bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of lncRNA-mediated ceRNA regulatory networks in pancreatic cancer
Authors: Xu Jichuan , Xu Jian , Liu Xinyuan , Jiang Jianxin
Published: June 2022

Non-coding RNAs (ncRNAs), which occupy the vast majority of human transcripts are known for their inability to encode proteins. NcRNAs consist of a diverse range of RNA species, including long non-coding RNAs (lncRNAs), which have significant meaning for epigenetic modification, post-transcriptional regulation of target genes, molecular interference, etc. The dysregulation of ncRNAs will mediate the pathogenesis of diverse human diseases, like cancer. Pancreatic cancer, as one of the most lethal malignancies in the digestive system that is hard to make a definite diagnosis at an early clinicopathological stage with a miserable prognosis. Therefore, the identification of potential and clinically applicable biomarker is momentous to improve the overall survival rate and positively ameliorate the prognosis of patients with pancreatic carcinoma. LncRNAs as one kind of ncRNAs exert multitudinous biological functions, and act as molecular sponges, relying on microRNA response elements (MREs) to competitively target microRNAs (miRNAs), thereby attenuating the degradation or inhibition of miRNAs to their own downstream protein-coding target genes, also thus regulating the initiation and progression of neoplasms. LncRNAs, which emerge aforementioned function are called competing endogenous RNAs (ceRNAs). Consequently, abundant research of lncRNAs as potential biomarkers is of critical significance for the molecular diagnosis, targeted therapy, as well as prognosis monitoring of pancreatic cancer.
Beam steering at the nanosecond time scale with an atomically thin reflector
Authors: Andersen Trond I. , Gelly Ryan J. , Scuri Giovanni , Dwyer Bo L. , Wild Dominik S. , Bekenstein Rivka , Sushko Andrey , Sung Jiho , Zhou You , Zibrov Alexander A. , Liu Xiaoling , Joe Andrew Y. , Watanabe Kenji , Taniguchi Takashi , Yelin Susanne F. , Kim Philip , Park Hongkun , Lukin Mikhail D.
Published: June 2022

Techniques to mold the flow of light on subwavelength scales enable fundamentally new optical systems and device applications. The realization of programmable, active optical systems with fast, tunable components is among the outstanding challenges in the field. Here, we experimentally demonstrate a few-pixel beam steering device based on electrostatic gate control of excitons in an atomically thin semiconductor with strong light-matter interactions. By combining the high reflectivity of a MoSe2 monolayer with a graphene split-gate geometry, we shape the wavefront phase profile to achieve continuously tunable beam deflection with a range of 10°, two-dimensional beam steering, and switching times down to 1.6 nanoseconds. Our approach opens the door for a new class of atomically thin optical systems, such as rapidly switchable beam arrays and quantum metasurfaces operating at their fundamental thickness limit.
Identification, discrimination and heterogeneity of fibroblasts
Authors: Lendahl Urban , Muhl Lars , Betsholtz Christer
Published: June 2022

Fibroblasts, the principal cell type of connective tissue, secrete extracellular matrix components during tissue development, homeostasis, repair and disease. Despite this crucial role, the identification and distinction of fibroblasts from other cell types are challenging and laden with caveats. Rapid progress in single-cell transcriptomics now yields detailed molecular portraits of fibroblasts and other cell types in our bodies, which complement and enrich classical histological and immunological descriptions, improve cell class definitions and guide further studies on the functional heterogeneity of cell subtypes and states, origins and fates in physiological and pathological processes. In this review, we summarize and discuss recent advances in the understanding of fibroblast identification and heterogeneity and how they discriminate from other cell types.
Abruptly attenuated carbon sequestration with Weddell Sea dense waters by 2100
Authors: Nissen Cara , Timmermann Ralph , Hoppema Mario , Gürses Özgür , Hauck Judith
Published: June 2022

Antarctic Bottom Water formation, such as in the Weddell Sea, is an efficient vector for carbon sequestration on time scales of centuries. Possible changes in carbon sequestration under changing environmental conditions are unquantified to date, mainly due to difficulties in simulating the relevant processes on high-latitude continental shelves. Here, we use a model setup including both ice-shelf cavities and oceanic carbon cycling and demonstrate that by 2100, deep-ocean carbon accumulation in the southern Weddell Sea is abruptly attenuated to only 40% of the 1990s rate in a high-emission scenario, while the rate in the 2050s and 2080s is still 2.5-fold and 4-fold higher, respectively, than in the 1990s. Assessing deep-ocean carbon budgets and water mass transformations, we attribute this decline to an increased presence of modified Warm Deep Water on the southern Weddell Sea continental shelf, a 16% reduction in sea-ice formation, and a 79% increase in ice-shelf basal melt. Altogether, these changes lower the density and volume of newly formed bottom waters and reduce the associated carbon transport to the abyss.
Large-scale genomic analyses reveal insights into pleiotropy across circulatory system diseases and nervous system disorders
Authors: Zhang Xinyuan , Lucas Anastasia M. , Veturi Yogasudha , Drivas Theodore G. , Bone William P. , Verma Anurag , Chung Wendy K. , Crosslin David , Denny Joshua C. , Hebbring Scott , Jarvik Gail P. , Kullo Iftikhar , Larson Eric B. , Rasmussen-Torvik Laura J. , Schaid Daniel J. , Smoller Jordan W. , Stanaway Ian B. , Wei Wei-Qi , Weng Chunhua , Ritchie Marylyn D.
Published: June 2022

