bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Fibroblast Growth Factor 14 (FGF14) structural variants reveals the genetic basis of the early onset nystagmus locus NYS4 and variable ataxia
Authors: Ceroni Fabiola , Osborne Daniel , Clokie Samuel , Bax Dorine A. , Cassidy Emma J. , Dunn Matt J. , Harris Christopher M. , Self Jay E. , Ragge Nicola K. 
Published: October 2022

AbstractNystagmus (involuntary, rhythmical eye movements) can arise due to sensory eye defects, in association with neurological disorders or as an isolated condition. We identified a family with early onset nystagmus and additional neurological features carrying a partial duplication of FGF14, a gene associated with spinocerebellar ataxia type 27 (SCA27) and episodic ataxia. Detailed eye movement analysis revealed oculomotor anomalies strikingly similar to those reported in a previously described four-generation family with early onset nystagmus and linkage to a region on chromosome 13q31.3-q33.1 (NYS4). Since FGF14 lies within NYS4, we revisited the original pedigree using whole genome sequencing, identifying a 161 kb heterozygous deletion disrupting FGF14 and ITGBL1 in the affected individuals, suggesting an FGF14-related condition. Therefore, our study reveals the genetic variant underlying NYS4, expands the spectrum of pathogenic FGF14 variants, and highlights the importance of screening FGF14 in apparently isolated early onset nystagmus.
High-precision electron affinity of oxygen
Authors: Kristiansson Moa K. , Chartkunchand Kiattichart , Eklund Gustav , Hole Odd M. , Anderson Emma K. , de Ruette Nathalie , Kamińska Magdalena , Punnakayathil Najeeb , Navarro-Navarrete José E. , Sigurdsson Stefan , Grumer Jon , Simonsson Ansgar , Björkhage Mikael , Rosén Stefan , Reinhed Peter , Blom Mikael , Källberg Anders , Alexander John D. , Cederquist Henrik , Zettergren Henning , Schmidt Henning T. , Hanstorp Dag 
Published: October 2022

AbstractNegative ions are important in many areas of science and technology, e.g., in interstellar chemistry, for accelerator-based radionuclide dating, and in anti-matter research. They are unique quantum systems where electron-correlation effects govern their properties. Atomic anions are loosely bound systems, which with very few exceptions lack optically allowed transitions. This limits prospects for high-resolution spectroscopy, and related negative-ion detection methods. Here, we present a method to measure negative ion binding energies with an order of magnitude higher precision than what has been possible before. By laser-manipulation of quantum-state populations, we are able to strongly reduce the background from photodetachment of excited states using a cryogenic electrostatic ion-beam storage ring where keV ion beams can circulate for up to hours. The method is applicable to negative ions in general and here we report an electron affinity of 1.461 112 972(87) eV for 16O.
The spike gene is a major determinant for the SARS-CoV-2 Omicron-BA.1 phenotype
Authors: Barut G. Tuba , Halwe Nico Joel , Taddeo Adriano , Kelly Jenna N. , Schön Jacob , Ebert Nadine , Ulrich Lorenz , Devisme Christelle , Steiner Silvio , Trüeb Bettina Salome , Hoffmann Bernd , Veiga Inês Berenguer , Leborgne Nathan Georges François , Moreira Etori Aguiar , Breithaupt Angele , Wylezich Claudia , Höper Dirk , Wernike Kerstin , Godel Aurélie , Thomann Lisa , Flück Vera , Stalder Hanspeter , Brügger Melanie , Esteves Blandina I. Oliveira , Zumkehr Beatrice , Beilleau Guillaume , Kratzel Annika , Schmied Kimberly , Ochsenbein Sarah , Lang Reto M. , Wider Manon , Machahua Carlos , Dorn Patrick , Marti Thomas M. , Funke-Chambour Manuela , Rauch Andri , Widera Marek , Ciesek Sandra , Dijkman Ronald , Hoffmann Donata , Alves Marco P. , Benarafa Charaf , Beer Martin , Thiel Volker 
Published: October 2022

