bluuebunny/crossref_metadata_2025_split huggingface dataset:
Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies
Authors: Cao Yunlong , Wang Jing , Jian Fanchong , Xiao Tianhe , Song Weiliang , Yisimayi Ayijiang , Huang Weijin , Li Qianqian , Wang Peng , An Ran , Wang Jing , Wang Yao , Niu Xiao , Yang Sijie , Liang Hui , Sun Haiyan , Li Tao , Yu Yuanling , Cui Qianqian , Liu Shuo , Yang Xiaodong , Du Shuo , Zhang Zhiying , Hao Xiaohua , Shao Fei , Jin Ronghua , Wang Xiangxi , Xiao Junyu , Wang Youchun , Xie Xiaoliang Sunney 
Published: January 2022

AbstractThe SARS-CoV-2 B.1.1.529 (Omicron) variant contains 15 mutations of the receptor-binding domain (RBD). How Omicron evades RBD-targeted neutralizing antibodies requires immediate investigation. Here we use high-throughput yeast display screening1,2 to determine the profiles of RBD escaping mutations for 247 human anti-RBD neutralizing antibodies and show that the neutralizing antibodies can be classified by unsupervised clustering into six epitope groups (A–F)—a grouping that is highly concordant with knowledge-based structural classifications3–5. Various single mutations of Omicron can impair neutralizing antibodies of different epitope groups. Specifically, neutralizing antibodies in groups A–D, the epitopes of which overlap with the ACE2-binding motif, are largely escaped by K417N, G446S, E484A and Q493R. Antibodies in group E (for example, S309)6 and group F (for example, CR3022)7, which often exhibit broad sarbecovirus neutralizing activity, are less affected by Omicron, but a subset of neutralizing antibodies are still escaped by G339D, N440K and S371L. Furthermore, Omicron pseudovirus neutralization showed that neutralizing antibodies that sustained single mutations could also be escaped, owing to multiple synergetic mutations on their epitopes. In total, over 85% of the tested neutralizing antibodies were escaped by Omicron. With regard to neutralizing-antibody-based drugs, the neutralization potency of LY-CoV016, LY-CoV555, REGN10933, REGN10987, AZD1061, AZD8895 and BRII-196 was greatly undermined by Omicron, whereas VIR-7831 and DXP-604 still functioned at a reduced efficacy. Together, our data suggest that infection with Omicron would result in considerable humoral immune evasion, and that neutralizing antibodies targeting the sarbecovirus conserved region will remain most effective. Our results inform the development of antibody-based drugs and vaccines against Omicron and future variants.
A cell-free approach to identify binding hotspots in plant immune receptors
Authors: Markou George C. , Sarkar Casim A. 
Published: January 2022

AbstractPlant immune receptors are often difficult to express heterologously, hindering study of direct interactions between these receptors and their targets with traditional biochemical approaches. The cell-free method ribosome display (RD) enables expression of such recalcitrant proteins by keeping each nascent polypeptide chain tethered to its ribosome, which can enhance protein folding by virtue of its size and solubility. Moreover, in contrast to an in planta readout of receptor activity such as a hypersensitive response that conflates binding and signaling, RD enables direct probing of the interaction between plant immune receptors and their targets. Here, we demonstrate the utility of this approach using tomato recognition of Trichoderma viride ethylene-inducing xylanase (EIX) as a case study. Leveraging the modular nature of the tomato LeEIX2 and LeEIX1 leucine-rich repeat (LRR) receptors, we applied an entropy-informed algorithm to maximize the information content in our receptor segmentation RD experiments to identify segments implicated in EIX binding. Unexpectedly, two distinct EIX-binding hotspots were discovered on LeEIX2 and both hotspots are shared with decoy LeEIX1, suggesting that their contrasting receptor functions are not due to differential modes of ligand binding. Given that most plant immune receptors are thought to engage targets via their LRR sequences, this approach should be of broad utility in rapidly identifying their binding hotspots.
Conformal properties of hyperinvariant tensor networks
Authors: Steinberg Matthew , Prior Javier 
Published: January 2022

