bluuebunny/crossref_metadata_2025_split huggingface dataset:
4th generation synchrotron source boosts crystalline imaging at the nanoscale
Authors: Li Peng , Allain Marc , Grünewald Tilman A. , Rommel Marcus , Campos Andrea , Carbone Dina , Chamard Virginie 
Published: March 2022

AbstractNew 4th-generation synchrotron sources, with their increased brilliance, promise to greatly improve the performances of coherent X-ray microscopy. This perspective is of major interest for crystal microscopy, which aims at revealing the 3D crystalline structure of matter at the nanoscale, an approach strongly limited by the available coherent flux. Our results, based on Bragg ptychography experiments performed at the first 4th-generation synchrotron source, demonstrate the possibility of retrieving a high-quality image of the crystalline sample, with unprecedented quality. Importantly, the larger available coherent flux produces datasets with enough information to overcome experimental limitations, such as strongly deteriorated scanning conditions. We show this achievement would not be possible with 3rd-generation sources, a limit that has inhibited the development of this otherwise powerful microscopy method, so far. Hence, the advent of next-generation synchrotron sources not only makes Bragg ptychography suitable for high throughput studies but also strongly relaxes the associated experimental constraints, making it compatible with a wider range of experimental set-ups at the new synchrotrons.
Phosphodiesterase 2A inhibition corrects the aberrant behavioral traits observed in genetic and environmental preclinical models of Autism Spectrum Disorder
Authors: Schiavi Sara , Carbone Emilia , Melancia Francesca , di Masi Alessandra , Jarjat Marielle , Brau Fréderic , Cardarelli Silvia , Giorgi Mauro , Bardoni Barbara , Trezza Viviana 
Published: March 2022

AbstractPharmacological inhibition of phosphodiesterase 2A (PDE2A), which catalyzes the hydrolysis of cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), has recently been proposed as a novel therapeutic tool for Fragile X Syndrome (FXS), the leading monogenic cause of Autism Spectrum Disorder (ASD). Here, we investigated the role of PDE2A in ASD pathogenesis using two rat models that reflect one of either the genetic or environmental factors involved in the human disease: the genetic Fmr1-Δexon 8 rat model and the environmental rat model based on prenatal exposure to valproic acid (VPA, 500 mg/kg). Prior to behavioral testing, the offspring was treated with the PDE2A inhibitor BAY607550 (0.05 mg/kg at infancy, 0.1 mg/kg at adolescence and adulthood). Socio-communicative symptoms were assessed in both models through the ultrasonic vocalization test at infancy and three-chamber test at adolescence and adulthood, while cognitive impairments were assessed by the novel object recognition test in Fmr1-Δexon 8 rats (adolescence and adulthood) and by the inhibitory avoidance test in VPA-exposed rats (adulthood). PDE2A enzymatic activity in VPA-exposed infant rats was also assessed. In line with the increased PDE2A enzymatic activity previously observed in the brain of Fmr1-KO animals, we found an altered upstream regulation of PDE2A activity in the brain of VPA-exposed rats at an early developmental age (p < 0.05). Pharmacological inhibition of PDE2A normalized the communicative (p < 0.01, p < 0.05), social (p < 0.001, p < 0.05), and cognitive impairment (p < 0.001) displayed by both Fmr1-Δexon 8 and VPA-exposed rats. Altogether, these data highlight a key role of PDE2A in brain development and point to PDE2A inhibition as a promising pharmacological approach for the deficits common to both FXS and ASD.
A prognostic hypoxia gene signature with low heterogeneity within the dominant tumour lesion in prostate cancer patients
Authors: Salberg Unn Beate , Skingen Vilde Eide , Fjeldbo Christina Sæten , Hompland Tord , Ragnum Harald Bull , Vlatkovic Ljiljana , Hole Knut Håkon , Seierstad Therese , Lyng Heidi 
Published: March 2022

