bluuebunny/crossref_metadata_2025 huggingface dataset:
Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct long-read sequencing
Authors: Tavakoli Sepideh , Nabizadeh Mohammad , Makhamreh Amr , Gamper Howard , McCormick Caroline A. , Rezapour Neda K. , Hou Ya-Ming , Wanunu Meni , Rouhanifard Sara H.
Published: January 2023

Here, we develop and apply a semi-quantitative method for the high-confidence identification of pseudouridylated sites on mammalian mRNAs via direct long-read nanopore sequencing. A comparative analysis of a modification-free transcriptome reveals that the depth of coverage and specific k-mer sequences are critical parameters for accurate basecalling. By adjusting these parameters for high-confidence U-to-C basecalling errors, we identify many known sites of pseudouridylation and uncover previously unreported uridine-modified sites, many of which fall in k-mers that are known targets of pseudouridine synthases. Identified sites are validated using 1000-mer synthetic RNA controls bearing a single pseudouridine in the center position, demonstrating systematic under-calling using our approach. We identify mRNAs with up to 7 unique modification sites. Our workflow allows direct detection of low-, medium-, and high-occupancy pseudouridine modifications on native RNA molecules from nanopore sequencing data and multiple modifications on the same strand.
Electrochemical direct air capture of CO2 using neutral red as reversible redox-active material
Authors: Seo Hyowon , Hatton T. Alan
Published: January 2023

Direct air capture of carbon dioxide is a viable option for the mitigation of CO2 emissions and their impact on global climate change. Conventional processes for carbon capture from ambient air require 230 to 800 kJ thermal per mole of CO2, which accounts for most of the total cost of capture. Here, we demonstrate electrochemical direct air capture using neutral red as a redox-active material in an aqueous solution enabled by the inclusion of nicotinamide as a hydrotropic solubilizing agent. The electrochemical system demonstrates a high electron utilization of 0.71 in a continuous flow cell with an estimated minimum work of 35 kJe per mole of CO2 from 15% CO2. Further exploration using ambient air (410 ppm CO2 in the presence of 20% oxygen) as a feed gas shows electron utilization of 0.38 in a continuous flow cell to provide an estimated minimum work of 65 kJe per mole of CO2.
Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2
Authors: Huang Kuan-Ying A. , Chen Xiaorui , Mohapatra Arpita , Nguyen Hong Thuy Vy , Schimanski Lisa , Tan Tiong Kit , Rijal Pramila , Vester Susan K. , Hills Rory A. , Howarth Mark , Keeffe Jennifer R. , Cohen Alexander A. , Kakutani Leesa M. , Wu Yi-Min , Shahed-Al-Mahmud Md , Chou Yu-Chi , Bjorkman Pamela J. , Townsend Alain R. , Ma Che
Published: January 2023

Antibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural infection and vaccination and showed that they recognize an immunogenic patch on the internal surface of the core RBD, which faces inwards and is hidden in the “down” state. These antibodies broadly neutralize wild type (Wuhan-Hu-1) SARS-CoV-2, Beta and Delta variants and some are effective against other sarbecoviruses. We observed a continuum of partially overlapping antibody epitopes from lower to upper part of the inner face of the RBD and some antibodies extend towards the receptor-binding motif. The majority of antibodies are substantially compromised by three mutational hotspots (S371L/F, S373P and S375F) in the lower part of the Omicron BA.1, BA.2 and BA.4/5 RBD. By contrast, antibody IY-2A induces a partial unfolding of this variable region and interacts with a conserved conformational epitope to tolerate all antigenic variations and neutralize diverse sarbecoviruses as well. This finding establishes that antibody recognition is not limited to the normal surface structures on the RBD. In conclusion, the delineation of functionally and structurally conserved RBD epitopes highlights potential vaccine and therapeutic candidates for COVID-19.
scm6A-seq reveals single-cell landscapes of the dynamic m6A during oocyte maturation and early embryonic development
Authors: Yao Huan , Gao Chun-Chun , Zhang Danru , Xu Jiawei , Song Gege , Fan Xiu , Liang Dao-Bo , Chen Yu-Sheng , Li Qian , Guo Yanjie , Cai Yu-Ting , Hu Lulu , Zhao Yong-Liang , Sun Ying-Pu , Yang Ying , Han Jianyong , Yang Yun-Gui
Published: January 2023