Clinical and epidemiological studies have shown that circulatory system diseases and nervous system disorders often co-occur in patients. However, genetic susceptibility factors shared between these disease categories remain largely unknown. Here, we characterized pleiotropy across 107 circulatory system and 40 nervous system traits using an ensemble of methods in the eMERGE Network and UK Biobank. Using a formal test of pleiotropy, five genomic loci demonstrated statistically significant evidence of pleiotropy. We observed region-specific patterns of direction of genetic effects for the two disease categories, suggesting potential antagonistic and synergistic pleiotropy. Our findings provide insights into the relationship between circulatory system diseases and nervous system disorders which can provide context for future prevention and treatment strategies.
ChIP-Hub provides an integrative platform for exploring plant regulome
Authors: Fu Liang-Yu , Zhu Tao , Zhou Xinkai , Yu Ranran , He Zhaohui , Zhang Peijing , Wu Zhigui , Chen Ming , Kaufmann Kerstin , Chen Dijun
Published: June 2022

Plant genomes encode a complex and evolutionary diverse regulatory grammar that forms the basis for most life on earth. A wealth of regulome and epigenome data have been generated in various plant species, but no common, standardized resource is available so far for biologists. Here, we present ChIP-Hub, an integrative web-based platform in the ENCODE standards that bundles >10,000 publicly available datasets reanalyzed from >40 plant species, allowing visualization and meta-analysis. We manually curate the datasets through assessing ~540 original publications and comprehensively evaluate their data quality. As a proof of concept, we extensively survey the co-association of different regulators and construct a hierarchical regulatory network under a broad developmental context. Furthermore, we show how our annotation allows to investigate the dynamic activity of tissue-specific regulatory elements (promoters and enhancers) and their underlying sequence grammar. Finally, we analyze the function and conservation of tissue-specific promoters, enhancers and chromatin states using comparative genomics approaches. Taken together, the ChIP-Hub platform and the analysis results provide rich resources for deep exploration of plant ENCODE. ChIP-Hub is available at https://biobigdata.nju.edu.cn/ChIPHub/.
A multifunctional system for genome editing and large-scale interspecies gene transfer
Authors: Teufel Marc , Klein Carlo A. , Mager Maurice , Sobetzko Patrick
Published: June 2022

CRISPR SWAPnDROP extends the limits of genome editing to large-scale in-vivo DNA transfer between bacterial species. Its modular platform approach facilitates species specific adaptation to confer genome editing in various species. In this study, we show the implementation of the CRISPR SWAPnDROP concept for the model organism Escherichia coli, the fast growing Vibrio natriegens and the plant pathogen Dickeya dadantii. We demonstrate the excision, transfer and integration of large chromosomal regions between E. coli, V. natriegens and D. dadantii without size-limiting intermediate DNA extraction. CRISPR SWAPnDROP also provides common genome editing approaches comprising scarless, marker-free, iterative and parallel insertions and deletions. The modular character facilitates DNA library applications, and recycling of standardized parts. Its multi-color scarless co-selection system significantly improves editing efficiency and provides visual quality controls throughout the assembly and editing process.
SpG and SpRY variants expand the CRISPR toolbox for genome editing in zebrafish
Authors: Liang Fang , Zhang Yu , Li Lin , Yang Yexin , Fei Ji-Feng , Liu Yanmei , Qin Wei
Published: June 2022

Precise genetic modifications in model organisms are essential for biomedical research. The recent development of PAM-less base editors makes it possible to assess the functional impact and pathogenicity of nucleotide mutations in animals. Here we first optimize SpG and SpRY systems in zebrafish by purifying protein combined with synthetically modified gRNA. SpG shows high editing efficiency at NGN PAM sites, whereas SpRY efficiently edit PAM-less sites in the zebrafish genome. Then, we generate the SpRY-mediated cytosine base editor SpRY-CBE4max and SpRY-mediated adenine base editor zSpRY-ABE8e. Both target relaxed PAM with up to 96% editing efficiency and high product purity. With these tools, some previously inaccessible disease-relevant genetic variants are generated in zebrafish, supporting the utility of high-resolution targeting across genome-editing applications. Our study significantly improves CRISPR-Cas targeting in the genomic landscape of zebrafish, promoting the application of this model organism in revealing gene function, physiological mechanisms, and disease pathogenesis.
Approaching intrinsic dynamics of MXenes hybrid hydrogel for 3D printed multimodal intelligent devices with ultrahigh superelasticity and temperature sensitivity
Authors: Liu Haodong , Du Chengfeng , Liao Liling , Zhang Hongjian , Zhou Haiqing , Zhou Weichang , Ren Tianning , Sun Zhicheng , Lu Yufei , Nie Zhentao , Xu Feng , Zhu Jixin , Huang Wei
Published: June 2022

