bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryoprotective Effect of Pentoxifylline on Spermatogonial Stem Cell During Transplantation into Azoospermic Torsion Mouse Model
Authors: malekzadeh mehrnoush , Takzaree Nasrin , toolee heidar , kazemzadeh shokoofe , khanmohammadi Nasrin , Solhjoo Somayeh , Sadeghiani Ghazaleh , shabani maryam , Rastegar Tayebeh 
Published: July 2021

Abstract
Preserving the spermatogonial stem cells (SSCs) in long periods of time during the treatment of male infertility using stem cell banking systems and transplantation is an important issue. Therefore, this study was conducted to develop an optimal cryopreservation protocol for SSCs using 10 mM pentoxifylline (PTX) as an antioxidant in basal freezing medium. Testicular torsion - a mouse model for long-term infertility- was used to transplant fresh SSCs (n = 6), fresh SSCs treated with PTX (n = 6), cryopreserved SSCs with basal freezing medium (n = 6) and cryopreserved SSCs treated with PTX (n = 6). Eight weeks after germ cell transplantation, samples were assessed for proliferation, through evaluation of Ddx4 and Id4 markers, and differentiation via evaluation of C-Kit and Sycp3, Tnp1, Tnp2, and Prm1 markers. According to morphological and flow cytometry results, SSCs are able to form colonies and express Gfra1, ID4, α6‐integrin and β1‐integrin markers. We found positive influence from PTX on proliferative and differentiative markers in SSCs transplanted to azoospermic mice. In the recipient testis, donor SSCs formed spermatogenic colonies and sperm. Respecting these data, adding pentoxifylline is a practical way to precisely cryopreserve germ cells enriched for SSCs in cryopreservation, and this procedure could become an efficient method to restore fertility in a clinical setup. However, more studies are needed to ensure its safety in the long term.
Secure Multi-Label Tumor Classification Using Homomorphic Encryption
Authors: Hong Seungwan , Park Jai Hyun , Cho Wonhee , Choe Hyeongmin , Cheon Jung Hee 
Published: July 2021

Abstract
Background: In a secure genome analysis competition called iDASH 2020, the homomorphic encryption task was to develop a multi-label tumor classification method for predicting the classes of samples based on genetic information. The scenario is that a data holder encrypts a genetic variant dataset from tumor samples and provides the encrypted data to an untrusted server. Then, the server evaluates homomorphically encrypted data in its model which is trained in plaintext using the published data or own genetic data and outputs the result in an encrypted state so that there is no leakage of genetic information. Methods: We develop a secure multi-label tumor classification method using the CKKS scheme, the approximate homomorphic encryption scheme. We first propose a new data preprocessing method to reduce the size of large-scale genetic data of tumor samples. Our method aims to analyze the dataset from iDASH 2020 competition track I, which originated from The Cancer Genome Atlas (TCGA) dataset, which consists of 2,713 samples from 11 types of cancers, genetic features from more than 25,000 genes. Secondly, we propose the new data packing method for CKKS ciphertext to provide a trade-off between the number of ciphertexts and the number of rotations in matrix multiplication. Lastly, we suggest the approximation method for softmax activation of a neural network model.Results: Our preprocessing method reduces the number of genes from more than 25,000 to 2048 or less and achieves a microAUC value of 0.9865 with a 1-layer shallow neural network. Using our model, we successfully compute the tumor classification inference steps on the encrypted test data in 4.5 minutes. Despite using the approximate softmax function, the difference in microAUC value from our implementation results in the encrypted state is less than 10-3 compared to the plain result.Conclusions: We present preprocessing and evaluation methods for secure multi-label tumor classification based on approximate homomorphic encryption using a shallow neural network model with the softmax activation function.
On The Exact Counting of Tree-Child Networks
Authors: Pons Miquel , Batle Josep 
Published: July 2021

