bluuebunny/crossref_metadata_2025 huggingface dataset:
USP11 controls R-loops by regulating senataxin proteostasis
Authors: Jurga Mateusz , Abugable Arwa A. , Goldman Alastair S. H. , El-Khamisy Sherif F.
Published: September 2021

R-loops are by-products of transcription that must be tightly regulated to maintain genomic stability and gene expression. Here, we describe a mechanism for the regulation of the R-loop-specific helicase, senataxin (SETX), and identify the ubiquitin specific peptidase 11 (USP11) as an R-loop regulator. USP11 de-ubiquitinates SETX and its depletion increases SETX K48-ubiquitination and protein turnover. Loss of USP11 decreases SETX steady-state levels and reduces R-loop dissolution. Ageing of USP11 knockout cells restores SETX levels via compensatory transcriptional downregulation of the E3 ubiquitin ligase, KEAP1. Loss of USP11 reduces SETX enrichment at KEAP1 promoter, leading to R-loop accumulation, enrichment of the endonuclease XPF and formation of double-strand breaks. Overexpression of KEAP1 increases SETX K48-ubiquitination, promotes its degradation and R-loop accumulation. These data define a ubiquitination-dependent mechanism for SETX regulation, which is controlled by the opposing activities of USP11 and KEAP1 with broad applications for cancer and neurological disease.
Functional and molecular characterization of a non-human primate model of autism spectrum disorder shows similarity with the human disease
Authors: Watanabe Satoshi , Kurotani Tohru , Oga Tomofumi , Noguchi Jun , Isoda Risa , Nakagami Akiko , Sakai Kazuhisa , Nakagaki Keiko , Sumida Kayo , Hoshino Kohei , Saito Koichi , Miyawaki Izuru , Sekiguchi Masayuki , Wada Keiji , Minamimoto Takafumi , Ichinohe Noritaka
Published: September 2021

Autism spectrum disorder (ASD) is a multifactorial disorder with characteristic synaptic and gene expression changes. Early intervention during childhood is thought to benefit prognosis. Here, we examined the changes in cortical synaptogenesis, synaptic function, and gene expression from birth to the juvenile stage in a marmoset model of ASD induced by valproic acid (VPA) treatment. Early postnatally, synaptogenesis was reduced in this model, while juvenile-age VPA-treated marmosets showed increased synaptogenesis, similar to observations in human tissue. During infancy, synaptic plasticity transiently increased and was associated with altered vocalization. Synaptogenesis-related genes were downregulated early postnatally. At three months of age, the differentially expressed genes were associated with circuit remodeling, similar to the expression changes observed in humans. In summary, we provide a functional and molecular characterization of a non-human primate model of ASD, highlighting its similarity to features observed in human ASD.
Evidence from a long-term experiment that collective risks change social norms and promote cooperation
Authors: Szekely Aron , Lipari Francesca , Antonioni Alberto , Paolucci Mario , Sánchez Angel , Tummolini Luca , Andrighetto Giulia
Published: September 2021

Social norms can help solve pressing societal challenges, from mitigating climate change to reducing the spread of infectious diseases. Despite their relevance, how norms shape cooperation among strangers remains insufficiently understood. Influential theories also suggest that the level of threat faced by different societies plays a key role in the strength of the norms that cultures evolve. Still little causal evidence has been collected. Here we deal with this dual challenge using a 30-day collective-risk social dilemma experiment to measure norm change in a controlled setting. We ask whether a looming risk of collective loss increases the strength of cooperative social norms that may avert it. We find that social norms predict cooperation, causally affect behavior, and that higher risk leads to stronger social norms that are more resistant to erosion when the risk changes. Taken together, our results demonstrate the causal effect of social norms in promoting cooperation and their role in making behavior resilient in the face of exogenous change.
Identification of a prismatic P3N3 molecule formed from electron irradiated phosphine-nitrogen ices
Authors: Zhu Cheng , Eckhardt André K. , Chandra Sankhabrata , Turner Andrew M. , Schreiner Peter R. , Kaiser Ralf I.
Published: September 2021

Polyhedral nitrogen containing molecules such as prismatic P3N3 - a hitherto elusive isovalent species of prismane (C6H6) - have attracted particular attention from the theoretical, physical, and synthetic chemistry communities. Here we report on the preparation of prismatic P3N3 [1,2,3-triaza-4,5,6-triphosphatetracyclo[2.2.0.02,6.03,5]hexane] by exposing phosphine (PH3) and nitrogen (N2) ice mixtures to energetic electrons. Prismatic P3N3 was detected in the gas phase and discriminated from its isomers utilizing isomer selective, tunable soft photoionization reflectron time-of-flight mass spectrometry during sublimation of the ices along with an isomer-selective photochemical processing converting prismatic P3N3 to 1,2,4-triaza-3,5,6-triphosphabicyclo[2.2.0]hexa-2,5-diene (P3N3). In prismatic P3N3, the P–P, P–N, and N–N bonds are lengthened compared to those in, e.g., diphosphine (P2H4), di-anthracene stabilized phosphorus mononitride (PN), and hydrazine (N2H4), by typically 0.03–0.10 Å.  These findings advance our fundamental understanding of the chemical bonding of poly-nitrogen and poly-phosphorus systems and reveal a versatile pathway to produce exotic, ring-strained cage molecules.
Getting a tool gives wings even in schizophrenia: underestimation of tool-related effort in a motor imagery task
Authors: Décombe Amandine , Brunel Lionel , Murday Vincent , Osiurak François , Capdevielle Delphine , Raffard Stéphane
Published: September 2021