Hydrogels are investigated broadly in flexible sensors which have been applied into wearable electronics. However, further application of hydrogels is restricted by the ambiguity of the sensing mechanisms, and the multi-functionalization of flexible sensing systems based on hydrogels in terms of cost, difficulty in integration, and device fabrication remains a challenge, obstructing the specific application scenarios. Herein, cost-effective, structure-specialized and scenario-applicable 3D printing of direct ink writing (DIW) technology fabricated two-dimensional (2D) transition metal carbides (MXenes) bonded hydrogel sensor with excellent strain and temperature sensing performance is developed. Gauge factor (GF) of 5.7 (0 − 191% strain) and high temperature sensitivity (−5.27% °C−1) within wide working range (0 − 80 °C) can be achieved. In particular, the corresponding mechanisms are clarified based on finite element analysis and the first use of in situ temperature-dependent Raman technology for hydrogels, and the printed sensor can realize precise temperature indication of shape memory solar array hinge.
Ursodeoxycholic acid reduces antitumor immunosuppression by inducing CHIP-mediated TGF-β degradation
Authors: Shen Yingying , Lu Chaojie , Song Zhengbo , Qiao Chenxiao , Wang Jiaoli , Chen Jinbiao , Zhang Chengyan , Zeng Xianchang , Ma Zeyu , Chen Tao , Li Xu , Lin Aifu , Guo Jufeng , Wang Jianli , Cai Zhijian
Published: June 2022

TGF-β is essential for inducing systemic tumor immunosuppression; thus, blocking TGF-β can greatly enhance antitumor immunity. However, there are still no effective TGF-β inhibitors in clinical use. Here, we show that the clinically approved compound ursodeoxycholic acid (UDCA), by degrading TGF-β, enhances antitumor immunity through restraining Treg cell differentiation and activation in tumor-bearing mice. Furthermore, UDCA synergizes with anti-PD-1 to enhance antitumor immunity and tumor-specific immune memory in tumor-bearing mice. UDCA phosphorylates TGF-β at T282 site via TGR5-cAMP-PKA axis, causing increased binding of TGF-β to carboxyl terminus of Hsc70-interacting protein (CHIP). Then, CHIP ubiquitinates TGF-β at the K315 site, initiating p62-dependent autophagic sorting and subsequent degradation of TGF-β. Notably, results of retrospective analysis shows that combination therapy with anti-PD-1 or anti-PD-L1 and UDCA has better efficacy in tumor patients than anti-PD-1 or anti-PD-L1 alone. Thus, our results show a mechanism for TGF-β regulation and implicate UDCA as a potential TGF-β inhibitor to enhance antitumor immunity.
Prognostic significance of RNA-based TP53 pathway function among estrogen receptor positive and negative breast cancer cases
Authors: Hurson Amber N. , Abubakar Mustapha , Hamilton Alina M. , Conway Kathleen , Hoadley Katherine A. , Love Michael I. , Olshan Andrew F. , Perou Charles M. , Garcia-Closas Montserrat , Troester Melissa A.
Published: June 2022

TP53 and estrogen receptor (ER) are essential in breast cancer development and progression, but TP53 status (by DNA sequencing or protein expression) has been inconsistently associated with survival. We evaluated whether RNA-based TP53 classifiers are related to survival. Participants included 3213 women in the Carolina Breast Cancer Study (CBCS) with invasive breast cancer (stages I–III). Tumors were classified for TP53 status (mutant-like/wildtype-like) using an RNA signature. We used Cox proportional hazards models to estimate covariate-adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) for breast cancer-specific survival (BCSS) among ER- and TP53-defined subtypes. RNA-based results were compared to DNA- and IHC-based TP53 classification, as well as Basal-like versus non-Basal-like subtype. Findings from the diverse (50% Black), population-based CBCS were compared to those from the largely white METABRIC study. RNA-based TP53 mutant-like was associated with BCSS among both ER-negatives and ER-positives (HR (95% CI) = 5.38 (1.84–15.78) and 4.66 (1.79–12.15), respectively). Associations were attenuated when using DNA- or IHC-based TP53 classification. In METABRIC, few ER-negative tumors were TP53-wildtype-like, but TP53 status was a strong predictor of BCSS among ER-positives. In both populations, the effect of TP53 mutant-like status was similar to that for Basal-like subtype. RNA-based measures of TP53 status are strongly associated with BCSS and may have value among ER-negative cancers where few prognostic markers have been robustly validated. Given the role of TP53 in chemotherapeutic response, RNA-based TP53 as a prognostic biomarker could address an unmet need in breast cancer.
Large-scale programmable assembly of functional micro-components for advanced electronics via light-regulated adhesion and polymer growth
Authors: Guo Chan , Pan Zhangxu , Li Changhao , Zou Shenghan , Pang Chao , Wang Jiantai , Hu Jinhua , Gong Zheng
Published: June 2022

Large-area, programmable assembly of diverse micro-objects onto arbitrary substrates is a fundamental yet challenging task. Herein a simple wafer-level micro-assembly technique based on the light-triggered change in both surface topography and interfacial adhesion of a soft photo-sensitive polymer is proposed. In particular, the light-regulated polymer growth creates locally indented and elevated zones on the stamp surface. The light-mediated adhesion reduction, on the other hand, facilitates the inks to be released from the polymer. The interplay of these two effects makes it feasible for the programmable assembly of ultra-small components onto various substrates coated with supplementary adhesive layers. The fidelity of this technique is validated by assembling diverse materials and functional devices, with the printing size up to 4-inch. This work provides a rational strategy for large-scale and programmable assembly of diverse delicate micro-objects, bypassing the common issues of some existing techniques such as poor transfer uniformity, small printing area, and high cost.
Metabolic profilings of rat INS-1 β-cells under changing levels of essential amino acids
Authors: Xu Lianbin , Lin Xueyan , Li Xiuli , Hu Zhiyong , Hou Qiuling , Wang Yun , Wang Zhonghua
Published: June 2022

