bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cancer cells adapt FAM134B/BiP mediated ER-phagy to survive hypoxic stress
Authors: Chipurupalli Sandhya , Ganesan Raja , Martini Giulia , Mele Luigi , Reggio Alessio , Esposito Marianna , Kannan Elango , Namasivayam Vigneshwaran , Grumati Paolo , Desiderio Vincenzo , Robinson Nirmal 
Published: April 2022

AbstractIn the tumor microenvironment, cancer cells experience hypoxia resulting in the accumulation of misfolded/unfolded proteins largely in the endoplasmic reticulum (ER). Consequently, ER proteotoxicity elicits unfolded protein response (UPR) as an adaptive mechanism to resolve ER stress. In addition to canonical UPR, proteotoxicity also stimulates the selective, autophagy-dependent, removal of discrete ER domains loaded with misfolded proteins to further alleviate ER stress. These mechanisms can favor cancer cell growth, metastasis, and long-term survival. Our investigations reveal that during hypoxia-induced ER stress, the ER-phagy receptor FAM134B targets damaged portions of ER into autophagosomes to restore ER homeostasis in cancer cells. Loss of FAM134B in breast cancer cells results in increased ER stress and reduced cell proliferation. Mechanistically, upon sensing hypoxia-induced proteotoxic stress, the ER chaperone BiP forms a complex with FAM134B and promotes ER-phagy. To prove the translational implication of our mechanistic findings, we identified vitexin as a pharmacological agent that disrupts FAM134B-BiP complex, inhibits ER-phagy, and potently suppresses breast cancer progression in vivo.
Mesenchymal stem cells empower T cells in the lymph nodes via MCP-1/PD-L1 axis
Authors: He Yifan , Qu Yan , Meng Bowen , Huang Weiying , Tang Jianxia , Wang Runci , Chen Zetao , Kou Xiaoxing , Shi Songtao 
Published: April 2022

AbstractMesenchymal stem cells (MSCs) are a type of immunosuppressive stromal cell found in multiple tissues and organs. However, whether MSCs possess immunosupportive characteristics remains unclear. In this study, we showed that the lymph nodes contain immunosupportive MSCs. They produce and secrete a high level of MCP-1 to promote T-cell proliferation and differentiation, in contrast to bone marrow MSCs (BMMSCs), which repress T-cell activation. Unlike BMMSCs, lymph node MSCs (LNMSCs) fail to respond to activated T-cell-induced production of PD-L1 to induce T-cell apoptosis. Mechanistically, MCP-1 activates phospho-Erk to sustain T-cell proliferation and activation while it represses NF-κB/PD-L1 pathway to avoid induction of T-cell apoptosis. Interestingly, inflammatory lymph node-derived LNMSCs abolish their immunosupportive function due to reduction of MCP-1 expression. Finally, we show that systemic infusion of LNMSCs rescues immunosuppression in cytoxan (CTX)-treated mice. This study reveals a previously unrecognized mechanism underlying MSC-based immunoregulation using the MCP-1/PD-L1 axis to energize T cells and suggests a potential to use MSCs to treat immunosuppressive disorders.
The Cycas genome and the early evolution of seed plants
Authors: Liu Yang , Wang Sibo , Li Linzhou , Yang Ting , Dong Shanshan , Wei Tong , Wu Shengdan , Liu Yongbo , Gong Yiqing , Feng Xiuyan , Ma Jianchao , Chang Guanxiao , Huang Jinling , Yang Yong , Wang Hongli , Liu Min , Xu Yan , Liang Hongping , Yu Jin , Cai Yuqing , Zhang Zhaowu , Fan Yannan , Mu Weixue , Sahu Sunil Kumar , Liu Shuchun , Lang Xiaoan , Yang Leilei , Li Na , Habib Sadaf , Yang Yongqiong , Lindstrom Anders J. , Liang Pei , Goffinet Bernard , Zaman Sumaira , Wegrzyn Jill L. , Li Dexiang , Liu Jian , Cui Jie , Sonnenschein Eva C. , Wang Xiaobo , Ruan Jue , Xue Jia-Yu , Shao Zhu-Qing , Song Chi , Fan Guangyi , Li Zhen , Zhang Liangsheng , Liu Jianquan , Liu Zhong-Jian , Jiao Yuannian , Wang Xiao-Quan , Wu Hong , Wang Ertao , Lisby Michael , Yang Huanming , Wang Jian , Liu Xin , Xu Xun , Li Nan , Soltis Pamela S. , Van de Peer Yves , Soltis Douglas E. , Gong Xun , Liu Huan , Zhang Shouzhou 
Published: April 2022

AbstractCycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists.
Development of a clinical polygenic risk score assay and reporting workflow
Authors: Hao Limin , Kraft Peter , Berriz Gabriel F. , Hynes Elizabeth D. , Koch Christopher , Korategere V Kumar Prathik , Parpattedar Shruti S. , Steeves Marcie , Yu Wanfeng , Antwi Ashley A. , Brunette Charles A. , Danowski Morgan , Gala Manish K. , Green Robert C. , Jones Natalie E. , Lewis Anna C. F. , Lubitz Steven A. , Natarajan Pradeep , Vassy Jason L. , Lebo Matthew S. 
Published: April 2022

AbstractImplementation of polygenic risk scores (PRS) may improve disease prevention and management but poses several challenges: the construction of clinically valid assays, interpretation for individual patients, and the development of clinical workflows and resources to support their use in patient care. For the ongoing Veterans Affairs Genomic Medicine at Veterans Affairs (GenoVA) Study we developed a clinical genotype array-based assay for six published PRS. We used data from 36,423 Mass General Brigham Biobank participants and adjustment for population structure to replicate known PRS–disease associations and published PRS thresholds for a disease odds ratio (OR) of 2 (ranging from 1.75 (95% CI: 1.57–1.95) for type 2 diabetes to 2.38 (95% CI: 2.07–2.73) for breast cancer). After confirming the high performance and robustness of the pipeline for use as a clinical assay for individual patients, we analyzed the first 227 prospective samples from the GenoVA Study and found that the frequency of PRS corresponding to published OR > 2 ranged from 13/227 (5.7%) for colorectal cancer to 23/150 (15.3%) for prostate cancer. In addition to the PRS laboratory report, we developed physician- and patient-oriented informational materials to support decision-making about PRS results. Our work illustrates the generalizable development of a clinical PRS assay for multiple conditions and the technical, reporting and clinical workflow challenges for implementing PRS information in the clinic.
Computational characterization of the behavior of a saliva droplet in a social environment
Authors: Ugarte-Anero Ainara , Fernandez-Gamiz Unai , Portal-Porras Koldo , Zulueta Ekaitz , Urbina-Garcia Oskar 
Published: April 2022

AbstractThe conduct of respiratory droplets is the basis of the study to reduce the spread of a virus in society. The pandemic suffered in early 2020 due to COVID-19 shows the lack of research on the evaporation and fate of droplets exhaled in the environment. The current study, attempts to provide solution through computational fluid dynamics techniques based on a multiphase state with the help of Eulerian–Lagrangian techniques to the activity of respiratory droplets. A numerical study has shown how the behavior of droplets of pure water exhaled in the environment after a sneeze or cough have a dynamic equal to the experimental curve of Wells. The droplets of saliva have been introduced as a saline solution. Considering the mass transferred and the turbulence created, the results has showed that the ambient temperature and relative humidity are parameters that significantly affect the evaporation process, and therefore to the fate. Evaporation time tends to be of a higher value when the temperature affecting the environment is lower. With constant parameters of particle diameter and ambient temperature, an increase in relative humidity increases the evaporation time. A larger particle diameter is consequently transported at a greater distance, since the opposite force it affects is the weight. Finally, a neural network-based model is presented to predict particle evaporation time.
Clinical Impact of Research: Introduction to the Forum
Authors: Spencer Trina D. 
Published: April 2022