AbstractVariant of concern (VOC) Omicron-BA.1 has achieved global predominance in early 2022. Therefore, surveillance and comprehensive characterization of Omicron-BA.1 in advanced primary cell culture systems and animal models are urgently needed. Here, we characterize Omicron-BA.1 and recombinant Omicron-BA.1 spike gene mutants in comparison with VOC Delta in well-differentiated primary human nasal and bronchial epithelial cells in vitro, followed by in vivo fitness characterization in hamsters, ferrets and hACE2-expressing mice, and immunized hACE2-mice. We demonstrate a spike-mediated enhancement of early replication of Omicron-BA.1 in nasal epithelial cultures, but limited replication in bronchial epithelial cultures. In hamsters, Delta shows dominance over Omicron-BA.1, and in ferrets Omicron-BA.1 infection is abortive. In hACE2-knock-in mice, Delta and a Delta spike clone also show dominance over Omicron-BA.1 and an Omicron-BA.1 spike clone, respectively. Interestingly, in naïve K18-hACE2 mice, we observe Delta spike-mediated increased replication and pathogenicity and Omicron-BA.1 spike-mediated reduced replication and pathogenicity, suggesting that the spike gene is a major determinant of replication and pathogenicity. Finally, the Omicron-BA.1 spike clone is less well-controlled by mRNA-vaccination in K18-hACE2-mice and becomes more competitive compared to the progenitor and Delta spike clones, suggesting that spike gene-mediated immune evasion is another important factor that led to Omicron-BA.1 dominance.
Past and present giant viruses diversity explored through permafrost metagenomics
Authors: Rigou Sofia , Santini Sébastien , Abergel Chantal , Claverie Jean-Michel , Legendre Matthieu 
Published: October 2022

AbstractGiant viruses are abundant in aquatic environments and ecologically important through the metabolic reprogramming of their hosts. Less is known about giant viruses from soil even though two of them, belonging to two different viral families, were reactivated from 30,000-y-old permafrost samples. This suggests an untapped diversity of Nucleocytoviricota in this environment. Through permafrost metagenomics we reveal a unique diversity pattern and a high heterogeneity in the abundance of giant viruses, representing up to 12% of the sum of sequence coverage in one sample. Pithoviridae and Orpheoviridae-like viruses were the most important contributors. A complete 1.6 Mb Pithoviridae-like circular genome was also assembled from a 42,000-y-old sample. The annotation of the permafrost viral sequences revealed a patchwork of predicted functions amidst a larger reservoir of genes of unknown functions. Finally, the phylogenetic reconstructions not only revealed gene transfers between cells and viruses, but also between viruses from different families.
Enhancement of single upconversion nanoparticle imaging by topologically segregated core-shell structure with inward energy migration
Authors: Zhang Yanxin , Wen Rongrong , Hu Jialing , Guan Daoming , Qiu Xiaochen , Zhang Yunxiang , Kohane Daniel S. , Liu Qian 
Published: October 2022

AbstractManipulating topological arrangement is a powerful tool for tuning energy migration in natural photosynthetic proteins and artificial polymers. Here, we report an inorganic optical nanosystem composed of NaErF4 and NaYbF4, in which topological arrangement enhanced upconversion luminescence. Three architectures are designed for considerations pertaining to energy migration and energy transfer within nanoparticles: outside-in, inside-out, and local energy transfer. The outside-in architecture produces the maximum upconversion luminescence, around 6-times brighter than that of the inside-out at the single-particle level. Monte Carlo simulation suggests a topology-dependent energy migration favoring the upconversion luminescence of outside-in structure. The optimized outside-in structure shows more than an order of magnitude enhancement of upconversion brightness compared to the conventional core-shell structure at the single-particle level and is used for long-term single-particle tracking in living cells. Our findings enable rational nanoprobe engineering for single-molecule imaging and also reveal counter-intuitive relationships between upconversion nanoparticle structure and optical properties.
The clinical significance of preoperative serum triglyceride, high-density lipoprotein, and low-density lipoprotein levels in lung squamous cell carcinoma
Authors: Li Zhupeng , Xu Jianfeng , Feng Weizhong , Ma Zhifeng , Wu Yuanling , Zhu Ting , Xu Peng , Dong Lingjun , Ding JianYi , Zhou Junqing , Yu Guangmao 
Published: October 2022

