bluuebunny/crossref_metadata_2025_split huggingface dataset:
uniPort: a unified computational framework for single-cell data integration with optimal transport
Authors: Cao Kai , Gong Qiyu , Hong Yiguang , Wan Lin 
Published: June 2022

Abstract
Single-cell data integration can provide a comprehensive molecular view of cells. Here we introduce uniPort, a unified single-cell data integration framework which combines a coupled Variational Autoencoder (coupled-VAE) and Minibatch Unbalanced Optimal Transport (Minibatch-UOT). It leverages both highly variable common and dataset-specific genes for integration and is scalable to large-scale and partially overlapping datasets. uniPort jointly embeds heterogeneous single-cell multi-omics datasets into a shared latent space. It can further construct a reference atlas for online prediction across datasets. Meanwhile, uniPort provides a flexible label transfer framework to deconvolute heterogeneous spatial transcriptomic data using optimal transport space, instead of embedding latent space. We demonstrate the capability of uniPort by integrating a variety of datasets, including single-cell transcriptomics, chromatin accessibility and spatially resolved transcriptomic data. uniPort software is available at https://github.com/caokai1073/uniPort.
Influence of thinning intensity and frequency on the provision of ecosystem services in Mediterranean mountain pine forests under climate change scenarios
Authors: Simon Diana Cristina , Ameztegui Aitor 
Published: June 2022

Abstract
Thinnings are silvicultural operations that repetitively reduce tree density to improve the ecological, economic, and social benefits of the stands. Thus, the correct choice of the thinning regime can enhance stand structure and the provision of various ecosystem services throughout the rotation period. In this study, we use a modelling approach to evaluate stand dynamics and the provision of ecosystem services (mushroom production, wood for timber, carbon storage, blue water, and habitat for biodiversity) in Mediterranean mountain pine forests under different thinning regimes – defined by intensity and frequency – and under two different climate change scenarios. We implemented the thinning regimes using SORTIE-ND, an individual-based model that simulates forest dynamics, and then we integrated models developed for the study area to calculate the provision of services. We used as a case study a Pinus sylvestris and a Pinus nigra stand and we evaluated the effect of the thinning regime, in terms of intensity and frequency, the effect of climate change, and the effect of forest type over a rotation period. Our results show that overall, the production of mushrooms, timber, and carbon decreased with increasing intensity and shortening frequency, while the blue water increased under those conditions. The application of thinnings favoured the habitat for biodiversity by producing more large dead trees and faster. Large timber was better supported by a thinning regime with heavy intensity and shorter frequencies. We found synergies between the production of mushrooms, timber, and carbon, while blue water is in a trade-off relationship with these services. Biodiversity showed a weak relationship with the rest of studied services. Furthermore, our results have shown that climate change will lower the production of ecosystem services under the most severe climate predictions. Based on our results, we can conclude that our modelling approach is a useful and efficient tool for answering questions that would otherwise require long-term studies, and that it can provide useful information to guide management efforts to adapt forest management to the challenges of climate change.
Developing Total Force Fitness and Its Components to Achieve Optimal Military Performance in Iran
Authors: Shakibaei Abolfazl , Alishiri Gholamhossein , Hosseiniara Reza 
Published: June 2022

Abstract
Background Military personnel is the most valuable asset of the armed forces to carry out missions. The Iranian Armed Forces have not provided a comprehensive definition of Total Force Fitness (TFF), and the present study will be a pioneer in this regard.AimThe aim of this study was to provide a TFF model, and its components to achieve optimal military performance in Iran.MethodsThe present study is an analytical study that was conducted cross-sectionally at Baqiyatallah University of Medical Sciences, Tehran, Iran from 2020-to 2021. Thirty-nine specialists related to TFF in 10 domains including medical fitness, physical fitness, nutritional fitness, environmental fitness, psychological fitness, spiritual fitness, behavioral fitness, social fitness, occupational fitness, and family fitness were consulted to develop the questionnaire for TFF.FindingsIn this study, for each panel, a specific questionnaire was developed by consulting the experts in order to design a TFF measurement pattern, among fitnesses, occupational fitness was eliminated by experts and the rest of the fitness including Physical, Nutrition, Medical, Psychological, Spiritual, environmental, social, family and Behavioral Fitness was confirmed. TOPSIS method showed that the first priority is spiritual fitness and then physical fitness, and family fitness and nutritional fitness were the last priority.ConclusionIn the present study, as one of the first comprehensive studies in Iran, components of TFF were identified and confirmed. The finding showed that spiritual fitness is most important for the Iranian armed force. Given that manpower is the most valuable resource and that every effort should be made to maximize its potential, further studies are needed.
Trogocytic-molting of T-cell microvilli controls T-cell clonal expansion
Authors: Park Jeong-Su , Kim Jun-Hyeong , Soh Won-Chang , Lee Kyung-Sik , Kim Chang-Hyun , Chung Ik Joo , Lee Sunjae , Kim Hye-Ran , Jun Chang-Duk 
Published: June 2022

