bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early-stage spatial disease surveillance of novel SARS-CoV-2 variants of concern in Germany with crowdsourced data
Authors: Mitze Timo , Rode Johannes 
Published: January 2022

AbstractThe emergence and rapid spread of novel variants of concern (VOC) of the coronavirus 2 constitute a major challenge for spatial disease surveillance. We explore the possibility to use close to real-time crowdsourced data on reported VOC cases (mainly the Alpha variant) at the local area level in Germany. The aim is to use these data for early-stage estimates of the statistical association between VOC reporting and the overall COVID-19 epidemiological development. For the first weeks in 2021 after international importation of VOC to Germany, our findings point to significant increases of up to 35–40% in the 7-day incidence rate and the hospitalization rate in regions with confirmed VOC cases compared to those without such cases. This is in line with simultaneously produced international evidence. We evaluate the sensitivity of our estimates to sampling errors associated with the collection of crowdsourced data. Overall, we find no statistical evidence for an over- or underestimation of effects once we account for differences in data representativeness at the regional level. This points to the potential use of crowdsourced data for spatial disease surveillance, local outbreak monitoring and public health decisions if no other data on new virus developments are available.
Accurate determination of marker location within whole-brain microscopy images
Authors: Tyson Adam L. , Vélez-Fort Mateo , Rousseau Charly V. , Cossell Lee , Tsitoura Chryssanthi , Lenzi Stephen C. , Obenhaus Horst A. , Claudi Federico , Branco Tiago , Margrie Troy W. 
Published: January 2022

AbstractHigh-resolution whole-brain microscopy provides a means for post hoc determination of the location of implanted devices and labelled cell populations that are necessary to interpret in vivo experiments designed to understand brain function. Here we have developed two plugins (brainreg and brainreg-segment) for the Python-based image viewer napari, to accurately map any object in a common coordinate space. We analysed the position of dye-labelled electrode tracks and two-photon imaged cell populations expressing fluorescent proteins. The precise location of probes and cells were physiologically interrogated and revealed accurate segmentation with near-cellular resolution.
Laser-induced thermal source for cold atoms
Authors: Hsu Chung Chuan , Larue Rémy , Kwong Chang Chi , Wilkowski David 
Published: January 2022

AbstractWe demonstrate a simple and compact approach to laser cool and trap atoms based on laser-induced thermal ablation (LITA) of a pure solid granule. A rapid thermalisation of the granule leads to a fast recovery of the ultra-high vacuum condition required for a long trapping lifetime of the cold gas. We give a proof-of-concept of the technique, performing a magneto-optical trap on the 461 nm $$^1S_0\rightarrow \,^1P_1$$

1

S
0

→

1

P
1

transition of strontium. We get up to 3.5 million of cold strontium-88 atoms with a trapping lifetime of more than 4 s. The lifetime is limited by the pressure of the strontium-free residual background vapour. We also implement an original configuration of permanent magnets to create the quadruple magnetic field of the magneto-optical trap. The LITA technique can be generalized to other atomic elements such as transition metals and lanthanide atoms, and shows a strong potential for applications in quantum technologies ranging from quantum computing to precision measurements such as outdoor inertial sensing.
Mutations affecting the N-terminal domains of SHANK3 point to different pathomechanisms in neurodevelopmental disorders
Authors: Woike Daniel , Wang Emily , Tibbe Debora , Hassani Nia Fatemeh , Failla Antonio Virgilio , Kibæk Maria , Overgård Tinett Martesen , Larsen Martin J. , Fagerberg Christina R. , Barsukov Igor , Kreienkamp Hans-Jürgen 
Published: January 2022

