bluuebunny/crossref_metadata_2025_split huggingface dataset:
To unwind the biological knots: The DNA/RNA G‐quadruplex resolvase RHAU (DHX36) in development and disease
Authors: Yang Chensi , Yao Jie , Yi Huijuan , Huang Xinyi , Zhao Wukui , Yang Zhongzhou 
Published: July 2022

AbstractThe G‐quadruplex (G4) sequences are short fragments of 4‐interval triple guanine (G) with frequent and ubiquitous distribution in the genome and RNA transcripts. The G4 sequences are usually folded into secondary “knot” structure via Hoogsteen hydrogen bond to exert negative regulation on a variety of biological processes, including DNA replication and transcription, mRNA translation, and telomere maintenance. Recent structural biological and mouse genetics studies have demonstrated that RHAU (DHX36) can bind and unwind the G4 “knots” to modulate embryonic development and postnatal organ function. Deficiency of RHAU gives rise to embryonic lethality, impaired organogenesis, and organ dysfunction. These studies uncovered the pivotal G4 resolvase function of RHAU to release the G4 barrier, which plays fundamental roles in development and physiological homeostasis. This review discusses the latest advancements and findings in deciphering RHAU functions using animal models.
An Activity‐Based Fluorescent Probe for Imaging Fluctuations of Peroxynitrite (ONOO−) in the Alzheimer's Disease Brain
Authors: Wang Pengzhan , Yu Le , Gong Jiankang , Xiong Jianhua , Zi Soyu , Xie Hua , Zhang Fan , Mao Zhiqiang , Liu Zhihong , Kim Jong Seung 
Published: July 2022

AbstractPeroxynitrite (ONOO−) plays a critical role in Alzheimer's disease (AD). To reveal the ONOO− influx in AD brains, an activatable activity‐based fluorescence probe Rd‐DPA3 was designed by a structure‐modulated strategy. Taking advantage of ONOO−‐initiated two‐step cascade reactions of a novel chemical trigger, Rd‐DPA3 specifically responds to ONOO− in 0.3 mM of other reactive oxygen species (ROS) and varied proteins, and gives an intensive fluorescence enhancement (F/F0=50). Moreover, with its mitochondria‐targeting ability, Rd‐DPA3 can be used to efficiently monitor the alternations of intracellular ONOO− levels in cerebral cells during oxidative stress. Significantly, due to NIR emission and good blood–brain barrier (BBB) crossing ability, Rd‐DPA3 is suitable for in vivo imaging of cerebral ONOO− influx and illustrating an age‐dependent accumulation of ONOO− in AD mice brains.
Direct Oxygen Transfer from H2O to Cyclooctene over Electron‐Rich RuO2 Nanocrystals for Epoxidation and Hydrogen Evolution
Authors: Lin Xiu , Zhou Zhaoyu , Li Qi‐Yuan , Xu Dong , Xia Si‐Yuan , Leng Bing‐Liang , Zhai Guang‐Yao , Zhang Shi‐Nan , Sun Lu‐Han , Zhao Guohua , Chen Jie‐Sheng , Li Xin‐Hao 
Published: July 2022

AbstractProduction of more than 20 million tons of epoxides per year from olefins suffers from low atom economy due to the use of oxidants and complex catalysts with unsatisfactory selectivity, leading to huge environmental and economic costs. We present a proof‐of‐concept application of electron‐rich RuO2 nanocrystals to boost the highly selective epoxidation of cyclooctene via direct oxygen transfer from water as the sole oxygen source under mild conditions. The enhanced electron enrichment of RuO2 nanocrystals via the Schottky effect with nitrogen‐doped carbons largely promotes the capture and activation of cyclooctene to give a high turnover frequency (260 h−1) of cyclooctene oxide, far surpassing the reported values (<20 h−1) of benchmarked catalysts at room temperature with oxidants. Our electron‐rich RuO2 electrocatalysts enable efficient and durable hydrogen production (Faradaic efficiency >90 %) on the cathode without impacting on the selectivity to epoxide (>99 %) on the anode.
Role‐Specialized Division of Labor in CO2Reduction with Doubly‐Functionalized Iron Porphyrin Atropisomers
Authors: Guo Kai , Li Xialiang , Lei Haitao , Guo Hongbo , Jin Xiaotong , Zhang Xue‐Peng , Zhang Wei , Apfel Ulf‐Peter , Cao Rui 
Published: July 2022

