bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preparing Active Recombinant AEP free of Acid-activation.
Authors: Ma Muge , Tang Simon TM , Luk Louis YP 
Published: August 2022

Abstract
Asparaginyl endopeptidase is a useful biocatalyst for site-specific protein bioconjugation. However, existing recombinant protocol is lengthy requiring cap removal of the zymogenic enzymes through acid activation and extra chromatographic steps. Here, we describe an activation-free approach for AEP preparation where the cap and core domains are prepared as separate entities during gene expression. An AEP variant from Oldenlandia affinis (OaAEP1b-C247A) can be prepared without the need of acid treatment giving a yield of ~1.5-2.2 mg of enzyme per litre of culture. Likely because of a decrease in chromatography time and an increase of homogeneity, activity of the split AEP was found to be ~3-fold higher than those obtained using existing protocols, highlighting its potential usefulness.
Stem cell-derived mouse embryos develop within an extra-embryonic yolk sac to form anterior brain regions and a beating heart-like structure.
Authors: Amadei Gianluca , Handford Charlotte E. , Glover David , Zernicka-Goetz Magdalena 
Published: August 2022

Abstract
Mouse embryos are an invaluable tool to study mammalian development but establishment of novel transgenic mouse lines is a costly and time-consuming endeavour. Stem cell models, on the other hand, lend themselves to quick genetic manipulation and are easily scalable, yet they do not successfully capture morphogenesis.Here, we report stem cell-based structures called ETiX-embryoids that can recapitulate mouse post-implantation morphogenesis. ETiX-embryoids form by aggregating embryonic and trophoblast stem cells to embryonic stem cells transiently expressing Gata4. Over the course of 4 days, these structures develop like mouse post-implantation egg cylinders; they then undertake and complete gastrulation on day 5 and 6, respectively. On day 7, ETiX-embryoids undergo neural induction and form the mouse anterior-posterior axis from neural folds to tail bud by movements of convergent extension. On day 8 they form a brain, establish a beating heart-like structure and a gut tube, as they develop inside extraembryonic membranes equivalent to amnion and yolk sac. We detail here the experimental set up and procedure required to generate ETiX-embryoids, and anticipate that they will establish themselves as a novel, powerful tool to study mammalian development without generating a novel mouse lines.
Spatial and molecular profiling reveals an immunosuppressive mononuclear phagocyte network in Classic Hodgkin lymphoma
Authors: Stewart Benjamin , Fergie Martin , Young Matthew , Jones Claire , Sachdeva Ashwin , Blain Alex , Bacon Chris , Rand Vikki , Ferdinand John , James Kylie , Mahbubani Krishnaa , Hook Liz , Jonas Nicolaas , Coleman Nicholas , Saeb-Parsy Kourosh , Collin Matthew , Clatworthy Menna , Behjati Sam , Carey Christopher 
Published: August 2022

Abstract
Classic Hodgkin lymphoma (cHL) has a rich immune infiltrate, which is an intrinsic component of the neoplastic process. Malignant Hodgkin Reed-Sternberg cells (HRSC) create an immunosuppressive microenvironment by the expression of regulatory molecules, preventing T-cell activation. It has also been demonstrated that mononuclear phagocytes (MNP) in the vicinity of HRSC express similar regulatory mechanisms in parallel, and their presence in tissue is associated with inferior patient outcomes. MNP in cHL have hitherto been identified with a small number of canonical markers and are usually described as ‘tumor-associated macrophages’. The organization of MNP networks and interactions with HRSC remains unexplored at high resolution. Here, we defined the global immune cell composition of cHL and non-lymphoma lymph nodes, integrating data across single-cell RNA sequencing, spatial transcriptomics and multiplexed immunofluorescence. We observed that MNP comprise multiple subsets of monocytes, macrophages and dendritic cells (DC). Classical monocytes, macrophages and conventional DC2 were enriched in the vicinity of HRSC, but plasmacytoid DC and activated DC were excluded. Unexpectedly, cDC and monocytes expressed immunoregulatory checkpoints PD-L1, TIM-3, and the tryptophan-catabolizing protein IDO, at the same level as macrophages. Expression of these molecules increased with age. We also found that classical monocytes are important signaling hubs, potentially controlling the retention of cDC2 and ThExh via CCR1-, CCR4-, CCR5-, and CXCR3-dependent signaling. Enrichment of the cDC2-monocyte-macrophage network in diagnostic biopsies is associated with early treatment failure. These results reveal unanticipated complexity and spatial polarization within the MNP compartment, further demonstrating their potential roles in immune evasion by cHL.
Enzymatic Extraction and Characterization of Nanocellulose from Cornhusk Fiber
Authors: Jin Haiyan , tian yinghua , Teng Liqian , Yang Jiaqi , Wu Hongyan , Liu Xiaolan 
Published: August 2022

