bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crosstalk between SUMOylation and ubiquitylation controls DNA end resection by maintaining MRE11 homeostasis on chromatin
Authors: Zhang Tao , Yang Han , Zhou Zenan , Bai Yongtai , Wang Jiadong , Wang Weibin 
Published: September 2022

AbstractDNA end resection is delicately regulated through various types of post-translational modifications to initiate homologous recombination, but the involvement of SUMOylation in this process remains incompletely understood. Here, we show that MRE11 requires SUMOylation to shield it from ubiquitin-mediated degradation when resecting damaged chromatin. Upon DSB induction, PIAS1 promotes MRE11 SUMOylation on chromatin to initiate DNA end resection. Then, MRE11 is deSUMOylated by SENP3 mainly after it has moved away from DSB sites. SENP3 deficiency results in MRE11 degradation failure and accumulation on chromatin, causing genome instability. We further show that cancer-related MRE11 mutants with impaired SUMOylation exhibit compromised DNA repair ability. Thus, we demonstrate that MRE11 SUMOylation in coordination with ubiquitylation is dynamically controlled by PIAS1 and SENP3 to facilitate DNA end resection and maintain genome stability.
Dynamic genome evolution in a model fern
Authors: Marchant D. Blaine , Chen Guang , Cai Shengguan , Chen Fei , Schafran Peter , Jenkins Jerry , Shu Shengqiang , Plott Chris , Webber Jenell , Lovell John T. , He Guifen , Sandor Laura , Williams Melissa , Rajasekar Shanmugam , Healey Adam , Barry Kerrie , Zhang Yinwen , Sessa Emily , Dhakal Rijan R. , Wolf Paul G. , Harkess Alex , Li Fay-Wei , Rössner Clemens , Becker Annette , Gramzow Lydia , Xue Dawei , Wu Yuhuan , Tong Tao , Wang Yuanyuan , Dai Fei , Hua Shuijin , Wang Hua , Xu Shengchun , Xu Fei , Duan Honglang , Theißen Günter , McKain Michael R. , Li Zheng , McKibben Michael T. W. , Barker Michael S. , Schmitz Robert J. , Stevenson Dennis W. , Zumajo-Cardona Cecilia , Ambrose Barbara A. , Leebens-Mack James H. , Grimwood Jane , Schmutz Jeremy , Soltis Pamela S. , Soltis Douglas E. , Chen Zhong-Hua 
Published: September 2022

AbstractThe large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.
Atmospheric temperature, water vapour and liquid water path from two microwave radiometers during MOSAiC
Authors: Walbröl Andreas , Crewell Susanne , Engelmann Ronny , Orlandi Emiliano , Griesche Hannes , Radenz Martin , Hofer Julian , Althausen Dietrich , Maturilli Marion , Ebell Kerstin 
Published: September 2022

AbstractThe microwave radiometers HATPRO (Humidity and Temperature Profiler) and MiRAC-P (Microwave Radiometer for Arctic Clouds - Passive) continuously measured radiation emitted from the atmosphere throughout the Multidisciplinary drifting Observatory for the Study of the Arctic Climate (MOSAiC) expedition on board the research vessel Polarstern. From the measured brightness temperatures, we have retrieved atmospheric variables using statistical methods in a temporal resolution of 1 s covering October 2019 to October 2020. The integrated water vapour (IWV) is derived individually from both radiometers. In addition, we present the liquid water path (LWP), temperature and absolute humidity profiles from HATPRO. To prove the quality and to estimate uncertainty, the data sets are compared to radiosonde measurements from Polarstern. The comparison shows an extremely good agreement for IWV, with standard deviations of 0.08–0.19 kg m−2 (0.39–1.47 kg m−2) in dry (moist) situations. The derived profiles of temperature and humidity denote uncertainties of 0.7–1.8 K and 0.6–0.45 gm−3 in 0–2 km altitude.
A large EEG dataset for studying cross-session variability in motor imagery brain-computer interface
Authors: Ma Jun , Yang Banghua , Qiu Wenzheng , Li Yunzhe , Gao Shouwei , Xia Xinxing 
Published: September 2022