Application of mass spectrometry enables the detection of metabolic differences between organisms with different nutritional settings. Divergence in the metabolic fingerprints of rat pancreatic INS-1 β-cells were systematically captured with regard to ten individual essential amino acid (EAA) availability. A high-resolution tandem mass spectrometry system coupled to liquid chromatography produced a horizontal comparison of metabolic profilings of β-cells with individual EAA elevated to 10 mmol/L by turn or removal individual EAA from the medium one by one. Quality control samples were injected at regular intervals throughout the analytical run to monitor and evaluate the stability of the system. The raw data of samples and reference compounds including study protocols have been deposited in the open metabolomics database MetaboLights to enable efficient reuse of the datasets, such as investigating the difference in metabolic process between diverse EAAs as well as screening and verifying potential metabolites affecting insulin secretion and β-cell function.
Preparation and application of chikungunya pseudovirus containing double reporter genes
Authors: Su Chunyan , Ding Kaiyun , Xu Jingwen , Wu Jianchao , Liu Jiansheng , Shen Jiayuan , Zhou Hongning , Liu Hongqi
Published: June 2022

Chikungunya virus (CHIKV), a highly infectious and rapidly spread viral pathogen, is classified as a pathogenic agent at the biosafety level 3. Operation of live authentic CHIKV needs a specific laboratory with the P3 or above containment, which greatly confines the CHIKV-associated studies. To establish an evaluation system of CHIKV that can be utilized in a BSL2 laboratory, we constructed a pseudovirus (PsV) system of CHIKV containing double reporter genes (ZsGreen1 and luciferase). The fluorescent ZsGreen1 is a convenient and cheap reporter for monitoring the efficiency of transfection and titration of PsV. The enzyme luciferase is a sensitive reporter for the application of PsV to neutralization assay or drug screening. The CHIKV PsV produced in this study, with a titer of up to 3.16 × 106 TU/ml, was confirmed by Western blotting and transmission electronic microscopy (TEM). Finally, we developed a microneutralization assay with the CHIKV PsV produced in this study, which was successfully applied to evaluate neutralizing activities of convalescent sera from CHIKV-infected patients. In summary, we have established a convenient and sensitive double-reporter CHIKV pseudovirus system, which provides a safe and effective platform for screening anti-CHIKV drugs and evaluating vaccines against CHIKV.
The human “contaminome”: bacterial, viral, and computational contamination in whole genome sequences from 1000 families
Authors: Chrisman Brianna , He Chloe , Jung Jae-Yoon , Stockham Nate , Paskov Kelley , Washington Peter , Wall Dennis P.
Published: June 2022

The unmapped readspace of whole genome sequencing data tends to be large but is often ignored. We posit that it contains valuable signals of both human infection and contamination. Using unmapped and poorly aligned reads from whole genome sequences (WGS) of over 1000 families and nearly 5000 individuals, we present insights into common viral, bacterial, and computational contamination that plague whole genome sequencing studies. We present several notable results: (1) In addition to known contaminants such as Epstein-Barr virus and phiX, sequences from whole blood and lymphocyte cell lines contain many other contaminants, likely originating from storage, prep, and sequencing pipelines. (2) Sequencing plate and biological sample source of a sample strongly influence contamination profile. And, (3) Y-chromosome fragments not on the human reference genome commonly mismap to bacterial reference genomes. Both experiment-derived and computational contamination is prominent in next-generation sequencing data. Such contamination can compromise results from WGS as well as metagenomics studies, and standard protocols for identifying and removing contamination should be developed to ensure the fidelity of sequencing-based studies.
A prime-masked ERP investigation on phonology in visual word processing among bilingual speakers of alphasyllabic and alphabetic orthographies
Authors: Shetty Adhvika , Hebbar Sanjana P. , Shenoy Rajath , Peter Varghese , Krishnan Gopee
Published: June 2022

In this study, we experimentally manipulated the phonology of the cross-script prime-target dyads in an ERP-coupled masked priming paradigm to explore the role phonology plays in visual word processing. The written characters of certain bilingual dyads seldom show any visual/orthographic similarity, yet have the same phonological representation. While the Bilingual Interactive Activation (BIA) model relies on the orthographic similarity between the languages in a bilingual dyad, its revised version (BIA + model) additionally banks on the phonological (and semantic) similarity between the words in such dyads. Thus, there exists the need to investigate the role of phonological (and semantic) similarity between the words of a bilingual dyad, especially in the absence of orthographic similarity. Borrowed words from one language to another provide a suitable avenue to explore this question. Cross-orthographic (or cross-script) bilingual participants of this study performed the semantic judgment of visually presented words in a masked priming paradigm in each of their languages while we simultaneously collected the event-related potentials (ERPs). The primes were either translations (different phonology & orthography: P–O–; phonologically incongruent) or transliterations (same phonology & different orthography: P + O–; phonologically congruent) of the target. Overall, the results showed no difference between the two prime conditions. We discuss our findings in light of the BIA and BIA + models of bilingual visual word processing and discuss the relevance of the former model in orthographically distinct bilingual language dyads.
Simulation platform for pattern recognition based on reservoir computing with memristor networks
Authors: Tanaka Gouhei , Nakane Ryosho
Published: June 2022