N6-methyladenosine (m6A) has been demonstrated to regulate RNA metabolism and various biological processes, including gametogenesis and embryogenesis. However, the landscape and function of m6A at single cell resolution have not been extensively studied in mammalian oocytes or during pre-implantation. In this study, we developed a single-cell m6A sequencing (scm6A-seq) method to simultaneously profile the m6A methylome and transcriptome in single oocytes/blastomeres of cleavage-stage embryos. We found that m6A deficiency leads to aberrant RNA clearance and consequent low quality of Mettl3Gdf9 conditional knockout (cKO) oocytes. We further revealed that m6A regulates the translation and stability of modified RNAs in metaphase II (MII) oocytes and during oocyte-to-embryo transition, respectively. Moreover, we observed m6A-dependent asymmetries in the epi-transcriptome between the blastomeres of two-cell embryo. scm6A-seq thus allows in-depth investigation into m6A characteristics and functions, and the findings provide invaluable single-cell resolution resources for delineating the underlying mechanism for gametogenesis and early embryonic development.
General low-temperature growth of two-dimensional nanosheets from layered and nonlayered materials
Authors: Qin Biao , Saeed Muhammad Zeeshan , Li Qiuqiu , Zhu Manli , Feng Ya , Zhou Ziqi , Fang Jingzhi , Hossain Mongur , Zhang Zucheng , Zhou Yucheng , Huangfu Ying , Song Rong , Tang Jingmei , Li Bailing , Liu Jialing , Wang Di , He Kun , Zhang Hongmei , Wu Ruixia , Zhao Bei , Li Jia , Liao Lei , Wei Zhongming , Li Bo , Duan Xiangfeng , Duan Xidong
Published: January 2023

Most of the current methods for the synthesis of two-dimensional materials (2DMs) require temperatures not compatible with traditional back-end-of-line (BEOL) processes in semiconductor industry (450 °C). Here, we report a general BiOCl-assisted chemical vapor deposition (CVD) approach for the low-temperature synthesis of 27 ultrathin 2DMs. In particular, by mixing BiOCl with selected metal powders to produce volatile intermediates, we show that ultrathin 2DMs can be produced at 280–500 °C, which are ~200–300 °C lower than the temperatures required for salt-assisted CVD processes. In-depth characterizations and theoretical calculations reveal the low-temperature processes promoting 2D growth and the oxygen-inhibited synthetic mechanism ensuring the formation of ultrathin nonlayered 2DMs. We demonstrate that the resulting 2DMs exhibit electrical, magnetic and optoelectronic properties comparable to those of 2DMs grown at much higher temperatures. The general low-temperature preparation of ultrathin 2DMs defines a rich material platform for exploring exotic physics and facile BEOL integration in semiconductor industry.
Integrated interfacial design of covalent organic framework photocatalysts to promote hydrogen evolution from water
Authors: He Ting , Zhen Wenlong , Chen Yongzhi , Guo Yuanyuan , Li Zhuoer , Huang Ning , Li Zhongping , Liu Ruoyang , Liu Yuan , Lian Xu , Xue Can , Sum Tze Chien , Chen Wei , Jiang Donglin
Published: January 2023

Attempts to develop photocatalysts for hydrogen production from water usually result in low efficiency. Here we report the finding of photocatalysts by integrated interfacial design of stable covalent organic frameworks. We predesigned and constructed different molecular interfaces by fabricating ordered or amorphous π skeletons, installing ligating or non-ligating walls and engineering hydrophobic or hydrophilic pores. This systematic interfacial control over electron transfer, active site immobilisation and water transport enables to identify their distinct roles in the photocatalytic process. The frameworks, combined ordered π skeletons, ligating walls and hydrophilic channels, work under 300–1000 nm with non-noble metal co-catalyst and achieve a hydrogen evolution rate over 11 mmol g–1h–1, a quantum yield of 3.6% at 600 nm and a three-order-of-magnitude-increased turnover frequency of 18.8 h–1compared to those obtained with hydrophobic networks. This integrated interfacial design approach is a step towards designing solar-to-chemical energy conversion systems.
Ultralow contact resistance in organic transistors via orbital hybridization
Authors: Zeng Junpeng , He Daowei , Qiao Jingsi , Li Yating , Sun Li , Li Weisheng , Xie Jiacheng , Gao Si , Pan Lijia , Wang Peng , Xu Yong , Li Yun , Qiu Hao , Shi Yi , Xu Jian-Bin , Ji Wei , Wang Xinran
Published: January 2023