AbstractIn building a practical and robust brain-computer interface (BCI), the classification of motor imagery (MI) from electroencephalography (EEG) across multiple days is a long-standing challenge due to the large variability of the EEG signals. We collected a large dataset of MI from 5 different days with 25 subjects, the first open-access dataset to address BCI issues across 5 different days with a large number of subjects. The dataset includes 5 session data from 5 different days (2–3 days apart) for each subject. Each session contains 100 trials of left-hand and right-hand MI. In this report, we provide the benchmarking classification accuracy for three conditions, namely, within-session classification (WS), cross-session classification (CS), and cross-session adaptation (CSA), with subject-specific models. WS achieves an average classification accuracy of up to 68.8%, while CS degrades the accuracy to 53.7% due to the cross-session variability. However, by adaptation, CSA improves the accuracy to 78.9%. We anticipate this new dataset will significantly push further progress in MI BCI research in addressing the cross-session and cross-subject challenge.
Ecological and human health risk assessment of heavy metal(loid)s in agricultural soil in hotbed chives hometown of Tangchang, Southwest China
Authors: Gong Cang , Wang Shunxiang , Wang Dewei , Lu Haichuan , Dong Hang , Liu Jiufen , Yan Buqing , Wang Liang 
Published: September 2022

AbstractTo determine the heavy metal(loid)s (HMs) contamination of agricultural soil in hotbed chives hometown of Tangchang, 788 topsoil samples were collected and analyzed for their heavy metal(loid)s concentration. The index of geo-accumulation (Igeo), pollution index (PI) and potential ecological risk index (EIi) were used to assess the degree of pollution. Correlation analysis and principal component analysis (PCA) were used to determine the sources of soil HMs. Human health risks estimated with hazard index (HI) and carcinogenic risk (CR) indices based on ingestion, inhalation and dermal exposure pathways for adults and children. The mean values of Cd, Hg, As, Pb, Cr, Cu, Ni and Zn were 0.221, 0.155, 9.76, 32.2, 91.9, 35.2, 37.1 and 108.8 mg kg−1, respectively, which did not exceed the threshold values of the risk screening value for soil contamination. The potential ecological risk of soil heavy metal(loid)s was low level and there was no significant human health risk. Based on PCA, Pb and Hg may originate from transportation and atmospheric deposition, Zn, Cr and Ni may originate from natural sources and industrial activities, and Cu and Cd may originate from agricultural activities. Overall, from the perspective of HMs content, the soil quality in this study area was at a clean level. This study provides a reference and a basis for formulating effective measures to prevent and control HMs enrichment in agricultural soils.
Ganglion cell inner plexiform layer thickness measured by optical coherence tomography to predict visual outcome in chiasmal compression
Authors: Lee Ga-In , Kim Joonhyoung , Lee Dongyoung , Park Kyung-Ah , Oh Sei Yeul , Kong Doo-Sik , Hong Sang Duk 
Published: September 2022

AbstractWe evaluated the prognostic value of the preoperative macular ganglion cell inner plexiform layer (mGCIPL) thickness along with peripapillary retinal nerve fiber layer (pRNFL) thickness measured by optical coherence tomography (OCT) and estimated an optimal cut-off value to predict postoperative visual field (VF) recovery in adult patients with chiasmal compression after decompression surgery. Two hundred forty eyes of 240 patients aged 20 years or older for which preoperative high-definition Cirrus OCT parameters and pre- and postoperative visual function data were available. The prognostic power of pRNFL and mGCIPL thicknesses for complete postoperative VF recovery or significant VF improvement (improvement ≥ 2 dB in the mean deviation) were assessed. The cut-off values for OCT parameters for VF recovery were estimated. The study found that the higher the preoperative pRNFL and mGCIPL thicknesses, the higher the probability of complete postoperative VF recovery (p = 0.0378 and p = 0.0051, respectively) or significant VF improvement (p = 0.0436 and p = 0.0177, respectively). The area under the receiver operating characteristic analysis of preoperative OCT parameters demonstrated that the mGCIPL thickness showed an area under the curve (AUC) of more than 0.7 for complete VF recovery after decompression surgery (AUC = 0.725, 95% CI: 0.655, 0.795), and the optimal mGCIPL thickness cut-off value for complete VF recovery was 77.25 µm (sensitivity 69% and specificity 69%). Preoperative mGCIPL thickness was a powerful predictor of visual functional outcome after decompression surgery for chiasmal compression.
Breast cancer detection by analyzing the volatile organic compound (VOC) signature in human urine
Authors: Giró Benet Judit , Seo Minjun , Khine Michelle , Gumà Padró Josep , Pardo Martnez Antonio , Kurdahi Fadi 
Published: September 2022