AbstractTo evaluate the prognostic role of the preoperative plasma lipid profile, including triglycerides (TG), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C) in patients with lung squamous cell carcinoma (LUSC) who underwent complete resection. Clinical data, including preoperative plasma profile levels, were retrospectively collected and reviewed in 300 patients with LUSC who underwent radical lung resection between 2016 and 2017. The overall survival (OS) and disease-free survival (DFS) were assessed by the Kaplan–Meier method and the Cox proportional hazards regression model. TG ≤ 1.35, HDL-C ≤ 1.17, and LDL-C ≤ 2.32 were deemed as independent preoperative risk factors for OS, and HDL-C ≤ 1.17 was an independent preoperative risk factor for DFS. In the multivariate analyses involving OS and DFS, a decreased HDL-C level was significantly associated with worse OS (HR, 0.546; 95% CI, 0.380–0.784, P = 0.001) and DFS (HR, 0.644; 95% CI, 0.422–0.981, P = 0.041). Additionally, an increased TG (HR, 0.546; 95% CI, 0.366–0.814, P = 0.003) or LDL-C (HR, 0.652; 95% CI, 0.456–0.933, P = 0.019) level was significantly associated with better OS. In patients with LUSC, decreased levels of HDL-C may predict worse outcomes for both DFS and OS, while increased TG or LDL-C levels may predict better OS.
Rehabilitative strategies after filtering procedure in glaucoma
Authors: Vingolo Enzo Maria , Casillo Lorenzo , Mecarelli Giulia , Limoli Paolo Giuseppe 
Published: October 2022

AbstractGlaucoma is one of the leading causes of non-reversible blindness worldwide, and almost 6 million people are estimated to be impaired visually in advanced stage of glaucoma. Recently, several studies on glaucoma has been focused towards new therapeutic approaches based on mechanisms independent from IOP control. Effects of new therapeutic agents, visual psychophysical training, or complementary medications targeting optic pathways today seem to be a relevant and effervescent field of research. The goal of the study is to evaluate in glaucoma patients if a rehabilitative strategy with a biofeedback training with microperimetry may be useful after surgery in recovery visual performance even when visual field defects are present in IOP is well controlled environment. Were enrolled 24 patients (28 eyes) with Primary Open Angle Glaucoma (POAG) (mean 63 range: 49–75 years) from our Glaucoma Center after filtering surgery. All patients after one months from surgical intervention underwent to a complete ophthalmologic examination: IOP measurement, gonioscopy, visual field and SD-OCT at baseline of RNFL thickness. In some cases, were included in the study both eyes because in POAG frequently clinical conditions are different in each eye, and secondarily new fixation target retinal location (TRL) was chosen based on single eye retinal sensitivity. Best corrected visual acuity was significantly increased after the training from 0.61 to 0.479 (p = 0.00058) with no change in refractive error. After the biofeedback patients presented increased value in Mean retinal sensitivity from 14.91 to 15.96 (p = 0.0078).Fixation stabilitywas improved either according to Fuji classification (increased from 75.1 to 81.3% p = 0.0073) or BCEA value, reduced from 8.7 to 6.0 square degrees (p = 0.013) we noted a marked increase in this parameter with better performances and satisfaction by the patient. RFNL thickness: no change was noted (p = 0.505) in this value as an indicator of disease’s stability. Our data indicate that MP-3 Biofeedback may be a good strategy to reduce the impairment of the Glaucoma Patient.
Expansion of the osteocytic lacunar-canalicular system involved in pharmacological action of PTH revealed by AI-driven fluorescence morphometry in female rabbits
Authors: Takakura Aya , Sato Takanori , Lee Ji-Won , Hirano Kyoko , Takao-Kawabata Ryoko , Ishizuya Toshinori , Iimura Tadahiro 
Published: October 2022

AbstractOsteoporosis is an age-related disorder that is characterized by reduced bone mass. Its prevention and treatment are important healthcare issues for maintaining social activity in aged societies. Although bone fractures mostly occur at sites of weakened cortical bone, pathophysiological and pharmacological evaluations of bone mass have tended to be predominantly assessed in trabecular bone. To statistically characterize cortical bone remodeling, we originally established multimode fluorescence imaging and artificial intelligence (AI)-driven morphometric analyses in six-month-old female rabbits with well-defined cortical remodeling, similar to that in humans. We evaluated three distinct administration frequencies of teriparatide [TPTD; human parathyroid hormone, hPTH (1–34)]: once (1/w), twice (2/w), and seven times (7/w) a week, with the same total dose (140 μg/kg/week). Our analyses revealed significant expansions of the osteocytic lacunar-canalicular system and Haversian canals accompanied by the development of cortical porosity and endosteal naïve bone formation induced by a frequent administration regimen (7/w) of TPTD; however, once-weekly (1/w) and twice-weekly (2/w) administration of TPTD showed little effect. These findings demonstrate a clear contrast between the effects of frequent and infrequent administration of TPTD on cortical bone metabolism and suggest that osteocytic bone remodeling is involved in the pharmacological action of PTH.
An assessment tool for computer-assisted semen analysis (CASA) algorithms
Authors: Choi Ji-won , Alkhoury Ludvik , Urbano Leonardo F. , Masson Puneet , VerMilyea Matthew , Kam Moshe 
Published: October 2022