Memristive systems and devices are potentially available for implementing reservoir computing (RC) systems applied to pattern recognition. However, the computational ability of memristive RC systems depends on intertwined factors such as system architectures and physical properties of memristive elements, which complicates identifying the key factor for system performance. Here we develop a simulation platform for RC with memristor device networks, which enables testing different system designs for performance improvement. Numerical simulations show that the memristor-network-based RC systems can yield high computational performance comparable to that of state-of-the-art methods in three time series classification tasks. We demonstrate that the excellent and robust computation under device-to-device variability can be achieved by appropriately setting network structures, nonlinearity of memristors, and pre/post-processing, which increases the potential for reliable computation with unreliable component devices. Our results contribute to an establishment of a design guide for memristive reservoirs toward the realization of energy-efficient machine learning hardware.
Disruption of spatiotemporal clustering in dengue cases by wMel Wolbachia in Yogyakarta, Indonesia
Authors: Dufault Suzanne M. , Tanamas Stephanie K. , Indriani Citra , Utarini Adi , Ahmad Riris Andono , Jewell Nicholas P. , Simmons Cameron P. , Anders Katherine L.
Published: June 2022

Dengue exhibits focal clustering in households and neighborhoods, driven by local mosquito population dynamics, human population immunity, and fine scale human and mosquito movement. We tested the hypothesis that spatiotemporal clustering of homotypic dengue cases is disrupted by introduction of the arbovirus-blocking bacteriumWolbachia(wMel-strain) into theAedes aegyptimosquito population. We analysed 318 serotyped and geolocated dengue cases (and 5921 test-negative controls) from a randomized controlled trial in Yogyakarta, Indonesia ofwMel deployments. We find evidence of spatial clustering up to 300 m among the 265 dengue cases (3083 controls) in the untreated trial arm. Participant pairs enrolled within 30 days and 50 m had a 4.7-fold increase (compared to 95% CI on permutation-based null distribution: 0.1, 1.2) in the odds of being homotypic (i.e. potentially transmission-related) as compared to pairs occurring at any distance. In contrast, we find no evidence of spatiotemporal clustering among the 53 dengue cases (2838 controls) resident in thewMel-treated arm. Introgression ofwMelWolbachiaintoAedes aegyptimosquito populations interrupts focal dengue virus transmission leading to reduced case incidence; the true intervention effect may be greater than the 77% efficacy measured in the primary analysis of the Yogyakarta trial.
Change detection based on unsupervised sparse representation for fundus image pair
Authors: Fu Yinghua , Zhao Xing , Liang Yong , Zhao Tiejun , Wang Chaoli , Zhang Dawei
Published: June 2022

Detecting changes is an important issue for ophthalmology to compare longitudinal fundus images at different stages and obtain change regions. Illumination variations bring distractions on the change regions by the pixel-by-pixel comparison. In this paper, a new unsupervised change detection method based on sparse representation classification (SRC) is proposed for the fundus image pair. First, the local neighborhood patches are extracted from the reference image to build a dictionary of the local background. Then the current image patch is represented sparsely and its background is reconstructed by the obtained dictionary. Finally, change regions are given through background subtracting. The SRC method can correct automatically illumination variations through the representation coefficients and filter local contrast and global intensity effectively. In experiments of this paper, the AUC and mAP values of SRC method are 0.9858 and 0.8647 respectively for the image pair with small lesions; the AUC and mAP values of the fusion method of IRHSF and SRC are 0.9892 and 0.9692 separately for the image pair with the big change region. Experiments show that the proposed method in this paper is more robust than RPCA for the illumination variations and can detect change regions more effectively than pixel-wised image differencing.
Population structure of blackfin tuna (Thunnus atlanticus) in the western Atlantic Ocean inferred from microsatellite loci
Authors: Saillant Eric A. , Luque Patricia L. , Short Emily , Antoni Luca , Reynal Lionel , Pau Cedric , Arocha Freddy , Roque Pollyana , Hazin Fabio
Published: June 2022

The blackfin tuna,Thunnus atlanticus, is a small tropical tuna exploited by recreational and commercial fisheries in various parts of its range. Information on stock structure is needed to develop management plans for this species but is currently lacking. In this work, 470 blackfin tuna from nine geographic populations were assayed at 13 homologous microsatellite markers to provide a first assessment of stock structure across the species range. The overall divergence among locality samples was very low (overall FST = 0.0004) indicating high connectivity of blackfin tuna across their range. No clear grouping of localities in differentiated units was inferred but structuring followed a weak isolation by distance pattern (r = 0.16, P = 0.032). Pairwise exact tests and spatial analysis of molecular variance suggested divergence of the sample collected offshore Baía Formosa (Brazil) possibly reflecting reproductive isolation of Brazilian populations from those in the Caribbean region and further north. Further study of the status of Brazilian populations and the transition between this region and the Caribbean is warranted. Cryptic subdivision within the Northern Hemisphere part of the range is possible and should be evaluated using increased marker density and a more comprehensive geographic coverage.
Identification of Adamts4 as a novel adult cardiac injury biomarker with therapeutic implications in patients with cardiac injuries
Authors: Khanam Riffat , Sengupta Arunima , Mukhopadhyay Dipankar , Chakraborty Santanu
Published: June 2022