Abstract

Cornhusk is a renewable and abundant crop by-product whose diverse applications must be studied more extensively. However, thus far, cornhusk, as a raw material, has not been employed for production of cornhusk fiber (CF) nanocellulose (CNC). This study aims to extract and characterize nanocellulose using CF as a raw material by high-shear-assisted enzyme hydrolysis. The extraction process was optimized by investigating the particle size distribution. The optimal extraction conditions of CNC were as follows: cellulase concentration of 1 mg/g, pH of 4.8, temperature of 50 ℃, and 24 h treatment under high-shear conditions for 20 min. The morphological characteristics of the CNC and CF were investigated, and FTIR，XRD, and TGA analyses were performed. Compared with CF, CNC exhibited slenderer nanofibrils with a smoother surface. FTIR analysis showed that the peaks that represented hemicellulose, lignin, and pectin disappeared or diminished in the CNC spectrum. The crystal type of CNC did not change and was identical to that of CF (cellulose type I). The TGA results showed that CNC possessed a lower thermal stability and higher char residuals than those of CF.
A Stretchable and Conformable Sensor Fabricated by PVDF Film for human dynamic monitoring
Authors: Hongying Tian , Lisheng Han , Xiangrong Wang , Huimin Hao , Kaili Zhao , Juanjuan Wu , Peiyuan Wang , Huang Jia-hai 
Published: August 2022

Abstract
With the increasing demand for self-adaptive electronics, stretchable and conformable sensors with merits of high sensitivity, stretchability, and self-adhesive have taken great proportion on the advanced intelligent devices. Herein, a novel tactile sensor that can always maintain conformal contact to the measuring object for efficient movement monitoring was demonstrated, whose structure contains the “H” well-manicured thermoplastic elastomer (TPE), rectangular PVDF film coupled with silver electrode and clamped into the copper-clad signal line ends (CCSLE), and “U” shaped super-elastic silica gel layer, can satisfy the above performances to the maximum extent. Thus, by ingenious designing and association, the output signals of the arch device have been explored, which can serve as dynamic monitoring sensor owing to the stretchable and conformal configuration. Besides, the mechanical stability, high sensitivity suggested that when attached to the skin of participates’ joints, the sensor would be able to detect strains induced by different motion postures, and it was confirmed in the paper experimentally. The results show that the novel biomimetic sensor is effective in monitoring human dynamic, with a success rate of more than 98.3 percent. The stretchable and conformable sensor is highly used for low-cost, non-toxic, breathable, and has further potential in clinical, conformal detection, and artificial intelligence.
scCapsNet-mask: an updated version of scCapsNet with extended applicability in functional analysis related to scRNA-seq data
Authors: Wang Lifei , Nie Rui , Zhang Jiang , Cai Jun 
Published: August 2022