AbstractHyperinvariant tensor networks (hyMERA) were introduced as a way to combine the successes of perfect tensor networks (HaPPY) and the multiscale entanglement renormalization ansatz (MERA) in simulations of the AdS/CFT correspondence. Although this new class of tensor network shows much potential for simulating conformal field theories arising from hyperbolic bulk manifolds with quasiperiodic boundaries, many issues are unresolved. In this manuscript we analyze the challenges related to optimizing tensors in a hyMERA with respect to some quasiperiodic critical spin chain, and compare with standard approaches in MERA. Additionally, we show two new sets of tensor decompositions which exhibit different properties from the original construction, implying that the multitensor constraints are neither unique, nor difficult to find, and that a generalization of the analytical tensor forms used up until now may exist. Lastly, we perform randomized trials using a descending superoperator with several of the investigated tensor decompositions, and find that the constraints imposed on the spectra of local descending superoperators in hyMERA are compatible with the operator spectra of several minimial model CFTs.
Evaluation of multiple satellite precipitation products for rainfed maize production systems over Vietnam
Authors: Gummadi Sridhar , Dinku Tufa , Shirsath Paresh B. , Kadiyala M. D. M. 
Published: January 2022

AbstractHigh-resolution reliable rainfall datasets are vital for agricultural, hydrological, and weather-related applications. The accuracy of satellite estimates has a significant effect on simulation models in particular crop simulation models, which are highly sensitive to rainfall amounts, distribution, and intensity. In this study, we evaluated five widely used operational satellite rainfall estimates: CHIRP, CHIRPS, CPC, CMORPH, and GSMaP. These products are evaluated by comparing with the latest improved Vietnam-gridded rainfall data to determine their suitability for use in impact assessment models. CHIRP/S products are significantly better than CMORPH, CPC, and GsMAP with higher skill, low bias, showing a high correlation coefficient with observed data, and low mean absolute error and root mean square error. The rainfall detection ability of these products shows that CHIRP outperforms the other products with a high probability of detection (POD) scores. The performance of the different rainfall datasets in simulating maize yields across Vietnam shows that VnGP and CHIRP/S were capable of producing good estimates of average maize yields with RMSE ranging from 536 kg/ha (VnGP), 715 kg/ha (CHIRPS), 737 kg/ha (CHIRP), 759 kg/ha (GsMAP), 878 kg/ha (CMORPH) to 949 kg/ha (CPC). We illustrated that there is a potential for use of satellite rainfall estimates to overcome the issues of data scarcity in regions with sparse rain gauges.
Ecoregional and temporal dynamics of dugong habitat use in a complex coral reef lagoon ecosystem
Authors: Derville Solène , Cleguer Christophe , Garrigue Claire 
Published: January 2022

AbstractMobile marine species display complex and nonstationary habitat use patterns that require understanding to design effective management measures. In this study, the spatio-temporal habitat use dynamics of the vulnerable dugong (Dugong dugon) were modelled from 16 satellite-tagged individuals in the coral reef lagoonal ecosystems of New Caledonia, South Pacific. Dugong residence time was calculated along the interpolated tracks (9371 hourly positions) to estimate intensity of use in three contrasting ecoregions, previously identified through hierarchical clustering of lagoon topographic characteristics. Across ecoregions, differences were identified in dugong spatial intensity of use of shallow waters, deeper lagoon waters and the fore-reef shelf outside the barrier reef. Maps of dugong intensity of use were predicted from these ecological relationships and validated with spatial density estimates derived from aerial surveys conducted for population assessment. While high correlation was found between the two datasets, our study extended the spatial patterns of dugong distribution obtained from aerial surveys across the diel cycle, especially in shallow waters preferentially used by dugongs at night/dusk during high tide. This study has important implications for dugong conservation and illustrates the potential benefits of satellite tracking and dynamic habitat use modelling to inform spatial management of elusive and mobile marine mammals.
Polymorphism analysis of pfmdr1 gene in Plasmodium falciparum isolates 11 years post-adoption of artemisinin-based combination therapy in Saudi Arabia
Authors: Al-Mekhlafi Hesham M. , Madkhali Aymen M. , Abdulhaq Ahmed A. , Atroosh Wahib M. , Ghzwani Ahmad Hassn , Zain Khalid Ammash , Ghailan Khalid Y. , Hamali Hassan A. , Mobarki Abdullah A. , Alharazi Talal H. , Eisa Zaki M. , Lau Yee-Ling 
Published: January 2022