Abstract
The combinatorial study of phylogenetic networks has attracted much attention in recent times. In particular, one class of them, the so-called tree-child networks, are becoming the most prominent ones. However, their combinatorial properties are largely unknown. In this paper we address the problem of exactly counting them. We conjecture a bijection with a certain class of words, and from this assumption a simple recurrence formula arises. It is able to determine the number of all subclasses, as well as a direct formula, a simple enumeration procedure and precise
asympotics. Our results coincide with all currently proved formulas for particular subclasses of tree-child networks, as well as with numerical results obtained for small networks. Since, as we will show, working with words greatly simplies the problem, we expect to contribute to further combinatoric characterizations of this class of networks.
Gene Deletion Algorithms for Minimum Reaction Network Design by Mixed-integer Linear Programming for Metabolite Production in Constraint-based Models: gDel_minRN
Authors: Tamura Takeyuki , Muto-Fujita Ai , Tohsato Yukako , Kosaka Tomoyuki 
Published: July 2021

Abstract
Background: Genome-scale constraint-based metabolic networks play an important role in the simulation of growth coupling, which means that cell growth and target metabolite production are simultaneously achieved. To achieve growth coupling, a minimal reaction-network-based design is known to be effective. However, the obtained reaction networks often fail to be realized by gene deletions due to conflicts with gene-protein-reaction relations.Results: Here, we developed gDel_minRN that determines gene deletion strategies using mixed-integer linear programming to achieve growth coupling by repressing the maximum number of reactions via gene-protein-reaction relations. Computational experiments were conducted in which gDel_minRN was applied to iML1515, a genome-scale model of Escherichia coli. The target metabolites were three vitamins that are highly valuable and require cost-effective bioprocesses for economics and the environment. gDel_minRN successfully calculated gene deletion strategies that achieve growth coupling for the production of biotin (vitamin B7), riboflavin (vitamin B2), and pantothenate (vitaminB5).Conclusion: Since gDel_minRN calculates a constraint-based model of the minimum number of gene-associated reactions without conflict with gene-protein-reaction relations, it helps biological analysis of the core parts essential for growth coupling for each target metabolite. The source codes are implemented in MATLAB, CPLEX, and COBRA Toolbox. The obtained data and source codes are available on https://github.com/taketam/gDel-minRN
Formulation, Development and Assessment of Novel Phyto-Elastosomes Loaded with Devil’s Claw Extract
Authors: Ntemi Pascal , Walker Roderick B , Khamanga Sandile 
Published: July 2021

Abstract
Background: Management of arthritis requires frequent administration of medications at high doses that may lead to unwanted side effects and diminished patient adherence to the therapy. Devil’s claw extract, a herbal medicine from the Kalahari sands possess similar therapeutic efficacy with less side effects as the commercialized NSAIDs. The objectives of this study were to formulate, develop and assess novel phyto-elastosomes loaded with Devil’s claw extract in order to combat the toxicity levels associated with Devil’s claw and enhance penetration of harpagoside to intended targeted site.Methods: Screening studies were undertaken to determine the ideal amount of Tween® 80, cholesterol, ethanol, diacetyl phosphate and the pH of the hydration medium necessary to produce stable Devil’s claw-loaded phyto-elastosomes. Parameters monitored were particle size, polydispersity index, zeta potential, entrapment efficiency and deformability index.Results: The use of 20 % v/v ethanol was sufficient to produce novel phyto-elastosomes capable of deforming with minimal size alterations. Hydration of thin films in acidic solution produced phyto-elastosomal dispersions with high entrapment efficiency. The presence of cholesterol impeded harpagoside entrapment and increased cholesterol content affected the stability of vesicles by causing agglomeration. Conversely, increasing Tween® 80 concentration promoted harpagoside entrapment. Diacetyl phosphate promoted the stability of vesicle through charge induction.Conclusions: Development of Devil’s claw loaded phyto-elastosomes is useful in ensuring harpagoside reach the target site of action in arthritis-affected patients. Incorporation of these elastic vesicles in transdermal dosage forms may significantly improve the management of arthritis in the near future.
WITHDRAWN: Ecc-bAsed ScalablE Revocation(EASER) scheme for selective sharing in resource-constrained devices
Authors: Sethia Divyashikha , Sahu Raj , Yadav Sandeep 
Published: July 2021

