bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring the Genomic Landscape of Cancer Patient Cohorts with GenVisR
Authors: Skidmore Zachary L. , Campbell Katie M. , Cotto Kelsy C. , Griffith Malachi , Griffith Obi L.
Published: September 2021

The creation of visualizations to interpret genomics data remains an important aspect of data science within computational biology. The GenVisR Bioconductor package was created to lower the entry point for publication‐quality graphics and has remained a popular suite of tools within this domain. GenVisR supports visualizations covering a breadth of topics including functions to produce visual summaries of copy‐number alterations, somatic variants, sequence quality metrics, and more. Recently, the GenVisR package has undergone significant updates to increase performance and functionality. To demonstrate the utility of GenVisR, we present protocols for use of the updated Waterfall() function to create a customizable Oncoprint‐style plot of the mutational landscape of a tumor cohort. We explain the basics of installation, data import, configuration, plotting, clinical annotation, and customization. A companion online workshop describing the GenVisR library, Waterfall() function, and other genomic visualization tools is available at genviz.org. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Generating a Waterfall() plot from original mutation data

Basic Protocol 2: Adding clinical data to a Waterfall() plot

Basic Protocol 3: Customizing mutation burden in Waterfall() plots

Basic Protocol 4: Brief exploration of customizable options

Support Protocol 1: Installing GenVisR
50,000 years of ice and seals: Impacts of the Last Glacial Maximum on Antarctic fur seals
Authors: Cleary Alison C. , Hoffman Joseph I. , Forcada Jaume , Lydersen Christian , Lowther Andrew D. , Kovacs Kit M.
Published: September 2021

Ice is one of the most important drivers of population dynamics in polar organisms, influencing the locations, sizes, and connectivity of populations. Antarctic fur seals, Arctocephalus gazella, are particularly interesting in this regard, as they are concomitantly reliant on both ice‐associated prey and ice‐free coastal breeding areas. We reconstructed the history of this species through the Last Glacial Maximum (LGM) using genomic sequence data from seals across their range. Population size trends and divergence events were investigated using continuous‐time size estimation analysis and divergence time estimation models. The combined results indicated that a panmictic population present prior to the LGM split into two small refugial populations during peak ice extent. Following ice decline, the western refugial population founded colonies at the South Shetlands, South Georgia, and Bouvetøya, while the eastern refugial population founded the colony on Iles Kerguelen. Postglacial population divergence times closely match geological estimates of when these coastal breeding areas became ice free. Given the predictions regarding continued future warming in polar oceans, these responses of Antarctic fur seals to past climate variation suggest it may be worthwhile giving conservation consideration to potential future breeding locations, such as areas further south along the Antarctic Peninsula, in addition to present colony areas.
Spin‐State‐Switching Rearrangements of Bis(dioxolene)‐Bridged CrCo Complexes: A DFT Study
Authors: Starikov Andrey G. , Starikova Alyona A. , Chegerev Maxim G. , Aldoshin Sergey M. , Metelitsa Anatoly V. , Minkin Vladimir I.
Published: September 2021

Density functional theory calculations (UTPSSh/6‐311++G(d,p)) of electronic structure, energy characteristics and magnetic properties of a series of heterometallic CrCo complexes comprising redox‐active bis(dioxolene) bridging ligands (3,3,3’,3’‐tetramethyl‐5,6,5’,6’‐tetrahydroxy‐1,1’‐spiro‐bis(indan) and 2,3,6,7‐tetrahydroxy‐9,10‐dimethyl‐9,10‐dihydro‐9,10‐ethanoanthracene) and ancillary tetradentate nitrogen‐containing bases (tris(2‐pyridylmethyl)amine and N,N′‐dialkyl‐2,11‐diaza[3.3]‐(2,6)pyridinophane derivatives) were performed. The compounds prone to manifest spin‐state switching rearrangements involving cobalt centre have been revealed. Analysis of the results obtained and their comparison with those found previously open wide prospects for the purposeful search for a broad variety of new magnetically bistable heterometallic dinuclear paramagnetic species with a prospect of useful application in the design of smart dynamic materials.
TaERF73 is associated with root depth, thousand‐grain weight and plant height in wheat over a range of environmental conditions
Authors: Du Yan , Li Chaonan , Mao Xinguo , Wang Jingyi , Li Long , Yang Jinwen , Zhuang Mengjia , Sun Daizhen , Jing Ruilian
Published: September 2021

AP2/ERF is a plant‐specific transcription factor superfamily regulating plant growth, development and responses to multiple stresses. However, the roles of ERF genes in the growth and development of wheat (Triticum aestivum L.) remain elusive. In this study, a novel ERF gene TaERF73 was cloned from wheat. qRT‐PCR analysis showed that TaERF73 is predominantly expressed in roots. It responds to treatments of auxin, MeJA, ABA, low temperature and drought stresses. Ectopic expression of TaERF73 in rice caused short root length, indicating that TaERF73 is a negative regulator of root growth. Four SNPs were detected in TaERF73‐4B coding region through sequence polymorphism analysis. A dCAPS (derived cleaved amplified polymorphic sequence) molecular marker was developed based on the SNP at 119 bp (G/C) of TaERF73‐4B. Association analysis between genotypes and agronomic traits revealed that Hap‐4B‐2 is a haplotype of TaERF73‐4B associated with shorter plant height, higher thousand‐grain weight and longer root depth. The distributions of haplotypes in ten Chinese major wheat zones suggested that Hap‐4B‐2 has been positively selected in the breeding process. Together, the ERF gene TaERF73 is associated with root depth, plant height and thousand‐grain weight under drought, heat and well‐watered conditions. The molecular marker developed in this study could be a valuable source for marker‐assisted selection and genetic improvement in wheat.
Neuropsychological basis of impaired gesture imitations in patients with Alzheimer's disease and dementia with Lewy bodies
Authors: Nagahama Yasuhiro , Okina Tomoko , Suzuki Norio
Published: September 2021