Purpose:In communication sciences and disorders (CSD), clinical impact is paramount. Without clinical impact of research, evidence-based practice is not possible. Unfortunately, clinical impact of research is often overlooked or underappreciated. The purpose of this forum is to provide guidance to current and future CSD researchers about how to maximize the clinical impact of their research. A secondary purpose is to increase researchers’ and their institutions’ awareness of the importance of clinical impact and the need to document it for tenure and promotion. The prologue introduces four articles that cover topics related to clinical practice research, knowledge brokering, disseminating via social media, and documenting impact for promotion.
Apple appearance quality classification method based on double branch feature fusion network
Authors: Yin Ji‐zhe , Geng Lei , Guo Yong‐min , Huang Ya‐long , Song Ye , Zhao Heng 
Published: April 2022

AbstractThis paper carried out a classification study on the quality of different types of apples. In order to achieve a high‐precision classification of high‐quality apples in various dimensions, shorten the classification time, improve efficiency, and make it feasible for practical applications. This paper proposes an automatic recognition and classification model OB‐Net (for apple appearance quality) based on a dual‐branch structure. The model consists of two branches, an O branch and a B branch. The O branch extracts the shape and contour features of the apple surface defect by decomposing the feature map into high and low frequencies. The B branch extracts the shape size and texture characteristics of the apple surface defect by fusing channel attention and spatial attention mechanisms; this is done to further increase the feature distance between different types of defects. Experimental results show that the classification accuracy rates of rot, insect bites, russeting, scratches, and intact apples are 95.65%, 98.17%, 94.62%, 92.02% and 97.67%, respectively; the overall classification and recognition accuracy rate reaches 95.64%. Finally, the three aspects of the feature map, heat map and category probability statistics map extracted from the OB‐Net network model prove the validity of the network model in the classification of apple appearance quality.
Self‐compensation of torque reaction in an induction contra‐rotating propulsion motor
Authors: Hassannia Amir 
Published: April 2022

AbstractTorque reaction is one of the most critical issues with current aerial and undersea vehicles. Contra‐Rotating Propulsion (CRP) systems are the most popular technique for compensating the torque reaction of floating vehicles. However, the unbalanced load conditions are inescapable in CRP systems, which eliminate the net zero torque reaction and impulse unwanted spinning on vehicle. A new single‐phase dual rotor axial flux induction motor has been investigated in this paper that has the ability of self‐compensate reaction torque against unbalanced loads. The proposed motor can eliminate the requirement for complicated torque reaction control systems. Finite element simulation shows the expected performance of proposed motor under unbalanced conditions. The simulation results have been verified by experimental testing of a motor prototype.
Reflex and Spontaneous Movements in Pediatric Patients with Brain Death
Authors: Kim Juhyeon , Kwon Oh-Young , Kim Do-Hyung , Yang Tae-Won , Kim Minhwa , Lee Jeongrim , Cho Wonhyun , Yeom Jung Sook , Kim Young-Soo 
Published: April 2022

Abstract
Background Reflex and spontaneous movements are not uncommon in brain death patients. However, most studies have been conducted in adults, while reports in infants and children are rare. Thus, we aimed to evaluate the frequency and characteristics of these movements in pediatric patients declared as brain death.
Methods Records of pediatric patients who were diagnosed as brain death from 15 hospitals in the Yeongnam region, South Korea, between January 2013 and September 2016 were analyzed. All body movements in patients who met the criteria for brain death as established by the Korea Medical Association were assessed by medical doctors and trained organ transplant coordinators. The frequency and characteristics of these movements were identified. Additionally, the demographic and clinical factors of the brain death patients with and without these movements were compared.
Results A total of 31 patients who met the criteria for brain death were enrolled. Seven patients (22.6%) showed either reflex or spontaneous movements; six of them (85.7%) showed reflex movements only, and one patient (14.3%) showed both types of movements. The most common types of reflex movements were the flexor/extensor plantar response and isolated finger jerk. Four of seven patients (57.1%) showed a single movement pattern, while three (42.9%) showed two different movement patterns.
Conclusion It is essential for physicians who perform pediatric brain death examinations to recognize the frequency and characteristics of reflex and spontaneous movements, and this article may help in the accurate and prompt diagnosis of brain death.
Platelet Toll-Like-Receptor-2 and -4 Mediate Different Immune-Related Responses to Bacterial Ligands
Authors: Niklaus Marius , Klingler Philipp , Weber Katja , Koessler Angela , Kuhn Sabine , Boeck Markus , Kobsar Anna , Koessler Juergen 
Published: April 2022