AbstractIn enzymes, the active site residues function differently to promote chemical reactions. Such a role‐specialized division of labor has been rarely realized by synthetic catalysts. We report herein on catalytic CO2reduction with Fe porphyrins decorated with two cationicN,N,N‐trimethylbenzylamine groups incis‐ ortrans‐arrangement. Thecis‐isomer outperforms thetrans‐isomer and reaches a TOFmaxof 4.4×105 s−1in acetonitrile using phenol proton source. Theoretical studies revealed that the two cationic units in thecis‐isomer are more effective than a single cationic unit to improve the CO2binding, and more importantly, they function differently but cooperatively to promote the C−O bond cleavage: one interacts with the CO2‐adduct, while the other one interacts with the phenol molecule through electrostatic interactions. This work therefore presents a significant example of synthetic catalysts, which boost chemical reactions using a role‐specialized strategy for substrate activation.
Recent advances in the utilization of glycerol for the production of lactic acid by catalysis
Authors: Wang Ke , Yang Zhiyun , Ma Yangyang , Zhao Wei , Sun Junyang , Lu Tianliang , He Hao 
Published: July 2022

AbstractIn this review, the research progress on catalytic conversion of glycerol to lactic acid or lactate esters and the reaction mechanisms with different catalysis systems are summarized. Both homogeneous catalysts, including inorganic bases and metal complexes, and heterogeneous catalysts, including metal oxides, molecular sieves, polyoxometalates and noble and non‐noble metals, are discussed. In particular, the influence of catalyst components, the physical and chemical properties of the catalysts and additives and solvents on the catalytic performances are highlighted. In comparison, nano‐metal particles or bimetal catalysts could achieve good catalytic performance, in which the alloy and synergistic effects might form under certain conditions. For further improvement of the sustainable transformation of glycerol to lactic acid or lactate esters, attention should still be paid to rational design of novel cost‐effective, high‐efficiency and green catalytic systems. © 2022 Society of Chemical Industry and John Wiley & Sons, Ltd.
Selective and Reversible Ligand Assembly on the DNA and RNA Repeat Sequences in Myotonic Dystrophy
Authors: Krueger Sarah B. , Lanzendorf Amie N. , Jeon Hyoeun (Heather) , Zimmerman Steven C. 
Published: July 2022

AbstractSmall molecule targeting of DNA and RNA sequences has come into focus as a therapeutic strategy for diseases such as myotonic dystrophy type 1 (DM1), a trinucleotide repeat disease characterized by RNA gain‐of‐function. Herein, we report a novel template‐selected, reversible assembly of therapeutic agents in situ via aldehyde‐amine condensation. Rationally designed small molecule targeting agents functionalized with either an aldehyde or an amine were synthesized and screened against the target nucleic acid sequence. The assembly of fragments was confirmed by MALDI‐MS in the presence of DM1‐relevant nucleic acid sequences. The resulting hit combinations of aldehyde and amine inhibited the formation of r(CUG)exp in vitro in a cooperative manner at low micromolar levels and rescued mis‐splicing defects in DM1 model cells. This reversible template‐selected assembly is a promising approach to achieve cell permeable and multivalent targeting via in situ synthesis and could be applied to other nucleic acid targets.
Mixed Convection in a Lid‐Driven Cavity with Triangular Corrugations and Built‐in Triangular Block
Authors: Kumar Sudhanshu , Panda Sibasish , Gangawane Krunal M. , Vijayan Aparna , Oztop Hakan F. , Hamdeh Nidal-Abu 
Published: July 2022

AbstractThe influence of triangular surface corrugations on the mixed convection characteristics in a tall lid‐driven cavity for non‐Newtonian power‐law fluids is reported. In particular, numerical experimentations are executed for a range of parameters, such as aspect ratio of cavity, number of triangular corrugations, Richardson numbers, Prandtl numbers (Pr), power‐law indexes, and at a constant Grashof number. The corrugation number seems to be the maximum impact for higher Prandtl number fluids. For taller cavities, higher Nusselt number values were obtained for Pr = 100. Triangular corrugations showed a modest change in the heat transfer augmentation in most of the considered parameters.
Fabrication of Vertex‐type‐selectively Reinforced PtCu@PtCuNi Double‐layered Nanoframes for Efficient Methanol Electrooxidation Catalysis
Authors: Wang Jingwei , Ling Yiwei , Yan Hongliang , Li Xinxue 
Published: July 2022