AbstractShank proteins are major scaffolds of the postsynaptic density of excitatory synapses. Mutations in SHANK genes are associated with autism and intellectual disability. The effects of missense mutations on Shank3 function, and therefore the pathomechanisms are unclear. Several missense mutations in SHANK3 affect the N-terminal region, consisting of the Shank/ProSAP N-terminal (SPN) domain and a set of Ankyrin (Ank) repeats. Here we identify a novel SHANK3 missense mutation (p.L270M) in the Ankyrin repeats in patients with an ADHD-like phenotype. We functionally analysed this and a series of other mutations, using biochemical and biophysical techniques. We observe two major effects: (1) a loss of binding to δ-catenin (e.g. in the p.L270M variant), and (2) interference with the intramolecular interaction between N-terminal SPN domain and the Ank repeats. This also interferes with binding to the α-subunit of the calcium-/calmodulin dependent kinase II (αCaMKII), and appears to be associated with a more severe neurodevelopmental pathology.
Harnessing Artificial Intelligence to assess the impact of nonpharmaceutical interventions on the second wave of the Coronavirus Disease 2019 pandemic across the world
Authors: Tao Sile , Bragazzi Nicola Luigi , Wu Jianhong , Mellado Bruce , Kong Jude Dzevela 
Published: January 2022

AbstractIn the present paper, we aimed to determine the influence of various non-pharmaceutical interventions (NPIs) enforced during the first wave of COVID-19 across countries on the spreading rate of COVID-19 during the second wave. For this purpose, we took into account national-level climatic, environmental, clinical, health, economic, pollution, social, and demographic factors. We estimated the growth of the first and second wave across countries by fitting a logistic model to daily-reported case numbers, up to the first and second epidemic peaks. We estimated the basic and effective (second wave) reproduction numbers across countries. Next, we used a random forest algorithm to study the association between the growth rate of the second wave and NPIs as well as pre-existing country-specific characteristics. Lastly, we compared the growth rate of the first and second waves of COVID-19. The top three factors associated with the growth of the second wave were body mass index, the number of days that the government sets restrictions on requiring facial coverings outside the home at all times, and restrictions on gatherings of 10 people or less. Artificial intelligence techniques can help scholars as well as decision and policy-makers estimate the effectiveness of public health policies, and implement “smart” interventions, which are as efficacious as stringent ones.
Responsiveness of PNPLA3 and lipid-related transcription factors is dependent upon fatty acid profile in primary bovine hepatocytes
Authors: Erb Sophia J. , Chandler Tawny L. , White Heather M. 
Published: January 2022

AbstractKnockdown of patatin-like phospholipase domain-containing protein 3 (PNPLA3) increased triglycerides (TG) in primary bovine hepatocytes, suggesting that PNPLA3 plays a causal role in hepatic TG clearing. In vivo, PNPLA3 abundance across the periparturient period is inversely related to hepatic TG accumulation and circulating fatty acid (FA) concentrations. The purpose of this research was to determine if PNPLA3, as well as other lipases, transcription factors, or FA-mediated genes, are regulated by FA mimicking liver lipid accumulation (ACCUM) and liver lipid clearing (RECOV) or singular FA physiologically found in dairy cows at 0.5 mM of circulating RECOV (iRECOV). Abundance of PNPLA3 tended to decrease with ACCUM and increased quadratically with RECOV (P ≤ 0.10), differing from PNPLA3 expression, but consistent with previous in vivo research. Adipose TG lipase abundance, but not other lipase abundances, was quadratically responsive to both ACCUM and RECOV (P ≤ 0.005). Abundance of PNPLA3 and SREBP1c and expression of LXRA responded similarly to iRECOV, with C18:0 tending to decrease abundance (P ≤ 0.07). Results indicate that bovine PNPLA3 is translationally regulated by FA and although a LXRA-SREBP1c pathway mediation is possible, the mechanism warrants further investigation.
Physical simulation study on grouting water plugging of flexible isolation layer in coal seam mining
Authors: Li Ang , Ji Bingnan , Ma Qiang , Ji Yadong , Mu Qian , Zhang Wenzhong , Mu Pengfei , Li Liang , Zhao Chunhu 
Published: January 2022

