bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectral extension and synchronization of microcombs in a single microresonator
Authors: Zhang Shuangyou , Silver Jonathan M. , Bi Toby , Del’Haye Pascal 
Published: December 2020

AbstractBroadband optical frequency combs are extremely versatile tools for precision spectroscopy, ultrafast ranging, as channel generators for telecom networks, and for many other metrology applications. Here, we demonstrate that the optical spectrum of a soliton microcomb generated in a microresonator can be extended by bichromatic pumping: one laser with a wavelength in the anomalous dispersion regime of the microresonator generates a bright soliton microcomb while another laser in the normal dispersion regime both compensates the thermal effect of the microresonator and generates a repetition-rate-synchronized second frequency comb. Numerical simulations agree well with experimental results and reveal that a bright optical pulse from the second pump is passively formed in the normal dispersion regime and trapped by the primary soliton. In addition, we demonstrate that a dispersive wave can be generated and influenced by cross-phase-modulation-mediated repetition-rate synchronization of the two combs. The demonstrated technique provides an alternative way to generate broadband microcombs and enables the selective enhancement of optical power in specific parts of a comb spectrum.
Activation of the IRE1 RNase through remodeling of the kinase front pocket by ATP-competitive ligands
Authors: Ferri Elena , Le Thomas Adrien , Wallweber Heidi Ackerly , Day Eric S. , Walters Benjamin T. , Kaufman Susan E. , Braun Marie-Gabrielle , Clark Kevin R. , Beresini Maureen H. , Mortara Kyle , Chen Yung-Chia A. , Canter Breanna , Phung Wilson , Liu Peter S. , Lammens Alfred , Ashkenazi Avi , Rudolph Joachim , Wang Weiru 
Published: December 2020

AbstractInositol-Requiring Enzyme 1 (IRE1) is an essential component of the Unfolded Protein Response. IRE1 spans the endoplasmic reticulum membrane, comprising a sensory lumenal domain, and tandem kinase and endoribonuclease (RNase) cytoplasmic domains. Excess unfolded proteins in the ER lumen induce dimerization and oligomerization of IRE1, triggering kinase trans-autophosphorylation and RNase activation. Known ATP-competitive small-molecule IRE1 kinase inhibitors either allosterically disrupt or stabilize the active dimeric unit, accordingly inhibiting or stimulating RNase activity. Previous allosteric RNase activators display poor selectivity and/or weak cellular activity. In this study, we describe a class of ATP-competitive RNase activators possessing high selectivity and strong cellular activity. This class of activators binds IRE1 in the kinase front pocket, leading to a distinct conformation of the activation loop. Our findings reveal exquisitely precise interdomain regulation within IRE1, advancing the mechanistic understanding of this important enzyme and its investigation as a potential small-molecule therapeutic target.
Revealing 3D magnetization of thin films with soft X-ray tomography: magnetic singularities and topological charges
Authors: Hierro-Rodriguez A. , Quirós C. , Sorrentino A. , Alvarez-Prado L. M. , Martín J. I. , Alameda J. M. , McVitie S. , Pereiro E. , Vélez M. , Ferrer S. 
Published: December 2020

AbstractThe knowledge of how magnetization looks inside a ferromagnet is often hindered by the limitations of the available experimental methods which are sensitive only to the surface regions or limited in spatial resolution. Here we report a vector tomographic reconstruction based on soft X-ray transmission microscopy and magnetic dichroism data, which has allowed visualizing the three-dimensional magnetization in a ferromagnetic thin film heterostructure. Different non-trivial topological textures have been resolved and the determination of their topological charge has allowed us to identify a Bloch point and a meron-like texture. Our method relies only on experimental data and might be of wide application and interest in 3D nanomagnetism.
Isolation of a member of the candidate phylum ‘Atribacteria’ reveals a unique cell membrane structure
Authors: Katayama Taiki , Nobu Masaru K. , Kusada Hiroyuki , Meng Xian-Ying , Hosogi Naoki , Uematsu Katsuyuki , Yoshioka Hideyoshi , Kamagata Yoichi , Tamaki Hideyuki 
Published: December 2020