Abstract
Internalization of the T-cell antigen receptor (TCR) is intimately linked to T-cell activation: a phenomenon thought to be related to the “exhaustion” of T-cell responses. To date, however, no report has considered that during physical interaction with cognate antigen-presenting cells, T cells release many TCRs via T-cell microvilli particles, which are derived from finger-like membrane structures (microvilli) in a combined process of trogocytosis and enzymatic vesiculation and correspond with the loss of membrane TCRs and many external membrane components. Surprisingly, in contrast to TCR internalization, this event leads to rapid upregulation of surface TCRs and remarkable metabolic reprogramming of cholesterol and fatty acids synthesis to meet the demands of clonal expansion, which drives multiple rounds of division and cell survival. We called this event “trogocytic-molting,” which represents an intrinsic molecular basis of T-cell clonal expansion by which T cells gain increased sensitivity to low antigen concentrations.
Affine-Mapping based Variational Ensemble Kalman Filter
Authors: Wen Linjie , Li Jinglai 
Published: June 2022

Abstract
We propose an affine-mapping based variational Ensemble Kalman filter for sequential Bayesian filtering problems with generic observation models. Specifically, the proposed method is formulated as to construct an affine mapping from the prior ensemble to the posterior one, and the affine mapping is computed via a variational Bayesian formulation, i.e., by minimizing the Kullback-Leibler divergence between the transformed distribution through the affine mapping and the actual posterior. Some theoretical properties of resulting optimization problem are studied and a gradient descent scheme is proposed to solve the resulting optimization problem. With numerical examples we demonstrate that the method has competitive performance against existing methods.Mathematics Subject Classification (2000) 65C05 · 62F15
The GPR83, CA1, AWP1, and WTAP genes expression evaluation in AGS cells Stimulated by Helicobacter pylori cagC gene
Authors: khoshfetrat Zahra , doosti Abbas 
Published: June 2022

Abstract
Background
Gastric carcinoma (GC) is the third leading cause of malignancies-related deaths worldwide, and Helicobacter pylori is one of the identified causes of gastric cancer. The Cag pathogenicity island (cagA, cagC, virB2) is one of the major pathogens of H. pylori, which increased the risk of gastric cancer development. Some studies have shown that H. pylori significantly alter some gastric epithelial cells genes expression. This study aimed to investigate the expression of the GPR83, CA1, AWP1, and WTAP genes in AGS cells transfected with the recombinant pIRES2-EGFP-cagC vector.
Materials and methods
The pIRES2-EGFP-cagC and pIRES2-EGFP plasmids (as control) were transfected into AGS cells by lipofectamine 2000 solution. Then, RNA extraction and cDNA synthesis was performed. The expression of GPR83, CA1, AWP1, and WTAP genes was evaluated using the Real-Time PCR method. Finally, the expression of each gene was evaluated using SPSS software and t-test independent statistical tests.
Results
Our findings indicated that the expression of the GPR83 gene in AGS cells treated with cagC statistically significantly increased compared to control cells (P = 0.0327). On the contrary, the WTAP expression was significantly decreased (P = 0.0132), whereas the AWP1 and CA1 mRNA expression were not statistically significant.
Conclusion
This study shows that GPR83 and WTAP genes's expression in the host is significantly altered through cagC gene expression. Hence, it seems that the cagC gene's presence can explain some alterations in the expression of gastric epithelial cell genes and the cause of gastric cancer pathogenesis caused by H. pylori infection.
Video-Based Communication Assessment for Weight Management Counseling Training in Medical Residents: A Mixed Methods Study
Authors: Faro Jamie M , D'Addario Angelo , King Ann M , Mazor Kathleen M , Pbert Lori , Sadasivam Rajani S , Geller Alan C , Murphy Elizabeth A , Ockene Judith K 
Published: June 2022