AbstractDeep coal seam mining often leads to water resource loss due to bedrock water entering the workings of the mine and is discharged adjacent to the mining area. Using the geological conditions of the Maiduoshan coal mine, this paper applied a physical simulation experiment. The specified rock above the coal seam was hydraulically fractured in advance to form a postmining grouted fracture network, followed by grouting to construct a flexible isolation layer that blocked the infiltration of groundwater from the aquifer into the water-conducting fracture zone. Stress sensors, flow sensors and strata displacement monitoring technology were deployed inside the experimental material to study the spatial distribution characteristics and evolution law of the water-conducting fracture zone in the overlying rocks. Analysis of the water-conducting fracture zone development law, stress variation, overburden evolution characteristics, fracturing and grouting sequence of the flexible isolation layer and the effect of postmining grouting on the water barrier was conducted. These experiments verified the feasibility of fracture and grouting of the flexible isolation layer. These research results will provide practical guidance for the transition from the current safe and efficient mining methods to safe and green mining methods of deep coal mining in the western mining areas of China.
Novel regulation mechanism of adrenal cortisol and DHEA biosynthesis via the endogen ERAD inhibitor small VCP-interacting protein
Authors: Ilhan Recep , Üner Göklem , Yilmaz Sinem , Atalay Sahar Esra , Cayli Sevil , Erzurumlu Yalcin , Gozen Oguz , Ballar Kirmizibayrak Petek 
Published: January 2022

AbstractEndoplasmic reticulum-associated degradation (ERAD) is a well-characterized mechanism of protein quality control by removal of misfolded or unfolded proteins. The tight regulation of ERAD is critical for protein homeostasis as well as lipid metabolism. Although the mechanism is complex, all ERAD branches converge on p97/VCP, a key protein in the retrotranslocation step. The multifunctionality of p97/VCP relies on its multiple binding partners, one of which is the endogenous ERAD inhibitor, SVIP (small VCP-interacting protein). As SVIP is a promising target for the regulation of ERAD, we aimed to assess its novel physiological roles. We revealed that SVIP is highly expressed in the rat adrenal gland, especially in the cortex region, at a consistently high level during postnatal development, unlike the gradual increase in expression seen in developing nerves. Steroidogenic stimulators caused a decrease in SVIP mRNA expression and increase in SVIP protein degradation in human adrenocortical H295R cells. Interestingly, silencing of SVIP diminished cortisol secretion along with downregulation of steroidogenic enzymes and proteins involved in cholesterol uptake and cholesterol biosynthesis. A certain degree of SVIP overexpression mainly increased the biosynthesis of cortisol as well as DHEA by enhancing the expression of key steroidogenic proteins, whereas exaggerated overexpression led to apoptosis, phosphorylation of eIF2α, and diminished adrenal steroid hormone biosynthesis. In conclusion, SVIP is a novel regulator of adrenal cortisol and DHEA biosynthesis, suggesting that alterations in SVIP expression levels may be involved in the deregulation of steroidogenic stimulator signaling and abnormal adrenal hormone secretion.
Accumulation and ecotoxicological risk assessment of heavy metals in surface sediments of the Olt River, Romania
Authors: Iordache Andreea Maria , Nechita Constantin , Zgavarogea Ramona , Voica Cezara , Varlam Mihai , Ionete Roxana Elena 
Published: January 2022

AbstractHeavy metal pollution of river freshwater environments currently raises significant concerns due to the toxic effects and the fact that heavy metal behavior is not fully understood. This study assessed the contamination level of eight heavy metals and trace elements (Cr, Ni, Cu, Zn, As, Pb, Cd, and Hg) in the surface sediments of 19 sites in 2018 during four periods (March, May, June, and October) in Olt River sediments. Multivariate statistical techniques were used, namely, one-way ANOVA, person product-moment correlation analysis, principal component analysis, hierarchical cluster analysis, and sediment quality indicators such as the contamination factor and pollution load index. The results demonstrated higher contents of Ni, Cu, Zn, As, Pb, Cd, and Hg, with values that were over 2.46, 4.40, 1.15, 8.28, 1.10, 1.53, and 3.71 times more, respectively, compared with the national quality standards for sediments. We observed a positive significant statistical correlation (p < 0.001) in March between elevation and Pb, Ni, Cu, Cr, and Zn and a negative correlation between Pb and elevation (p = 0.08). Intermetal associations were observed only in March, indicating a relationship with river discharge from spring. The PCA sustained mainly anthropogenic sources of heavy metals, which were also identified through correlation and cluster analyses. We noted significant differences between the Cr and Pb population means and variances (p < 0.001) for the data measured in March, May, June, and October. The contamination factor indicated that the pollution level of heavy metals was high and significant for As at 15 of the 19 sites. The pollution load index showed that over 89% of the sites were polluted by metals to various degrees during the four periods investigated. Our results improve the knowledge of anthropogenic versus natural origins of heavy metals in river surface sediments, which is extremely important in assessing environmental and human health risks and beneficial for decision-maker outcomes for national freshwater management plans.
Identification of a fall armyworm (Spodoptera frugiperda)-specific gene and development of a rapid and sensitive loop-mediated isothermal amplification assay
Authors: Osabutey Angelina F. , Seo Bo Yoon , Kim A-Young , Ha Thu Anh Thi , Jung JinKyo , Goergen Georg , Owusu Ebenezer Oduro , Lee Gwan-Seok , Koh Young Ho 
Published: January 2022