AbstractA key feature that differentiates prokaryotic cells from eukaryotes is the absence of an intracellular membrane surrounding the chromosomal DNA. Here, we isolate a member of the ubiquitous, yet-to-be-cultivated phylum ‘Candidatus Atribacteria’ (also known as OP9) that has an intracytoplasmic membrane apparently surrounding the nucleoid. The isolate, RT761, is a subsurface-derived anaerobic bacterium that appears to have three lipid membrane-like layers, as shown by cryo-electron tomography. Our observations are consistent with a classical gram-negative structure with an additional intracytoplasmic membrane. However, further studies are needed to provide conclusive evidence for this unique intracellular structure. The RT761 genome encodes proteins with features that might be related to the complex cellular structure, including: N-terminal extensions in proteins involved in important processes (such as cell-division protein FtsZ); one of the highest percentages of transmembrane proteins among gram-negative bacteria; and predicted Sec-secreted proteins with unique signal peptides. Physiologically, RT761 primarily produces hydrogen for electron disposal during sugar degradation, and co-cultivation with a hydrogen-scavenging methanogen improves growth. We propose RT761 as a new species, Atribacter laminatus gen. nov. sp. nov. and a new phylum, Atribacterota phy. nov.
Disulfide stabilization of human norovirus GI.1 virus-like particles focuses immune response toward blockade epitopes
Authors: Verardi Raffaello , Lindesmith Lisa C. , Tsybovsky Yaroslav , Gorman Jason , Chuang Gwo-Yu , Edwards Caitlin E. , Brewer-Jensen Paul D. , Mallory Michael L. , Ou Li , Schön Arne , Shi Wei , Tully Ena S. , Georgiou George , Baric Ralph S. , Kwong Peter D. 
Published: December 2020

AbstractHuman noroviruses are non-enveloped, single-strand RNA viruses that cause pandemic outbreaks of acute gastroenteritis. A bivalent vaccine containing GI.1 and GII.4 virus-like particles (VLPs) has been shown to be safe and highly immunogenic, but its efficacy and durability have been limited. Here, we show that norovirus GI.1 VLPs are unstable and contain a substantial fraction of dissociated VLP components. Broadly reactive, non-neutralizing antibodies isolated from vaccinated donors bound to the dissociated components, but not to the intact VLPs. Engineering of interprotomer disulfide bonds within the shell domain prevented disassembly of the VLPs, while preserving antibody accessibility to blockade epitopes. Without adjuvant, mice immunized with stabilized GI.1 VLPs developed faster blockade antibody titers compared to immunization with wild-type GI.1 VLPs. In addition, immunization with stabilized particles focused immune responses toward surface-exposed epitopes and away from occluded epitopes. Overall, disulfide-stabilized norovirus GI.1 VLPs elicited improved responses over the non-disulfide-stabilized version, suggesting their promise as candidate vaccines.
Dynamics of social network emergence explain network evolution
Authors: Pomeroy Caleb , Bond Robert M. , Mucha Peter J. , Cranmer Skyler J. 
Published: December 2020

AbstractNetworked systems emerge and subsequently evolve. Although several models describe the process of network evolution, researchers know far less about the initial process of network emergence. Here, we report temporal survey results of a real-world social network starting from its point of inception. We find that individuals’ ties undergo an initial cycle of rapid expansion and contraction. This process helps to explain the eventual interactions and working structure in the network (in this case, scientific collaboration). We propose a stylized concept and model of “churn” to describe the process of network emergence and stabilization. Our empirical and simulation results suggest that these network emergence dynamics may be instrumental for explaining network details, as well as behavioral outcomes at later time periods.
Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole
Authors: Guerrero-Cózar Israel , Perez-Garcia Cathaysa , Benzekri Hicham , Sánchez J. J. , Seoane Pedro , Cruz Fernando , Gut Marta , Zamorano Maria Jesus , Claros M. Gonzalo , Manchado Manuel 
Published: December 2020

AbstractThe Senegalese sole (Solea senegalensis) is an economically important flatfish species. In this study, a genome draft was analyzed to identify microsatellite (SSR) markers for whole-genome genotyping. A subset of 224 contigs containing SSRs were preselected and validated by using a de novo female hybrid assembly. Overall, the SSR density in the genome was 886.7 markers per megabase of genomic sequences and the dinucleotide motif was the most abundant (52.4%). In silico comparison identified a set of 108 SSRs (with di-, tetra- or pentanucleotide motifs) widely distributed in the genome and suitable for primer design. A total of 106 markers were structured in thirteen multiplex PCR assays (with up to 10-plex) and the amplification conditions were optimized with a high-quality score. Main genetic diversity statistics and genotyping reliability were assessed. A subset of 40 high polymorphic markers were selected to optimize four supermultiplex PCRs (with up to 11-plex) for pedigree analysis. Theoretical exclusion probabilities and real parentage allocation tests using parent–offspring information confirmed their robustness and effectiveness for parental assignment. These new SSR markers were combined with previously published SSRs (in total 229 makers) to construct a new and improved integrated genetic map containing 21 linkage groups that matched with the expected number of chromosomes. Synteny analysis with respect to C. semilaevis provided new clues on chromosome evolution in flatfish and the formation of metacentric and submetacentric chromosomes in Senegalese sole.
CoMix: comparing mixing patterns in the Belgian population during and after lockdown
Authors: Coletti Pietro , Wambua James , Gimma Amy , Willem Lander , Vercruysse Sarah , Vanhoutte Bieke , Jarvis Christopher I. , Van Zandvoort Kevin , Edmunds John , Beutels Philippe , Hens Niel 
Published: December 2020