Abstract
Background
We recently developed the single cell Capsule Network (scCapsNet), an interpretable deep learning classifier for single cell RNA sequencing (scRNA-seq) data based on Capsule Network (CapsNet). Although scCapsNet could identify cell type related genes that determine the classification process, the random association with one-to-many and many-to-one relationships between primary capsules and type capsules adds complexity and difficulty for model interpretation.
Results
Here we introduce scCapsNet-mask, an updated version of scCapsNet that utilizes a mask to ease the task of model interpretation. To assess the performance of scCapsNet-mask, we conducted experiments on two scRNA-seq datasets. The results of experiments on two scRNA-seq datasets show that scCapsNet-mask could constrain the coupling coefficients, the internal parameters of the model, and make a one-to-one correspondence between the primary capsules and type capsules. Therefore, scCapsNet-mask keeps the virtue of high classification accuracy and high interpretability of the original scCapsNet, and has the advantages of automatic processing and easy interpretation. Furthermore, we show that scCapsNet-mask could extend its applicability in functional analysis. Firstly, scCapsNet-mask could estimate the lineage (fate) bias of cells with less differentiated states. After deducing the fate bias, a pseudo-temporal order of cells could be established for each lineage. Following these pseudo-temporal order, lineage specific genes exhibit a gradual increase expression pattern and HSC associated genes exhibit a gradual decrease expression pattern. Secondly, scCapsNet-mask was applied to the cell type assignment in spatial transcriptomics. Training on scRNA-seq data, the spatial map of predicted cell types generated by scCapsNet-mask model is consistent with that generated by RCTD and the anatomical structure of the mouse hippocampus, with much less time and computing resources.
Conclusions
scCapsNet-mask source code is freely available at https://github.com/wanglf19/scCapsNet_mask. It is an updated version of scCapsNet to identify cell type associated genes more easily, and can extend its applicability in functional analysis such as fate bias prediction in less differentiated cells and cell type assignment in spatial transcriptomics.
Analysis of Seismic Noise of Broadband Seismological Stations installed along the Western Ghats
Authors: Jha Krishna , B Padma Rao , C Sribin , S Silpa 
Published: August 2022

Abstract
The Western Ghats (WG) is one of the great escarpments that extend ~ 1500 km parallel to the west coast of India in the NNW-SSE. We deployed a network of seven broadband seismological stations along the WG to decipher it’s evolution. In the present study, we investigate the characteristics of different kinds of noises at the stations by utilizing the power spectral density measurements. Further, the results are compared with the global standard noise models to assess the data quality. The PSD results reveal that the short period (cultural) noise is more prominent at stations AGMB, SDPR, MGLI when compared to the other stations, especially during day hours since these sites were in the proximity of roads. The seasonal variations are observed especially in the microseismic period range and noise levels are more prominent in the months of July to August since the western part of India experiences peak monsoon during this period. These variations are observed especially at PCH and KNUR stations as their locations were near the coastline. Further, the results indicate that the noise levels are more prominent in vertical component than that of horizontal components in the microseismic period range whereas it is reversed in the short and long period ranges. Later, the results indicate that the noise levels at all the localities of stations are within the global standard noise models, which suggest that our installation of broadband seismological stations have been successful and has good data quality.
Chen’s Penetrating-Suture Technique for Pancreaticojejunostomy Following Pancreaticoduodenectomy
Authors: Zhang Lihong , Zhu Xuefeng , Zhu Yongsheng , Huang Jianjun , Tao Lide , Chen Yijun 
Published: August 2022

Abstract
Background and purpose: Postoperative pancreatic fistula (POPF) is the most serious complication and the main reason for morbidity and mortality after pancreaticoduodenectomy (PD). Currently, there exists no flawless pancreaticojejunal anastomosis approach. We presents a new approach called Chen’s penetrating-suture technique for pancreaticojejunostomy (PPJ), which involves end-to-side pancreaticojejunostomy by suture penetrating the full-thickness of the pancreas and jejunum, and evaluates its safety and efficacy.Methods: To assess this new approach, between May 2006 and July 2018, 193 consecutive patients who accepted the new Chen’s Penetrating-Suture technique after a PD were enrolled in this study. Postoperative morbidity and mortality were evaluated.Results: All cases recovered well after PD. The median operative time was 256 (range 208–352) min, with a median time of 12 (range 8–25) min for performing pancreaticojejunostomy. Postoperative morbidity was 19.7% (38/193) and mortality was zero. The POPF rate was 4.7 % (9/193) for Grade A, 1.0 % (2/193) for Grade B, and no Grade C cases. and one urinary tract infection.Conclusion: PPJ is a simple, safe, and reliable technique with ideal postoperative clinical results.
Estimations of energy-based criteria in nonlinear phenomena in peridynamic micromechanics of random structure composites
Authors: Buryachenko Valeriy 
Published: August 2022