Abstract
IoT is one of the most promising technologies in modern industry. IoT devices are resource-constrained and hence require efficient and lightweight encryption schemes to provide data security. Fine-grained selective access control is required to share sensitive data with different stakeholders. There must be support for scalable revocation to revoke unsolicited users and provide uninterrupted access to valid users. In this paper, we propose a novel lightweight Ecc bAsed ScalablE Revocation (EASER) CP-ABE scheme. It extends an existing CPABE-CSSK to mitigate a key collusion attack and extends it for scalable revocation without any need for any redistribution of keys, re-encryption of ciphertext, or requirement of any revocation lists beforehand. EASER CP-ABE scheme is lightweight and pairing-free with constant -size secret keys. Detailed qualitative and quantitative analysis of the EASER CP-ABE scheme proves that it outperforms the existing related schemes with acceptable storage and computational overheads.
Simplified Cultivation Methods for Rice Production in a Rice-ratoon Rice Cropping System in Southwestern China
Authors: Jiang Peng , Xu Fuxian , Zhang Lin , Mao Liu , Xiong Hong , Guo Xiaoyi , Zhu Yongchuan , Zhou Xingbing 
Published: July 2021

Abstract
Simplified cultivation methods for rice production offer considerable social, economic, and environmental benefits. However, limited information is available on yield components of rice grown using simplified cultivation methods in a rice-ratoon rice cropping system. A field experiment using two hybrids and two rice cultivars was conducted to compare four cultivation methods (conventional tillage and transplanting, CTTP; conventional tillage and direct seeding, CTDS; no-tillage and transplanting, NTTP; no-tillage and direct seeding, NTDS) in a rice-ratoon rice system from 2017–2020. Main season yields for CTDS and NTDS were higher than for CTTP, whereas ratoon season yields for CTDS and NTDS were equal to or higher than for CTTP. Annual grain yields for CTDS and NTDS were higher than for CTTP. The higher CTDS and NTDS yields were associated with higher panicle numbers per m2 and biomass production. Rice hybrids had significantly higher yields than inbred cultivars, which was attributed to high grain weight and biomass production. Our results suggest that CTTP can be replaced by CTDS and NTDS to maintain high grain yields and save labor costs. Developing cultivars with high grain weight could be a feasible approach to achieve high rice yields in the rice-ratoon rice cropping system in southwest China.
An integrated design for collecting and recycling of space debris
Authors: Kamal Sherif , Gaber Ahmed , El-Baz Farouk 
Published: July 2021

Abstract
Today, as estimated by the U.S. Space Surveillance Network, there are 14,000 pieces of debris larger than 10 cm in Earth-orbit. That is in addition to thousands of satellites for various applications. As time passes, these satellites represent debris that might represent dangerous space waste. Such accumulated items orbit the Earth at very high speed and might threaten the daily uses of space-based applications, such as satellites that are needed for weather forecasting, telecommunications, and global positioning systems (GPS). In addition, this might negatively affect future missions -- unless the international space community considers the risks and joins forces to mitigate them. Today, only ideas have been proposed by the various space agencies without taking much action. Each proposed idea deals with a specific size of debris. This paper proposes an integrated approach to collect most of the debris to be recycled for use as a source of raw material in construction equipment, which are used in maintenance of the International Space Station (ISS) and other equipment needed by future space missions and spacecraft. Furthermore, this proposal might solve the problem of the lack of space in the ISS, which served as home to numerous astronauts for more two decades. The proposed design could be implemented through cooperative programs by the world’s space agencies. Because few countries represent the main source of this space wastes, it is here proposed that a financing source would be established by assigning a tariff for each future space flight, as a percentage of the cost of each mission. For example, fees could be determined based on; the extent of the mission’s lifetime, the size and weight of the satellites, and the purpose of the mission.
Evaluation of Strategies for Pumping Optimization of Coastal Aquifers Using Numerical Simulation and Game Theory
Authors: Beheshti Javid , Javadi Saman , Hosseini Seyed Abbas , Moghadam Hamid Kardan 
Published: July 2021

Abstract
In this study, after simulating five years of saltwater intrusion with SEAWAT package in Astaneh-Kouchesfahan coastal aquifer, Iran, 19 strategies, including managerial, structural, and combined strategies, were investigated to reduce the saltwater intrusion. Since managerial solutions cause users’ dissatisfaction and structural solutions increase the costs, two-player game theory was used to identify the most appropriate solution. According to the results obtained from game theory, the two strategies of artificial recharge and underground dam had the greatest impact on preventing the saltwater intrusion with the highest satisfaction of stakeholders, so that they decreased the saltwater intrusion from 740 m by 150 and 300 m, respectively, after five years. Therefore, the combined simulator-optimizer method presented in this study can evaluate various solutions, and the most appropriate solution can be proposed with the lowest cost and maximum satisfaction for the sustainable management of coastal aquifers.
Knockdown of PGM1 Synergistically Enhances Anticancer Effects of Orlistat in Gastric Cancer Under Glucose Deprivation
Authors: Cao Bo , Deng Huan , Cui Hao , Zhao Ruiyang , Li Hanghang , Wei Bo , Chen Lin 
Published: July 2021