Pathological cardiac remodeling as an aftermath of a severe cardiac injury can lead to ventricular dysfunction and subsequent heart failure. Adamts4, a metalloproteinase, and disintegrin with thrombospondin-like motif, involved in the turnover of certain extracellular matrix molecules and pathogenesis of osteoarthritis, also plays a role in cardiac remodeling although little is presently known about its expression and function in the heart. Here, we have investigated the dynamic expression pattern of Adamts4 during cardiogenesis and also in the adult heart. To our surprise, adult cardiac injury reactivated Adamts4 expression concomitant with fibrosis induction. To better understand the mechanism, cultured H9c2 cardiomyocyte cells were subjected to ROS injury and Hypoxia. Moreover, through combinatorial treatment with SB431542 (an inhibitor of Tgf-β1), and Adamts4 siRNA mediated gene knockdown, we were able to decipher a regulatory hierarchy to the signal cascade being at the heart of Tgf-β regulation. Besides the hallmark expression of Adamts4 and Tgf-β1, expression of other fibrosis-related markers like Collagen-III, alpha-SMA and Periostin were also assessed. Finally, increased levels of Adamts4 and alpha-SMA proteins in cardiac patients also resonated well with our animal and cell culture studies. Overall, in this study, we highlight, Adamts4 as a novel biomarker of adult cardiac injury.
Real-time laser ultrasonic monitoring of laser-induced thermal processes
Authors: Morales Rosa E. , Harke Kathryn J. , Tringe Joseph W. , Stobbe David M. , Murray Todd W.
Published: June 2022

Intra- and inter-layer integrity of components fabricated with advanced manufacturing techniques, such as laser powder bed fusion, is dependent upon rapid heating, melting, and solidification processes. There is a need for new techniques to provide in situ feedback of these processes. Here a laser-based ultrasonic technique to probe thermal effects induced by a high-power continuous wave laser in titanium samples is described. Numerical simulations were performed to show that, for a spatially uniform heating beam, laser-induced surface acoustic waves are strongly influenced by surface heating conditions, are dispersive in the case of rapid heating, and that an abrupt velocity reduction happens upon the onset of surface melting. Furthermore, laser-based ultrasound experimental results which monitor the transient change of surface wave travel time associated with high power laser surface heating are provided. A pulsed laser is used to generate high frequency surface acoustic waves that propagate through the laser-heated region and are detected using a photorefractive crystal-based interferometer. Qualitative agreement is observed between theory and experiment with both showing a rapid reduction in the surface wave velocity at the onset of illumination and further decrease in surface wave velocity associated with melting. It is demonstrated that changes in the surface wave velocity can be used to track local heating and detect the onset of surface melting in real time.
EM-driven size reduction and multi-criterial optimization of broadband circularly-polarized antennas using pareto front traversing and design extrapolation
Authors: Ullah Ubaid , Al-Hasan Muath , Koziel Slawomir , Mabrouk Ismail Ben
Published: June 2022

Maintaining small size has become an important consideration in the design of contemporary antenna structures. In the case of broadband circularly polarized (CP) antennas, miniaturization is a challenging process due to the necessity of simultaneous handling of electrical and field properties (reflection, axial ratio, gain), as well as ensuring sufficient frequency range of operation, especially at the lower edge of the antenna bandwidth. An additional difficulty is that—for the sake of reliability—the design process has to be based on full-wave electromagnetic simulation tools. This is a computationally expensive endeavor because rendering the minimum-size design under the assumed constraints concerning the operating frequencies requires rigorous numerical optimization, which entails massive evaluations of the structure at hand. This paper describes an algorithmic framework for efficient identification of broadband CP antenna designs that realize the best possible trade-offs (Pareto set) between the antenna size and its operating bandwidth. The designs are generated sequentially by solving local optimization tasks targeting explicit reduction of the antenna footprint with implicit constraints imposed on the reflection and axial ratio characteristics. The data accumulated during the previous iterations is employed to yield good initial points for further stages by means of inverse surrogates and extrapolation. Low cost of the process is ensured by sparse sensitivity updates within the trust-region gradient-based algorithm being the main optimization engine. The proposed methodology is demonstrated using three examples of wide-slot CP structures with the trade-off designs representing broad ranges of achievable antenna sizes and operating bandwidth. The framework can be used to assess the antenna suitability for particular application areas as well to conclusively compare alternative CP geometries from the point of view of achievable miniaturization rate and capability of fulfilling given performance requirements.
Deep convolutional neural networks for automated scoring of pentagon copying test results
Authors: Maruta Jumpei , Uchida Kentaro , Kurozumi Hideo , Nogi Satoshi , Akada Satoshi , Nakanishi Aki , Shinoda Miki , Shiba Masatsugu , Inoue Koki
Published: June 2022

This study aims to investigate the accuracy of a fine-tuned deep convolutional neural network (CNN) for evaluating responses to the pentagon copying test (PCT). To develop a CNN that could classify PCT images, we fine-tuned and compared the pre-trained CNNs (GoogLeNet, VGG-16, ResNet-50, Inception-v3). To collate our training dataset, we collected 1006 correct PCT images and 758 incorrect PCT images drawn on a test sheet by dementia suspected patients at the Osaka City Kosaiin Hospital between April 2009 and December 2012. For a validation dataset, we collected PCT images from consecutive patients treated at the facility in April 2020. We examined the ability of the CNN to detect correct PCT images using a validation dataset. For a validation dataset, we collected PCT images (correct, 41; incorrect, 16) from 57 patients. In the validation testing for an ability to detect correct PCT images, the fine-tuned GoogLeNet CNN achieved an area under the receiver operating characteristic curve of 0.931 (95% confidence interval 0.853–1.000). These findings indicate that our fine-tuned CNN is a useful method for automatically evaluating PCT images. The use of CNN-based automatic scoring of PCT can potentially reduce the burden on assessors in screening for dementia.
Influence of moisture content, temperature, and time on free fatty acid in stored crude palm oil
Authors: Emebu Samuel , Osaikhuiwuomwan Omokaro , Mankonen Aleksi , Udoye Chinweike , Okieimen Charity , Janáčová Dagmar
Published: June 2022