AbstractA total of 227 Plasmodium falciparum isolates from Jazan region, southwestern Saudi Arabia were amplified for the P. falciparum multi-drug resistance 1 (pfmdr1) gene to detect point mutations 11 years after the introduction of artemisinin-based combination therapy (ACT) in Saudi Arabia. The pfmdr1 86Y mutation was found in 11.5% (26/227) of the isolates while the N86 wild allele was detected in 88.5%. Moreover, 184F point mutations dominated (86.3%) the instances of pfmdr1 polymorphism while no mutation was observed at codons 1034, 1042 and 1246. Three pfmdr1 haplotypes were identified, NFSND (74.9%), NYSND (13.7%) and YFSND (11.4%). Associations of the prevalence of 86Y mutation and YFSND haplotype with participants’ nationality, residency and parasitaemia level were found to be significant (P < 0.05). The findings revealed significant decline in the prevalence of the pfmdr1 86Y mutation in P. falciparum isolates from Jazan region over a decade after the implementation of ACT treatment. Moreover, the high prevalence of the NFSND haplotype might be indicative of the potential emergence of CQ-sensitive but artemether-lumefantrine-resistant P. falciparum strains since the adoption of ACT. Therefore, continuous monitoring of the molecular markers of antimalarial drug resistance in Jazan region is highly recommended.
Free-water diffusion tensor imaging detects occult periependymal abnormality in the AQP4-IgG-seropositive neuromyelitis optica spectrum disorder
Authors: Kim Minchul , Choi Kyu Sung , Hyun Ryoo Chang , Hwang Inpyeong , Yun Tae Jin , Kim Sung Min , Kim Ji-hoon 
Published: January 2022

AbstractTo compare free-water corrected diffusion tensor imaging (DTI) measures in the normal-appearing periependymal area between AQP4-IgG-seropositive NMOSD and multiple sclerosis (MS) to investigate occult pathophysiology.
This prospective study included 44 patients (mean age, 39.52 ± 11.90 years; 14 men) with AQP4-IgG-seropositive NMOSD (n = 20) and MS (n = 24) who underwent DTI between April 2014 and April 2020. Based on free-water corrected DTI measures obtained from normal-appearing periependymal voxels of (1) lateral ventricles and (2) the 3rd and 4th ventricles as dependent variables, MANCOVA was conducted to compare the two groups, using clinical variables as covariates. A significant difference was found between AQP4-IgG-seropositive NMOSD and MS in the 3rd and 4th periependymal voxels (λ = 0.462, P = 0.001). Fractional anisotropy, axial diffusivity was significantly decreased and radial diffusivity was increased in AQP4-IgG-seropositive NMOSD in post-hoc analysis, compared with MS (F = 27.616, P < 0.001, F = 7.336, P = 0.011, and F = 5.800, P = 0.022, respectively). Free-water corrected DTI measures differ in the periependymal area surrounding the diencephalon and brain stem/cerebellum between MS and NMOSD, which may suggest occult white matter injury in areas with distribution of AQP-4 in NMOSD.
Spread of variants of epidemic disease based on the microscopic numerical simulations on networks
Authors: Okabe Yutaka , Shudo Akira 
Published: January 2022

AbstractViruses constantly undergo mutations with genomic changes. The propagation of variants of viruses is an interesting problem. We perform numerical simulations of the microscopic epidemic model based on network theory for the spread of variants. Assume that a small number of individuals infected with the variant are added to widespread infection with the original virus. When a highly infectious variant that is more transmissible than the original lineage is added, the variant spreads quickly to the wide space. On the other hand, if the infectivity is about the same as that of the original virus, the infection will not spread. The rate of spread is not linear as a function of the infection strength but increases non-linearly. This cannot be explained by the compartmental model of epidemiology but can be understood in terms of the dynamic absorbing state known from the contact process.
A rapid influenza diagnostic test based on detection of viral neuraminidase activity
Authors: Lin Xuexiang , Liu Xiao-Yu , Zhang Bo , Qin Ai-Qing , Hui Kwok-Min , Shi Kevin , Liu Yang , Gabriel Don , Li X. James 
Published: January 2022