Abstract
Background
Physician delivered weight management counseling (WMC) occurs infrequently and physicians report lack of training and poor self-efficacy. The purpose of this study was to develop and test the Video-based Communication Assessment (VCA) for weight management counseling (WMC) training in medical residents.
Methods
This study was a mixed methods pilot conducted in 3 phases. First, we created five vignettes based on our prior data and expert feedback, then administered the vignettes via the VCA to Internal Medicine categorical residents (n = 16) from a University Medical School. Analog patients rated responses and also provided comments. We created individualized feedback reports which residents were able to view on the VCA. Lastly, we conducted debriefing interviews with the residents (n = 11) to obtain their feedback on the vignettes and personalized feedback. Interviews were transcribed, and we used thematic analysis to generate and apply codes, followed by identifying themes.
Results
Descriptive statistics were calculated and learning points were created for the individualized feedback reports. In VCA debriefing interviews with residents, five themes emerged: 1) Overall the VCA was easy to use, helpful and more engaging than traditional learning and assessment modes, 2) Patient scenarios were similar to those encountered in the clinic, including diversity, health literacy and different stages of change, 3) The knowledge, skills, and reminders from the VCA can be transferred to practice, 4) Feedback reports were helpful, to the point and informative, including the exemplar response of how to best respond to the scenario, and 5) The VCA provide alternatives and practice scenarios to real-life patient situations when they aren’t always accessible.
Conclusions
We demonstrated the feasibility and acceptability of the VCA, a technology delivered platform, for delivering WMC to residents. The VCA exposed residents to diverse patient experiences and provided potential opportunities to tailor providers responses to sociological and cultural factors in WMC scenarios. Future work will examine the effect of the VCA on WMC in actual clinical practice.
Influence of Heat Source Arrangement on Coupling Characteristics of Low Power Pulsed Laser-MAG Hybrid Welding
Authors: Tao Xingkong , Yang Huanyu , Ba Xianli , Liu Liming 
Published: June 2022

Abstract
Low power pulsed laser-MAG hybrid welding was carried out by different heat source arrangement methods (lead mode, distance between laser spot and welding wire tip (DLA)). The coupling effect and welding characteristics of hybrid heat sources under different modes were studied by using high speed image (HSI) and real-time electrical signals. HSI observation and electronic signals showed that the lead mode and DLA significantly affect the coupling state of heat source and welding characteristics (weld morphology, process stability and droplet transfer). The influence of lead mode on weld forming was more significant than that of DLA. In laser-lead mode, when DLA = 1~2mm, the laser and arc had perfect coupling effect, good weld formation, less spatter and greater penetration. In arc-lead mode, the weld formation was poor and undercut defects were common, while the overall penetration was greater than that in laser-lead mode. In terms of welding process stability, arc-lead mode was better than laser-lead mode. The pulsed laser increased the stability of projected transition, produced more fine droplets and reduced the generation of spatter. When DLA = 1~2mm, stable droplet transfer could be realized under both modes.
Accelerating effect of Shilajit on osteogenic property of adipose derived mesenchymal stem cells (ASCs)
Authors: Kangari Parisa , Roshangar Leila , Iraji Aida , Talaei-Khozani Tahereh , Razmkhah Mahboobeh 
Published: June 2022