Introduction

The aim of this study was to examine the neuropsychological factors that may be related to the impaired gesture imitations in patients with dementia.

Methods

The imitation of unilateral finger and bimanual gestures was evaluated in 162 patients with Alzheimer's disease (AD) and 103 patients with dementia with Lewy bodies (DLB). The relationships of gesture imitation performance to global cognition, semantic fluency, phonemic fluency, figure copying, clock drawing, and trail‐making test part A (TMT‐A) scores were examined.

Results

Mean scores for unilateral finger imitation were significantly lower in DLB patients than in AD patients, and significantly more DLB patients showed impaired performance in unilateral finger imitation than AD patients. In contrast, the percentage of patients with impaired bimanual gesture imitation was not significantly different between AD and DLB patients. Unilateral finger imitation performance was predicted by pentagon copying in the AD patients, and was predicted by cube copying in the DLB patients. Bimanual gesture imitation performance was predicted by TMT‐A scores and phonemic fluency in the AD patients but was predicted by TMT‐A scores, cube copying, and parkinsonism severity in the DLB patients.

Discussion

Our study suggested that bimanual gesture imitation is a complex task that is supported by a wide range of neuropsychological processes, such as visuospatial attention, executive function, and visuomotor control, and therefore, it was easily impaired in early dementia. Unilateral finger imitation was more similar to constructional tasks, such as figure drawing, and was impaired more often in DLB patients than in AD patients.
A case of perirenal non‐specific lymphadenitis mimicking a solitary renal mass
Authors: Umeda Shun , Hatano Koji , Kato Taigo , Kawashima Atsunari , Abe Toyofumi , Fukuhara Shinichiro , Uemura Motohide , Kiuchi Hiroshi , Imamura Ryoichi , Nonomura Norio
Published: September 2021

Introduction

Since the diagnosis of small renal masses is often a challenge despite improvements in imaging modalities, renal tumor biopsy provides useful information regarding treatment decisions. However, there is no established treatment strategy when renal biopsy shows lymphoid tissue.

Case presentation

A 63‐year‐old woman was referred to our department for the investigation of a small renal mass. Contrast‐enhanced computed tomography showed a weakly enhancing mass 39 × 17 mm in diameter in the left kidney. A renal tumor biopsy was performed, and histopathological examination showed lymphoid tissue, but the diagnosis was not confirmed. The tumor was bluntly dissected from the renal capsule via robotic‐assisted laparoscopic surgery without renal artery clamping. The pathological diagnosis was non‐specific lymphadenitis.

Conclusion

We report a rare case of perirenal non‐specific lymphadenitis mimicking a solitary renal mass. Non‐specific lymphadenitis is a possible differential diagnosis of renal masses.
Synthesis, characterization, thermal degradation, docking, DFT calculation, and biological activity of dimethyltin(IV) complex with homopiperazine
Authors: Shoukry Mohamed M. , Shehata Mohamed R. , Abdel Wahab Amira M.
Published: September 2021

The dimethyltin(IV) complex with 1,4‐dizacycloheptane (homopiperazine) was synthesized. The complex is of 1:1 stoichiometry. The complex was characterized by elemental analysis, spectroscopic techniques as infrared (IR) and nuclear magnetic resonance (NMR), and thermal measurements. Homopiperazine coordinates to dimethyltin(IV) by the two nitrogen atoms. The complex decomposes in two steps. The kinetic parameters of thermal decomposition process have been calculated using Coats–Redfern and Horowitz–Metzger methods. The high values of the energy of activation of the complexes reveal the high stability of the complex due to their covalent bond character. The two decomposition steps are endothermic. Density Functional Theory (DFT) calculations have been carried out to investigate the equilibrium geometry of homopiperazine and its complex. The calculated total energies, energies of highest occupied molecular orbital (HOMO), energies of lowest unoccupied molecular orbital (LUMO), and dipole moments are reported. Antibacterial, antifungal, and anticancer activities of homopiperazine and its dimethyltin(IV) complex were tested. The molecular docking studies were performed to find the possible binding modes to the most active sites of the receptor of breast cancer oxidoreductase and those of Escherichia coli.
Association between urinary VEGFA and renal pathology of IgA nephropathy patients
Authors: Feng Shaozhen , Huang Naya , Xue Miaorong , Zhang Puhua , Zhong Zhong , Guo Qunying , Li Zhijian
Published: September 2021

Background

Renal biopsy remains the golden standard for diagnosing and monitoring IgA nephropathy (IgAN). Vascular endothelial growth factor A (VEGFA) was crucial for the survival of glomerular cells. Our aim was to screen the expression pattern of urinary, circulating and renal VEGFA in IgAN patients to reveal their relationship with renal pathology and outcomes.