AbstractComputer-Assisted Semen Analysis (CASA) enables reliable analysis of semen images, and is designed to process large number of images with high consistency, accuracy, and repeatability. Design and testing of CASA algorithms can be accelerated greatly if reliable simulations of semen images under a variety of conditions and sample quality modes are available. Using life-like simulation of semen images can quantify the performance of existing and proposed CASA algorithms, since the parameters of the simulated image are known and controllable. We present simulation models for sperm cell image and swimming modes observed in real 2D (top-down) images of sperm cells in laboratory specimen. The models simulate human sperm using four (4) types of swimming, namely linear mean, circular, hyperactive, and immotile (or dead). The simulation models are used in studying algorithms for segmentation, localization, and tracking of sperm cells. Several segmentation and localization algorithms were tested under varying levels of noise, and then compared using precision, recall, and the optimal subpattern assignment (OSPA) metric. Images of real human semen sample were used to validate the segmentation and localization observations obtained from simulations. An example is given of sperm cell tracking on simulated semen images of cells using the different tracking algorithms (nearest neighbor (NN), global nearest neighbor (GNN), probabilistic data association filter (PDAF), and joint probabilistic data association filter (JPDAF)). Tracking performance was evaluated through multi-object tracking precision (MOTP) and multi-object tracking accuracy (MOTA). Simulation models enable objective assessments of semen image processing algorithms. We demonstrate the use of a new simulation tool to assess and compare segmentation, localization, and tracking methods. The simulation software allows testing along a large spectrum of parameter values that control the appearance and behavior of simulated semen images. Users can generate scenarios of different characteristics and assess the effectiveness of different CASA algorithms in these environments. The simulation was used to assess and compare algorithms for segmentation and tracking of sperm cells in semen images.
Community detection in networks by dynamical optimal transport formulation
Authors: Leite Daniela , Baptista Diego , Ibrahim Abdullahi A. , Facca Enrico , De Bacco Caterina 
Published: October 2022

AbstractDetecting communities in networks is important in various domains of applications. While a variety of methods exist to perform this task, recent efforts propose Optimal Transport (OT) principles combined with the geometric notion of Ollivier–Ricci curvature to classify nodes into groups by rigorously comparing the information encoded into nodes’ neighborhoods. We present an OT-based approach that exploits recent advances in OT theory to allow tuning between different transportation regimes. This allows for better control of the information shared between nodes’ neighborhoods. As a result, our model can flexibly capture different types of network structures and thus increase performance accuracy in recovering communities, compared to standard OT-based formulations. We test the performance of our algorithm on both synthetic and real networks, achieving a comparable or better performance than other OT-based methods in the former case, while finding communities that better represent node metadata in real data. This pushes further our understanding of geometric approaches in their ability to capture patterns in complex networks.
Large in-plane vibrational and optical anisotropy in natural 2D heterostructure abramovite
Authors: Dasgupta Arindam , Belakovskiy Dmitriy I. , Chaplygin Ilya V. , Gao Jie , Yang Xiaodong 
Published: October 2022