AbstractBackgroundGene signatures measured in a biopsy have been proposed as hypoxia biomarkers in prostate cancer. We assessed a previously developed signature, and aimed to determine its relationship to hypoxia and its heterogeneity within the dominant (index) lesion of prostate cancer.MethodsThe 32-gene signature was assessed from gene expression data of 141 biopsies from the index lesion of 94 patients treated with prostatectomy. A gene score calculated from the expression levels was applied in the analyses. Hypoxic fraction from pimonidazole immunostained whole-mount and biopsy sections was used as reference standard for hypoxia.ResultsThe gene score was correlated with pimonidazole-defined hypoxic fraction in whole-mount sections, and the two parameters showed almost equal association with clinical markers of tumour aggressiveness. Based on the gene score, incorrect classification according to hypoxic fraction in whole-mount sections was seen in one third of the patients. The incorrect classifications were apparently not due to intra-tumour heterogeneity, since the score had low heterogeneity compared to pimonidazole-defined hypoxic fraction in biopsies. The score showed prognostic significance in uni-and multivariate analysis in independent cohorts.ConclusionsOur signature from the index lesion reflects tumour hypoxia and predicts prognosis in prostate cancer, independent of intra-tumour heterogeneity in pimonidazole-defined hypoxia.
LncRNA SNHG5 promotes the proliferation and cancer stem cell-like properties of HCC by regulating UPF1 and Wnt-signaling pathway
Authors: Li Yarui , Hu Junbi , Guo Dan , Ma Wenhui , Zhang Xu , Zhang Zhiyong , Lu Guifang , He Shuixiang 
Published: March 2022

AbstractThe role of long noncoding RNA (lncRNAs) had been demonstrated in different types of cancer, including hepatocellular carcinoma. This study was intended to investigate the role of lncRNA small nucleolar RNA host gene 5 (SNHG5) in HCC proliferation and the liver CSC-like properties. Through functional experiments, we determined that knockdown of SNHG5 repressed HCC cell proliferation and CSC-like properties, while over-expression of SNHG5 promoted cell growth. At the same time, CSC markers (CD44, CD133, and ALDH1) and related transcription factors (OCT4, SOX2, and NANOG) were downregulated when SNHG5 was knocked down. Mechanically, RNA immunoprecipitation (RIP) and RNA pulldown assay showed that SNHG5 regulated the proliferation and CSC-like properties of HCC by binding UPF1. Further investigations showed that expression of critical components of Wnt/β-catenin pathway (β-catenin, TCF4, c-myc, cyclinD1, and c-Jun) were upregulated with depletion of UPF1 in liver CSCs, which were downregulated with depletion of SNHG5. After use of the inhibitor of Wnt/β-catenin pathway, the formation of liver CSCs sphere decreased. Taken together, SNHG5 plays a critical role to promote HCC cell proliferation and cancer stem cell-like properties via UPF1 and Wnt/β-catenin pathway.
Long noncoding RNA NEAT1 promotes ferroptosis by modulating the miR-362-3p/MIOX axis as a ceRNA
Authors: Zhang Ying , Luo Meiying , Cui Xiaohong , O’Connell Douglas , Yang Yongfei 
Published: March 2022

AbstractFerroptosis, a novel form of regulated cell death induced by iron-dependent lipid peroxidation, plays an essential role in the development and drug resistance of tumors. Long noncoding RNA (lncRNA) nuclear paraspeckle assembly transcript 1 (NEAT1) has been reported to be involved in the regulation of cell cycle, proliferation, apoptosis, and migration of tumor cells. However, the function and molecular mechanism of NEAT1 in regulating ferroptosis in tumors remain unclear. Here, we found that ferroptosis inducers erastin and RSL3 increased NEAT1 expression by promoting the binding of p53 to the NEAT1 promoter. Induced NEAT1 promoted the expression of MIOX by competitively binding to miR-362-3p. MIOX increased ROS production and decreased the intracellular levels of NADPH and GSH, resulting in enhanced erastin- and RSL3-induced ferroptosis. Importantly, overexpression of NEAT1 increased the anti-tumor activity of erastin and RSL3 by enhancing ferroptosis both in vitro and in vivo. Collectively, these data suggest that NEAT1 plays a novel and indispensable role in ferroptosis by regulating miR-362-3p and MIOX. Considering the clinical findings that HCC patients are insensitive to chemotherapy and immunotherapy, ferroptosis induction may be a promising therapeutic strategy for HCC patients with high NEAT1 expression.
MicroRNA-495 suppresses pre-eclampsia via activation of p53/PUMA axis
Authors: Zhao Yi , Zhao Ge , Li Weiwei 
Published: March 2022