AbstractCurrent methods used for diagnosis of acute infection of pathogens rely on detection of nucleic acids, antigens, or certain classes of antibodies such as IgM. Here we report a virus enzyme assay as an alternative to these methods for detection of acute viral infection. In this method, we used a luciferin derivative as the substrate for detection of the enzyme activity of influenza viral neuraminidase as a means for diagnosis of influenza. The resulting commercial test, the qFLU Dx Test, uses a different supply chain that does not compete with those for the current tests. The assay reagents were formulated as a master mix that accommodated both the neuraminidase and luciferase reactions, thereby enabling rapid and prolonged production of stable light signal in the presence of influenza virus in the sample. The assay was evaluated using depository throat swab specimens. As expected, the assay exhibited similar detection rates for all influenza types and subtypes except for A(H7N9), which exhibited lower detection rate due to lower viral titer in the specimens. When throat swab specimens were diluted with the sample buffer of the test kit and tested with the qFLU Dx Test. The sensitivity and specificity were 82.41% (95% confidence interval: 79.66–85.84%) and 95.39% (95% confidence interval: 94.32–96.46%), respectively, for these diluted specimens in comparison to a real-time polymerase chain reaction assay. The uniqueness of the qFLU Dx Test as an enzymatic assay makes it highly complementary with currently available methods.
Retrospective analysis of OCT on MB characteristics and 1-year follow-up of the ISR incidence after the DES implantation in patients with MB
Authors: Xu Tian , You Wei , Wu Zhiming , Meng Peina , Ye Fei , Wu Xiangqi , Chen Shaoliang 
Published: January 2022

AbstractWe used optical coherence tomography (OCT) to analyze the "half-moon" like phenomenon and its characteristics and observe 1-year follow-up of the in-stent restenosis (ISR) incidence after the drug eluted stent (DES) implantation in patients with the myocardial bridge (MB). Patients were retrospectively analyzed from January 2013 to December 2019. We used OCT to check 45 patients with MB and found a visible muscle layer (VML) around the vessel adventitia with the same or high density compared to the vessel media layer. There was not any significant difference in maximal thickness, maximal arch, and total length between the half-moon layer and the visible muscle layer groups (p > 0.05). Maximal thickness, arch, and total length of the half-moon layer were significantly positively related to VML, respectively (r = 0.962, 0.985, 0.742, p < 0.01). Of these 626 patients with MB seen by OCT, only 300 could be checked out by coronary angiography (CAG). Besides, the larger the thickness and arch of the VML around the vessel adventitia, the more severe the MB in these patients (p < 0.05). After the OCT use, there was no coronary perforation in these patients with MB covered with DES. After 1-year follow-up, ISR in MB covered with DES showed a notable difference among no MB, mild MB, moderate MB, and severe MB groups (p < 0.05), and ISR in DES aggravated with the MB severity. However, ISR in MB with and without covered with DES had no significant difference among the 4 groups (p > 0.05). OCT could evaluate MB characteristics accurately compared to IVUS and had a higher rate of detecting MB than CAG. Moreover, it is safe and effective to guide DES covering the mild MB segment in patients with severe coronary lesions detected by the OCT.
Calculation of blast hole charge amount based on three-dimensional solid model of blasting rock mass
Authors: Chen YingXian , Wang PengFei , Chen Jian , Zhou Meng , Yang HongXia , Li JiaYing 
Published: January 2022

AbstractThe development and use of intelligent drilling rigs make it available to obtain accurate lithology data of blast drilling. In order to make full use of drilling data to improve blasting efficiency, the following research was carried out. First, a database is established to manage and store the blast hole data recognized by the intelligent drill. Secondly, the blast hole lithology data is taken as a sample, and the inverse distance square method is used to interpolate the blasting range's solid elements to generate a three-dimensional solid model of the blasting rock mass. Afterward, the blasting range polygon and stope triangle grid are used successively in the solid model to obtain the cut 3D solid model of the blasting rock mass; finally, the blast hole charge is calculated based on the cut 3D solid model of the blasting rock. The C++ programming language is used to realize all the blast hole charge amount processes based on the three-dimensional solid model of the blasting rock mass. With the application example of No. 918 bench blasting of Shengli Open-pit Coal Mine in Xilinhot, Inner Mongolia, the blast hole charge amount in the blasting area is calculated and compared with the results of single hole rock property calculation, the results show that the blast hole charge calculated by three-dimensional rock mass model can be effectively reduced.
Multifocal Oral Epstein–Barr Virus-Positive Mucocutaneous Ulcers Associated with Dual Methotrexate and Leflunomide Therapy: A Case Report
Authors: Kunmongkolwut Sumana , Amornkarnjanawat Chatchawan , Phattarataratip Ekarat 
Published: January 2022