Abstract
Background
Shilajit, as a herbomineral natural substance, has been most widely used remedy for treating a numerous of illness such as bone defects in Iran traditional folk medicine since hundreds of years ago. The aim of the present study was to explore the effect of Shilajit on the osteogenic differentiation of human adipose-derived mesenchymal stem cells (ASCs) in two- and three-dimensional cultures.
Materials and methods
ASCs were isolated and seeded in three-dimensional (3D) 1% alginate (Alg) hydrogel with or without Shilajit at a density of 3 × 105 cell/mL. For two-dimensional (2D) cultures, 3 × 104 ASCs /mL were seeded into culture plates and treated with 500µg/mL Shilajit. Then, characterization was done using electron microscopy (SEM)/energy dispersive X-ray spectroscopy (EDX), alkaline phosphatase (ALP) activity, Alizarin red staining, and Raman confocal microscopy.
Results
Adding Shilajit had no impact on the Alg scaffold degradability. In the 3D Alg hydrogel and in the present of osteogenic medium (OM), Shilajit acted as enhancer to increase ALP activity, also showed osteoinductive property in the absence of OM compared to the 2D matched groups at all time points (days 7 and 21 both P < 0.001, for 14 days P < 0.001 and P < 0.05, respectively). In addition, calcium deposition was significantly increased in the cultures exposed to Shilajit compared to 2D matched groups on days 14 (P < 0.0001), and 21 (P < 0.001and P < 0.01, respectively). In both 3D and 2D conditions, Shilajit induced osteogenic differentiation, but Shilajit/Alg combination starts osteogenic differentiation in a short period of time.
Conclusion
As Shilajit accelerates the differentiation of ASCs into the osteoblasts, without changing the physical properties of the Alg hydrogel, this combination may pave the way for more promising remedies considering bone defects.
Study on Tool wear mechanism under Cryogenic CO2-Assisted Minimum Quantity Lubrication Technology
Authors: Cheng Lin , Qiu Tian , Huang Shizhan , Xie Hong , Liu Chao , Li Yousheng , Lin Liangliang , Xiang Zhiyang , Shui Yan , Wang Fuzeng , Wu Xian , Yan Lan , Jiang Feng 
Published: June 2022

Abstract
Cryogenic CO2-assisted minimum quantity lubrication milling technology is a green processing technology with broad application prospects. Aiming at the problem of tool wear in the application of cryogenic CO2 cooling assisted minimum quantity lubrication in difficult-to-machine materials and the influence of relevant parameters on tool wear, this study used coated cemented carbide tools to perform milling experiments under cryogenic CO2-assisted minimum quantity lubrication technology conditions. The micromorphology of the tool rake face and chip was observed, and the energy spectrum of the tool chip contact area was analyzed. The results showed that reducing CO2 temperature and increasing the oil flow of minimum quantity lubrication can improve the tool wear. The tool wear mechanisms under cryogenic CO2-assisted minimum quantity lubrication were mainly abrasive wear, diffusion wear, and oxidation wear. The chip sawtooth degree of the optimal parameter group was more conducive to chip breaking than that of dry cutting and wet cutting groups. The temperature of the tool-chip contact area is an important factor affecting tool wear, the higher the temperature, the faster the tool wear. At the same time, it is verified that cryogenic CO2-assisted minimum quantity lubrication technology can replace cutting fluid in hard-to-machine materials under certain conditions.
Investigating the origin of TMS-evoked brain potentials using topographic analysis
Authors: Šulcová Dominika , Salatino Adriana , Ivanoiu Adrian , Mouraux André 
Published: June 2022

Abstract
The combination of transcranial magnetic stimulation (TMS) and electroencephalography (EEG) represents an increasingly popular tool to non-invasively probe cortical excitability in humans. TMS-evoked brain potentials (TEPs) are composed of successive components reflecting the propagation of activity from the site of stimulation, thereby providing information on the state of brain networks. However, TMS also generates peripherally evoked sensory activity which contributes to TEP waveforms and hinders their interpretation. In the present study, we examined whether topographic analysis of TEPs elicited by stimulation of two distinct cortical targets can disentangle confounding signals from the genuine TMS-evoked cortical response. In 20 healthy subjects, TEPs were evoked by stimulation of the left primary motor cortex (M1) and the left angular gyrus (AG). Topographic dissimilarity analysis and microstate analysis were used to identify target-specific TEP components. Furthermore, we explored the contribution of cortico-spinal activation by comparing TEPs elicited by stimulation below and above the threshold to evoke motor responses. We observed topographic dissimilarity between M1 and AG TEPs until approximately 80 ms post-stimulus and identified early TEP components that likely reflect specific TMS-evoked activity. Later components peaking at 100 and 180 ms were similar in both datasets and attributed to sensory-evoked activity. Analysis of sub- and supra-threshold M1 TEPs revealed a component at 17 ms that possibly reflects the cortico-spinal output of the stimulated area. Moreover, supra-threshold M1 activation influenced the topography of almost all later components. Together, our results demonstrate the utility of topographic analysis for the evaluation and interpretation of TMS-evoked EEG responses.
Multilayer encapsulation using Atomic Layer Deposition and a moisture- stable silica containing nanocomposite polymer: correlation between gas permeation measurement on plastic film and performances obtained on top-emitting Organic Light-Emitting Diodes
Authors: Provost Marion , Maindron Tony , Cros Stephane 
Published: June 2022