AbstractLinkage between microRNAs (miRNAs) and pre-eclampsia (PE) has been documented. Here, we focused on miR-495 in PE and its underlying mechanism in regulation of trophoblast cells. Expression of miR-495, HDAC2, p53 and PUMA was determined in collected placental tissue samples. Loss- and gain-function was performed to determine the roles of miR-495, HDAC2, p53, and PUMA in biological processes of HTR8/SVneo cells and primary trophoblast cells. The relationships among miR-495, HDAC2, and p53 were pinpointed. PE patients presented with higher expression of miR-495, p53, and PUMA in placental tissues, but lower HDAC2. miR-495 negatively targeted HDAC2 expression. HDAC2 suppressed p53 expression via deacetylation. Overexpression of miR-495, p53, or PUMA inhibited biological properties of HTR8/SVneo cells and primary trophoblast cells, while opposite trends were observed in response to oe-HDAC2. In conclusion, miR-495 knockdown can suppress p53/PUMA axis by targeting HDAC2 to enhance biological behaviors of trophoblast cells, which may prevent occurrence of PE.
Sulforaphane suppresses metastasis of triple-negative breast cancer cells by targeting the RAF/MEK/ERK pathway
Authors: Zhang Ying , Lu Qian , Li Nan , Xu Ming , Miyamoto Tatsuo , Liu Jing 
Published: March 2022

AbstractBreast cancer metastasis is the main cause of cancer death in women, so far, no effective treatment has inhibited breast cancer metastasis. Sulforaphane (SFN), a natural compound derived from broccoli, has shown potential health benefits in many cancers. However, research on breast cancer metastasis is still insufficient. Here, we showed that SFN, including its two isomers of R-SFN and S-SFN, significantly inhibited TGF-β1-induced migration and invasion in breast cancer cells. Proteomic and phosphoproteomic analysis showed that SFN affected the formation of the cytoskeleton. Subsequent experiments confirmed that SFN significantly inhibited TGF-β1-induced actin stress fiber formation and the expression of actin stress fiber formation-associated proteins, including paxillin, IQGAP1, FAK, PAK2, and ROCK. Additionally, SFN is directly bound to RAF family proteins (including ARAF, BRAF, and CRAF) and inhibited MEK and ERK phosphorylation. These in vitro results indicate that SFN targets the RAF/MEK/ERK signaling pathway to inhibit the formation of actin stress fibers, thereby inhibiting breast cancer cell metastasis.
Gate- versus defect-induced voltage drop and negative differential resistance in vertical graphene heterostructures
Authors: Kim Tae Hyung , Lee Juho , Lee Ryong-Gyu , Kim Yong-Hoon 
Published: March 2022

AbstractTo enable the computer-aided design of vertically stacked two-dimensional (2D) van der Waals (vdW) heterostructure devices, we here introduce a non-equilibrium first-principles simulation method based on the multi-space constrained-search density functional formalism. Applying it to graphene/few-layer hBN/graphene field-effect transistors, we show that the negative differential resistance (NDR) characteristics can be produced not only from the gating-induced mismatch between two graphene Dirac cones in energy-momentum space but from the bias-dependent energetic shift of defect levels. Specifically, for a carbon atom substituted for a nitrogen atom (CN) within inner hBN layers, the increase of bias voltage is found to induce a self-consistent electron filling of in-gap CN states, which in turn changes voltage drop profiles and produces symmetric NDR characteristics. With the CN placed on outer hBN layers, however, the pinning of CN states to nearby graphene significantly modifies device characteristics, demonstrating the critical impact of atomic details for 2D vdW devices.
Spin-triplet superconductivity in Weyl nodal-line semimetals
Authors: Shang Tian , Ghosh Sudeep K. , Smidman Michael , Gawryluk Dariusz Jakub , Baines Christopher , Wang An , Xie Wu , Chen Ye , Ajeesh Mukkattu O. , Nicklas Michael , Pomjakushina Ekaterina , Medarde Marisa , Shi Ming , Annett James F. , Yuan Huiqiu , Quintanilla Jorge , Shiroka Toni 
Published: March 2022