Abstract
The basic feature of the peridynamic model considered is a continuum description of a material behavior as the integrated nonlocal force interactions between infinitesimal particles. In contrast to these classical local and nonlocal theories, the peridynamic equation of motion introduced by Silling (J. Mech. Phys. Solids 2000; 48:175--209) is free of any spatial derivatives of displacement. For random structure composite materials (CMs) being considered, a linearized theory of bond-based peridynamics was proposed before for multiphase constituents of arbitrary geometry. It is demonstrated that many nonlinear phenomena (such as, e.g. plasticity, damage, and fatigue) in both local micromechanics and peridynamic one are described by energy-based criteria which are, in its turn, depend on the second moments of the local fields. Analyses of these nonlinear phenomena in peridynamics imply the availability of the direct numerical simulation that is only possible for CMs of deterministic structure (e.g. either a finite sample or periodic structure CMs). Consideration of random structure CMs with nonlinear phenomena requires an acceptance of some additional assumptions. The corresponding approaches in local micromechanics are well developed. A goal of the current study is bridging the gap between the linearized peridynamic micromechanics gathering momentum and a wide class of nonlinear phenomena for random structure CMs. It is performed by a straightforward generalization of the concept of the field second moments (used in energy-based criteria) developed before in nonlinear local micromechanics to their peridynamic counterparts. The method proposed is most advantageously applicable due to identity (with an accuracy to notations) of the operator forms of the new general integral equations (GIEs) for both the local micromechanics of random structure CMs and peridynamic one.
A study on the relationship between succinate dehydrogenase and mitoKATPC in the mechanism of ischemic postconditioning protecting against MIRI under CPB in adult rats
Authors: Du Kang , Wang Yan , Tang Kun , Chen Wei , Zhou Wenjing , Zhang Yu , Wang Haiying 
Published: August 2022

Abstract
Objective: To explore the relationship between succinate dehydrogenase and mitoKATPC in the mechanism of ischemic postconditioning (IPO) attenuating myocardial ischemia-reperfusion injury (MIRI) under CPB in adult rats. Methods: 160 adult male SD rats, SPF grade, weighing 300-350g. Established adult rat CPB ischemia-reperfusion and IPO models. Randomly divided into 8 groups with 20 animals in each group: normal group (Nor), SDH competitive inhibitor Dimethyl malonate (dm) control group (dm+ Nor), ischemia-reperfusion group (I// R), dm+ ischemia-reperfusion group (dm+ I/R), ischemia postconditioning group (IPO), dm+ ischemic postconditioning group (dm+ IPO), mitoKATPC specific inhibitor 5-hydroxydecanoic acid (5-HD) + ischemic postconditioning group (5-HD+IPO), dm+5-HD+ischemic postconditioning group (dm+5-HD+IPO). The blood was collected at the end of reperfusion and the rat hearts were harvested for the following tests: 1. Measure the myocardial infarct size (IS); 2. Observing the ultrastructure of the myocardium and calculating the mitochondrial Flameng score of the myocardial cells; 3. Creatine kinase-MB (CK-MB) and cardiac troponin I (cTnI) concentrations; 4. Reactive oxygen species (ROS) generation under confocal microscopy; 5. Myocardial determination SDH activity, content of succinic acid (SA) and fumaric acid (FA); 6. Determination of mRNA and protein expression of succinate dehydrogenase flavoprotein (SDHA) in myocardial tissue. Results: Compared with the Nor group, IS, mitochondrial Flameng score, CK-MB, cTnI, ROS content, SDH activity, SA content, SDHA mRNA expression and SDHA protein expression were significantly increased in the I/R group (P<0.05). Compared with the dm+ Nor group, there was no statistical difference (P>0.05); compared with the I/R group, both were decreased in the dm+ I/R group and the IPO group (P<0.05); compared with the IPO group, the dm+ IPO group decreased, and the 5-HD+IPO group increased (P＜0.05); there was no significant difference between the 5-HD+IPO group and the dm+5-HD+IPO group (P＞0.05) . The FA content is the opposite of the above results. Conclusion: The activity of SDH in myocardial ischemia is significantly increased, which leads to a significant increase in the expression of SDHA, which is involved in the mechanism of myocardial ischemia-reperfusion injury and inhibits the activity of SDH, which can effectively reduce MIRI. Ischemic postconditioning can open mitoKATPC and inhibit the activity of SDH to protect MIRI. The inhibitory effect of ischemic postconditioning on SDH activity is achieved by opening mitoKATPC.
"We hear and we fear" – preferences of 1,203 women regarding conversations of the personnel during cesarean delivery.
Authors: Sagi-Dain Lena 
Published: August 2022