AbstractEpstein–Barr virus (EBV)-positive mucocutaneous ulcer (EBVMCU) is a unique clinicopathologic entity of lymphoproliferative disorder, occurring in immunosuppressed patients. Due to its rarity, EBVMCU may be under-recognized by clinicians as well as pathologists. In addition, its clinical and histopathologic features overlap with other benign and malignant conditions, making a diagnosis challenging. This report presents an unusual case of multifocal oral EBVMCUs in a 52-year-old female patient with rheumatoid arthritis, receiving the combination of methotrexate and leflunomide for 5 years. The patient presented with persistent multiple large painful ulcers involving her palate and gingiva for 6 months. The histopathologic examination revealed extensive ulceration with diffuse polymorphic inflammatory infiltrate admixed with scattered atypical lymphoid cells showing occasional Hodgkin and Reed/Sternberg-like cell features. These atypical cells showed immunoreactivity for CD20, CD30 and MUM1/IRF4. EBV-encoded small RNA in situ hybridization was positive, validating the presence of EBV-infected cells. Two months after discontinuation of both immunosuppressive medications, oral lesions gradually regressed. At 9-month follow-up, no evidence of relapsing oral EBVMCU has been observed. The multifocal presentation of EBVMCU is rare and could be resulted from the overwhelming immune suppression by long-term use of dual immunosuppressants. Its diagnosis requires comprehensive correlation of patient history, clinical findings, histopathologic, and immunophenotypic features. The ability of EBVMCU to regress following removal of immunosuppressive causes is in drastic contrast to a variety of its potential clinical and histopathologic mimics. Therefore, accurate diagnosis is crucial to avoid unnecessary patient management and achieve optimal patient outcomes.
Cervical Spine Inhomogeneously Enhancing Lesion: Avoiding Confirmation Bias
Authors: Penner Federica , Zeppa Pietro , Cofano Fabio , Bianconi Andrea , Ajello Marco , Zenga Francesco 
Published: January 2022

Abstract
Confirmation bias is the tendency to seek information and evidence in order to confirm a preexisting hypothesis while giving less importance and overlook an alternative solution. This report describes the case of a 52-year-old man with a long history of neck pain and bilateral upper limbs paresthesias with a cervical intracanal inhomogeneously enhancing lesion. Despite all the preoperative radiological findings, a spinal meningioma an anterior approach was performed. The mass ended up being a large migrated hernia with the involvement of two levels. Before suggesting treatment, especially surgery, physicians and practitioners need to evaluate all of the possible alternatives in order to optimize patient outcome.
Clinical Outcome of Neoplastic Meningitis Associated with Breast Cancer
Authors: Abraham Anju Anna , T.M Anoop , P. Rona Joseph , Vasudevan Arun , Kumar Bhavya S. 
Published: January 2022

Abstract

Background Neoplastic meningitis (NM) is considered as a terminal event with poor prognosis. Its impact in clinical oncology is growing.

Objective To analyze the clinical outcome of patients with carcinoma breast diagnosed with NM.

Materials and Methods This study was an observational study in breast cancer patients diagnosed with NM. Patients with typical clinical symptoms and signs with either presence of cerebrospinal fluid (CSF) cytology positive for neoplastic cells or typical radiological features of leptomeningeal involvement in the presence of neurological symptoms or signs were taken as leptomeningeal metastasis (LM) or NM. The estimation of survival was done by Kaplan–Meier method.

Results Out of 1,200 patients diagnosed with carcinoma breast during the study period, 15 developed NM. The median age of study population was 51 (range: 44–55) years. Most common presentations were headache (47%), vomiting (47%), diplopia (20%), seizure (20%), and cerebellar signs (7%). Seven (46%) patients were hormone receptor positive, four (30%) were HER2 (Human epidermal growth factor receptor 2) positive and seven (46%) were triple-negative breast cancer. Median time to develop LM from the time of diagnosis of breast cancer was 6 (range: 3–8) months. Nine patients (90%) had features of NM in CSF cytology. Thirteen patients received palliative whole brain radiotherapy (20 Gy in five fractions). Nine out of 12 patients received single-agent Capecitabine as first-line chemotherapy after palliative radiation therapy (RT). Intrathecal methotrexate was given for seven patients. The median overall survival was 3 (range: 0.5–4) months.

Conclusion LM is a very aggressive metastatic disease with poor outcome. There is an unmet need for proper guidelines and an overwhelming necessity for a better focus on research for new modalities of disease in this scenario.