Humans frequently use tools to reduce action-related efforts. Interestingly, several studies have demonstrated that individuals had tool-related biases in terms of perceived effort reduction during motor imagery tasks, despite the lack of evidence of real benefits. Reduced effort allocation has been repeatedly found in schizophrenia, but it remains unknown how schizophrenia patients perceive tool-related benefits regarding effort. Twenty-four schizophrenia patients and twenty-four nonclinical participants were instructed to move the same quantities of objects with their hands or with a tool in both real and imagined situations. Imagined and real movement durations were recorded. Similarly to nonclinical participants, patients overestimated tool-related benefits and underestimated tool-related effort in terms of time when they mentally simulated a task requiring the use of a tool. No association between movement durations and psychotic symptoms was found. Our results open new perspectives on the issue of effort in schizophrenia.
Dairying enabled Early Bronze Age Yamnaya steppe expansions
Authors: Wilkin Shevan , Ventresca Miller Alicia , Fernandes Ricardo , Spengler Robert , Taylor William T.-T. , Brown Dorcas R. , Reich David , Kennett Douglas J. , Culleton Brendan J. , Kunz Laura , Fortes Claudia , Kitova Aleksandra , Kuznetsov Pavel , Epimakhov Andrey , Zaibert Victor F. , Outram Alan K. , Kitov Egor , Khokhlov Aleksandr , Anthony David , Boivin Nicole
Published: September 2021

During the Early Bronze Age, populations of the western Eurasian steppe expanded across an immense area of northern Eurasia. Combined archaeological and genetic evidence supports widespread Early Bronze Age population movements out of the Pontic–Caspian steppe that resulted in gene flow across vast distances, linking populations of Yamnaya pastoralists in Scandinavia with pastoral populations (known as the Afanasievo) far to the east in the Altai Mountains1,2 and Mongolia3. Although some models hold that this expansion was the outcome of a newly mobile pastoral economy characterized by horse traction, bulk wagon transport4–6 and regular dietary dependence on meat and milk5, hard evidence for these economic features has not been found. Here we draw on proteomic analysis of dental calculus from individuals from the western Eurasian steppe to demonstrate a major transition in dairying at the start of the Bronze Age. The rapid onset of ubiquitous dairying at a point in time when steppe populations are known to have begun dispersing offers critical insight into a key catalyst of steppe mobility. The identification of horse milk proteins also indicates horse domestication by the Early Bronze Age, which provides support for its role in steppe dispersals. Our results point to a potential epicentre for horse domestication in the Pontic–Caspian steppe by the third millennium bc, and offer strong support for the notion that the novel exploitation of secondary animal products was a key driver of the expansions of Eurasian steppe pastoralists by the Early Bronze Age.
Structural basis of human transcription–DNA repair coupling
Authors: Kokic Goran , Wagner Felix R. , Chernev Aleksandar , Urlaub Henning , Cramer Patrick
Published: September 2021

Transcription-coupled DNA repair removes bulky DNA lesions from the genome1,2 and protects cells against ultraviolet (UV) irradiation3. Transcription-coupled DNA repair begins when RNA polymerase II (Pol II) stalls at a DNA lesion and recruits the Cockayne syndrome protein CSB, the E3 ubiquitin ligase, CRL4CSA and UV-stimulated scaffold protein A (UVSSA)3. Here we provide five high-resolution structures of Pol II transcription complexes containing human transcription-coupled DNA repair factors and the elongation factors PAF1 complex (PAF) and SPT6. Together with biochemical and published3,4 data, the structures provide a model for transcription–repair coupling. Stalling of Pol II at a DNA lesion triggers replacement of the elongation factor DSIF by CSB, which binds to PAF and moves upstream DNA to SPT6. The resulting elongation complex, ECTCR, uses the CSA-stimulated translocase activity of CSB to pull on upstream DNA and push Pol II forward. If the lesion cannot be bypassed, CRL4CSA spans over the Pol II clamp and ubiquitylates the RPB1 residue K1268, enabling recruitment of TFIIH to UVSSA and DNA repair. Conformational changes in CRL4CSA lead to ubiquitylation of CSB and to release of transcription-coupled DNA repair factors before transcription may continue over repaired DNA.
Underwater noise mitigation in the Santa Barbara Channel through incentive-based vessel speed reduction
Authors: ZoBell Vanessa M. , Frasier Kaitlin E. , Morten Jessica A. , Hastings Sean P. , Peavey Reeves Lindsey E. , Wiggins Sean M. , Hildebrand John A.
Published: September 2021

Commercial shipping is the dominant source of low-frequency noise in the ocean. It has been shown that the noise radiated by an individual vessel depends upon the vessel’s speed. This study quantified the reduction in source levels (SLs) and sound exposure levels (SELs) for ships participating in two variations of a vessel speed reduction (VSR) program. SLs and SELs of individual ships participating in the program between 2014 and 2017 were statistically lower than non-participating ships (p < 0.001). In the 2018 fleet-based program, there were statistical differences between the SLs and SELs of fleets that participated with varying degrees of cooperation. Significant reductions in SL and SEL relied on cooperation of 25% or more in slowing vessel speed. This analysis highlights how slowing vessel speed to 10 knots or less is an effective method in reducing underwater noise emitted from commercial ships.
Predicting the gender of individuals with tinnitus based on daily life data of the TrackYourTinnitus mHealth platform
Authors: Allgaier Johannes , Schlee Winfried , Langguth Berthold , Probst Thomas , Pryss Rüdiger
Published: September 2021