AbstractA rising number of authors are drawing evidence on the diagnostic capacity of specific volatile organic compounds (VOCs) resulting from some body fluids. While cancer incidence in society is on the rise, it becomes clear that the analysis of these VOCs can yield new strategies to mitigate advanced cancer incidence rates. This paper presents the methodology implemented to test whether a device consisting of an electronic nose inspired by a dog’s olfactory system and olfactory neurons is significantly informative to detect breast cancer (BC). To test this device, 90 human urine samples were collected from control subjects and BC patients at a hospital. To test this system, an artificial intelligence-based classification algorithm was developed. The algorithm was firstly trained and tested with data resulting from gas chromatography-mass spectrometry (GC–MS) urine readings, leading to a classification rate of 92.31%, sensitivity of 100.00%, and specificity of 85.71% (N = 90). Secondly, the same algorithm was trained and tested with data obtained with our eNose prototype hardware, and class prediction was achieved with a classification rate of 75%, sensitivity of 100%, and specificity of 50%.
Remarks on phylogeny and molecular variations of criconematid species (Nematoda: Criconematidae) with case studies from Vietnam
Authors: Nguyen Huu Tien , Nguyen Thi Duyen , Le Thi Mai Linh , Trinh Quang Phap , Bert Wim 
Published: September 2022

AbstractThe family Criconematidae is a remarkable group of nematodes, containing roughly 600 nominal root-ectoparasitic species, of which many species are known to be significant agricultural pests. Strikingly, our phylogenetic analyses based on 18S, D2-D3 of 28S rRNA, and COI mtDNA sequences of criconematid species, supported by tree topology tests (SH and AU tests), revealed that almost all studied genera, including Criconema, Ogma, Crossonema, Discocriconema, Hemicriconemoides, Criconemoides, Mesocriconema, and Lobocriconema, are not monophyletic groups, a finding that is partly contrary to those of previous studies on these groups. Our results suggest that key morphological characters used in the classification of Criconematidae are the consequence of convergent evolution. It is clear from our studies that the species status of at least 40 sequences of criconematid species from GenBank must be either revised or reconsidered, with analyses based on a polyphasic approach that includes different tree- and distance-based molecular species-delimitation methods (bPTP, GMYC, ABGD1, and ABGD2). Our studies found the ABGD2 output of the automatic barcode method to agree remarkably well with established species delimitations, while in general, the four species-delimitation results corresponding to three barcode regions forwarded significantly more putative species compared to those originally considered. This study also characterised for the first time the populations of Criconemoides myungsugae and Discocriconemella hensungica associated with Vietnamese ginseng, one of the most precious and rare ginseng varieties in the world. Although these populations are morphologically in agreement with the original descriptions of C. myungsugae and D. hengsungica, their molecular data display notable variations compared to the sequences deposited in GenBank. These species demonstrate clearly the immense molecular variations that can be observed in several species of the family Criconematidae.
Accurate magnetic field imaging using nanodiamond quantum sensors enhanced by machine learning
Authors: Tsukamoto Moeta , Ito Shuji , Ogawa Kensuke , Ashida Yuto , Sasaki Kento , Kobayashi Kensuke 
Published: September 2022

AbstractNanodiamonds can be excellent quantum sensors for local magnetic field measurements. We demonstrate magnetic field imaging with high accuracy of 1.8 $$\upmu $$
μ
T combining nanodiamond ensemble (NDE) and machine learning without any physical models. We discover the dependence of the NDE signal on the field direction, suggesting the application of NDE for vector magnetometry and the improvement of the existing model. Our method enhances the NDE performance sufficiently to visualize nano-magnetism and mesoscopic current and expands the applicability of NDE in arbitrarily shaped materials, including living organisms. This accomplishment bridges machine learning to quantum sensing for accurate measurements.
Effect of a 16-week multi-level classroom standing desk intervention on cognitive performance and academic achievement in adolescents
Authors: Silva Danilo R. , Machado Daniel G. S. , Pinto Fernando , Júdice Pedro B. , Minderico Cláudia S. , Collings Paul J. , Cyrino Edilson S. , Sardinha Luís B. 
Published: September 2022