Abstract
Thin Film Encapsulation (TFE) using a multilayer stack of inorganic and organic films is now a well-known encapsulation technology for organic electronics such as Organic Light-Emitting Diodes (OLED). It shows excellent gas barrier properties with very low WVTR, and good compatibility with flexible and transparent substrates. In this study, low-temperature Atomic Layer Deposition (ALD) serves for the fabrication of high performance Al2O3 inorganic barrier layers. A silica nanocomposite polymer serves as a moisture-stable interface layer in a very high barrier quality architecture of the kind [Al2O3 (25 nm)/nano-CP (1 µm)/Al2O3 (25 nm)/nano-CP (5 µm)]. The helium and water vapor quantitative gas permeation properties (HeTR and WVTR) of different intermediate TFE architectures deposited on plastic substrate (PET) are analyzed using a permeameter. These results are compared to an accelerated weathering test standard, for monolithic TFE deposited in-situ on top-emitting OLED circuits. On PET, the best TFE stack decreases the steady state permeation rate by a factor 1180 and 1650 respectively for helium and water vapor. Onto a top-emitting OLED, the long-term black spot occurrence rate drastically decreased from 100 %.h− 1 to 3.210− 3 %.h− 1, attesting the successful implementation of this TFE architecture from ex-situ on PET substrate to in-situ on OLED circuits.
Identification of risk factors for 1-year mortality among elderly and critically ill patients with hip fractures surgery: A single medical center retrospective study
Authors: luo Taijun , Zhang Juxia , Zhou Haibin , Xu Tao , Zhang Wenchao , Wang Geng 
Published: June 2022

Abstract
AIM: The aim of this study is to examine potential risk factors for 1-year mortality after hip fracture surgery.METHODS: We reviewed 591 elderly and critically ill patients who underwent hip surgery at our institution from January 2018 to April 2021 retrospectively. The baseline demographic, clinical data and 1-year survival status in both groups were collected through the medical record system and follow-up phone calls. Patients were divided into survival group and death group according to the survival status within the first postoperative year. RESULTS: According to the results from 1year follow-up, 117 cases were classified into the death group while 474 cases were in the survival group, and it was calculated that the 1-year mortality rate of elderly and critically ill patients with hip fracture was 19.8% (117/591) in our hospital. The identified risk factors for 1-year mortality were advanced age (HR:1.04, 95%:1.01- 1.06), preoperative arrhythmia (HR: 1.95, 95%: 1.26 - 2.70), high level of NLR (HR:1.03, 95%:1.01 - 1.06), respiratory failure (HR: 2.63, 95%:1.32 - 5.23) and acute cardiovascular events (HR: 1.65, 95%:1.05 - 2.59).CONCLUSION: Advanced age, preoperative comorbid arrhythmias, preoperative high level of NLR, respiratory failure and acute cardiovascular events postoperatively were independently associated with increased risk of 1-year mortality rate of critically ill elderly patients with hip fracture. Laboratory tests such as high level of NLR preoperative can be used as important indicators to determine the prognosis of patients.
A Wideband Circularly Polarized Antenna Using Substrate Integrated Waveguide and Truncated-Corner Patch Loaded Slot
Authors: Agrawal Meha , Kumar Trivesh 
Published: June 2022

Abstract
A wideband circularly polarized antenna based on the substrate integrated waveguide (SIW) is investigated and presented for mobile satellite applications. Initially, a rectangular-slot is etched on the top layer of the SIW cavity. A truncated patch from the one corner (top left) is loaded inside the slot to obtain the two pairs of orthogonal degenerate modes TE130/TE310 and TE230/TE320. This truncated-corner patch helps to bring the orthogonal modes closer to obtain the wideband circular polarization. Further, a rotated rectangular-slot is incorporated inside the patch to enhance the circular polarization bandwidth. The antenna exhibits a relative impedance bandwidth of 20% (10.87GHz-3.275GHz) and the axial ratio bandwidth 11.50GHz-12.26GHz (6.4%). The broadside radiation characteristics are achieved with the peak gain of 6.3dBic and 7.0dBic at the two working frequencies 11.5GHz and 12.0GHz respectively