Tinnitus is an auditory phantom perception in the absence of an external sound stimulation. People with tinnitus often report severe constraints in their daily life. Interestingly, indications exist on gender differences between women and men both in the symptom profile as well as in the response to specific tinnitus treatments. In this paper, data of the TrackYourTinnitus platform (TYT) were analyzed to investigate whether the gender of users can be predicted. In general, the TYT mobile Health crowdsensing platform was developed to demystify the daily and momentary variations of tinnitus symptoms over time. The goal of the presented investigation is a better understanding of gender-related differences in the symptom profiles of users from TYT. Based on two questionnaires of TYT, four machine learning based classifiers were trained and analyzed. With respect to the provided daily answers, the gender of TYT users can be predicted with an accuracy of 81.7%. In this context, worries, difficulties in concentration, and irritability towards the family are the three most important characteristics for predicting the gender. Note that in contrast to existing studies on TYT, daily answers to the worst symptom question were firstly investigated in more detail. It was found that results of this question significantly contribute to the prediction of the gender of TYT users. Overall, our findings indicate gender-related differences in tinnitus and tinnitus-related symptoms. Based on evidence that gender impacts the development of tinnitus, the gathered insights can be considered relevant and justify further investigations in this direction.
Secondary predation constrains DNA-based diet reconstruction in two threatened shark species
Authors: de Bruyn Mark , Barbato Matteo , DiBattista Joseph D. , Broadhurst Matt K.
Published: September 2021

Increasing fishing effort, including bycatch and discard practices, are impacting marine biodiversity, particularly among slow-to-reproduce taxa such as elasmobranchs, and specifically sharks. While some fisheries involving sharks are sustainably managed, collateral mortalities continue, contributing towards > 35% of species being threatened with extinction. To effectively manage shark stocks, life-history information, including resource use and feeding ecologies is pivotal, especially among those species with wide-ranging distributions. Two cosmopolitan sharks bycaught off eastern Australia are the common blacktip shark (Carcharhinus limbatus; globally classified as Near Threatened) and great hammerhead (Sphyrna mokarran; Critically Endangered). We opportunistically sampled the digestive tracts of these two species (and also any whole prey; termed the ‘Russian-doll’ approach), caught in bather-protection gillnets off northern New South Wales, to investigate the capacity for DNA metabarcoding to simultaneously determine predator and prey regional feeding ecologies. While sample sizes were small,S. mokkaranfed predominantly on stingrays and skates (Myliobatiformes and Rajiformes), but also teleosts, whileC. limbatusmostly consumed teleosts. Metabarcoding assays showed extensive intermixing of taxa from the digestive tracts of predators and their whole prey, likely via the predator’s stomach chyme, negating the opportunity to distinguish between primary and secondary predation. This Russian-doll effect requires further investigation in DNA metabarcoding studies focussing on dietary preferences and implies that any outcomes will need to be interpreted concomitant with traditional visual approaches.
The nucleolar DExD/H protein Hel66 is involved in ribosome biogenesis in Trypanosoma brucei
Authors: Bakari-Soale Majeed , Ikenga Nonso Josephat , Scheibe Marion , Butter Falk , Jones Nicola G. , Kramer Susanne , Engstler Markus
Published: September 2021

The biosynthesis of ribosomes is a complex cellular process involving ribosomal RNA, ribosomal proteins and several further trans-acting factors. DExD/H box proteins constitute the largest family of trans-acting protein factors involved in this process. Several members of this protein family have been directly implicated in ribosome biogenesis in yeast. In trypanosomes, ribosome biogenesis differs in several features from the process described in yeast. Here, we have identified the DExD/H box helicase Hel66 as being involved in ribosome biogenesis. The protein is unique to Kinetoplastida, localises to the nucleolus and its depletion via RNAi caused a severe growth defect. Loss of the protein resulted in a decrease of global translation and accumulation of rRNA processing intermediates for both the small and large ribosomal subunits. Only a few factors involved in trypanosome rRNA biogenesis have been described so far and our findings contribute to gaining a more comprehensive picture of this essential process.
CRISPR/Cas9 small promoter deletion in H19 lncRNA is associated with altered cell morphology and proliferation
Authors: da Silva Santos Renan , Pinheiro Daniel Pascoalino , Teixeira Louhanna Pinheiro Rodrigues , Sales Sarah Leyenne Alves , dos Santos Luciano Maria Claudia , de Lima Melo Mayara Magna , Pinheiro Ronald Feitosa , Tavares Kaio César Simiano , Furtado Gilvan Pessoa , Pessoa Claudia , Furtado Cristiana Libardi Miranda
Published: September 2021

The imprinted H19 long non-coding RNA, a knowing oncofetal gene, presents a controversial role during the carcinogenesis process since its tumor suppressor or oncogenic activity is not completely elucidated. Since H19 lncRNA is involved in many biological pathways related to tumorigenesis, we sought to develop a non-cancer lineage with CRISPR-Cas9-mediated H19 knockdown (H19-) and observe the changes in a cellular context. To edit the promoter region of H19, two RNA guides were designed, and the murine C2C12 myoblast cells were transfected. H19 deletion was determined by DNA sequencing and gene expression by qPCR. We observed a small deletion (~ 60 bp) in the promoter region that presented four predicted transcription binding sites. The deletion reduced H19 expression (30%) and resulted in increased proliferative activity, altered morphological patterns including cell size and intracellular granularity, without changes in viability. The increased proliferation rate in the H19- cell seems to facilitate chromosomal abnormalities. The H19- myoblast presented characteristics similar to cancer cells, therefore the H19 lncRNA may be an important gene during the initiation of the tumorigenic process. Due to CRISPR/Cas9 permanent edition, the C2C12 H19- knockdown cells allows functional studies of H19 roles in tumorigenesis, prognosis, metastases, as well as drug resistance and targeted therapy.
Plateaus, rebounds and the effects of individual behaviours in epidemics
Authors: Berestycki Henri , Desjardins Benoît , Heintz Bruno , Oury Jean-Marc
Published: September 2021

