophages.
The impact of sleep, physical activity and sedentary behaviour on symptoms of depression and anxiety before and during the COVID-19 pandemic in a sample of South African participants
Authors: Lewis R. , Roden L. C. , Scheuermaier K. , Gomez-Olive F. X. , Rae D. E. , Iacovides S. , Bentley A. , Davy J. P. , Christie C. J. , Zschernack S. , Roche J. , Lipinska G. 
Published: December 2021

AbstractDuring lockdowns associated with the COVID-19 pandemic, individuals have experienced poor sleep quality and sleep regularity, changes in lifestyle behaviours, and heightened depression and anxiety. However, the inter-relationship and relative strength of those behaviours on mental health outcomes is still unknown. We collected data between 12 May and 15 June 2020 from 1048 South African adults (age: 32.76 ± 14.43 years; n = 767 female; n = 473 students) using an online questionnaire. Using structural equation modelling, we investigated how insomnia symptoms, sleep regularity, exercise intensity/frequency and sitting/screen-use (sedentary screen-use) interacted to predict depressive and anxiety-related symptoms before and during lockdown. We also controlled for the effects of sex and student status. Irrespective of lockdown, (a) more severe symptoms of insomnia and greater sedentary screen-use predicted greater symptoms of depression and anxiety and (b) the effects of sedentary screen-use on mental health outcomes were mediated by insomnia. The effects of physical activity on mental health outcomes, however, were only significant during lockdown. Low physical activity predicted greater insomnia symptom severity, which in turn predicted increased depressive and anxiety-related symptoms. Overall, relationships between the study variables and mental health outcomes were amplified during lockdown. The findings highlight the importance of maintaining physical activity and reducing sedentary screen-use to promote better sleep and mental health.
Burial of microplastics in freshwater sediments facilitated by iron-organo flocs
Authors: Leiser Rico , Schumann Maja , Dadi Tallent , Wendt-Potthoff Katrin 
Published: December 2021

AbstractMicroplastics are ubiquitous in standing freshwater bodies, consequently lakes and reservoirs may be important sinks for these contaminants. However, the mechanisms governing the deposition of microplastics and their interactions with the sediments are understudied. We demonstrate how aggregation-based transport facilitates the sinking and infiltration of buoyant microplastics into freshwater reservoir sediments by employing experiments with intact sediment cores. Buoyant polyethylene microplastics were rapidly (1–4 h) incorporated into sinking iron-organic aggregates, followed by swift deposition into sediments. Ingression of microplastic bearing flocs into sediments was completed within 6 days and led to stable deposition of the incorporated particles for at least 2 months. Most microplastics were deposited in the top 2 cm of the sediments and few particles (5–15%) were re-released into the water. Our results show at least 85% burial of microplastics, indicating the significant role of freshwaters with low flow velocities in reducing microplastic loads to the oceans.
Causal motifs and existence of endogenous cascades in directed networks with application to company defaults
Authors: Barjašić Irena , Štefančić Hrvoje , Pribičević Vedrana , Zlatić Vinko 
Published: December 2021

AbstractMotivated by the problem of detection of cascades of defaults in economy, we developed a detection framework for an endogenous spreading based on causal motifs we define in this paper. We assume that the change of state of a vertex can be triggered either by an endogenous (related to the network) or an exogenous (unrelated to the network) event, that the underlying network is directed and that times when vertices changed their states are available. After simulating default cascades driven by different stochastic processes on different synthetic networks, we show that some of the smallest causal motifs can robustly detect endogenous spreading events. Finally, we apply the method to the data of defaults of Croatian companies and observe the time window in which an endogenous cascade was likely happening.
A functional spleen contributes to afucosylated IgG in humans
Authors: Wojcik Iwona , Schmidt David E. , de Neef Lisa A. , Rab Minke A. E. , Meek Bob , de Weerdt Okke , Wuhrer Manfred , van der Schoot C. Ellen , Zwaginga Jaap J. , de Haas Masja , Falck David , Vidarsson Gestur 
Published: December 2021