Abstract
Background Like immune cells, platelets express toll-like receptors (TLRs) on their surface membrane. TLR2 and TLR4 are able to recognize bacterial antigens and have the potential to influence hemostatic functions and classical intracellular signaling pathways. This study investigated the role of TLR2 and TLR4 for immune-related functions in human platelets.
Materials and Methods Washed platelets and neutrophils were prepared from fresh human peripheral blood. Basal-, Pam3CSK4- (as TLR2 agonist) and Lipopolysaccharides (LPS; as TLR4 agonist) -induced CD62P expression, fibrinogen binding and TLR2 or TLR4 expression, intracellular reactive oxygen species (ROS) production in H2DCFDA-loaded platelets and uptake of fluorescence-labeled TLR ligands, and fluorophore-conjugated fibrinogen were evaluated by flow cytometry. Analysis of platelet–neutrophil complexes was performed after coincubation of washed platelets and neutrophils in the presence and absence of TLR2 or TLR4 agonists on poly-L-lysine coated surfaces, followed by immunostaining and immunofluorescence imaging.
Results Pam3CSK4 rapidly and transiently increased TLR2 and TLR4 expression. Over the course of 30 minutes after activation with Pam3CSK4 and LPS, the expression of both receptors decreased. Pam3CSK4-stimulated intracellular ROS production and the uptake of TLR ligands or fibrinogen much stronger than LPS. Besides, TLR4 activation led to a significant increase of platelet–neutrophil contacts.
Conclusion Stimulation leads to rapid mobilization of TLR2 or TLR4 to the platelet surface, presumably followed by receptor internalization along with bound TLR ligands. After activation, platelet TLR2 and TLR4 mediate different immune-related reactions. In particular, TLR2 induces intracellular responses in platelets, whereas TLR4 initiates interactions with other immune cells such as neutrophils.
High Factor VIII Levels and Recurrent Thromboembolism in Patients with and without Inflammatory Bowel Disease: A Retrospective Comparative Study
Authors: Eagle G E. , Schulman Sam 
Published: April 2022

Abstract
Background The natural course of elevated factor VIII (FVIII) in patients with venous thromboembolism (VTE) and with or without inflammatory bowel disease (IBD) is not well described. Furthermore, the data on effectiveness and safety of extended anticoagulation in these patients are limited.
Methods We performed a retrospective chart review of all patients with VTE who had an elevated FVIII level (>1.5 IU/mL) during a period of 16 years. FVIII levels, duration of anticoagulation, recurrent thromboembolic events, and bleeding requiring hospitalization were captured and compared between patients with and without IBD.
Results Fourteen patients with IBD and 66 without IBD were followed for 8.0 years (standard deviation [SD] =  ±  3.5) and 5.6 years (SD =  ±  5.1), respectively. Among the 41 patients with repeat levels, FVIII remained elevated in most patients. None of the IBD patients had thromboembolic events or major bleeding during a mean of 5.6 years (SD =  ±  5.1) of anticoagulation. Three of five IBD patients who stopped anticoagulation had thromboembolic events at a median of 9 months after stopping, observed event rate of 12 per 100 patient-years. For the 66 non-IBD patients, the event rates of thromboembolism on and off anticoagulation were 1.6 and 7.2 per 100 patient-years, respectively, and of major bleeding on anticoagulation 0.8 per 100 patient-years.
Conclusion Elevated FVIII in patients with VTE is often a persistent risk factor. The cohort with VTE and elevated FVIII that we analyzed appeared to have a favorable benefit/risk ratio of extended anticoagulation.
Effect of Ozone Gas on Removal of Airborne Particles
Authors: Agra Priscilla Alvarenga , Agra Patricia Alvarenga , Marceliano-Alves Marilia Fagury Videira , Conceição Greice Maria Silva da , Assumpção Sérgio Luiz de Lima , Crespo Celso de Farias , Philippi Letícia Maria Borsarini , Lins Renata Ximenes 
Published: April 2022