Plateaus and rebounds of various epidemiological indicators are widely reported in Covid-19 pandemics studies but have not been explained so far. Here, we address this problem and explain the appearance of these patterns. We start with an empirical study of an original dataset obtained from highly precise measurements of SARS-CoV-2 concentration in wastewater over nine months in several treatment plants around the Thau lagoon in France. Among various features, we observe that the concentration displays plateaus at different dates in various locations but at the same level. In order to understand these facts, we introduce a new mathematical model that takes into account the heterogeneity and the natural variability of individual behaviours. Our model shows that the distribution of risky behaviours appears as the key ingredient for understanding the observed temporal patterns of epidemics.
Short-term facilitation of breathing upon cessation of hypoxic challenge is impaired in male but not female endothelial NOS knock-out mice
Authors: Getsy Paulina M. , Sundararajan Sripriya , May Walter J. , von Schill Graham C. , McLaughlin Dylan K. , Palmer Lisa A. , Lewis Stephen J.
Published: September 2021

Decreases in arterial blood oxygen stimulate increases in minute ventilation via activation of peripheral and central respiratory structures. This study evaluates the role of endothelial nitric oxide synthase (eNOS) in the expression of the ventilatory responses during and following a hypoxic gas challenge (HXC, 10% O2, 90% N2) in freely moving male and female wild-type (WT) C57BL6 and eNOS knock-out (eNOS–/–) mice. Exposure to HXC caused an array of responses (of similar magnitude and duration) in both male and female WT mice such as, rapid increases in frequency of breathing, tidal volume, minute ventilation and peak inspiratory and expiratory flows, that were subject to pronounced roll-off. The responses to HXC in male eNOS–/– mice were similar to male WT mice. In contrast, several of the ventilatory responses in female eNOS–/– mice (e.g., frequency of breathing, and expiratory drive) were greater compared to female WT mice. Upon return to room-air, male and female WT mice showed similar excitatory ventilatory responses (i.e., short-term potentiation phase). These responses were markedly reduced in male eNOS–/– mice, whereas female eNOS–/– mice displayed robust post-HXC responses that were similar to those in female WT mice. Our data demonstrates that eNOS plays important roles in (1) ventilatory responses to HXC in female compared to male C57BL6 mice; and (2) expression of post-HXC responses in male, but not female C57BL6 mice. These data support existing evidence that sex, and the functional roles of specific proteins (e.g., eNOS) have profound influences on ventilatory processes, including the responses to HXC.
Standard hospital blanket warming cabinets can be utilized for complete moist heat SARS-CoV2 inactivation of contaminated N95 masks for re-use
Authors: Kumar Anand , Kasloff Samantha B. , Cutts Todd , Leung Anders , Sharma Naresh , Vazquez-Grande Gloria , Drew Tracy , Laframboise Denis , Orofino Olivero , Tanelli Joe , Krishnan Jay
Published: September 2021

Shortages of personal protective equipment for use during the SARS-CoV-2 pandemic continue to be an issue among health-care workers globally. Extended and repeated use of N95 filtering facepiece respirators without adequate decontamination is of particular concern. Although several methods to decontaminate and re-use these masks have been proposed, logistic or practical issues limit adoption of these techniques. In this study, we propose and validate the use of the application of moist heat (70 °C with humidity augmented by an open pan of water) applied by commonly available hospital (blanket) warming cabinets to decontaminate N95 masks. This report shows that a variety of N95 masks can be repeatedly decontaminated of SARS-CoV-2 over 6 h moist heat exposure without compromise of their filtering function as assessed by standard fit and sodium chloride aerosol filtration efficiency testing. This approached can easily adapted to provide point-of-care N95 mask decontamination allowing for increased practical utility of mask recycling in the health care setting.
Generalized and social anxiety disorder interactomes show distinctive overlaps with striosome and matrix interactomes
Authors: Karunakaran Kalyani B. , Amemori Satoko , Balakrishnan N. , Ganapathiraju Madhavi K. , Amemori Ken-ichi
Published: September 2021

Mechanisms underlying anxiety disorders remain elusive despite the discovery of several associated genes. We constructed the protein–protein interaction networks (interactomes) of six anxiety disorders and noted enrichment for striatal expression among common genes in the interactomes. Five of these interactomes shared distinctive overlaps with the interactomes of genes that were differentially expressed in two striatal compartments (striosomes and matrix). Generalized anxiety disorder and social anxiety disorder interactomes showed exclusive and statistically significant overlaps with the striosome and matrix interactomes, respectively. Systematic gene expression analysis with the anxiety disorder interactomes constrained to contain only those genes that were shared with striatal compartment interactomes revealed a bifurcation among the disorders, which was influenced by the anterior cingulate cortex, nucleus accumbens, amygdala and hippocampus, and the dopaminergic signaling pathway. Our results indicate that the functionally distinct striatal pathways constituted by the striosome and the matrix may influence the etiological differentiation of various anxiety disorders.
Limit of detection in different matrices of 19 commercially available rapid antigen tests for the detection of SARS-CoV-2
Authors: Cubas-Atienzar Ana I. , Kontogianni Konstantina , Edwards Thomas , Wooding Dominic , Buist Kate , Thompson Caitlin R. , Williams Christopher T. , Patterson Edward I. , Hughes Grant L. , Baldwin Lisa , Escadafal Camille , Sacks Jilian A. , Adams Emily R.
Published: September 2021