AbstractThe COVID-19 pandemic has shown how a newly emergent communicable disease can lay considerable burden on public health. To avoid system collapse, governments have resorted to several social distancing measures. In Belgium, this included a lockdown and a following period of phased re-opening. A representative sample of Belgian adults was asked about their contact behaviour from mid-April to the beginning of August, during different stages of the intervention measures in Belgium. Use of personal protection equipment (face masks) and compliance to hygienic measures was also reported. We estimated the expected reproduction number computing the ratio of $$\hbox {R}_{0}$$

R
0

with respect to pre-pandemic data. During the first two waves (the first month) of the survey, the reduction in the average number of contacts was around 80% and was quite consistent across all age-classes. The average number of contacts increased over time, particularly for the younger age classes, still remaining significantly lower than pre-pandemic values. From the end of May to the end of July , the estimated reproduction number has a median value larger than one, although with a wide dispersion. Estimated $$\hbox {R}_{0}$$

R
0

fell below one again at the beginning of August. We have shown how a rapidly deployed survey can measure compliance to social distancing and assess its impact on COVID-19 spread. Monitoring the effectiveness of social distancing recommendations is of paramount importance to avoid further waves of COVID-19.
Impact of needle positioning on ablation success of irreversible electroporation: a unicentric retrospective analysis
Authors: Mathy René Michael , Tinoush Parham , da Florencia Ricardo Daniel , Braun Alexander , Ghamarnejad Omid , Radeleff Boris , Kauczor Hans-Ulrich , Chang De-Hua 
Published: December 2020

AbstractIrreversible electroporation (IRE) is an ablation procedure in which cell death is induced by ultrashort electrical pulses. In this unicentric retrospective study we investigated the influence of needle positioning on ablation success. 15 IREs with residual tumor after ablation, detected in the first follow-up MRI, were included, and compared with 30 successful ablations. Evaluation of needle geometry revealed significantly higher values for needle divergence (NDiv, 7.0° vs. 3.7°, p = 0.02), tumor-center-to-ablation-center distance (TACD, 11.6 vs. 3.2 mm, p < 0.001), tumor-to-needle distance (4.7 vs. 1.9 mm, p = 0.04), and tumor diameter per needle (7.5 vs. 5.9 mm/needle, p = 0.01) in patients with residual tumor. The average number of needles used was higher in the group without residual tumor after ablation (3.1 vs. 2.4, p = 0.04). In many cases with residual tumor, needle depth was too short (2.1 vs. 6.8 mm tumor overlap beyond the most proximal needle tip, p < 0.01). The use of a stereotactic navigation system in 10 cases resulted in a lower NDiv value (2.1° vs. 5.6°, p < 0.01). Thus, correct needle placement seems to be a crucial factor for success and the assistance of a stereotactic navigation system might be helpful. As most important geometrical parameter TACD could be identified. Main reasons for high TACD were insufficient needle depth and a lesion location out of the needle plane.
Endoscopic vs. microscopic transsphenoidal pituitary surgery: a single centre study
Authors: Møller Morten Winkler , Andersen Marianne Skovsager , Glintborg Dorte , Pedersen Christian Bonde , Halle Bo , Kristensen Bjarne Winther , Poulsen Frantz Rom 
Published: December 2020