AbstractAs a lymphoid organ, the spleen hosts a wide range of immune cell populations, which not only remove blood-borne antigens, but also generate and regulate antigen-specific immune responses. In particular, the splenic microenvironment has been demonstrated to play a prominent role in adaptive immune responses to enveloped viral infections and alloantigens. During both types of immunizations, antigen-specific immunoglobulins G (IgGs) have been characterized by the reduced amount of fucose present on N-linked glycans of the fragment crystallizable (Fc) region. These glycans are essential for mediating the induction of immune effector functions. Therefore, we hypothesized that a spleen may modulate humoral responses and serve as a preferential site for afucosylated IgG responses, which potentially play a role in immune thrombocytopenia (ITP) pathogenesis. To determine the role of the spleen in IgG-Fc glycosylation, we performed IgG subclass-specific liquid chromatography–mass spectrometry (LC–MS) analysis of Fc glycosylation in a large cohort of individuals splenectomized due to trauma, due to ITP, or spherocytosis. IgG-Fc fucosylation was consistently increased after splenectomy, while no effects for IgG-Fc galactosylation and sialylation were observed. An increase in IgG1- and IgG2/3-Fc fucosylation level upon splenectomy has been reported here for the first time, suggesting that immune responses occurring in the spleen may be particularly prone to generate afucosylated IgG responses. Surprisingly, the level of total IgG-Fc fucosylation was decreased in ITP patients compared to healthy controls. Overall, our results suggest a yet unrecognized role of the spleen in either the induction or maintenance of afucosylated IgG responses by B cells.
A data-driven approach to measuring epidemiological susceptibility risk around the world
Authors: Bitetto Alessandro , Cerchiello Paola , Mertzanis Charilaos 
Published: December 2021

AbstractEpidemic outbreaks are extreme events that become more frequent and severe, associated with large social and real costs. It is therefore important to assess whether countries are prepared to manage epidemiological risks. We use a fully data-driven approach to measure epidemiological susceptibility risk at the country level using time-varying information. We apply both principal component analysis (PCA) and dynamic factor model (DFM) to deal with the presence of strong cross-section dependence in the data. We conduct extensive in-sample model evaluations of 168 countries covering 17 indicators for the 2010–2019 period. The results show that the robust PCA method accounts for about 90% of total variability, whilst the DFM accounts for about 76% of the total variability. Our index could therefore provide the basis for developing risk assessments of epidemiological risk contagion. It could be also used by organizations to assess likely real consequences of epidemics with useful managerial implications.
Preliminary feasibility assessment of CDM-based active surveillance using current status of medical device data in medical records and OMOP-CDM
Authors: Choi Sooin , Choi Soo Jeong , Kim Jin Kuk , Nam Ki Chang , Lee Suehyun , Kim Ju Han , Lee You Kyoung 
Published: December 2021

AbstractIn recent years, there has been an emerging interest in the use of claims and electronic health record (EHR) data for evaluation of medical device safety and effectiveness. In Korea, national insurance electronic data interchange (EDI) code has been used as a medical device data source for common data model (CDM). This study performed a preliminary feasibility assessment of CDM-based vigilance. A cross-sectional study of target medical device data in EHR and CDM was conducted. A total of 155 medical devices were finally enrolled, with 58.7% of them having EDI codes. Femoral head prosthesis was selected as a focus group. It was registered in our institute with 11 EDI codes. However, only three EDI codes were converted to systematized nomenclature of medicine clinical terms concept. EDI code was matched in one-to-many (up to 104) with unique device identifier (UDI), including devices classified as different global medical device nomenclature. The use of UDI rather than EDI code as a medical device data source is recommended. We hope that this study will share the current state of medical device data recorded in the EHR and contribute to the introduction of CDM-based medical device vigilance by selecting appropriate medical device data sources.
Determinants of falls after stroke based on data on 5065 patients from the Swedish Väststroke and Riksstroke Registers
Authors: Persson Carina U. , Hansson Per-Olof 
Published: December 2021