In the context of the coronavirus disease 2019 (COVID-19) pandemic there has been an increase of the use of antigen-detection rapid diagnostic tests (Ag-RDT). The performance of Ag-RDT vary greatly between manufacturers and evaluating their analytical limit of detection (LOD) has become high priority. Here we describe a manufacturer-independent evaluation of the LOD of 19 marketed Ag-RDT using live SARS-CoV-2 spiked in different matrices: direct culture supernatant, a dry swab, and a swab in Amies. Additionally, the LOD using dry swab was investigated after 7 days’ storage at − 80 °C of the SARS-CoV-2 serial dilutions. An LOD of ≈ 5.0 × 102 pfu/ml (1.0 × 106 genome copies/ml) in culture media is defined as acceptable by the World Health Organization. Fourteen of 19 Ag-RDTs (ActiveXpress, Espline, Excalibur, Innova, Joysbio, Mologic, NowCheck, Orient, PanBio, RespiStrip, Roche, Standard-F, Standard-Q and Sure-Status) exceeded this performance criteria using direct culture supernatant applied to the Ag-RDT. Six Ag-RDT were not compatible with Amies media and a decreased sensitivity of 2 to 20-fold was observed for eleven tests on the stored dilutions at − 80 °C for 7 days. Here, we provide analytical sensitivity data to guide appropriate test and sample type selection for use and for future Ag-RDT evaluations.
Versatile cell-based assay for measuring DNA alkylation damage and its repair
Authors: Li Yong , Mao Peng , Basenko Evelina Y. , Lewis Zachary , Smerdon Michael J. , Czaja Wioletta
Published: September 2021

DNA alkylation damage induced by environmental carcinogens, chemotherapy drugs, or endogenous metabolites plays a central role in mutagenesis, carcinogenesis, and cancer therapy. Base excision repair (BER) is a conserved, front line DNA repair pathway that removes alkylation damage from DNA. The capacity of BER to repair DNA alkylation varies markedly between different cell types and tissues, which correlates with cancer risk and cellular responses to alkylation chemotherapy. The ability to measure cellular rates of alkylation damage repair by the BER pathway is critically important for better understanding of the fundamental processes involved in carcinogenesis, and also to advance development of new therapeutic strategies. Methods for assessing the rates of alkylation damage and repair, especially in human cells, are limited, prone to significant variability due to the unstable nature of some of the alkyl adducts, and often rely on indirect measurements of BER activity. Here, we report a highly reproducible and quantitative, cell-based assay, named alk-BER (alkylation Base Excision Repair) for measuring rates of BER following alkylation DNA damage. The alk-BER assay involves specific detection of methyl DNA adducts (7-methyl guanine and 3-methyl adenine) directly in genomic DNA. The assay has been developed and adapted to measure the activity of BER in fungal model systems and human cell lines. Considering the specificity and conserved nature of BER enzymes, the assay can be adapted to virtually any type of cultured cells. Alk-BER offers a cost efficient and reliable method that can effectively complement existing approaches to advance integrative research on mechanisms of alkylation DNA damage and repair.
Research on routing and scheduling algorithms for the simultaneous transmission of diverse data streaming services on the industrial internet
Authors: Song Yan , Guo Chenyang , Xu Panfeng , Li Lina , Zhang Rui
Published: September 2021

OPC UA PubSub Over TSN is the core of the Industrial Internet and guarantees flexible interaction features for multiple parties in real-time for industrial communication. To achieve the transmission of time-triggered traffic in PubSub NetworkMessage, routing and scheduling data need to be analyzed. Traditional routing and scheduling methods have disadvantages such as low calculation efficiency, slow convergence speed, and poor reliability. Therefore, a routing and scheduling method for OPC UA PubSub NetworkMessage time-triggered traffic based on an improved ant colony algorithm is proposed. First, we analyze the network topology model, traffic model, and traffic transmission constraints of TSN; then, we apply the K-means clustering algorithm, the KSP algorithm based on the shortest path idea, and an improved ant colony algorithm for traffic classification, routing, and scheduling calculation. Experimental results show that this method can effectively reduce the delay increase caused by link congestion, improve the ability to schedule time-triggered traffic, and accelerate the convergence rate of iteration.
Machine learning risk prediction model for acute coronary syndrome and death from use of non-steroidal anti-inflammatory drugs in administrative data
Authors: Lu Juan , Wang Ling , Bennamoun Mohammed , Ward Isaac , An Senjian , Sohel Ferdous , Chow Benjamin J. W. , Dwivedi Girish , Sanfilippo Frank M.
Published: September 2021