Consequent to the importance of crude palm oil (CPO) to global food processing industries, and the need for quality assurance of CPO. A kinetic model that describes changes of free fatty acid (FFA) in industrially stored CPO has been developed. CPO FFA is a well-known indicator of the deterioration of CPO. The effect of initial moisture content, storage temperature, and time on CPO FFA have been investigated in this work. Specifically, statistical multi-regression models for changes in FFA and moisture content (MC) were developed at P-value < 0.05 or 95% confidence interval fence. It was found that CPO FFA increases with an increase in moisture content, temperature, and time in their linear term and in respect to decreases in their quadratic term, and interaction between moisture content and temperature. The CPO MC was also found to decrease with an increase in temperature and time and increases in the quadratic term of temperature. Although while the model for CPO FFA, based on Fisher's F-test: $${\mathrm{F}}_{\mathrm{model}}(6.80)<{\mathrm{F}}_{95\mathrm{\%}}(19.30)$$

F
model

(
6.80
)

<

F

95
%

(
19.30
)

, showed no lack-of-fit; that of CPO MC showed lack-of-fit, $${\mathrm{F}}_{\mathrm{model}}(13.67)\nless {\mathrm{F}}_{95\mathrm{\%}}(4.39)$$

F
model

(
13.67
)

≮

F

95
%

(
4.39
)

. Furthermore, based on inference from the statistical model, their kinetic models were also developed. While the CPO FFA kinetic, found to be a half-order kinetic model and its other auxiliary models showed a very good fit (R2 {0.9933–0.8614} and RMSE {0.0020–3.6716}); that of CPO MC was a poorly fitted first-order kinetic model (R2 {0.9885–0.3935} and RMSE {0.0605–17.8501}).
Riemannian geometry-based transfer learning for reducing training time in c-VEP BCIs
Authors: Ying Jiahui , Wei Qingguo , Zhou Xichen
Published: June 2022

One of the main problems that a brain-computer interface (BCI) face is that a training stage is required for acquiring training data to calibrate its classification model just before every use. Transfer learning is a promising method for addressing the problem. In this paper, we propose a Riemannian geometry-based transfer learning algorithm for code modulated visual evoked potential (c-VEP)-based BCIs, which can effectively reduce the calibration time without sacrificing the classification accuracy. The algorithm includes the main procedures of log-Euclidean data alignment (LEDA), super-trial construction, covariance matrix estimation, training accuracy-based subject selection (TSS) and minimum distance to mean classification. Among them, the LEDA reduces the difference in data distribution between subjects, whereas the TSS promotes the similarity between a target subject and the source subjects. The resulting performance of transfer learning is improved significantly. Sixteen subjects participated in a c-VEP BCI experiment and the recorded data were used in offline analysis. Leave-one subject-out (LOSO) cross-validation was used to evaluate the proposed algorithm on the data set. The results showed that the algorithm achieved much higher classification accuracy than the subject-specific (baseline) algorithm with the same number of training trials. Equivalently, the algorithm reduces the training time of the BCI at the same performance level and thus facilitates its application in real world.
Three-dimensional foot trajectory in female patients with end-stage hip osteoarthritis during walking
Authors: Kiko Yu , Ogata Taiki , Uchitomi Hirotaka , Matsubara Masaaki , Miyake Yoshihiro , Wada Yoshiaki
Published: June 2022

Osteoarthritis (OA) is a risk factor for falls. To decrease the fall risk, it is important to evaluate the detailed features of the gait of patients with OA. This study aimed to investigate the spatio-temporal parameters of gait in patients with end-stage hip OA, especially foot trajectory. We measured normal speed gait in patients with hip OA and in healthy controls (HCs) using inertial measurement units attached to shanks. The stride lengths in the affected and unaffected sides in the patients with hip OA were shorter than those in the HCs, but the position of maximum foot clearance was not significantly different between the two groups. The patients with hip OA compensated the position of maximum foot clearance to avoid fall risk. The horizontal plane foot trajectory in patients with hip OA suggests that the lateral bending of the trunk during walking, which is frequently seen in them, was a result of the lateral distance at swing down being located significantly more medially on the unaffected side than on the affected side. Herein, a new gait parameter of lateral distance at swing was discovered by a detailed evaluation of three-dimensional foot trajectory of female patients with end-stage hip OA.
An optimized protocol for single nuclei isolation from clinical biopsies for RNA-seq
Authors: Rousselle Thomas V. , McDaniels Jennifer M. , Shetty Amol C. , Bardhi Elissa , Maluf Daniel G. , Mas Valeria R.
Published: June 2022