AbstractWe aimed to identify determinants in acute stroke that are associated with falls during the stroke unit stay. In order to enable individualized preventive actions, this knowledge is fundamental. Based on local and national quality register data on an unselected sample of 5065 stroke patients admitted to a stroke unit at a Swedish university hospital, univariable and multivariable logistic regression analyses were performed. The dependent variable was any fall during stroke unit stay. The independent variables related to function, activity, personal factors, time to assessment, comorbidities and treatments. Determinants of falls were: being male (odds ratio (OR) 2.25, 95% confidence interval (95% CI) 1.79–2.84), haemorrhagic stroke (OR 1.39, 95% CI 1.05–1.86), moderate stroke symptoms according to the National Institutes of Health Stroke Scale (NIHSS score 2–5 vs. NIHSS score 0–1) (OR 1.43, 95% CI 1.08–1.90), smoking (OR 1.70, 95% CI 1.29–2.25), impaired postural control in walking (OR 4.61, 95% CI 3.29–6.46), impaired postural control in standing (OR 1.60, 95% CI 1.25–2.05), stroke-related arm- and hand problems, OR 1.45, 95% CI 1.11–1.91), impaired cognition (OR 1.43, 95% CI 1.04–1.95), and urinary tract infection (OR 1.91, 95% CI 1.43–2.56). The findings from this study are useful in clinical practice and might help to improve patient safety after stroke.
RETRACTED ARTICLE: A brief comparative examination of tangent hyperbolic hybrid nanofluid through a extending surface: numerical Keller–Box scheme
Authors: Jamshed Wasim , Prakash M. , Devi S. Suriya Uma , Ibrahim Rabha W. , Shahzad Faisal , Nisar Kottakkaran Sooppy , Eid Mohamed R. , Abdel-Aty Abdel-Haleem , Khashan M. Motawi , Yahia I. S. 
Published: December 2021

AbstractA novel hybrid nanofluid was explored in order to find an efficient heat-transmitting fluid to replace standard fluids and revolutionary nanofluids. By using tangent hyperbolic hybrid combination nanoliquid with non-Newtonian ethylene glycol (EG) as a basis fluid and a copper (Cu) and titanium dioxide (TiO2) mixture, this work aims to investigate the viscoelastic elements of the thermal transferring process. Flow and thermal facts, such as a slippery extended surface with magnetohydrodynamic (MHD), suction/injection, form factor, Joule heating, and thermal radiation effects, including changing thermal conductivity, were also integrated. The Keller–Box method was used to perform collective numerical computations of parametric analysis using governing equivalences. In the form of graphs and tables, the results of TiO2–Cu/EG hybrid nanofluid were compared to those of standard Cu/EG nanofluid in important critical physical circumstances. The entropy generation study was used to examine energy balance and usefulness for important physically impacting parameters. Detailed scrutiny on entropy development get assisted with Weissenberg number, magnetic parameter, fractional volumes, injection parameter, thermal radiation, variable thermal conductivity, Biot number, shape variation parameter, Reynolds and Brinkman number. Whereas the entropy gets resisted for slip and suction parameter. In this case, spotted entropy buildup with important parametric ranges could aid future optimization.
DNA barcodes evidence the contact zone of eastern and western caddisfly lineages in the Western Carpathians
Authors: Bozáňová Jana , Čiampor Fedor , Mamos Tomasz , Grabowski Michal , Čiamporová-Zat’ovičová Zuzana 
Published: December 2021