Methods

Baseline VEGFA levels were determined with ELISA, real‐time PCR and immunohistochemistry. Associations between VEGFA expression and clinical–pathological parameters, and renal outcomes were evaluated.

Results

Compared with healthy controls, urinary VEGFA level was obviously elevated in IgAN patients (76.19 ± 63.67 pg/mg Cr vs 146.67 ± 232.71 pg/mg Cr, p = 0.0291) and not correlated with serum VEGFA level. Baseline urinary VEGFA was significantly associated with gender and tubular atrophy/interstitial fibrosis by stepwise multivariate regression analysis. Urinary VEGFA was higher in male patients accompanied with higher serum creatinine, larger proportion of hypertension and recurrent hematuria than in female patients. In the kidney of IgAN patients, VEGFA were robustly expressed in the parietal epithelial cells, podocytes, mesangial cells and tubular epithelial cells. After a follow‐up duration of 38.53 ± 27.14 months, IgAN patients with higher urinary VEGFA level were found to have a poorer renal outcome of renal replacement therapy (HR = 1.027, p = 0.037) or composite outcome (HR = 1.023, p = 0.039) after adjusting for confounders.

Conclusions

Increased urinary VEGFA might reflect certain renal pathology and, although not fully specific, still could be served as a valuable noninvasive indicator in predicting renal progression of IgAN.
Sulfonylamidine‐substituted derivatives of avibactam: Synthesis and antibacterial activity
Authors: Ji Jingwen , Zhai Lijuan , Sun Jian , He Lili , Ji Jinbo , Ma Xueqin , Liu Yuanbai , Tang Dong , Mu Yangxiu , Gao Yuanyu , Yang Haikang , Iqbal Zafar , Yang Zhixiang
Published: September 2021

Avibactam is a clinically approved non‐β‐lactam based β‐lactamase inhibitor. Derivatization of this scaffold with improved inhibition profile is the demand of the day to cope with the future challenges. We successfully synthesized new derivatives of avibactam containing sulfonylamidine moieties at C2 position of the diazabicyclooctane ring. We tested in vitro antibacterial activities of newly synthesized compounds against 10 bacterial strains expressing variable β‐lactamases. All compounds did not exhibit antimicrobial profile when assayed individually; however, all compounds minimized the MIC value of the imipenem in combination. Compound 5l proved most potent against all 10 bacterial strains, and showed improved inhibition against six bacterial strains as compared with the control inhibitor, relebactam. The compound 5l may be a lead hit for future development.
Providing multicolor plasmonic patterns with graphene quantum dots functionalized d‐penicillamine for visual recognition of V(V), Cu (II), and Fe(III): Colorimetric fingerprints of GQDs‐DPA for discriminating ions in human urine samples
Authors: Abdollahiyan Parinaz , Heidari Hassan , Hassanzadeh Soheila , Hasanzadeh Mohammad , Seidi Farzad , Pashazadeh‐Panahi Paria
Published: September 2021

In this study, a novel fluorescent probe (graphene quantum dots functionalized d‐penicillamine [GQDs‐DPA]) was developed for the selective identification of Cu2+, V5+, and Fe3+ among 26 types of metal ions, which considerably quench the fluorescence intensity of GQD. So, GQDs‐DPA was applied as a simple fluorescent probe for facile metal ions recognition in standard solution. The proposed DPA‐GQD supported amino acids respond to Cu2+, V5+, and Fe3+, with high sensitivity. The intensity of the fluorescence histogram of this probe significantly diminished in exposure to metal ions such as Cu(II), V(V), and Fe(III). Moreover, a microfluidic paper‐based device (μPAD) was fabricated through a facile and cost‐effective protocol. Cu2+, V5+, and Fe3+ can be selectively recognized by GQDs‐DPA using μPAD by naked eye. Also, GQDs‐DPA exhibits a linear response for the detection of ions in concentrations ranging from 0.01 to 1 ppm, with a low limit of quantification of 0.01 ppm in standards samples. The boosted color uniformity, low instrumental needs of the stamp, and disposability of μPADs enable the application of the proposed device for commercial applications in environmental science and technology.
Dynamical downscaling projections of extreme temperature for the major river basins in China under shared socioeconomic pathway scenarios
Authors: Zou Liwei
Published: September 2021