Organic field-effect transistors (OFETs) are of interest in unconventional form of electronics. However, high-performance OFETs are currently contact-limited, which represent a major challenge toward operation in the gigahertz regime. Here, we realize ultralow total contact resistance (Rc) down to 14.0 Ω ∙ cm in C10-DNTT OFETs by using transferred platinum (Pt) as contact. We observe evidence of Pt-catalyzed dehydrogenation of side alkyl chains which effectively reduces the metal-semiconductor van der Waals gap and promotes orbital hybridization. We report the ultrahigh performance OFETs, including hole mobility of 18 cm2 V−1 s−1, saturation current of 28.8 μA/μm, subthreshold swing of 60 mV/dec, and intrinsic cutoff frequency of 0.36 GHz. We further develop resist-free transfer and patterning strategies to fabricate large-area OFET arrays, showing 100% yield and excellent variability in the transistor metrics. As alkyl chains widely exist in conjugated molecules and polymers, our strategy can potentially enhance the performance of a broad range of organic optoelectronic devices.
Sex-specificity of the C. elegans metabolome
Authors: Burkhardt Russell N. , Artyukhin Alexander B. , Aprison Erin Z. , Curtis Brian J. , Fox Bennett W. , Ludewig Andreas H. , Palomino Diana Fajardo , Luo Jintao , Chaturbedi Amaresh , Panda Oishika , Wrobel Chester J. J. , Baumann Victor , Portman Douglas S. , Lee Siu Sylvia , Ruvinsky Ilya , Schroeder Frank C.
Published: January 2023

Recent studies of animal metabolism have revealed large numbers of novel metabolites that are involved in all aspects of organismal biology, but it is unclear to what extent metabolomes differ between sexes. Here, using untargeted comparative metabolomics for the analysis of wildtype animals and sex determination mutants, we show thatC. eleganshermaphrodites and males exhibit pervasive metabolomic differences. Several hundred small molecules are produced exclusively or in much larger amounts in one sex, including a host of previously unreported metabolites that incorporate building blocks from nucleoside, carbohydrate, lipid, and amino acid metabolism. A subset of male-enriched metabolites is specifically associated with the presence of a male germline, whereas enrichment of other compounds requires a male soma. Further, we show that one of the male germline-dependent metabolites, an unusual dipeptide incorporatingN,N-dimethyltryptophan, increases food consumption, reduces lifespan, and accelerates the last stage of larval development in hermaphrodites. Our results serve as a foundation for mechanistic studies of how the genetic sex of soma and germline shape theC. elegansmetabolome and provide a blueprint for the discovery of sex-dependent metabolites in other animals.
Cryo-EM reveals the molecular basis of laminin polymerization and LN-lamininopathies
Authors: Kulczyk Arkadiusz W. , McKee Karen K. , Zhang Ximo , Bizukojc Iwona , Yu Ying Q. , Yurchenco Peter D.
Published: January 2023

Laminin polymerization is the major step in basement membranes assembly. Its failures cause laminin N-terminal domain lamininopathies including Pierson syndrome. We have employed cryo-electron microscopy to determine a 3.7 Å structure of the trimeric laminin polymer node containing α1, β1 and γ1 subunits. The structure reveals the molecular basis of calcium-dependent formation of laminin lattice, and provides insights into polymerization defects manifesting in human disease.
Solids that are also liquids: elastic tensors of superionic materials
Authors: Materzanini Giuliana , Chiarotti Tommaso , Marzari Nicola
Published: January 2023

Superionics are fascinating materials displaying both solid- and liquid-like characteristics: as solids, they respond elastically to shear stress; as liquids, they display fast-ion diffusion at normal conditions. In addition to such scientific interest, superionics are technologically relevant for energy, electronics, and sensing applications. Characterizing and understanding their elastic properties is, e.g., urgently needed to address their feasibility as solid-state electrolytes in all-solid-state batteries. However, static approaches to elasticity assume well-defined reference positions around which atoms vibrate, in contrast with the quasi-liquid motion of the mobile ions in fast ionic conductors. Here, we derive the elastic tensors of superionics from ensemble fluctuations in the isobaric-isothermal ensemble, exploiting extensive Car-Parrinello simulations. We apply this approach to paradigmatic Li-ion conductors, and complement with a block analysis to compute statistical errors. Static approaches sampled over the trajectories often overestimate the response, highlighting the importance of a dynamical treatment in determining elastic tensors in superionics.
Probing magnetic orbitals and Berry curvature with circular dichroism in resonant inelastic X-ray scattering
Authors: Schüler Michael , Schmitt Thorsten , Werner Philipp
Published: January 2023

Resonant inelastic X-ray scattering (RIXS) can probe localized excitations at selected atoms in materials, including particle-hole transitions between the valence and conduction bands. These transitions are governed by fundamental properties of the corresponding Bloch wave functions, including orbital and magnetic degrees of freedom, and quantum geometric properties such as the Berry curvature. In particular, orbital angular momentum (OAM), which is closely linked to the Berry curvature, can exhibit a nontrivial momentum dependence. We demonstrate how information on such OAM textures can be extracted from the circular dichroism in RIXS. Based on accurate modeling with a first-principles treatment of the key ingredient—the light–matter interaction—we simulate dichroic RIXS spectra for the prototypical transition-metal dichalcogenide MoSe2 and the two-dimensional topological insulator 1T$${}^{{\prime}}$$