Our aim was to investigate the usefulness of machine learning approaches on linked administrative health data at the population level in predicting older patients’ one-year risk of acute coronary syndrome and death following the use of non-steroidal anti-inflammatory drugs (NSAIDs). Patients from a Western Australian cardiovascular population who were supplied with NSAIDs between 1 Jan 2003 and 31 Dec 2004 were identified from Pharmaceutical Benefits Scheme data. Comorbidities from linked hospital admissions data and medication history were inputs. Admissions for acute coronary syndrome or death within one year from the first supply date were outputs. Machine learning classification methods were used to build models to predict ACS and death. Model performance was measured by the area under the receiver operating characteristic curve (AUC-ROC), sensitivity and specificity. There were 68,889 patients in the NSAIDs cohort with mean age 76 years and 54% were female. 1882 patients were admitted for acute coronary syndrome and 5405 patients died within one year after their first supply of NSAIDs. The multi-layer neural network, gradient boosting machine and support vector machine were applied to build various classification models. The gradient boosting machine achieved the best performance with an average AUC-ROC of 0.72 predicting ACS and 0.84 predicting death. Machine learning models applied to linked administrative data can potentially improve adverse outcome risk prediction. Further investigation of additional data and approaches are required to improve the performance for adverse outcome risk prediction.
Impact of salt and exogenous AM inoculation on indigenous microbial community structure in the rhizosphere of dioecious plant, Populus cathayana
Authors: Wu Na , Li Zhen , Tang Ming
Published: September 2021

The sex-specific physical and biochemical responses in dioecious plants to abiotic stresses could result in gender imbalance, and how to ease the current situation by microorganisms is still unclear. Using native soil where poplars were grown, growth parameters, soil physicochemical properties in the rhizosphere soil of different sexes of Populus cathayana exposed to salt stress and exogenous arbuscular mycorrhizal (AM) inoculation were tested. Besides, the sex-specific microbial community structures in the rhizosphere soil of different sexes of Populus cathayana were compared under salt stress. To identify the sex-specific microbial community characteristics related to salinity and AM symbiosis, a combined qPCR and DGGE method was used to monitor microbial community diversity. Seedlings suffered severe pressure by salt stress, reflected in limited growth, biomass, and nutrient element accumulation, especially on females. Exogenous AM inoculation treatment alleviated these negative effects, especially under salt treatment of 75 mM. Compared with salt effect, exogenous AM inoculation treatment showed a greater effect on soil physical–chemical properties of both sexes. Based on DGGE results, salt stress negatively affected fungal richness but positively affected fungal Simpson diversity index, while exogenous AM inoculation treatment showed the opposite effect. Structural equation modeling (SEM) was performed to show the causal relationships between salt and exogenous AM inoculation treatments with biomass accumulation and microbial community: salt and exogenous AM inoculation treatment showed complicated effects on elementary concentrations, soil properties, which resulted in different relationship with biomass accumulation and microbial community. Salt stress had a negative effect on soil properties and microbial community structure in the rhizosphere soil of P. cathayana, whereas exogenous AM inoculation showed positive impacts on most of the soil physical–chemical properties and microbial community status.
Antennal and palpal sensilla of three predatory Lispe species (Diptera: Muscidae): an ultrastructural investigation
Authors: Liu Genting , Wang Qike , Liu Xianhui , Li Xinyu , Pang Xiunan , Zhang Dong
Published: September 2021

Antennae and maxillary palps are the most important chemical reception organs of flies. So far, the morphology of antennae and maxillary palps of flies of most feeding habits have been well described, except for that of relatively rare aquatic predatory species. This study describes sensilla on antennae and maxillary palps of three aquatic predatory Lispe species: Lispe longicollis, L. orientalis and L. pygmaea. Types, distribution, and density of sensilla are characterised via light and scanning electron microscopy. One type of mechanoreceptors is found on antennal scape. Mechanoreceptors (two subtypes) and one single pedicellar button (in L. pygmaea) are located on antennal pedicel. Four types of sensilla are discovered on antennal postpedicel: trichoid sensilla, basiconic sensilla (three subtypes), coeloconic sensilla and clavate sensilla. A unique character of these Lispe species is that the coeloconic sensilla are distributed sparsely on antennal postpedicel. Mechanoreceptors and basiconic sensilla are observed on the surface of maxillary palps in all three species. We demonstrated clear sexual dimorphism of the maxillary palps in some of the Lispe species, unlike most other Muscidae species, are larger in males than females. This, along with their courtship dance behaviour, suggest their function as both chemical signal receiver and visual signal conveyer, which is among the few records of a chemical reception organ act as a signal conveyer in insects.
Features of structure, magnetic state and electrodynamic performance of SrFe12−xInxO19
Authors: Turchenko V. A. , Trukhanov S. V. , Kostishin V. G. , Damay F. , Porcher F. , Klygach D. S. , Vakhitov M. G. , Lyakhov D. , Michels D. , Bozzo B. , Fina I. , Almessiere M. A. , Slimani Y. , Baykal A. , Zhou D. , Trukhanov A. V.
Published: September 2021

Indium-substituted strontium hexaferrites were prepared by the conventional solid-phase reaction method. Neutron diffraction patterns were obtained at room temperature and analyzed using the Rietveld methods. A linear dependence of the unit cell parameters is found. In3+ cations are located mainly in octahedral positions of 4fVI and 12 k. The average crystallite size varies within 0.84–0.65 μm. With increasing substitution, the TC Curie temperature decreases monotonically down to ~ 520 K. ZFC and FC measurements showed a frustrated state. Upon substitution, the average and maximum sizes of ferrimagnetic clusters change in the opposite direction. The Mr remanent magnetization decreases down to ~ 20.2 emu/g at room temperature. The Ms spontaneous magnetization and the keff effective magnetocrystalline anisotropy constant are determined. With increasing substitution, the maximum of the ε/ real part of permittivity decreases in magnitude from ~ 3.3 to ~ 1.9 and shifts towards low frequencies from ~ 45.5 GHz to ~ 37.4 GHz. The maximum of the tg(α) dielectric loss tangent decreases from ~ 1.0 to ~ 0.7 and shifts towards low frequencies from ~ 40.6 GHz to ~ 37.3 GHz. The low-frequency maximum of the μ/ real part of permeability decreases from ~ 1.8 to ~ 0.9 and slightly shifts towards high frequencies up to ~ 34.7 GHz. The maximum of the tg(δ) magnetic loss tangent decreases from ~ 0.7 to ~ 0.5 and shifts slightly towards low frequencies from ~ 40.5 GHz to ~ 37.7 GHz. The discussion of microwave properties is based on the saturation magnetization, natural ferromagnetic resonance and dielectric polarization types.
Toward enhanced catalytic activity of magnetic nanoparticles integrated into 3D reduced graphene oxide for heterogeneous Fenton organic dye degradation
Authors: Sadegh Fatemeh , Politakos Nikolaos , de San Roman Estibaliz Gonzalez , Sanz Oihane , Modarresi-Alam Ali Reza , Tomovska Radmila
Published: September 2021