AbstractThe fall armyworm [FAW, Spodoptera frugiperda (J E Smith)], a moth native to America, has spread throughout the world since it was first discovered in Africa in 2016. The FAW is a polyphagous migratory pest that can travel over long distances using seasonal winds or typhoons because of its excellent flying ability, causing serious damage to many crops. For effective FAW control, accurate species identification is essential at the beginning of the invasion. In this study, the FAW-specific gene Sf00067 was discovered by performing bioinformatics to develop a fast and accurate tool for the species-specific diagnosis of this pest. An Sf00067 loop-mediated isothermal amplification (LAMP) assay was developed, and optimal conditions were established. The Sf00067 6 primer LAMP (Sf6p-LAMP) assay established in this study was able to diagnose various genotype-based strains of FAW captured in Korea and FAWs collected from Benin, Africa. Our FAW diagnostic protocol can be completed within 30 min, from the process of extracting genomic DNA from an egg or a 1st instar larva to species determination.
brca2-mutant zebrafish exhibit context- and tissue-dependent alterations in cell phenotypes and response to injury
Authors: Kouprianov Vassili A. , Selmek Aubrie A. , Ferguson Jordan L. , Mo Xiaokui , Shive Heather R. 
Published: January 2022

AbstractCancer cells frequently co-opt molecular programs that are normally activated in specific contexts, such as embryonic development and the response to injury. Determining the impact of cancer-associated mutations on cellular phenotypes within these discrete contexts can provide new insight into how such mutations lead to dysregulated cell behaviors and subsequent cancer onset. Here we assess the impact of heritable BRCA2 mutation on embryonic development and the injury response using a zebrafish model (Danio rerio). Unlike most mouse models for BRCA2 mutation, brca2-mutant zebrafish are fully viable and thus provide a unique tool for assessing both embryonic and adult phenotypes. We find that maternally provided brca2 is critical for normal oocyte development and embryonic survival in zebrafish, suggesting that embryonic lethality associated with BRCA2 mutation is likely to reflect defects in both meiotic and embryonic developmental programs. On the other hand, we find that adult brca2-mutant zebrafish exhibit aberrant proliferation of several cell types under basal conditions and in response to injury in tissues at high risk for cancer development. These divergent effects exemplify the often-paradoxical outcomes that occur in embryos (embryonic lethality) versus adult animals (cancer predisposition) with mutations in cancer susceptibility genes such as BRCA2. The altered cell behaviors identified in brca2-mutant embryonic and adult tissues, particularly in adult tissues at high risk for cancer, indicate that the effects of BRCA2 mutation on cellular phenotypes are both context- and tissue-dependent.
Technical field measurements of muscular workload during stocking activities in supermarkets: cross-sectional study
Authors: Skovlund Sebastian Venge , Bláfoss Rúni , Skals Sebastian , Jakobsen Markus Due , Andersen Lars Louis 
Published: January 2022

AbstractMultiple studies have reported high prevalence of musculoskeletal disorders among supermarket workers. Technical field measurements can provide important knowledge about ergonomic risk factors for musculoskeletal disorders in the physical working environment, but these measurements are lacking in the supermarket sector. Therefore, using wearable electromyography and synchronous video recording in 75 supermarket workers, this cross-sectional study measured muscular workload during stocking activities in six different types of general store departments and during the thirteen most common work tasks across five different supermarket chains. Our results showed that muscular workload varies, especially for the low-back muscles, across (1) supermarket chains, (2) departments, and (3) specific stocking activities. Highest workloads of the low-back and neck/shoulders were seen in the fruit and vegetables department and during heavy, two-handed lifts of parcels (especially without using technical aids). In conclusion, physical work demands during supermarket stocking activities differ between chains, departments, and work tasks. These results can be used by company representatives and work environment professionals to specifically address and organize the stocking procedures to reduce the muscular workload during supermarket stocking.
Pathology and virology of natural highly pathogenic avian influenza H5N8 infection in wild Common buzzards (Buteo buteo)
Authors: Caliendo Valentina , Leijten Lonneke , van de Bildt Marco W. G. , Fouchier Ron A. M. , Rijks Jolianne M. , Kuiken Thijs 
Published: January 2022