Abstract
Objective Airborne particles are one of the most important factors in the spread of infectious pathogens and must be monitored in healthcare facilities. Viable particles are living microorganisms, whereas non-viable particles do not contain microorganisms but act as transport for viable particles. The effectiveness of ozone in reducing these particles in a non-controlled room and a controlled cleanroom using high-efficiency particles air (HEPA) filter was analyzed in this study.
Materials and Methods Viable particles and non-viable particles sized 0.5 and 5 μm were quantified before and after ozonation in two different health environments: non-controlled (group 1) and controlled area, which was associated with a HEPA filtering system (group 2). Active air sampling using a MAS 100 was used to count the number of viable particles, while the number of non-viable particles/m3 was obtained following the manufacturer's recommendations of the Lasair III 310C system.
Results Our results of the viable particles counting were not quantifiable and analyzed using statistical tests. Both groups showed a slight tendency to reduce the number of viable particles after ozonation of the environmental air. A statistically significant reduction of non-viable 5 μm particles after ozonation was observed in both groups (G1: p = 0,009; G2: p = 0,002). Reduction in the non-viable 0.5 μm particles after ozonation was observed only in group 2, associated with the HEPA filter. In group 1, after ozonation, a significant increase in 0.5 μm particles was observed, probably due to the breaking of 5 μm particles by ozone gas. Our results suggest that ozone gas can break 5 μm particles and, when associated with a HEPA filter, increases its effectiveness in removing 0.5 μm particles.
Conclusion Considering that 5 μm particles are important in the air transport of microorganisms, their reduction in the environment can be a relevant parameter in controlling the dissemination of infections.
Universal Screening of Patients with Cancer for COVID-19: Results from an Observational, Retrospective Cohort Study in Kerala, India
Authors: Pavithran Keechilat , Jayamohanan Hridya , Philp Arun , Vijaykumar D.K. , Kumar Anil , John Denny 
Published: April 2022

Abstract
Introduction There is high risk of contracting coronavirus disease 2019 (COVID-19) among patients with cancer with risk of mortality and morbidity being high. Limited data is available on the outcomes of universal screening of cancer patients with asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection from lower-middle-income countries (LMICs).
Objectives Our goal was to determine the prevalence of asymptomatic SARS-CoV-2 infection in patients with cancer attending the medical oncology department of a tertiary care hospital in Kerala and protect both patients and health care workers before proceeding with the systemic anticancer treatment.
Materials and Methods This was a retrospective cohort study of screening patients receiving systemic anticancer therapy for COVID-19 among hospitalized patients from August 1, 2020, and both outpatients and hospitalized patients from September 1 to November 15, 2020. After clinical triaging, patients were subjected to universal screening with rapid antigen tests and/or reverse transcriptase-polymerase chain reaction (RT-PCR).
Results A total of 1,722 SARS-CoV-2 tests (321 RT-PCR and 1,401 antigen tests) were performed among 1,496 asymptomatic patients before their scheduled chemotherapy/immunotherapy. Eight hundred forty-eight patients were screened more than twice. The patient cohort's median age was 59 years (range 01–92 years); 44.98% of patients were males, and 55.01% were females. 58.77% of patients were on adjuvant or neoadjuvant chemotherapy and 41.22% on chemotherapy for metastatic cancer. The most common malignancy was breast cancer (26.53%), followed by lung (8.35%) and gastrointestinal (16.4%) cancers. The prevalence of asymptomatic infections in our study was 0.86%. Only one patient who had undergone chemotherapy after a negative SARS-CoV-2 test developed confirmed COVID-19 during subsequent testing. From these index cases, none of the other patients, health care workers, or their caretakers contracted COVID-19.
Conclusion The prevalence of asymptomatic COVID-19 infections in our study was low (0.86%). With proper health education, clinical triaging, and screening of the high-risk group, it is possible to continue cancer treatment during the peak of the COVID-19 pandemic, even in LMICs.