AbstractHerein, we report a two‐step strategy for the preparation of vertex‐type‐selectively reinforced PtCu@PtCuNi double‐layered nanoframes (DNFs). In the first step, PtCuNi heterogeneous nanocrystals (HNCs) were synthesized by a facile one‐pot solvent method. The PtCuNi HNC is composed of a Cu‐enriched concave rhombic dodecahedral core, a double‐layered nanoframe consisting of an inner vertex‐selectively‐reinforced rhombic dodecahedral PtCu nanoframe and an outer concave rhombic dodecahedral PtCuNi nanoframe, and a Ni‐enriched shell. In the second step, PtCu@PtCuNi DNFs were prepared by selectively removing the leachable components via acid treatment. Strikingly, the inner rhombic dodecahedral nanoframe contained six nanopods sticking out from its ⟨100⟩ vertices rather than ⟨111⟩ ones, and the outer concave rhombic dodecahedral nanoframe is formed by interconnecting the adjacent vertices of the inner nanoframe. The electrocatalytic test for methanol oxidation reaction showed that the as‐prepared PtCu@PtCuNi DNFs exhibited enhanced electrocatalytic activity and improved stability compared to the commercial Pt/C catalyst.
The use of the connective tissue graft from the palate for vertical soft tissue augmentation during submerged dental implant placement: A case series
Authors: Vatėnas Imantas , Linkevičius Tomas 
Published: July 2022

AbstractObjectivesTo evaluate the efficacy of the soft tissue augmentation vertically, using connective tissue graft from the palate, during submerged dental implant placement.Material and MethodsVertical soft tissue augmentation, using connective tissue graft from the palate, combining with submerged dental implant placement was performed for 50 patients (10 males and 40 females, mean age 57.22 years). Soft tissue thickness vertically was measured in the middle of the alveolar crest with the periodontal probe. After 3 months, healing abutments or multiunits were connected to the dental implants, augmented soft tissue thickness was measured vertically in the middle of the alveolar crest. The vertical soft tissue volume gain was calculated using analysis of variance descriptive analysis, significance set to p = .05.ResultsAll 50 autogenous connective tissue grafts from the palate healed successfully. The average thickness of the soft tissue grafts from the palate was 1.8 ± 0.41 mm. After 3 months, soft tissue thickness vertically increased from 2.27 ± 0.64 mm to 4.35 ± 0.64 mm. This difference between mean figures, between the groups, before and after soft tissue augmentation was found to be statistically significant F (263;477). The mean increase in soft tissue thickness was 2.08 ± 0.71 mm.ConclusionIt can be concluded that soft tissue augmentation vertically, using connective tissue graft from the palate can be successfully used for vertical soft tissue augmentation.
Deconvolution analysis of cell‐type expression from bulk tissues by integrating with single‐cell expression reference
Authors: Luo Yutong , Fan Ruzong 
Published: July 2022

AbstractTo understand phenotypic variations and key factors which affect disease susceptibility of complex traits, it is important to decipher cell‐type tissue compositions. To study cellular compositions of bulk tissue samples, one can evaluate cellular abundances and cell‐type‐specific gene expression patterns from the tissue transcriptome profiles. We develop both fixed and mixed models to reconstruct cellular expression fractions for bulk‐profiled samples by using reference single‐cell (sc) RNA‐sequencing (RNA‐seq) reference data. In benchmark evaluations of estimating cellular expression fractions, the mixed‐effect models provide similar results as an elegant machine learning algorithm named cell‐type identification by estimating relative subsets of RNA transcripts (CIBERSORTx), which is a well‐known and reliable procedure to reconstruct cell‐type abundances and cell‐type‐specific gene expression profiles. In real data analysis, the mixed‐effect models outperform or perform similarly as CIBERSORTx. The mixed models perform better than the fixed models in both benchmark evaluations and data analysis. In simulation studies, we show that if the heterogeneity exists in scRNA‐seq data, it is better to use mixed models with heterogeneous mean and variance–covariance. As a byproduct, the mixed models provide fractions of covariance between subject‐specific gene expression and cell types to measure their correlations. The proposed mixed models provide a complementary tool to dissect bulk tissues using scRNA‐seq data.
Adult patients with Ph+ ALL benefit from conditioning regimen of medium‐dose VP16 plus CY/TBI
Authors: Morita‐Fujita Mari , Arai Yasuyuki , Kondo Tadakazu , Harada Kaito , Uchida Naoyuki , Toya Takashi , Ozawa Yukiyasu , Fukuda Takahiro , Ota Shuichi , Onizuka Makoto , Kanda Yoshinobu , Maruyama Yumiko , Takada Satoru , Kawakita Toshiro , Ara Takahide , Ichinohe Tatsuo , Kimura Takafumi , Atsuta Yoshiko , Kako Shinichi 
Published: July 2022