AbstractThe design and formation of van der Waals (vdW) heterostructures with different two-dimensional (2D) materials provide an opportunity to create materials with extraordinary physical properties tailored toward specific applications. Mechanical exfoliation of natural vdW materials has been recognized as an effective way for producing high-quality ultrathin vdW heterostructures. Abramovite is one of such naturally occurring vdW materials, where the superlattice is composed of alternating Pb2BiS3 and SnInS4 2D material lattices. The forced commensuration between the two incommensurate constituent 2D material lattices induces in-plane structural anisotropy in the formed vdW heterostructure of abramovite, even though the individual 2D material lattices are isotropic in nature. Here, we show that ultrathin layers of vdW heterostructures of abramovite can be achieved by mechanical exfoliation of the natural mineral. Furthermore, the structural anisotropy induced highly anisotropic vibrational and optical responses of abramovite thin flakes are demonstrated by angle-resolved polarized Raman scattering, linear dichroism, and polarization-dependent third-harmonic generation. Our results not only establish abramovite as a promising natural vdW material with tailored linear and nonlinear optical properties for building future anisotropic integrated photonic devices, but also provide a deeper understanding of the origin of structural, vibrational and optical anisotropy in vdW heterostructures.
The quantification of vaccine uptake in the Nordic countries and impact on key indicators of COVID-19 severity and healthcare stress level via age range comparative analysis
Authors: Islind Anna Sigridur , Óskarsdóttir María , Cot Corentin , Cacciapaglia Giacomo , Sannino Francesco 
Published: October 2022

AbstractIn this paper we analyze the impact of vaccinations on spread of the COVID-19 virus for different age groups. More specifically, we examine the deployment of vaccines in the Nordic countries in a comparative analysis where we focus on factors such as healthcare stress level and severity of disease through new infections, hospitalizations, intensive care unit (ICU) occupancy and deaths. Moreover, we analyze the impact of the various vaccine types, vaccination rate on the spread of the virus in each age group for Denmark, Finland, Iceland, Norway and Sweden from the start of the vaccination period in December 2020 until the end of September 2021. We perform a threefold analysis: (i) frequency analysis of infections and vaccine rates by age groups; (ii) rolling correlations between vaccination strategies, severity of COVID-19 and healthcare stress level and; (iii) we also employ the epidemic Renormalization Group (eRG) framework. The eRG is used to mathematically model wave structures, as well as the impact of vaccinations on wave dynamics. We further compare the Nordic countries with England. Our main results outline the quantification of the impact of the vaccination campaigns on age groups epidemiological data, across countries with high vaccine uptake. The data clearly shows that vaccines markedly reduce the number of new cases and the risk of serious illness.
Serum IL-1β predicts de novo hepatitis B virus reactivation during direct-acting antiviral therapy for hepatitis C, not during anti-cancer/immunosuppressive therapy
Authors: Kawagishi Naoki , Suda Goki , Sakamori Ryotaro , Matsui Takeshi , Onozawa Masahiro , Yang Zijian , Yoshida Sonoe , Ohara Masatsugu , Kimura Megumi , Kubo Akinori , Maehara Osamu , Fu Qingjie , Hosoda Shunichi , Tokuchi Yoshimasa , Suzuki Kazuharu , Nakai Masato , Sho Takuya , Morikawa Kenichi , Natsuizaka Mitsuteru , Ogawa Koji , Sakai Hajime , Ohnishi Shunsuke , Baba Masaru , Takehara Tetsuo , Sakamoto Naoya 
Published: October 2022

AbstractDe novo hepatitis B virus (HBV) reactivation occurs during direct-acting antiviral (DAA) treatment in hepatitis C virus (HCV)-infected patients with resolved HBV infection. We evaluated the predictive factors, mechanical insight, and differences of cytokine levels during anti-cancer/immunosuppressive and DAA. Eleven, 35, and 19 HCV-infected patients with previous HBV infection with HBV reactivation during DAA treatment, previous HBV infection without HBV reactivation during DAA treatment, and without HBV infection resolution receiving DAA treatment, respectively, were enrolled. Clinical data and baseline cytokine levels were analyzed. Low baseline serum interleukin (IL)-1β levels predicted de novo HBV reactivation during DAA treatment (odds ratio: 47.6, 95% confidence interval: 6.94–333.3). HCV-infected patients with the IL-1β gene single nucleotide polymorphism rs16944 AA allele had significantly higher IL-1β levels; no HCV-infected patient with the IL-1β AA allele experienced HBV reactivation during DAA treatment. Compared to HCV-infected patients with HBV infection resolution, non-HCV infected patients with or without HBV reactivation during anti-cancer/immunosuppressive therapy or bone marrow transplantation had remarkably lower baseline IL-1β levels. Low IL-1β levels were not associated with HBV reactivation. IL-1β levels before DAA for HCV-infected patients with resolved HBV infection could predict HBV reactivation during DAA treatment.