AbstractEndoscopic pituitary surgery has shown promising results. This study reports the experiences of experienced microscopic pituitary surgeons changing to the endoscopic technique, and the beneficial effects on the postoperative outcomes. 45 transsphenoidal endoscopic-assisted surgeries performed in 2016–2017 were compared with 195 microscope-assisted surgeries performed in 2007–2017 for pituitary adenoma. Tumour size, hormonal status and vision were assessed preoperatively and 3–5 months postoperatively. Cases were identified through electronic patient records. GTR was achieved in 39% of the endoscopic operations vs. 22% of microscopic operations, p = 0.018. Mean duration of surgery was 86 min (77–95) with the endoscopic technique vs. 106 min (101–111) with the microscopic technique, p < 0.001. New hypothalamus–pituitary–adrenal axis deficiencies were observed after 3% of endoscopic vs. 34% microscopic operations, p = 0.001, and overall fewer postoperative pituitary deficiencies were observed in the endoscope-assisted group. Complications within 30 days of surgery occurred in 17% of endoscopic operations vs. 27% of microscopic operations (p > 0.05). Normalization of visual impairment occurred in 37% of the cases with preoperative visual impairment in the endoscopic group vs. 35% of those in the microscopic group (p > 0.05). The endoscopic technique performed better as a surgical procedure for pituitary adenomas. We found no statistically significant differences in complication rate or visual improvement between the two techniques.
DUSP5 expression in left ventricular cardiomyocytes of young hearts regulates thyroid hormone (T3)-induced proliferative ERK1/2 signaling
Authors: Bogush Nikolay , Tan Lin , Naib Hussain , Faizullabhoy Ebrahim , Calvert John W. , Iismaa Siiri E. , Gupta Ankan , Ramchandran Ramani , Martin David I. K. , Graham Robert M. , Husain Ahsan , Naqvi Nawazish 
Published: December 2020

AbstractCardiomyocytes of newborn mice proliferate after injury or exposure to growth factors. However, these responses are diminished after postnatal day-6 (P6), representing a barrier to building new cardiac muscle in adults. We have previously shown that exogenous thyroid hormone (T3) stimulates cardiomyocyte proliferation in P2 cardiomyocytes, by activating insulin-like growth factor-1 receptor (IGF-1R)-mediated ERK1/2 signaling. But whether exogenous T3 functions as a mitogen in post-P6 murine hearts is not known. Here, we show that exogenous T3 increases the cardiomyocyte endowment of P8 hearts, but the proliferative response is confined to cardiomyocytes of the left ventricular (LV) apex. Exogenous T3 stimulates proliferative ERK1/2 signaling in apical cardiomyocytes, but not in those of the LV base, which is inhibited by expression of the nuclear phospho-ERK1/2-specific dual-specificity phosphatase, DUSP5. Developmentally, between P7 and P14, DUSP5 expression increases in the myocardium from the LV base to its apex; after this period, it is uniformly expressed throughout the LV. In young adult hearts, exogenous T3 increases cardiomyocyte numbers after DUSP5 depletion, which might be useful for eliciting cardiac regeneration.
Upregulation of PI3K/AKT/PTEN pathway is correlated with glucose and glutamine metabolic dysfunction during tamoxifen resistance development in MCF-7 cells
Authors: Hamadneh Lama , Abuarqoub Rama , Alhusban Ala , Bahader Mohamad 
Published: December 2020

AbstractTamoxifen resistance is emerging as a big challenge in endocrine therapy of luminal A breast cancer patients. In this study, we aimed to determine the molecular changes of PI3K/AKT/PTEN signaling pathway during tamoxifen-resistance development using gradually increased doses of tamoxifen in one model, while fixing tamoxifen treatment dose at 35 μM for several times in the second model. An upregulation of AKT/PI3K genes was noticed at 30 μM tamoxifen concentration in cells treated with a gradual increase of tamoxifen doses. In the second model, significant upregulation of AKT1 was seen in cells treated with 35 μM tamoxifen for three times. All genes studied showed a significant increase in expression in resistant cells treated with 50 µM and 35 µM six times tamoxifen. These genes’ upregulation was accompanied by PTEN and GSK3 ß genes’ down-regulation, and it was in correlation to the changes in the metabolic rate of glucose in tamoxifen-resistant models. A significant increase in glucose consumption rate from culture media was observed in tamoxifen resistant cells with the highest consumption rate reported in the first day of culturing. Increased glucose consumption rates were also correlated with GLUL significant gene expression and non-significant change in c-MYC gene expression that may lead to increased endogenous glutamine synthesis. As a result, several molecular and metabolic changes precede acquired tamoxifen resistance could be used as resistance biomarkers or targets to reverse tamoxifen resistance.
A comparative UHPLC-Q/TOF–MS-based eco-metabolomics approach reveals temperature adaptation of four Nepenthes species
Authors: Wong Changi , Ling Yee Soon , Wee Julia Lih Suan , Mujahid Aazani , Müller Moritz 
Published: December 2020