AbstractThe region of the Western Carpathians is, among other aspects, very important for survival and diversity of European freshwater fauna due to the presence of a large number of (sub)mountain springs and streams. However, these ecologically and faunistically diversified habitats are still understudied in the context of genetic diversity and population structure of their inhabitants. This study focuses on genetic diversity and distribution patterns of the caddisfly Rhyacophila tristis, common and widespread representative of mountain freshwater fauna. Analysis of the COI mitochondrial marker revealed presence of the western and eastern lineages, with samples from both lineages being grouped in BOLD (Barcode of Life Data System) into separate BINs (Barcode Index Numbers). Our data indicates that eastern lineage (BIN_E) is more closely related to the Balkan populations than to co-occurring western lineage (BIN_W), and that the contact zone of the lineages passes through the W Carpathians. The study revealed phylogeographic and demographic differences between lineages, supporting hypothesis of their evolutionary independence and specific ecological preferences. The obtained genetic data of the R. tristis population from W Carpathians improved our knowledge about population genetics of this aquatic species and can contribute to understanding the state and evolution of biodiversity of freshwater ecosystems in Europe.
Talar trochlear morphology may not be a good skeletal indicator of locomotor behavior in humans and great apes
Authors: Nozaki Shuhei , Oishi Motoharu , Ogihara Naomichi 
Published: December 2021

AbstractTo reconstruct locomotor behaviors of fossil hominins and understand the evolution of bipedal locomotion in the human lineage, it is important to clarify the functional morphology of the talar trochlea in humans and extant great apes. Therefore, the present study aimed to investigate the interspecific-differences
of the talar trochlear morphology among humans, chimpanzees, gorillas, and orangutans by means of cone frustum approximation to calculate an apical angle and geometric morphometrics for detailed variability in the shape of the talar trochlea. The apical angles in gorillas and orangutans were significantly greater than those in humans and chimpanzees, but no statistical difference was observed between humans and chimpanzees, indicating that the apical angle did not necessarily correspond with the degree of arboreality in hominoids. The geometric morphometrics revealed clear interspecific differences in the trochlear morphology, but no clear association between the morphological characteristics of the trochlea and locomotor behavior was observed. The morphology of the trochlea may not be a distinct skeletal correlate of locomotor behavior, possibly because the morphology is determined not only by locomotor behavior, but also by other factors such as phylogeny and body size.
Fe and Zn stress induced gene expression analysis unraveled mechanisms of mineral homeostasis in common bean (Phaseolus vulgaris L.)
Authors: Urwat Uneeb , Ahmad Syed Mudasir , Masi Antonio , Ganai Nazir Ahmad , Murtaza Imtiyaz , Khan Imran , Zargar Sajad Majeed 
Published: December 2021

AbstractIron (Fe) and zinc (Zn) stress significantly affects fundamental metabolic and physiological processes in plants that results in reduction of plant growth and development. In the present study, common bean variety; Shalimar French Bean-1 (SFB-1) was used as an experimental material. Four different MGRL media i.e. normal MGRL medium (Control), media without Fe (0-Fe), media without Zn (0-Zn) and media with excess Zn (300-Zn) were used for growing seeds of SFB-1 under in vitro condition for three weeks under optimum conditions. Three week old shoot and root tissues were harvested from the plants grown in these four different in vitro conditions and were, subjected to Fe and Zn estimation. Further, extraction of total RNA for differential gene expression of ten candidate genes selected based on our in silico investigation and their classification, phylogeny and expression pattern was unraveled. Expression analysis of three candidate genes (OPT3, NRAMP2 and NRAMP3) in roots revealed possible cross talk among Fe/Zn stress that was further confirmed by observing less accumulation of Fe in roots under both these conditions. However, we observed, higher accumulation of Fe in shoots under 0-Fe condition compared to control that suggests precise sensing for priority based compartmentalization and partitioning leading to higher accumulation of Fe in shoots. Furthermore, the expression analysis of IRT1, FRO1 and Ferritin 1 genes under Fe/Zn stress suggested their role in uptake/transport and signaling of Fe and Zn, whereas the expression of ZIP2, NRAMP1, HA2 and GLP1 genes were highly responsive to Zn in Phaseolus vulgaris. The identified genes highly responsive to Fe and Zn stress condition can be potential candidates for overcoming mineral stress in dicot crop plants.