AbstractHighly pathogenic avian influenza (HPAI) in wild birds is a major emerging disease, and a cause of increased mortality during outbreaks. The Common buzzard (Buteo buteo) has a considerable chance of acquiring the infection and therefore may function as bio-sentinel for the presence of virus in wildlife. This study aimed to determine the virus distribution and associated pathological changes in the tissues of Common buzzards that died with HPAI H5 virus infection during the 2020–2021 epizootic. Eleven freshly dead, HPAI H5 virus-positive Common buzzards were necropsied. Based on RT-PCR, all birds were systemically infected with HPAI H5N8 virus, as viral RNA was detected in cloacal and pharyngeal swabs and in all 10 selected tissues of the birds, with mean Ct values per tissue ranging from 22 for heart to 32 for jejunum. Based on histology and immunohistochemistry, the most common virus-associated pathological changes were necrotizing encephalitis (9/11 birds) and necrotizing myocarditis (7/11 birds). The proventriculus of two birds showed virus-associated necrosis, indicating tropism of this virus for the digestive tract. Our advice is to collect at least a miniset of samples including brain, heart, liver, and spleen, as these tissues were positive both by RT-PCR and for virus-antigen-associated lesions.
Cycloidal CT with CNN-based sinogram completion and in-scan generation of training data
Authors: Pelt Daniël M. , Roche i Morgó Oriol , Maughan Jones Charlotte , Olivo Alessandro , Hagen Charlotte K. 
Published: January 2022

AbstractIn x-ray computed tomography (CT), the achievable image resolution is typically limited by several pre-fixed characteristics of the x-ray source and detector. Structuring the x-ray beam using a mask with alternating opaque and transmitting septa can overcome this limit. However, the use of a mask imposes an undersampling problem: to obtain complete datasets, significant lateral sample stepping is needed in addition to the sample rotation, resulting in high x-ray doses and long acquisition times. Cycloidal CT, an alternative scanning scheme by which the sample is rotated and translated simultaneously, can provide high aperture-driven resolution without sample stepping, resulting in a lower radiation dose and faster scans. However, cycloidal sinograms are incomplete and must be restored before tomographic images can be computed. In this work, we demonstrate that high-quality images can be reconstructed by applying the recently proposed Mixed Scale Dense (MS-D) convolutional neural network (CNN) to this task. We also propose a novel training approach by which training data are acquired as part of each scan, thus removing the need for large sets of pre-existing reference data, the acquisition of which is often not practicable or possible. We present results for both simulated datasets and real-world data, showing that the combination of cycloidal CT and machine learning-based data recovery can lead to accurate high-resolution images at a limited dose.
Assay of honey freshness by a novel optical technique
Authors: Mashhadi Alireza , Bavali Ali , Mokhtari Farzad 
Published: January 2022

AbstractAssay of Maillard reaction products (e.g. furosine) is a reputable method for determination of the honey freshness. In this report, novel optical technique is proposed for real-time measurement of the changes of furosine content in honey. The method is based on the unidirectional energy transfer between two peaks of the doubled-peak fluorescence spectrum as secondary inner filter effect (2nd-IFE) in a specific arrangement of the laser induced fluorescence (LIF) setup. Proper optical parameters are defined accordingly, and affirmed to be dependent on the content of furosine in honey. It is shown that the introduced parameters are not sensitive to the LIF intensity fluctuations induced by the ambient noises and particularly alter due to the 2nd-IFE. Furosine level of 8 honey types with different botanical origin were chemically determined before and after the 1 year storage, and compared with the values of the devised spectral parameters. Proofs conducted that the proposed technique can be utilized for evaluation of the honey freshness.