AbstractThe medium‐dose etoposide (VP16) added on cyclophosphamide (CY)/total body irradiation (TBI) is one of the intensified myeloablative conditioning regimens used in allogenic hematopoietic stem cell transplantation (allo‐HSCT) for acute lymphoblastic leukemia (ALL). However, the patient subgroups who can actually benefit from VP16/CY/TBI compared to CY/TBI have not been precisely defined. Therefore, we conducted a multi‐center retrospective study using the Japanese nationwide registry database to elucidate the efficacy of VP16/CY/TBI on post‐transplant prognosis. Biological and clinical distinct subtypes (i.e., Philadelphia chromosome‐positive (Ph+) and ‐negative (Ph−) ALL) were evaluated separately, which included 820 Ph+ and 1463 patients with Ph− ALL, respectively. Compared with the CY/TBI group, the VP16/CY/TBI group showed superior progression‐free survival (PFS) in patients with Ph+ ALL (65% vs. 57% at 3 years after HSCT; adjusted hazard ratio (HR), 0.73; 95% confidence interval (CI), 0.55–0.98; p = 0.03), along with significantly reduced incidence of relapse (adjusted HR, 0.58; 95% CI, 0.37–0.90; p = 0.02) without the increase of non‐relapse mortality (NRM). By contrast, in patients with Ph− ALL, VP16/CY/TBI did not improve PFS nor incidence of relapse; addition of VP16 reduced relapse (HR, 0.65; p = 0.06) in patients with Ph− ALL transplanted at CR1, while improved PFS was not observed (HR, 0.90; p = 0.52) due to increased NRM. This study demonstrated that VP16/CY/TBI is a more effective and well‐tolerated regimen in comparison with CY/TBI in patients with myeloablative allo‐HSCT for adult Ph+ ALL. Our findings can provide a novel algorithm for conditioning regimen selection in patients with adult ALL.
Sarcomatoid variant of urothelial carcinoma of renal pelvis with direct invasion of the pancreas and descending colon
Authors: Nakano Yoshinori , Kitano Hiroyuki , Hieda Keisuke , Babasaki Takashi , Takemoto Kenshiro , Hayashi Tetsutaro , Kido Aya , Taniyama Daiki , Sentani Kazuhiro , Hinata Nobuyuki 
Published: July 2022

IntroductionSarcomatoid variant of urothelial carcinoma infiltrates the perimeter and occurs occasionally. However, there are only few case reports.Case presentationA left renal tumor was incidentally detected in a 75‐year‐old woman and protruded outside the kidney, infiltrating the pancreatic tail and spleen. Tumor invasion was observed in the adjacent organs; therefore, the left kidney, pancreatic tail, spleen, and, descending colon were resected. Histopathological examination revealed a sarcomatoid variant of invasive urothelial carcinoma. She received two cycles of gemcitabine and carboplatin combination chemotherapy but succumbed to the disease after 5 months.ConclusionSarcomatoid variant of urothelial carcinoma is rare, with aggressive malignancy. The diagnosis was difficult and required surgery. This is the first case of a sarcomatoid variant of urothelial carcinoma with direct invasion into the pancreas and descending colon.
Stakeholder Alignment/Capability Based Security Engineering: Capability Engineering vs “Problemeering” and “Solutioneering” – Prioritizing Stakeholder Needs Over Requirements
Authors: Hause Matthew , Brooks Mitchell 
Published: July 2022