AbstractThe replacement of traditional classroom desks for active-permissive desks has been tested to reduce sitting time during classes. However, their impact on other domains is still unclear. We aimed to verify the potential effects of a classroom standing desk intervention on cognitive function and academic achievement in 6th-grade students. This was a controlled trial conducted with two classes [intervention (n = 22) and control (n = 27)] from a public school in Lisbon, Portugal. The intervention was carried out for 16 weeks and consisted of multi-level actions (students, parents, and teachers) centered on the implementation of standing desks in the intervention classroom. The control group had traditional classes with no use of standing desks or any other interference/action from the research team. Pre- and post-assessments of executive functions (attention, inhibitory function, memory, and fluid intelligence) and academic achievement were obtained. No differences between groups were found at baseline. Both groups improved (time effect) academic achievement (p < 0.001), memory span (p < 0.001), and inhibitory function (p = 0.008). Group versus time interactions were observed regarding operational memory (intervention: + 18.0% and control: + 41.6%; p = 0.039) and non-verbal fluid intelligence (intervention: − 14.0% and control: + 3.9%; p = 0.017). We concluded that a 16-week classroom standing desk intervention did not improve cognitive performance or academic achievement more than the traditional sitting classes.Trial registration: ClinicalTrials.gov Identifier (NCT03137836) (date of first registration: 03/05/2017).
High-fat diet causes mechanical allodynia in the absence of injury or diabetic pathology
Authors: Tierney Jessica A. , Uong Calvin D. , Lenert Melissa E. , Williams Marisa , Burton Michael D. 
Published: September 2022

AbstractUnderstanding the interactions between diet, obesity, and diabetes is important to tease out mechanisms in painful pathology. Western diet is rich in fats, producing high amounts of circulating bioactive metabolites. However, no research has assessed how a high-fat diet (HFD) alone may sensitize an individual to non-painful stimuli in the absence of obesity or diabetic pathology. To investigate this, we tested the ability of a HFD to stimulate diet-induced hyperalgesic priming, or diet sensitization in male and female mice. Our results revealed that 8 weeks of HFD did not alter baseline pain sensitivity, but both male and female HFD-fed animals exhibited robust mechanical allodynia when exposed to a subthreshold dose of intraplantar Prostaglandin E2 (PGE2) compared to mice on chow diet. Furthermore, calcium imaging in isolated primary sensory neurons of both sexes revealed HFD induced an increased percentage of capsaicin-responsive neurons compared to their chow counterparts. Immunohistochemistry (IHC) showed a HFD-induced upregulation of ATF3, a neuronal marker of injury, in lumbar dorsal root ganglia (DRG). This suggests that a HFD induces allodynia in the absence of a pre-existing condition or injury via dietary components. With this new understanding of how a HFD can contribute to the onset of pain, we can understand the dissociation behind the comorbidities associated with obesity and diabetes to develop pharmacological interventions to treat them more efficiently.
Recognizing the new disorder “idiopathic hypocryoglobulinaemia” in patients with previously unidentified clinical conditions
Authors: Roccatello Dario , Sciascia Savino , Naretto Carla , Barreca Antonella , Solfietti Laura , Battaglia Laura , Viziello Lucia , Fenoglio Roberta , Rossi Daniela 
Published: September 2022