This study presents an analysis of the changes in extreme temperatures over major river basins in China under different shared socioeconomic pathway (SSP) scenarios based on a set of dynamical downscaling over CORDEX East Asia, performed with the regional climate model RegCM4 at a resolution of 25 km, driven by the global climate model FGOALS‐g3. The results indicated that the dynamical downscaling tended to reduce the warm (cold) biases of the present‐day daily maximum (TXx) and minimum temperatures (TNn) simulated by FGOALS‐g3. Under the SSP scenarios, substantial increases in TXx and TNn and the number of warm days and warm nights throughout China were projected by both models. The average increase in TXx in most of the river basins ranged from 1 to 2°C under the SSP1‐2.6 scenario, from 2 to 3°C under the SSP2‐4.5 scenario, and from 3 to 5°C under the SSP5‐8.5 scenario. Reductions in the number of cold days and cold nights were projected across China, but these reductions were smaller than the increases in the number of warm days and warm nights. The interregional variability in the increases in TXx and TNn was more pronounced in the SSP5‐8.5 scenario and the RegCM4 model than in the other SSP scenarios and the FGOALS‐g3 model, respectively. Larger percentages of the land area and population of China would be affected by greater increases in extreme high temperatures and TNn. Under the SSP2‐4.5 (SSP1‐2.6) scenario, 20–65% (50–95%) of the impacts of extreme temperatures under the SSP5‐8.5 scenario could be avoided across most regions in China. The avoided impacts of warm days and warm nights were greater than those of the other extreme temperature indices. More of the impacts of extreme temperatures could be avoided in the Huai River basin, Yellow River basin, Hai River basin, and Northwest Interior River basin than in the other river basins in China.
Nano‐liquid chromatography with a new nano‐structured monolithic nanocolumn for proteomics analysis
Authors: Günyel Zeynep , Aslan Hakiye , Demir Nurullah , Aydoğan Cemil
Published: September 2021

Herein, we report the preparation and application of a new nano‐structured monolithic nanocolumn based on modified graphene oxide using narrow fused silica capillary column (e.g., 50 μm internal diameter). The nanocolumn was prepared by an in situ polymerization using butyl methacrylate, ethylene dimethacrylate, and methacryloyl graphene oxide nanoparticles. Dimethyl formamide and water were used as the porogenic solvent. After polymerization, the obtained nanocolumn was coated with dimethyloctadecylchlorosilane in order to enhance the hydrophobicity. Both isocratic and gradient nano‐liquid chromatographic separations for small molecules (e.g., alkylbenzenes) and macromolecules (e.g., intact proteins) were performed. Theoretical plates number up to 3600 plates/m in isocratic mode for propylbenzene were achieved. It was demonstrated that the feasibility of graphene oxide modified monolithic nanocolumn for high‐efficiency and high‐throughput nanoscale proteomics analysis. The high resolving power of monolithic nanocolumn yielded sensitive protein separation with narrower peak width while a high‐resolution analysis of peptides from trypsin‐digested cytochrome C could be obtained. Graphene oxide based monolithic nanocolumns are promising and can allow to powerful tools for trace proteom sample analysis.
Bifunctional RAFT Agent Directed Preparation of Polymer/Graphene Oxide Composites
Authors: Hsia Tina , Wan Jing , Fan Bo , Thang San H.
Published: September 2021

Polymer/graphene oxide (GO) composites, which combine the physical properties of GO and the processability of polymers, are of increasing interest in a variety of applications ranging from conductive foams, sensors, to bioelectronics. However, the preparation of these composites through physical blending demands the polymers with functional groups that interact strongly with the GO. Here the design and synthesis of a new bifunctional reversible addition–fragmentation chain transfer (RAFT) agent are demonstrated, which allows the synthesis of polymers with predetermined molecular weights and low dispersibilities (Ð), while having functionalities at both polymer termini that allow strong binding to GO. To access polymers with diverse thermal and mechanical properties, acrylonitrile–styrene–acrylate (ASA) copolymers with different types of acrylates, both short and long side chains, are synthesized under the control of the bifunctional RAFT agent. Furthermore, the strong binding between GO and the synthesized polymers is verified and explored to prepare polymer/GO composites with diverse tensile strengths and conductivity in the range of semiconductors. Overall, this novel RAFT agent is expected to expand the utility of polymer/GO composites by providing well‐defined polymers with tunable properties and strong binding with GO.
Genetic testing and clinical relevance of patients with thoracic aortic aneurysm and dissection in northwestern China
Authors: Li Jinjie , Yang Liu , Diao Yanjun , Zhou Lei , Xin Yijuan , Jiang Liqing , Li Rui , Wang Juan , Duan Weixun , Liu Jiayun
Published: September 2021

Background

Thoracic aortic aneurysm and dissection (TAAD) is a life‐threatening pathology that remains a challenge worldwide. Up to 40% of TAAD cases are hereditary with complex heterogeneous genetic backgrounds. The purposes of this study were to determine the diagnostic rate of patients with TAAD, investigate the molecular pathologic spectrum of TAAD by next‐generation sequencing (NGS), and explore the future preclinical prospects of genetic diagnosis in patients at high ‐risk of study.

Methods

NGS was used to screen 15 genes associated with genetic TAAD in 212 patients from northwestern China. Clinical data of patients were gathered by electrocardiography, transthoracic echocardiography, and computed tomography.

Results

Of the 212 patients, 67 (31.60%) tested positive for a (likely) pathogenic variant, 42 (19.81%) had a variant of uncertain significance (VUS), and 103 (48.58%) had no variant (likely benign/benign/negative). A total of 135 reportable variants were detected in our test, among which 77 (57.04%) are first reported in this paper. A genotype–phenotype correlation of FBN1 was assessed, and the data showed that the patients with truncating and splicing mutations are more prone to developing severe aortic dissection than those with missense mutations, especially frameshift mutations (82.76% vs. 42.86%). In this study, 43 (20.28%) patients had a family history of sudden death or TAAD, whereas 132 (62.26%) did not (the remaining 37 were not available), and the positive rate of genetic testing was higher in TAAD patients with family history than in those without (76.74% vs. 18.94%).