Single nuclei RNA sequencing (snRNA-seq) has evolved as a powerful tool to study complex human diseases. Single cell resolution enables the study of novel cell types, biological processes, cell trajectories, and cell–cell signaling pathways. snRNA-seq largely relies on the dissociation of intact nuclei from human tissues. However, the study of complex tissues using small core biopsies presents many technical challenges. Here, an optimized protocol for single nuclei isolation is presented for frozen and RNAlater preserved human kidney biopsies. The described protocol is fast, low cost, and time effective due to the elimination of cell sorting and ultra-centrifugation. Samples can be processed in 90 min or less. This method is effective for obtaining normal nuclei morphology without signs of structural damage. Using snRNA-seq, 16 distinct kidney cell clusters were recovered from normal and peri-transplant acute kidney injury allograft samples, including immune cell clusters. Quality control measurements demonstrated that these optimizations eliminated cellular debris and allowed for a high yield of high-quality nuclei and RNA for library preparation and sequencing. Cellular disassociation did not induce cellular stress responses, which recapitulated transcriptional patterns associated with standardized methods of nuclei isolation. Future applications of this protocol will allow for thorough investigations of small biobank biopsies, identifying cell-specific injury pathways and driving the discovery of novel diagnostics and therapeutic targets.
Removal of Cr(VI) by biochar derived via co-pyrolysis of oily sludge and corn stalks
Authors: Han Lei , Li Jinling , Zhang Tiantian , Qu Chengtun , Yu Tao , Yang Bo , Shao Zhiguo
Published: June 2022

The co-pyrolysis of oily sludge with biomass to prepare carbon materials is not only an effective way to mitigate oily sludge pollution, but it is also a method of obtaining carbon materials. In this study, a carbon material (OS-CS AC) was obtained by the direct co-pyrolysis of oily sludge (OS) and corn stalks (CS) and then applied to Cr(VI) removal. According to the hydroxy and carboxy masking experiments and the characterization of OS-CS AC by FT-IR, SEM, XPS, XRD, and N2 physical adsorption–desorption, Cr(VI) can be adsorbed efficiently through pore filling, the surface oxygen-containing functional groups can promote the reduction of Cr(VI) to Cr(III) through electron donors, and the greater the electrostatic attraction between the electron-donating functional groups of OS-CS AC and the Cr(VI) is, the stronger the ability to remove Cr(VI). In addition, the removal process was discussed, and the results indicated that the McKay kinetic model, Langmuir isotherm model and Van't Hoff thermodynamic model were the most suitable models for removal. The main factors affecting the removal of Cr(VI) were discussed, and the removal of Cr(VI) reached 99.14%, which gives a comprehensive utilization way of oily sludge and corn stalks.
The physical and optical investigations of the tannic acid functionalised Cu-based oxide nanostructures
Authors: Che Lah Nurul Akmal , Murthy Puhanes , Mohd Zubir Mohd Nashrul
Published: June 2022

The need for a mild, low-cost, green environment that is able to produce exotic properties of output nanostructures is appealing nowadays. Employing these requirements, the copper (Cu)—based oxide nanostructures have been successfully synthesised via one-pot reaction using biocompatible natural polyphenol, tannic acid (TA) as both the reducing agent and stabiliser at 60, 70 and 80 °C. The structural and optical studies disclosed the effect of TA on the surface morphology, phase purity, elemental composition, optical microstrain and optical intrinsic energy of this mixed Cu2O and CuO nanostructures. The optically based method describes the comparative details of the multi-band gap in the presence of more than one element with overlapping spectra from the first-derivative absorbance curve $$\frac{\Delta E}{\Delta A}$$

Δ
E

Δ
A

and the exponential absorbance of Urbach tail energy $${E}_{U}$$

E
U

towards the conventional Tauc bandgap. The $$\frac{\Delta E}{\Delta A}$$

Δ
E

Δ
A

demonstrates that the pronounced effect of TA that Cu2O and CuO nanostructures creates much sensitive first-derivative bandgap output compared to the Tauc bandgap. The results also show that the $${E}_{U}$$

E
U

reduced as the temperature reaches 70 °C and then experienced sudden increase at 80 °C. The change in the pattern is parallel to the trend observed in the Williamson–Hall microstrain and is evident from the variations of the mean crystallite size $${D}_{m}$$

D
m

which is also a cause response to the change in temperature or pH. Therefore, the current work has elucidated that the structural and optical correlations on the as-synthesised Cu2O and CuO nanostructures in the presence of TA were the combined reaction of pH change and the ligand complexation reactions. The acquired results suggest a more comprehensive range of studies to further understand the extent relationship between the physical and optical properties of TA functionalised Cu-based oxide nanostructures.
Computational drug repurposing based on electronic health records: a scoping review
Authors: Zong Nansu , Wen Andrew , Moon Sungrim , Fu Sunyang , Wang Liwei , Zhao Yiqing , Yu Yue , Huang Ming , Wang Yanshan , Zheng Gang , Mielke Michelle M. , Cerhan James R. , Liu Hongfang
Published: June 2022

Computational drug repurposing methods adapt Artificial intelligence (AI) algorithms for the discovery of new applications of approved or investigational drugs. Among the heterogeneous datasets, electronic health records (EHRs) datasets provide rich longitudinal and pathophysiological data that facilitate the generation and validation of drug repurposing. Here, we present an appraisal of recently published research on computational drug repurposing utilizing the EHR. Thirty-three research articles, retrieved from Embase, Medline, Scopus, and Web of Science between January 2000 and January 2022, were included in the final review. Four themes, (1) publication venue, (2) data types and sources, (3) method for data processing and prediction, and (4) targeted disease, validation, and released tools were presented. The review summarized the contribution of EHR used in drug repurposing as well as revealed that the utilization is hindered by the validation, accessibility, and understanding of EHRs. These findings can support researchers in the utilization of medical data resources and the development of computational methods for drug repurposing.