Abstract
Background Phosphoglucomutase 1 (PGM1) acts as an important regulator in glucose metabolism. However, the role of PGM1 in gastric cancer (GC) remains unclear. This study aims to investigate the role of PGM1 and develop novel regimens based on metabolic reprogramming in GC. MethodsCorrelation and enrichment analysis of PGM1 was conducted based on The Cancer Genome Atlas database. Data derived from the Kaplan-Meier Plotter database were analyzed for correlations between PGM1 expression and survival time of GC patients. CCK-8, EdU, flow cytometry assays, generation of subcutaneous tumor and lung metastasis mouse models were used to determine growth and metastasis in vitro and in vivo. Cell glycolysis was detected by a battery of glycolytic indicators, including lactate, pyruvic acid, ATP production and glucose uptake. Fatty Acid Synthase (FASN) activity and detection of lipid regulators levels by western blot were used to reflect on the cell lipid metabolism. ResultsCorrelation and enrichment analysis suggested that PGM1 was closely associated with cell proliferation and metabolism. PGM1 was overexpressed in GC tissues and cell lines. High PGM1 expression served as an indicator of shorter survival for specific subpopulation of GC patients, which was also correlated with some clinicopathological features, including T stage and TNM stage. Under low glucose conditions, knockdown of PGM1 significantly suppressed cell proliferation and glycolysis levels, whereas lipid metabolism was enhanced. Orlistat, as a drug that was designed to inhibit FASN activity for obesity treatment, effectively induced apoptosis, suppressed FASN activity. However, orlistat conversely increased glycolytic levels in GC cells. Orlistat exhibited more significant inhibitive effects on GC progression after knockdown of PGM1 under glucose deprivation due to combination of glycolysis and lipid metabolism. ConclusionsDownregulation of PGM1 expression under glucose deprivation synergistically enhanced anti-cancer effects of orlistat. This combination application may serve as a novel strategy for GC treatment.
Employing Peer Support Workers in the Emergency Department to Help Care for Patients that Present After An Opioid-Related Overdose: Implementation Challenges and Recommendations From Key Stakeholders
Authors: Crisanti Annette S. , Earheart Jennifer 
Published: July 2021

Abstract
Background: The peer support model has been adapted in emergency departments (ED) throughout the country, specifically in response to increases in admissions resulting from opioid use disorder (OUD). The purpose of this study was to use community-engaged principles to identify implementation challenges and recommendations related to employing peer support workers (PSWs) in the ED to help care for patients that present after an opioid-related overdose. Methods: A qualitative study was conducted to identify challenges to and recommendations for implementing the peer support model in the ED to help care for patients that present after an opioid-related overdose. Nineteen stakeholders were interviewed, including directors/managers, nurses and PSWs. An inductive qualitative approach was used for the identification of themes from the interviews.Results: Three themes surfaced among the implementation challenges, including system level challenges, hospital level challenges, and challenges specific to PSWs (referred to as individual level challenges). Recommendations to address the challenges are presented for successful integration of PSWs in ED settings to help care for patients that present after an opioid-related overdose. Recommendations include, for example, clearly defined job descriptions and increasing understanding of what PSWs do among all hospital staff. Conclusions: PSWs can play a role in the care for patients that present to the ED after an opioid-related overdose and in doing so help address the opioid crisis. Through the identification of challenges, awareness of strategies to address these challenges, and proper planning, hospitals can implement PSWs into the ED successfully. Planning should include thoughtful conversations between leadership, ED staff and, PSWs, as well as a commitment from leadership and hospital staff to recovery-oriented care. For the successful employment and integration of PSWs into ED settings to help care for patients that present after an opioid-related overdose, planning should focus on four key areas, including (1) hiring the right PSWs for the position, (2) education ED and hospital staff, (3) establishing protocols, and (4) training and supervision.
A Supramolecular Heat-Pump: an Electrochemical Cooling System Utilizing the Enthalpy Change of a Host–Guest Interaction
Authors: Matoba Fumitoshi , Yamada Teppei , Kimizuka Nobuo 
Published: July 2021