Composite Fenton nanocatalyst was prepared by water-based in situ creation of Fe3O4nanoparticles integrated within the self-assembly 3D reduced graphene oxide (rGO) aerogel. The hybrid applied for the degradation of Acid Green 25 (AG-25) organic dye in an aqueous solution, in the presence of H2O2. By investigating the conditions that maximize the dye adsorption by the 3D composite, it was found that the pH of the solution should be adjusted between the pKa of the functional groups present on the rGO surface (carboxylic acid) and that of the dye (sulfonic acid) to promote electrostatic interactions dye—3D structure. Performed under these conditions, Fenton degradation of AG-25 in presence of H2O2was completed in less than 30 min, including all the intermediate products, as demonstrated by MALDI–TOF–MS analysis of the aqueous solution after discoloration. Moreover, this was achieved in a solution with as high a dye concentration of 0.5 mg/mL, with only 10 mg of 3D composite catalyst, at room temperature and without additional energy input. The high performance was attributed to the creation of charge-transfer complex between rGO and Fe3O4nanoparticles throughout covalent bond C–O–Fe, the formation of which was promoted by the in situ synthesis procedure. For the first time, up to the authors’ knowledge, AG-25 degradation mechanism was proposed.
Semiautomated 3D mapping of aneurysmal wall enhancement with 7T-MRI
Authors: Raghuram Ashrita , Varon Alberto , Roa Jorge A. , Ishii Daizo , Lu Yongjun , Raghavan Madhavan L. , Wu Chaorong , Magnotta Vincent A. , Hasan David M. , Koscik Timothy R. , Samaniego Edgar A.
Published: September 2021

Aneurysm wall enhancement (AWE) after the administration of contrast gadolinium is a potential biomarker of unstable intracranial aneurysms. While most studies determine AWE subjectively, this study comprehensively quantified AWE in 3D imaging using a semi-automated method. Thirty patients with 33 unruptured intracranial aneurysms prospectively underwent high-resolution imaging with 7T-MRI. The signal intensity (SI) of the aneurysm wall was mapped and normalized to the pituitary stalk (PS) and corpus callosum (CC). The CC proved to be a more reliable normalizing structure in detecting contrast enhancement (p < 0.0001). 3D-heatmaps and histogram analysis of AWE were used to generate the following metrics: specific aneurysm wall enhancement (SAWE), general aneurysm wall enhancement (GAWE) and focal aneurysm wall enhancement (FAWE). GAWE was more accurate in detecting known morphological determinants of aneurysm instability such as size ≥ 7 mm (p = 0.049), size ratio (p = 0.01) and aspect ratio (p = 0.002). SAWE and FAWE were aneurysm specific metrics used to characterize enhancement patterns within the aneurysm wall and the distribution of enhancement along the aneurysm. Blebs were easily identified on 3D-heatmaps and were more enhancing than aneurysm sacs (p = 0.0017). 3D-AWE mapping may be a powerful objective tool in characterizing different biological processes of the aneurysm wall.
Detection of CWD prions in naturally infected white-tailed deer fetuses and gestational tissues by PMCA
Authors: Bravo-Risi Francisca , Soto Paulina , Eckland Thomas , Dittmar Robert , Ramírez Santiago , Catumbela Celso S. G. , Soto Claudio , Lockwood Mitch , Nichols Tracy , Morales Rodrigo
Published: September 2021

Chronic wasting disease (CWD) is a prevalent prion disease affecting cervids. CWD is thought to be transmitted through direct animal contact or by indirect exposure to contaminated environmental fomites. Other mechanisms of propagation such as vertical and maternal transmissions have also been suggested using naturally and experimentally infected animals. Here, we describe the detection of CWD prions in naturally-infected, farmed white-tailed deer (WTD) fetal tissues using the Protein Misfolding Cyclic Amplification (PMCA) technique. Prion seeding activity was identified in a variety of gestational and fetal tissues. Future studies should demonstrate if prions present in fetuses are at sufficient quantities to cause CWD after birth. This data confirms previous findings in other animal species and furthers vertical transmission as a relevant mechanism of CWD dissemination.
Activation of β3-adrenoceptor increases the number of readily releasable glutamatergic vesicle via activating Ca2+/calmodulin/MLCK/myosin II pathway in the prefrontal cortex of juvenile rats
Authors: Wang Xing , Sun Xuan , Zhou Hou-Cheng , Luo Fei
Published: September 2021