Conclusion

Our study concludes that genetic variation is an important consideration in the risk stratification of individualized prediction and disease diagnosis.
Afghanistan war vets have new or worsening MH symptoms
Authors: Canady Valerie A.
Published: September 2021

A new survey examining Taliban control of Afghanistan and its impact on American war veterans found that the majority of Afghanistan veterans 18 and older have struggled with their mental health since serving in Afghanistan. During the month of August, the Taliban overran Afghanistan as U.S. troops left the country following a 20‐year war. The Afghanistan fall intensified veterans' mental health struggles, according to the survey.
Revisiting EXTREME in the Immuno-Oncology Era: How to Improve Its Outcomes
Authors: Szturz Petr , Vermorken Jan B.
Published: September 2021

The choice of first-line palliative treatment has always been one of the crucial decisions in the management of patients with recurrent and/or metastatic squamous cell carcinoma of the head and neck not suitable for salvage surgery or full-dose radiotherapy. This commentary highlights trial results that show the importance of treatment sequencing decisions that should be of interest for daily practice.
Assessing the implication of green revolution for food security in Pakistan: A multivariate cointegration decomposition analysis
Authors: Nouman Muhammad , Khan Dilawar , Ul Haq Ihtisham , Naz Nabeela , Zahra Bibi Taharat E. , Ullah Arif
Published: September 2021

Food security is a growing concern around the world and the agricultural sector plays a significant role in solving this problem to a large extent. In particular, the developing world has been highly affected by the food security challenge due to its large population since the last few decades. This study explored the impact of the green revolution on food security in Pakistan using annual time series data over the period 1975–2017. The findings of the Johansen co‐integration and F‐bounds tests found that the green revolution positively and significantly improves food security in Pakistan. The results of the autoregressive distributed lag model explored that agricultural machinery, agricultural credit, use of fertilizers, high quality seeds, fuel consumption and rise in area under cereal crops are the significant factors of the green revolution, which improve the food security in Pakistan. This study recommends that policies must be designed to guarantee farmers' access to quality production inputs.
Lifting the Spin‐Momentum Locking in Ultra‐Thin Topological Insulator Films
Authors: Leis Arthur , Schleenvoigt Michael , Cherepanov Vasily , Lüpke Felix , Schüffelgen Peter , Mussler Gregor , Grützmacher Detlev , Voigtländer Bert , Tautz F. Stefan
Published: September 2021

3D topological insulators are known to carry 2D Dirac‐like topological surface states in which spin‐momentum locking prohibits backscattering. When thinned down to a few nanometers, the hybridization between the topological surface states at the top and bottom surfaces results in a topological quantum phase transition, which can lead to the emergence of a quantum spin Hall phase. Here, the thickness‐dependent transport properties across the quantum phase transition are studied on the example of (Bi0.16Sb0.84.)2Te3 films, with a four‐tip scanning tunneling microscope. The findings reveal an exponential drop of the conductivity below the critical thickness. The steepness of this drop indicates the presence of spin‐conserving backscattering between the top and bottom surface states, effectively lifting the spin‐momentum locking and resulting in the opening of a gap at the Dirac point. The experiments provide a crucial step toward the detection of quantum spin Hall states in transport measurements.
Study on forearm swing recognition algorithms to drive the underwater power‐assisted device of frogman
Authors: Chen Longwen , Hu Dean , Han Xu
Published: September 2021

The frogmen have a great demand for the underwater power‐assisted device (UPaD) because of their poor working conditions and complex missions. Although the wearable power‐assisted device on land has been diversified, the development of UPaDs is relatively slow. Meanwhile, the most of current small frogman transport equipment is needed to be manipulated by the frogmen with their hands with the aim of changing their moving speed or posture, which increases the difficulty of frogmen executing their tasks. The major contribution of this paper is to develop a method that frees the hands and realizes power assisting at the same time for frogmen, which can be applied to drive the UPaDs of frogmen. Two posture recognition algorithms based on the Human–Computer Interface have been promoted. The algorithms can recognize the forearm swings of the wearer of UPaD, calculate the frequency of the wearer's forearm swing, and adjust the moving speed of the wearer's UPaD according to the wearer's forearm swing frequency. Moreover, we evaluate the performance of two algorithms recognizing forearm swings underwater from four different subjects. Meanwhile, one of the two algorithms is improved and evaluated by experiments from the previous four subjects. The results of accuracy of two algorithms recognizing the wearer's forearm swing are more than 90%. The performance of the speed regulating system of UPaD based on the designed two algorithms is also acceptable.
A new particle mounting method for surface analysis
Authors: Dundas Adam A. , Kern Stefanie , Cuzzucoli Crucitti Valentina , Scurr David J. , Wildman Ricky , Irvine Derek J. , Alexander Morgan R.
Published: September 2021