AbstractTopological semimetals are three dimensional materials with symmetry-protected massless bulk excitations. As a special case, Weyl nodal-line semimetals are realized in materials having either no inversion or broken time-reversal symmetry and feature bulk nodal lines. The 111-family, including LaNiSi, LaPtSi and LaPtGe materials (all lacking inversion symmetry), belongs to this class. Here, by combining muon-spin rotation and relaxation with thermodynamic measurements, we find that these materials exhibit a fully-gapped superconducting ground state, while spontaneously breaking time-reversal symmetry at the superconducting transition. Since time-reversal symmetry is essential for protecting the normal-state topology, its breaking upon entering the superconducting state should remarkably result in a topological phase transition. By developing a minimal model for the normal-state band structure and assuming a purely spin-triplet pairing, we show that the superconducting properties across this family can be described accurately. Our results demonstrate that the 111 materials reported here provide an ideal test-bed for investigating the rich interplay between the exotic properties of Weyl nodal-line fermions and unconventional superconductivity.
A single-cell atlas of non-haematopoietic cells in human lymph nodes and lymphoma reveals a landscape of stromal remodelling
Authors: Abe Yoshiaki , Sakata-Yanagimoto Mamiko , Fujisawa Manabu , Miyoshi Hiroaki , Suehara Yasuhito , Hattori Keiichiro , Kusakabe Manabu , Sakamoto Tatsuhiro , Nishikii Hidekazu , Nguyen Tran B. , Owada Yohei , Enomoto Tsuyoshi , Sawa Aya , Bando Hiroko , Yoshida Chikashi , Tabata Rikako , Terao Toshiki , Nakayama Masahiro , Ohshima Koichi , Usuki Kensuke , Oda Tatsuya , Matsue Kosei , Chiba Shigeru 
Published: March 2022

AbstractThe activities of non-haematopoietic cells (NHCs), including mesenchymal stromal cells and endothelial cells, in lymphomas are reported to underlie lymphomagenesis. However, our understanding of lymphoma NHCs has been hampered by unexplained NHC heterogeneity, even in normal human lymph nodes (LNs). Here we constructed a single-cell transcriptome atlas of more than 100,000 NHCs collected from 27 human samples, including LNs and various nodal lymphomas, and it revealed 30 distinct subclusters, including some that were previously unrecognized. Notably, this atlas was useful for comparative analyses with lymphoma NHCs, which revealed an unanticipated landscape of subcluster-specific changes in gene expression and interaction with malignant cells in follicular lymphoma NHCs. This facilitates our understanding of stromal remodelling in lymphoma and highlights potential clinical biomarkers. Our study largely updates NHC taxonomy in human LNs and analysis of disease status, and provides a rich resource and deeper insights into LN and lymphoma biology to advance lymphoma management and therapy.
Daily motionless activities: A dataset with accelerometer, magnetometer, gyroscope, environment, and GPS data
Authors: Pires Ivan Miguel , Garcia Nuno M. , Zdravevski Eftim , Lameski Petre 
Published: March 2022

AbstractThe dataset presented in this paper presents a dataset related to three motionless activities, including driving, watching TV, and sleeping. During these activities, the mobile device may be positioned in different locations, including the pants pockets, in a wristband, over the bedside table, on a table, inside the car, or on other furniture, for the acquisition of accelerometer, magnetometer, gyroscope, GPS, and microphone data. The data was collected by 25 individuals (15 men and 10 women) in different environments in Covilhã and Fundão municipalities (Portugal). The dataset includes the sensors’ captures related to a minimum of 2000 captures for each motionless activity, which corresponds to 2.8 h (approximately) for each one. This dataset includes 8.4 h (approximately) of captures for further analysis with data processing techniques, and machine learning methods. It will be useful for the complementary creation of a robust method for the identification of these type of activities.
Aggressiveness, ADHD-like behaviour, and environment influence repetitive behaviour in dogs
Authors: Sulkama Sini , Salonen Milla , Mikkola Salla , Hakanen Emma , Puurunen Jenni , Araujo César , Lohi Hannes 
Published: March 2022

AbstractRepetitive behaviour ranges from variants of normal repetitive behaviours to abnormal repetitive behaviours. The domestic dog spontaneously performs different repetitive behaviours, which can be severe and impair the quality of life and the dog-owner relationship. We collected comprehensive behavioural questionnaire data from almost 4500 Finnish pet dogs and studied the effect of several demographic, environmental, and behavioural factors on canine repetitive behaviour with logistic regression. We replicated findings from previous studies by revealing comorbidity between repetitive behaviour and behavioural factors aggressiveness, hyperactivity/impulsivity, and inattention. We also found a novel association between repetitive behaviour and the owner’s dog experience. In addition, we showed that repetitive behaviour is more common in dogs that live without conspecifics, dogs that were given a low amount of exercise, dogs that lived in larger families, young dogs and elderly dogs, and neutered dogs. Finally, we identified breed differences in repetitive behaviour, suggesting that some breeds are more vulnerable to repetitive behaviour and indicate a genetic susceptibility. As abnormal repetitive behaviour can considerably worsen the well-being of dogs and impair the dog-owner relationship, a better understanding of the environmental, lifestyle, and molecular factors affecting canine repetitive behaviour can benefit both dogs and humans.
Prognostic determinants of hearing outcomes in children with congenital cytomegalovirus infection
Authors: Lo Ta-Hsuan , Lin Pei-Hsuan , Hsu Wei-Chung , Tsao Po-Nien , Liu Tien-Chen , Yang Tzong-Hann , Hsu Chuan-Jen , Huang Li-Min , Lu Chun-Yi , Wu Chen-Chi 
Published: March 2022