It is well known that β3-adrenoceptor (β3-AR) in many brain structures including prefrontal cortex (PFC) is involved in stress-related behavioral changes. SR58611A, a brain-penetrant β3-AR subtypes agonist, is revealed to exhibit anxiolytic- and antidepressant-like effects. Whereas activation of β3-AR exerts beneficial effects on cognitive function, the underlying cellular and molecular mechanisms have not been fully determined. In this study, whole cell patch-clamp recordings were employed to investigate the glutamatergic transmission of layer V/VI pyramidal cells in slices of the rat PFC. Our result demonstrated that SR58611A increased AMPA receptor-mediated excitatory postsynaptic currents (AMPAR-EPSCs) through activating pre-synaptic β3-AR. SR58611A enhanced the miniature EPSCs (mEPSCs) and reduced paired-pulse ratio (PPR) of AMPAR-EPSCs suggesting that SR58611A augments pre-synaptic glutamate release. SR58611A increased the number of readily releasable vesicle (N) and release probability (Pr) with no effects on the rate of recovery from vesicle depletion. Influx of Ca2+ through L-type Ca2+ channel contributed to SR58611A-mediated enhancement of glutamatergic transmission. We also found that calmodulin, myosin light chain kinase (MLCK) and myosin II were involved in SR58611A-mediated augmentation of glutamate release. Our current data suggest that SR58611A enhances glutamate release by the Ca2+/calmodulin/MLCK/myosin II pathway.
Differential inflammation-mediated function of prokineticin 2 in the synovial fibroblasts of patients with rheumatoid arthritis compared with osteoarthritis
Authors: Noda Kentaro , Dufner Bianca , Ito Haruyasu , Yoshida Ken , Balboni Gianfranco , Straub Rainer H.
Published: September 2021

Prokineticin 2 (PK2) is a secreted protein involved in several pathological and physiological processes, including the regulation of inflammation, sickness behaviors, and circadian rhythms. Recently, it was reported that PK2 is associated with the pathogenesis of collagen-induced arthritis in mice. However, the role of PK2 in the pathogenesis of rheumatoid arthritis (RA) or osteoarthritis (OA) remains unknown. In this study, we collected synovial tissue, plasma, synovial fluid, and synovial fibroblasts (SF) from RA and OA patients to analyze the function of PK2 using immunohistochemistry, enzyme-linked immunosorbent assays, and tissue superfusion studies. PK2 and its receptors prokineticin receptor (PKR) 1 and 2 were expressed in RA and OA synovial tissues. PKR1 expression was downregulated in RA synovial tissue compared with OA synovial tissue. The PK2 concentration was higher in RA synovial fluid than in OA synovial fluid but similar between RA and OA plasma. PK2 suppressed the production of IL-6 from TNFα-prestimulated OA-SF, and this effect was attenuated in TNFα-prestimulated RA-SF. This phenomenon was accompanied by the upregulation of PKR1 in OA-SF. This study provides a new model to explain some aspects underlying the chronicity of inflammation in RA.
Decision making on vestibular schwannoma treatment: predictions based on machine-learning analysis
Authors: Profant Oliver , Bureš Zbyněk , Balogová Zuzana , Betka Jan , Fík Zdeněk , Chovanec Martin , Voráček Jan
Published: September 2021

Decision making on the treatment of vestibular schwannoma (VS) is mainly based on the symptoms, tumor size, patient’s preference, and experience of the medical team. Here we provide objective tools to support the decision process by answering two questions: can a single checkup predict the need of active treatment?, and which attributes of VS development are important in decision making on active treatment? Using a machine-learning analysis of medical records of 93 patients, the objectives were addressed using two classification tasks: a time-independent case-based reasoning (CBR), where each medical record was treated as independent, and a personalized dynamic analysis (PDA), during which we analyzed the individual development of each patient’s state in time. Using the CBR method we found that Koos classification of tumor size, speech reception threshold, and pure tone audiometry, collectively predict the need for active treatment with approximately 90% accuracy; in the PDA task, only the increase of Koos classification and VS size were sufficient. Our results indicate that VS treatment may be reliably predicted using only a small set of basic parameters, even without the knowledge of individual development, which may help to simplify VS treatment strategies, reduce the number of examinations, and increase cause effectiveness.
RETRACTED ARTICLE: Multivariate optimization of removing of cobalt(II) with an efficient aminated-GMA polypropylene adsorbent by induced-grafted polymerization under simultaneous gamma-ray irradiation
Authors: Maleki Fatemeh , Gholami Mobina , Torkaman Rezvan , Torab-Mostaedi Meisam , Asadollahzadeh Mehdi
Published: September 2021

Nowadays, radiation grafting polymer adsorbents have been widely developed due to their advantages, such as low operating cost, high efficiency. In this research, glycidyl methacrylate monomers were grafted on polypropylene polymer fibers by simultaneous irradiation of gamma-ray with a dose of 20 kGy. The grafted polymer was then modified using different amino groups and tested for adsorption of cobalt ions in an aqueous solution. Finally, the modified polymer adsorbent with a high efficiency for cobalt ions adsorption was synthesized and tested. Different modes of cobalt ions adsorption were tested in other adsorption conditions, including adsorption contact time, pH, different amounts of adsorbent mass, and different concentrations of cobalt ions solution. The adsorbent structure was characterized with FT-IR, XRD, TG and SEM techniques and illustrated having an efficient grafting percentage and adsorption capability for cobalt removing by batch experiments. The optimum conditions were obtained by a central composite design: adsorbent mass = 0.07 g, initial concentration = 40 mg/L, time = 182 min, and pH = 4.5 with ethylenediamine as a modified monomer and high amination percentage. Kinetics and equilibrium isotherms observation described that the experimental data followed pseudo-second-order and Langmuir models, respectively. The maximum adsorption capacity from Langmuir isotherm capacity is obtained equal to 68.02 mg/g.