Abstract
Redox-stimulated host–guest chemistry was applied for the electrochemical Peltier effect, which is a heat transportation phenomenon observed in redox-active electrolytes. The refrigeration capability was enhanced up to 70%. By the addition of alpha-Cyclodextrin (α-CD) into I−/I3− aqueous solution, the amount of heat transported from the cathode side to the anode side was observed. The enhancement of the heat transportation was derived from the elimination heat of I3− from α-CD associated with the shift of host–guest equilibrium caused by the exhausting of I3− by the reduction. This is the first report that utilized the stimuli-responsive supramolecular interaction for heat transportation.
Chicken miR-126-5p Negatively Regulates Antiviral Innate Immunity By Targeting TRAF3
Authors: Wang Jie , Cheng Yuqiang , Wang Longlong , Lin Zhenyu , Zhu Wenxian , Wang Zhaofei , Ma Jinjiao , Wang Henan , Sun JianHe 
Published: July 2021

Abstract
Background Innate immunity plays an essential role in preventing the invasion of pathogenic microorganisms. However, innate immunity is a double-edged sword, whose excessively activated is detrimental to immune homeostasis and even leads to "cytokine storm" of the infected host. A series of negative regulatory mechanisms are developed by the host to balance the immune response. Here, we report a negative regulatory mechanism of chicken innate immunity mediated by miRNA. Results In this study we found that the miR-126-5p is markedly up-regulated in RNA virus infected chickens in GEO database. Then, the upregulation of the miR-126-5p by RNA virus was further verified via both cell model and in vivo test. Overexpression of miR-126-5p significantly inhibits the expression of interferon related genes and inflammatory cytokines evoked by RNA virus. The opposite result was achieved after knocking down miR-126-5p expression. Bioinformatics analysis indicated TRAF3 as the candidate target gene of miR-126-5p, and experimental evidence, such as the effects of miR-126-5p on the endogenous expression of TRAF3, and the effect of miR-126-5p on TRAF3 3'UTR drove luciferase reporter assay, were provided to further verify that miR-126-5p targets TRAF3. Furthermore, we demonstrated that miR-126-5p negatively regulates innate immunity by blocking the MAVS-TRAF3-TBK1 axis, with co-expression assay. Conclusion Our results suggest that miR-126-5p is involved in the negative regulation of the chicken innate immunity, which might contribute to maintaining immune balance.
Computational Probing of Tin-based Lead-free Perovskite Solar Cells: Effects of Absorber Parameters and Various ETL Materials on Device Performance
Authors: Shyma Arunkumar Prabhakaran , Sellappan Raja 
Published: July 2021

Abstract
Tin-based perovskite solar cells have gained global research attention due to the lead toxicity and health risk associated with its lead-based analogue. The promising opto-electrical properties of the Tin-based perovskite have attracted researchers to work on developing solar cells with higher efficiencies comparable to Lead-based analogues. Tin-based perovskites outperform the lead-based ones in areas like optimal band gap and carrier mobility. A detailed understanding regarding the effects of each parameters and working conditions on Tin-based perovskite is crucial in order to improve the efficiency. In the present work, we have carried out a numerical simulation of planar heterojunction Tin-based (CH3NH3SnI3) perovskite solar cell employing SCAPS 1D simulator. Device parameters namely thickness of the absorber layer, defect density of the absorber layer, working temperature, series resistance, metal work function have been exclusively investigated. ZnO has been employed as the ETL (Electron transport layer) material in the initial simulation to obtain optimized parameters and attained a maximum efficiency of 19.62 % with 1.1089 V open circuit potential (Voc) at 700 nm thickness (absorber layer). Further, different ETL materials have been introduced into the optimized device architecture and Zn2SnO4 based device delivers an efficiency of 24.3 % with a Voc of 1.1857 V. The obtained results indicate a strong possibility to model and construct better performing perovskite solar cells based on Tin (Sn) with Zn2SnO4 as ETL layer.