ABSTRACTWhen building systems, it is tempting to start with the stakeholder requirements and jump straight into implementing a preconceived solution and then mapping it to the requirements as best one can. This is “solutioneering.” To avoid this, systems engineers build models of the requirements, elaborating them into use cases, activity diagrams, IBDs, and other more concrete modeling steps. However, part of a system engineer's job is to validate these requirements against the stakeholder needs, capabilities, and goals to ensure you build the right system. This assumes that the stakeholder knows and understands their needs and problems, which we have dubbed “Problemeering.” The systems engineer can never take the requirements at face value, assume that they are correct and have captured the stakeholder needs and can solve their problems. This is true across many cross‐cutting aspects and domains, requiring a Subject Matter Expert (SME). This is especially true regarding security issues where is it unlikely that stakeholders are aware of the current threat landscape and risks and can fully elaborate them. This will require the knowledge and experience of a cyber‐security SME who can adequately analyze the system vulnerabilities from the right perspective. In this article, we will detail how Capability‐Based security engineering ensures the articulation of the true needs of the stakeholder so that the engineers ultimately implement the needs in the delivered system.
Multilayered Network Models for Security: Enhancing System Security Engineering with Orchestration
Authors: Williams Adam D. 
Published: July 2022

ABSTRACTSecurity engineering approaches can often focus on a particular domain—physical security, cyber security, or personnel security, for example. Yet, security systems engineering consistently faces challenges requiring socio‐technical solutions to address evolving and dynamic complexity. While some drivers of this complexity stem from complex risk environments, innovative adversaries, and disruptive technologies, other drivers are endogenous and emerge from the interactions across security engineering approaches. In response, INCOSE's Systems Security Working Group identified the need to better coordinate “disparate security solutions [that] operate independently” as one of eleven key concepts in their IS21 FuSE Security Roadmap. From this perspective, this need for “security orchestration” aligns with the perspective that security is a property that emerges from interactions within complex systems. Current efforts at Sandia National Laboratories are developing a systems security engineering approach that describes high consequence facility (HCF) security as a multidomain set of interacting layers. The result is a multilayered network (MLN)‐based approach that captures the interactions between infrastructure, physical components, digital components, and humans in nuclear security systems. This article will summarize the MLN‐based approach to HCF security and describe two preliminary results demonstrating potential benefits from incorporating interactions across disparate security solutions. Leveraging the logical structure of networks, this MLN model‐based approach provides an example of how security orchestration provides enhanced systems security engineering solutions.
Making the Puzzle Pieces Fit – Utilizing UAF to Model a Cybersecurity SoS
Authors: Brooks Mitchell , Hause Matthew 
Published: July 2022

ABSTRACTWhile there are security bundles on the market, most IT departments operate with a wide range of products (an average of 75) just to secure their network (Zurkus 2016). Companies developed the security products independently and offer little to no cross‐product integration. Although many people treat cybersecurity infrastructures as systems, it is far better to view them as a System of Systems (SoS) as many different parts of an organization develop, manage, and operate the systems they must protect. So, for system engineers attempting to secure systems, utilizing the Unified Architecture Framework (UAF) to create a map of these systems and software and how they must integrate is a far better practice than SysML. Not only is UAF specifically designed to handle an SoS, but it includes Security Viewpoints which can more easily represent the complex interactions between individual security systems. In this article, we will briefly discuss an introduction to UAF, explain its benefits when modeling integrated security for complex systems of systems, offer solutions to the most common issues encountered when attempting to model the interactions between security elements, and demonstrate how they address the FuSE concepts of security orchestration and architectural agility.
Preparation of Complex Ratio‐Dependent Nanomaterials from Polymerizable Hydrogen‐Bonded Liquid Crystal
Authors: Tao Lei , Xiao Anqi , Lyu Xiaolin , Tang Zhehao , Yu Zhen‐Qiang , Shen Zhihao , Fan Xinghe 
Published: July 2022

AbstractA scalable approach to generating different nanomaterials from the same hydrogen‐bondeded complex by photo‐crosslinking is described. The hydrogen‐bonded complex exhibits a smectic or columnar mesophase, depending on the molar ratio between the donor and acceptor. The mesophase structure is effectively retained after photo‐crosslinking. Polymer nanosheets with negatively charged carboxylate groups can be prepared from the complex with the smectic mesophase after subsequent extraction and chemical treatment, and they show effective adsorption of Pd2+. Meanwhile, a nanoporous polymer is successfully achieved from the complex having the columnar mesophase by using the same technology of photo‐crosslinking and solvent treatment. This work provides a new strategy to fabricate different nanomaterials from the same hydrogen‐bonded complex system.