The chemical analysis of microparticles is challenging due to the need to mount the particles on a substrate for analysis; double‐sided adhesive tape is often used (sometimes conductive), however that is usually coated with poly (dimethyl siloxane) (PDMS) that is often used as a release agent. PDMS is a common surface contamination that can mask surface chemistries and hinder material performance where it is dependent on this contaminated interface. It is known that PDMS contains a very mobile oligomeric fraction that readily diffuses across surfaces resulting in the contamination of mounted particulate samples before and during surface chemistry analysis. This makes it impossible to determine whether the PDMS has arisen from the analysis procedure or from the sample itself. A new sample preparation method is proposed where polymer microparticles are mounted on a poly (hydroxyethyl methacrylate) (pHEMA) polymer solution, which we compare with particles that have been mounted on adhesive discs using time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) and 3D OrbiSIMS analysis. Particles mounted on the pHEMA substrate results in a reduction of PDMS signal by 99.8% compared with microparticles mounted on adhesive discs. This illustrates how a simple, quick and inexpensive polymer solution can be used to adhere particles for analysis by ToF‐SIMS, or other surface chemical analysis techniques such as X‐ray photoelectron spectroscopy (XPS), without introduction of large amounts of silicone contaminant.
Catalyst Design for Electrochemical Reduction of CO2 to Multicarbon Products
Authors: Xue Yuanyuan , Guo Yibo , Cui Huijuan , Zhou Zhen
Published: September 2021

Electrochemical reduction of CO2 (CO2RR), driven by renewable energy (such as wind and solar energy), is an effective route toward carbon neutralization. The multicarbon (C2+) products from CO2RR are highly desirable, since they are important fuels, chemicals, and industrial raw materials. However, selective reduction of CO2 to C2+ products is especially challenging, due to low selectivity, poor yield, and high overpotential. Since the performance of CO2RR is closely related to the structure and composition of catalysts, which alter the binding energy of intermediates generated in CO2RR, it is necessary to study these effects systematically to achieve possible design strategies. Herein, design strategies toward catalysts for CO2 conversion to C2+ products are discussed on the basis of the adjustment of the structure and composition of catalysts, such as morphology control, defect engineering, bimetal, and surface modification. Meanwhile the reaction mechanisms and structure evolution of catalysts during CO2RR are focused on in particular. Finally, challenges and perspectives are proposed for further improvement of CO2RR technologies.
Suppressing Polysulfide Shuttling in Lithium–Sulfur Batteries via a Multifunctional Conductive Binder
Authors: Chen Shiming , Song Zhibo , Ji Yuchen , Yang Kai , Fang Jianjun , Wang Lu , Wang Zijian , Zhao Yan , Zhao Yunlong , Yang Luyi , Pan Feng
Published: September 2021

Exhibiting high specific energy and low cost, lithium–sulfur batteries are considered promising candidates for the next‐generation battery. However, its wide applications are limited by the insulating nature of the sulfur, dissolution of polysulfide species, and large volume change of the sulfur cathode. In this work, a conductive binder, crosslinked polyfluorene (C‐PF) is synthesized and employed in Li–S batteries to enhance the overall electrochemical performance from the following three aspects: 1) possessing high electronic conductivity, C‐PF facilitates lowered areal resistance for the sulfur electrode and leads to an improved rate capability; 2) owing to the cross‐linked polymer structure, favorable mechanical properties of the electrode can be achieved, hence the well‐preserved electrode integrity; 3) forming strong binding with various polysulfide species, C‐PF manages to trap them from diffusing to the Li anode, which greatly improves the cycling stability of Li–S cells. Through designing a multifunctional binder to comprehensively enhance the Li–S cathode, this proposed approach could be broadly applied to fully harness the energy from S redox in addition to cathode material modifications.
Influence of new‐to‐old concrete interface on the damping behavior of recycled aggregate concrete
Authors: Li Tan , Xiao Jianzhuang , Singh Amardeep
Published: September 2021

The interface transition zone (ITZ) is a critical component of concrete, as it has a significant effect on the material's mechanical properties. This paper using specimens of bonded new and old concrete analyzes the effect of the interface in recycled concrete on damping performance using semi precast concrete specimens with old and new concrete. To determine the effect of the bonding zone between new and old concrete on the damping ratio of recycled concrete, the free vibration attenuation test method was used. When the acceleration signal from the specimen's transverse vibration is transformed to the frequency domain, the study observes two prominent peaks. The damping ratio is between 0.005 and 0.007 at the high‐frequency position and 0.06–0.08 at the low‐frequency position. When the excitation position is not in the bonding zone, the damping ratio measured in the bonding zone has a smaller average value. Under different recycled aggregate replacement rates, there is a significant difference in the damping ratio and frequency of old and new concrete bonded specimens, as well as complete recycled concrete specimens. The bonding zone's damping ratio data is more discrete than that of other locations. The damping ratio and the acceleration amplitude exhibit an excellent linear relationship, with the damping ratio increasing as the amplitude increases. The damping ratio varies significantly more in the longitudinal direction, with no apparent relationship to the acceleration amplitude.
Glycan Assembly Strategy: From Concept to Application
Authors: Liu Mingli , Qin Xianjin , Ye Xin‐Shan
Published: September 2021