AbstractA considerable number of patients with high clinical suspicion for cryoglobulinaemic vasculitis either show negative results for the detection of cryoglobulins or show only trace amounts which cannot be characterized for composition. We aimed at establishing whether the failure to detect or the detection of trace amounts of cryoglobulin with conventional methods either identifies a peculiar subset of low level cryoglobulinaemia (from now on hypocryoglobulinaemia) or represents a separate entity. Using a modified precipitation technique in hypo-ionic medium, we prospectively identified between 2008 and 2021 237 patients (median age 60.8 years [22–97], 137 females) having < 0.5% cryocrit and clinical suspicion of autoimmune disorder. Of these 237 patients, only 54 (22.7%) had a history of HCV infection. One hundred and sixty-nine out of 237 patients (71%) had an established underlying disease, while 68 patients (28.6%) (median age 62.9 years [29–93], 35 females) did not show either laboratory markers or clinical symptoms consonant with an underlying aetiology. These 68 cases with only trace amounts of cryoglobulins were defined as having a putatively idiopathic hypocryoglobulinaemia. Nineteen of these 68 patients (27.9%) had a history of HCV infection. Twenty-four patients out of 68 (35.3%) were positive for rheumatoid factor (RF), while 25 (36.7%) patients had signs of complement consumption (i.e., C4 < 15 mg/dl and/or C3 < 80 mg/dl ), and 36 (52.9%) had increased inflammatory indexes. Seven patients only had arthralgia and constitutional symptoms while 61 out of 68 (89.7%) presented with at least one of the three cardinal signs of cryoglobulinaemic vasculitis including skin lesions, peripheral nerve involvement, and glomerulonephritis. Seventy-five percent of the subjects had type III hypocryoglobulins. In patients with hypocryoglobulinaemia the histologic features of glomerulonephritis (also examined by electron microscopy) resembled those of mixed cryoglobulinaemia-associated glomerulonephritis. In conclusion, hypocryoglobulins are often polyclonal and are mainly unrelated to HCV infection. Patients who present high clinical suspicion for vasculitis, especially glomerulonephritis and yet test negative for cryoglobulinaemia detected by standard techniques, could require deeper investigation even in the absence of HCV infection, RF activity or signs of complement consumption.
Synthesis of tolyl guanidine as copper corrosion inhibitor with a complementary study on electrochemical and in silico evaluation
Authors: Abdou Moaz M. , EL-Haddad Mahmoud N. 
Published: September 2022

AbstractA rapid and new synthetic route forN,N′-di-o-tolyl guanidine (DTG) synthesis from cheap materials is reported. The performance ofDTGas an excellent inhibitor for delaying copper (Cu) corrosion with an efficiency higher than 98% at 20 × 10−6 M in an acidic solution was investigated via electrochemical measurements. These measurements included PDP, EFM, and EIS spectroscopy. The experimental data indicated thatDTGhas an efficient inhibiting effect on the corrosion of Cu in acidic media.TheDTGwas adsorbed on to the Cu surface via chemical adsorption and followed the Langmuir route. The PDP measurements revealed thatDTGacted as a mixed inhibitor. Furthermore, EIS data showed that theDTGadsorbed through the metal/electrolyte interface. This resulted in forming aDTGprotective layer on the Cu surface, thereby impeding the dissolution of Cu in the acidic solution. The corrosive solution containing theDTGinhibitor after immersion of the Cu specimen for 48 h, which promoted the formation of a complex between the Cu cation andDTG, was investigated via ultraviolet/visible spectroscopy. In addition, the formation of aDTGprotective layer on the Cu surface was confirmed via scanning electron microscopy and atomic force microscopy analysis of the Cu surface morphology. Moreover, the active centers for interaction with the Cu surface in an acidic solution were investigated via in silico evaluation ofDTG.
Dynamics of the secreted frizzled related protein Sizzled and potential implications for binding to bone morphogenetic protein-1 (BMP-1)
Authors: Sharma Urvashi , Vadon-Le Goff Sandrine , Harlos Karl , Zhao Yuguang , Mariano Natacha , Bijakowski Cecile , Bourhis Jean-Marie , Moali Catherine , Hulmes David J. S. , Aghajari Nushin 
Published: September 2022

AbstractSizzled (Szl) is both a secreted frizzled related protein (sFRP) and a naturally occurring inhibitor of the zinc metalloproteinase bone morphogenetic protein-1 (BMP-1), a key regulator of extracellular matrix assembly and growth factor activation. Here we present a new crystal structure for Szl which differs from that previously reported by a large scale (90°) hinge rotation between its cysteine-rich and netrin-like domains. We also present results of a molecular docking analysis showing interactions likely to be involved in the inhibition of BMP-1 activity by Szl. When compared with known structures of BMP-1 in complex with small molecule inhibitors, this reveals features that may be helpful in the design of new inhibitors to prevent the excessive accumulation of extracellular matrix that is the hallmark of fibrotic diseases.