Abstract
Purpose: To evaluate the preferences of women undergoing cesarean delivery regarding the conversations of the personnel during the operation. Methods: This cross-sectional study was conducted by distribution of an open anonymous questionnaire in social media platforms during March 2022, aiming for respondents who underwent cesarean delivery at any time during their lifetime. Results: The questionnaire was completed by 1,203 participants. Conversations between the staff members were reported in 97.6% of the cases. Casual conversations were considered as “disturbing” by higher proportion of the respondents compared to professional talk (33.4% vs. 27.6%, respectively, p=0.0077), and as “relaxing” by a lower proportion (22.8% vs. 32.2%, respectively, p<0.0001). According to logistic regression analysis, factors associated with being disturbed by the conversations were higher levels of stress and pain experienced during the operation, and for professional conversations - urgent operations and second and higher order cesarean compared to first cesarean delivery. Respondents recalling direct communication with the personnel reported significantly lower levels of stress compared to the remaining cohort (60.8% vs. 72.5%, p<0.001). Conclusion: Intraoperative conversations of the personnel occur during the vast majority of cesarean deliveries. For some patients, these talks can decrease the anxiety, while for others such conversations increase the stress; thus, the optimal approach would be a preliminary assessment of maternal preferences. In addition, communication with the women during the operative course is of great importance.
Shallow Parallel CNNs for contextual remote sensing image classification
Authors: Abdellatif Bassam , Laban Noureldin , Metwalli Mohamed R. 
Published: August 2022

Abstract

In this paper we present a new neural network structure that can better learn to classify remote sensing images of moderate and high spatial resolution where the main source of information about desired objects are the pixels themselves and the tight neighborhood. It enhances the pixel-based classification process by incorporating the contextual information in its surroundings.The proposed algorithm is an arrangement of small Shallow Parallel Convolutional Neural Network layers, SP-CNN, that are centered, each of them, over training or test pixels. Each SP-CNN drives information from the pixel to be classified and its contextual neighborhood. Depending on the information that may be found in the context of each pixel, the size and the number of SP-CNNs to be used in the proposed structure can be learned or optimized.The proposed method has been applied to Sentinel-2 (10 m resolution) and Pl\'eiades data (0.5 m resolution) and gave superior results when compared to 1-D CNN and other pixel-based methods such as KNN, SVM, and RF.The proposed method shows its suitability when the training and test data are pixel-based and in same time the spatial domain has valuable information to be incorporated in the classification process.
Relationship between physical activity and bone mineral density loss after gastrectomy in gastric cancer patients
Authors: Sakurai Yuto , Honda Michitaka , Kawamura Hidetaka , Kobayashi Hiroshi , Toshiyama Satoshi , Yamamoto Ryuya , Nakao Eiichi , Yue Cong , Takano Minoru , Hayao Keishi , Konno Shinichi 
Published: August 2022

Abstract
Purpose: The prevention of osteoporosis is a particularly relevant issue for gastric cancer survivors. We investigated the relationship between postoperative physical activity and the change of bone mineral density (BMD) in patients with gastric cancer.Methods: Patients who underwent radical gastrectomy for gastric cancer were enrolled in this single-center prospective cohort study. Physical activity was evaluated using the International Physical Activity Questionnaire Short Form at postoperative month (POM) 6 and patients were classified into high, middle, and low physical activity groups accordingly. The primary outcome was the change in BMD from baseline at POM 12, which was expressed as a percentage of the young adult mean (YAM). The YAM of the lumbar spine and femoral neck was measured by dual-energy X-ray absorptiometry. Results: One hundred ten patients were enrolled in this study. The physical activity level at POM6 was classified as high (n=50; 45%), middle (n=25; 23%), and low (n=35; 32%). The mean decrease of YAM% was 5.1% in the lumbar spine and 4.2% in the femoral neck at POM 12. A multivariable-adjusted logistic regression model revealed that low physical activity at POM 6 was a significant risk factor for BMD loss at POM 12 (odds ratio, 3.63; 95% confidence interval, 1.45–9.11; p=0.006).Conclusion: Low physical activity after gastrectomy is an independent risk factor for decreased BMD at POM12. The introduction of exercise may prevent osteoporosis after the surgical treatment of gastric cancer.