Glycans have been hot topics in recent years due to their exhibition of numerous biological activities. However, the heterogeneity of their natural source and the complexity of their chemical synthesis impede the progress in their biological research. Thus, the development of glycan assembly strategies to acquire plenty of structurally well‐defined glycans is an important issue in carbohydrate chemistry. In this review, the latest advances in glycan assembly strategies from concepts to their applications in carbohydrate synthesis, including chemical and enzymatic/chemo‐enzymatic approaches, as well as solution‐phase and solid‐phase/tag‐assisted synthesis, are summarized. Furthermore, the automated glycan assembly techniques are also outlined.
“Third‐wave” cognitive and behavioral therapies and the emergence of a process‐based approach to intervention in psychiatry
Authors: Hayes Steven C. , Hofmann Stefan G.
Published: September 2021

For decades, cognitive and behavioral therapies (CBTs) have been tested in randomized controlled trials for specific psychiatric syndromes that were assumed to represent expressions of latent diseases. Although these protocols were more effective as compared to psychological control conditions, placebo treatments, and even active pharmacotherapies, further advancement in efficacy and dissemination has been inhibited by a failure to focus on processes of change. This picture appears now to be evolving, due both to a collapse of the idea that mental disorders can be classified into distinct, discrete categories, and to the more central attention given to processes of change in newer, so‐called “third‐wave” CBTs. Here we review the context for this historic progress and evaluate the impact of these newer methods and models, not as protocols for treating syndromes, but as ways of targeting an expanded range of processes of change. Five key features of “third‐wave” therapies are underlined: a focus on context and function; the view that new models and methods should build on other strands of CBT; a focus on broad and flexible repertoires vs. an approach to signs and symptoms; applying processes to the clinician, not just the client; and expanding into more complex issues historically more characteristic of humanistic, existential, analytic, or system‐oriented approaches. We argue that these newer methods can be considered in the context of an idiographic approach to process‐based functional analysis. Psychological processes of change can be organized into six dimensions: cognition, affect, attention, self, motivation and overt behavior. Several important processes of change combine two or more of these dimensions. Tailoring intervention strategies to target the appropriate processes in a given individual would be a major advance in psychiatry and an important step toward precision mental health care.
Initial treatment choices to achieve sustained response in major depression: a systematic review and network meta‐analysis
Authors: Furukawa Toshi A. , Shinohara Kiyomi , Sahker Ethan , Karyotaki Eirini , Miguel Clara , Ciharova Marketa , Bockting Claudi L.H. , Breedvelt Josefien J.F. , Tajika Aran , Imai Hissei , Ostinelli Edoardo G. , Sakata Masatsugu , Toyomoto Rie , Kishimoto Sanae , Ito Masami , Furukawa Yuki , Cipriani Andrea , Hollon Steven D. , Cuijpers Pim
Published: September 2021

Major depression is often a relapsing disorder. It is therefore important to start its treatment with therapies that maximize the chance of not only getting the patients well but also keeping them well. We examined the associations between initial treatments and sustained response by conducting a network meta‐analysis of randomized controlled trials (RCTs) in which adult patients with major depression were randomized to acute treatment with a psychotherapy (PSY), a protocolized antidepressant pharmacotherapy (PHA), their combination (COM), standard treatment in primary or secondary care (STD), or pill placebo, and were then followed up through a maintenance phase. By design, acute phase treatment could be continued into the maintenance phase, switched to another treatment or followed by discretionary treatment. We included 81 RCTs, with 13,722 participants. Sustained response was defined as responding to the acute treatment and subsequently having no depressive relapse through the maintenance phase (mean duration: 42.2±16.2 weeks, range 24‐104 weeks). We extracted the data reported at the time point closest to 12 months. COM resulted in more sustained response than PHA, both when these treatments were continued into the maintenance phase (OR=2.52, 95% CI: 1.66‐3.85) and when they were followed by discretionary treatment (OR=1.80, 95% CI: 1.21‐2.67). The same applied to COM in comparison with STD (OR=2.90, 95% CI: 1.68‐5.01 when COM was continued into the maintenance phase; OR=1.97, 95% CI: 1.51‐2.58 when COM was followed by discretionary treatment). PSY also kept the patients well more often than PHA, both when these treatments were continued into the maintenance phase (OR=1.53, 95% CI: 1.00‐2.35) and when they were followed by discretionary treatment (OR=1.66, 95% CI: 1.13‐2.44). The same applied to PSY compared with STD (OR=1.76, 95% CI: 0.97‐3.21 when PSY was continued into the maintenance phase; OR=1.83, 95% CI: 1.20‐2.78 when PSY was followed by discretionary treatment). Given the average sustained response rate of 29% on STD, the advantages of PSY or COM over PHA or STD translated into risk differences ranging from 12 to 16 percentage points. We conclude that PSY and COM have more enduring effects than PHA. Clinical guidelines on the initial treatment choice for depression may need to be updated accordingly.
Closed string deformations in open string field theory. Part III. $$ \mathcal{N} $$ = 2 worldsheet localization
Authors: Maccaferri Carlo , Vošmera Jakub
Published: September 2021