AbstractNepenthes, as the largest family of carnivorous plants, is found with an extensive geographical distribution throughout the Malay Archipelago, specifically in Borneo, Philippines, and Sumatra. Highland species are able to tolerate cold stress and lowland species heat stress. Our current understanding on the adaptation or survival mechanisms acquired by the different Nepenthes species to their climatic conditions at the phytochemical level is, however, limited. In this study, we applied an eco-metabolomics approach to identify temperature stressed individual metabolic fingerprints of four Nepenthes species: the lowlanders N. ampullaria, N. rafflesiana and N. northiana, and the highlander N. minima. We hypothesized that distinct metabolite regulation patterns exist between the Nepenthes species due to their adaptation towards different geographical and altitudinal distribution. Our results revealed not only distinct temperature stress induced metabolite fingerprints for each Nepenthes species, but also shared metabolic response and adaptation strategies. The interspecific responses and adaptation of N. rafflesiana and N. northiana likely reflected their natural habitat niches. Moreover, our study also indicates the potential of lowlanders, especially N. ampullaria and N. rafflesiana, to produce metabolites needed to deal with increased temperatures, offering hope for the plant genus and future adaption in times of changing climate.
Relationship between fatty pancreas and hypertriglyceridemic waist phenotype: a cross-sectional study
Authors: Yu Xiaoping , Wang Dan , Xiao Weiming , Shi Xinlin , She Qiang , Sun Hongguang , Qi Tingyue , Xu Renyan , Li Guiqing , Liu Xinnong , Gong Weijuan , Yan Zhigang , Ding Yanbing , Lu Guotao 
Published: December 2020

AbstractHypertriglyceridemic waist phenotype (HTWP) and its quantitative indicator, waist circumference-triglyceride index (WTI), are common quantitative indices of visceral obesity and are closely related to metabolic diseases. The purpose of this study was to investigate the relationship between fatty pancreas (FP) and HTWP in China. FP was diagnosed using trans-abdominal ultrasonography in all participants. According to the waist circumference and serum triglyceride levels, the participants were divided into four phenotype groups: normal waist circumference-normal triglyceride, normal waist circumference-elevated triglyceride, elevated waist circumference-normal triglyceride, and elevated waist circumference-elevated triglyceride (indicating HTWP). Clinical characteristics and biochemical indices were compared among the groups. Receiver operating characteristic (ROC) curves were used to evaluate the utility of WTI as a reference factor for FP screening. The HTWP group had a higher prevalence of metabolic syndrome (84.2%), FP (10.4%), fatty liver (64.5%), and hypertension (15.8%) than the other three phenotype groups. The occurrence rate of HTWP and the median WTI were significantly higher in participants with FP than in those without FP (54.7% vs 21.0%, 222 ± 135 vs 142 ± 141, p < 0.001). In the ROC curve analysis, when the maximum area under the curve was 0.746, the WTI was 107.09 and the corresponding sensitivity and specificity were 90.6% and 51.9%, respectively. HTWP is closely associated with FP and can be used as a reference factor for FP screening.
Low-motion fMRI data can be obtained in pediatric participants undergoing a 60-minute scan protocol
Authors: Horien Corey , Fontenelle Scuddy , Joseph Kohrissa , Powell Nicole , Nutor Chaela , Fortes Diogo , Butler Maureen , Powell Kelly , Macris Deanna , Lee Kangjoo , Greene Abigail S. , McPartland James C. , Volkmar Fred R. , Scheinost Dustin , Chawarska Katarzyna , Constable R. Todd 
Published: December 2020

AbstractPerforming functional magnetic resonance imaging (fMRI) scans of children can be a difficult task, as participants tend to move while being scanned. Head motion represents a significant confound in fMRI connectivity analyses. One approach to limit motion has been to use shorter MRI protocols, though this reduces the reliability of results. Hence, there is a need to implement methods to achieve high-quality, low-motion data while not sacrificing data quantity. Here we show that by using a mock scan protocol prior to a scan, in conjunction with other in-scan steps (weighted blanket and incentive system), it is possible to achieve low-motion fMRI data in pediatric participants (age range: 7–17 years old) undergoing a 60 min MRI session. We also observe that motion is low during the MRI protocol in a separate replication group of participants, including some with autism spectrum disorder. Collectively, the results indicate it is possible to conduct long scan protocols in difficult-to-scan populations and still achieve high-quality data, thus potentially allowing more reliable fMRI findings.