AbstractCongenital cytomegalovirus (cCMV) infection is the most prevalent cause of non-genetic sensorineural hearing loss (SNHL) in children. However, the prognostic determinants of SNHL remain unclear. Children with cCMV infection in a tertiary hospital were enrolled. The presence of cCMV-related symptoms at birth, the newborn hearing screening (NHS) results, and the blood viral loads were ascertained. Audiologic outcomes and initial blood viral loads were compared between different groups. Of the 39 children enrolled, 16 developed SNHL. SNHL developed in 60% of children who were initially symptomatic, and in 34.5% of those who were initially asymptomatic with normal hearing or isolated hearing loss, respectively. Failuire in NHS was a reliable tool for early detection of SNHL. The initial viral loads were higher in children who were symptomatic at birth, those who failed NHS, and those who developed SNHL. We observed SNHL deterioration in a patient after CMV DNAemia clearance was achieved, and in another patient with the flare-up of viral load. The presence of cCMV-related symptoms at birth, failure in NHS, and blood viral load might be the prognostic factors for hearing outcomes. Regular audiologic examinations are necessary in all children with cCMV infection even after CMV DNAemia clearance.
Determining an effective short term COVID-19 prediction model in ASEAN countries
Authors: Sharif Omar , Hasan Md Zobaer , Rahman Azizur 
Published: March 2022

AbstractThe challenge of accurately short-term forecasting demand is due to model selection and the nature of data trends. In this study, the prediction model was determined based on data patterns (trend data without seasonality) and the accuracy of prediction measurement. The cumulative number of COVID-19 affected people in some ASEAN countries had been collected from the Worldometers database. Three models [Holt’s method, Wright’s modified Holt’s method, and unreplicated linear functional relationship model (ULFR)] had been utilized to identify an efficient model for short-time prediction. Moreover, different smoothing parameters had been tested to find the best combination of the smoothing parameter. Nevertheless, using the day-to-day reported cumulative case data and 3-days and 7-days in advance forecasts of cumulative data. As there was no missing data, Holt’s method and Wright’s modified Holt’s method showed the same result. The text-only result corresponds to the consequences of the models discussed here, where the smoothing parameters (SP) were roughly estimated as a function of forecasting the number of affected people due to COVID-19. Additionally, the different combinations of SP showed diverse, accurate prediction results depending on data volume. Only 1-day forecasting illustrated the most efficient prediction days (1 day, 3 days, 7 days), which was validated by the Nash–Sutcliffe efficiency (NSE) model. The study also validated that ULFR was an efficient forecasting model for the efficient model identifying. Moreover, as a substitute for the traditional R-squared, the study applied NSE and R-squared (ULFR) for model selection. Finally, the result depicted that the prediction ability of ULFR was superior to Holt’s when it is compared to the actual data.
Revealing microhabitat requirements of an endangered specialist lizard with LiDAR
Authors: Bradley Holly S. , Craig Michael D. , Cross Adam T. , Tomlinson Sean , Bamford Michael J. , Bateman Philip W. 
Published: March 2022

AbstractA central principle of threatened species management is the requirement for detailed understanding of species habitat requirements. Difficult terrain or cryptic behaviour can, however, make the study of habitat or microhabitat requirements difficult, calling for innovative data collection techniques. We used high-resolution terrestrial LiDAR imaging to develop three-dimensional models of log piles, quantifying the structural characteristics linked with occupancy of an endangered cryptic reptile, the western spiny-tailed skink (Egernia stokesii badia). Inhabited log piles were generally taller with smaller entrance hollows and a wider main log, had more high-hanging branches, fewer low-hanging branches, more mid- and understorey cover, and lower maximum canopy height. Significant characteristics linked with occupancy were longer log piles, an average of three logs, less canopy cover, and the presence of overhanging vegetation, likely relating to colony segregation, thermoregulatory requirements, and foraging opportunities. In addition to optimising translocation site selection, understanding microhabitat specificity of E. s. badia will help inform a range of management objectives, such as targeted monitoring and invasive predator control. There are also diverse opportunities for the application of this technology to a wide variety of future ecological studies and wildlife management initiatives pertaining to a range of cryptic, understudied taxa.