Abstract

In this paper, which is the last of a series including [1, 2] we first verify that the two open-closed effective potentials derived in the previous paper from the WZW theory in the large Hilbert space and the A∞ theory in the small Hilbert space have the same vacuum structure. In particular, we show that mass-term deformations given by the effective (open)2-closed couplings are the same, provided the effective tadpole is vanishing to first order in the closed string deformation. We show that this condition is always realized when the worldsheet BCFT enjoys a global $$ \mathcal{N} $$
N
= 2 superconformal symmetry and the deforming closed string belongs to the chiral ring in both the holomorphic and anti-holomorphic sector. In this case it is possible to explicitly evaluate the mass deformation by localizing the SFT Feynman diagrams to the boundary of world-sheet moduli space, reducing the amplitude to a simple open string two-point function. As a non-trivial check of our construction we couple a constant Kalb-Ramond closed string state to the OSFT on the D3–D(−1) system and we show that half of the bosonic blowing-up moduli become tachyonic, making the system condense to a bound state whose binding energy we compute exactly to second order in the closed string deformation, finding agreement with the literature.
Beyond Schrödinger-Poisson: nonrelativistic effective field theory for scalar dark matter
Authors: Salehian Borna , Zhang Hong-Yi , Amin Mustafa A. , Kaiser David I. , Namjoo Mohammad Hossein
Published: September 2021

Abstract

Massive scalar fields provide excellent dark matter candidates, whose dynamics are often explored analytically and numerically using nonrelativistic Schrödinger-Poisson (SP) equations in a cosmological context. In this paper, starting from the nonlinear and fully relativistic Klein-Gordon-Einstein (KGE) equations in an expanding universe, we provide a systematic framework for deriving the SP equations, as well as relativistic corrections to them, by integrating out ‘fast modes’ and including nonlinear metric and matter contributions. We provide explicit equations for the leading-order relativistic corrections, which provide insight into deviations from the SP equations as the system approaches the relativistic regime. Upon including the leading-order corrections, our equations are applicable beyond the domain of validity of the SP system, and are simpler to use than the full KGE case in some contexts. As a concrete application, we calculate the mass-radius relationship of solitons in scalar dark matter and accurately capture the deviations of this relationship from the SP system towards the KGE one.
Benchmarking and optimization of robot motion planning with motion planning pipeline
Authors: Liu Shuai , Liu Pengcheng
Published: September 2021

Algorithms have been designed for robot motion planning with various adaptability to different problems. However, how to choose the most suitable planner in a scene has always been a problem worthy of research. This paper aims to find the most suitable motion planner for each query under three different scenes and six different queries. The work lies in optimization of sampling-based motion planning algorithms through motion planning pipeline and planning request adapter. The idea is to use the pre-processing of the planning request adapter, to run OMPL as a pre-processer for the optimized CHOMP or STOMP algorithm, and connect through the motion planning pipeline, to realize the optimization of the motion trajectory. The optimized trajectories are compared with original trajectories through benchmarking. The benchmarking determines the most suitable motion planning algorithm for different scenarios and different queries. Experimental results show that after optimization, the planning time of the algorithm is longer, but the efficiency is significantly improved. In the low-complexity scenes, STOMP optimizes the sampling algorithm very well, improves the trajectory quality greatly, and has a higher success rate. CHOMP also has a good optimization of the sampling algorithm, but it reduces the success rate of the original algorithm. However, in more complex scenes, optimization performance of the two optimization methods may not be as good as the original algorithm. In future work, we need to find better algorithms and better optimization algorithms to tackle with complex scenes.
COVID-19 and Networks
Authors: Murata Tsuyoshi
Published: September 2021

Ongoing COVID-19 pandemic poses many challenges to the research of artificial intelligence. Epidemics are important in network science for modeling disease spread over networks of contacts between individuals. To prevent disease spread, it is desirable to introduce prioritized isolation of the individuals contacting many and unspecified others, or connecting different groups. Finding such influential individuals in social networks, and simulating the speed and extent of the disease spread are what we need for combating COVID-19. This article focuses on the following topics, and discusses some of the traditional and emerging research attempts: (1) topics related to epidemics in network science, such as epidemic modeling, influence maximization and temporal networks, (2) recent research of network science for COVID-19 and (3) datasets and resources for COVID-19 research.
Assessment of prospective memory after stroke utilizing virtual reality
Authors: Hogan Christy , Cornwell Petrea , Fleming Jennifer , Man David W. K. , Shum David H. K.
Published: September 2021

Prospective Memory (PM) is the ability to remember to do something in the future. It is often impaired after stroke and can impact on an individual’s level of independence and daily functioning. PM tasks have been criticized for their lack of ecological validity wherein test results may not be related to actual performance in daily life. With ecological validity in mind, the Virtual Reality Prospective Memory Shopping Task (VRPMST) was designed to assess two types of PM, time- and event-based. This study aimed to examine the ecological and convergent validity of the VRPMST in comparison to an experimental (Lexical Decision PM Task) and clinical measure of PM (Cambridge PM Test). Twelve individuals with stroke and 12 controls were administered three PM measures, three neuropsychological measures, and two user-friendliness questionnaires, one for the experimental PM measure and one for the VRPMST. Individuals with stroke showed impairments in PM compared to controls on all three PM measures, particularly time-based PM. Individuals with stroke were found to monitor time significantly less than controls on both the experimental PM measure and the VRPMST. The VRPMST was found to be sensitive in measuring PM, have better ecological validity when compared to the experimental PM measure, and good convergent validity. The findings of this study have helped to clarify that PM impairment does exist after stroke, possibly due to a problem in strategic monitoring. In addition, we have demonstrated how VR technology can be used to design a measure of cognitive function commonly impaired after stroke.