′

-MoS2. Guided by an intuitive picture of the optical selection rules, we discuss how the momentum-dependent OAM manifests itself in the dichroic RIXS signal if one controls the momentum transfer. Our calculations are performed for typical experimental geometries and parameter regimes, and demonstrate the possibility of observing the predicted circular dichroism in forthcoming experiments. Thus, our work establishes a new avenue for observing Berry curvature and topological states in quantum materials.
Mitochondria regulate intracellular coenzyme Q transport and ferroptotic resistance via STARD7
Authors: Deshwal Soni , Onishi Mashun , Tatsuta Takashi , Bartsch Tim , Cors Eileen , Ried Katharina , Lemke Kathrin , Nolte Hendrik , Giavalisco Patrick , Langer Thomas
Published: January 2023

Coenzyme Q (or ubiquinone) is a redox-active lipid that serves as universal electron carrier in the mitochondrial respiratory chain and antioxidant in the plasma membrane limiting lipid peroxidation and ferroptosis. Mechanisms allowing cellular coenzyme Q distribution after synthesis within mitochondria are not understood. Here we identify the cytosolic lipid transfer protein STARD7 as a critical factor of intracellular coenzyme Q transport and suppressor of ferroptosis. Dual localization of STARD7 to the intermembrane space of mitochondria and the cytosol upon cleavage by the rhomboid protease PARL ensures the synthesis of coenzyme Q in mitochondria and its transport to the plasma membrane. While mitochondrial STARD7 preserves coenzyme Q synthesis, oxidative phosphorylation function and cristae morphogenesis, cytosolic STARD7 is required for the transport of coenzyme Q to the plasma membrane and protects against ferroptosis. A coenzyme Q variant competes with phosphatidylcholine for binding to purified STARD7 in vitro. Overexpression of cytosolic STARD7 increases ferroptotic resistance of the cells, but limits coenzyme Q abundance in mitochondria and respiratory cell growth. Our findings thus demonstrate the need to coordinate coenzyme Q synthesis and cellular distribution by PARL-mediated STARD7 processing and identify PARL and STARD7 as promising targets to interfere with ferroptosis.
Widespread spring phenology effects on drought recovery of Northern Hemisphere ecosystems
Authors: Li Yang , Zhang Wen , Schwalm Christopher R. , Gentine Pierre , Smith William K. , Ciais Philippe , Kimball John S. , Gazol Antonio , Kannenberg Steven A. , Chen Anping , Piao Shilong , Liu Hongyan , Chen Deliang , Wu Xiuchen
Published: January 2023

The time required for an ecosystem to recover from severe drought is a key component of ecological resilience. The phenology effects on drought recovery are, however, poorly understood. These effects centre on how phenology variations impact biophysical feedbacks, vegetation growth and, ultimately, recovery itself. Using multiple remotely sensed datasets, we found that more than half of ecosystems in mid- and high-latitudinal Northern Hemisphere failed to recover from extreme droughts within a single growing season. Earlier spring phenology in the drought year slowed drought recovery when extreme droughts occurred in mid-growing season. Delayed spring phenology in the subsequent year slowed drought recovery for all vegetation types (with importance of spring phenology ranging from 46% to 58%). The phenology effects on drought recovery were comparable to or larger than other well-known postdrought climatic factors. These results strongly suggest that the interactions between vegetation phenology and drought must be incorporated into Earth system models to accurately quantify ecosystem resilience.
Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome
Authors: Laso-Pérez Rafael , Wu Fabai , Crémière Antoine , Speth Daan R. , Magyar John S. , Zhao Kehan , Krupovic Mart , Orphan Victoria J.
Published: January 2023

‘CandidatusMethanophagales’ (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus–host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, ‘CandidatusMethanospirareceae’, closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.
A wearable motion capture suit and machine learning predict disease progression in Friedreich’s ataxia
Authors: Kadirvelu Balasundaram , Gavriel Constantinos , Nageshwaran Sathiji , Chan Jackson Ping Kei , Nethisinghe Suran , Athanasopoulos Stavros , Ricotti Valeria , Voit Thomas , Giunti Paola , Festenstein Richard , Faisal A. Aldo
Published: January 2023

Friedreichʼs ataxia (FA) is caused by a variant of the Frataxin (FXN) gene, leading to its downregulation and progressively impaired cardiac and neurological function. Current gold-standard clinical scales use simplistic behavioral assessments, which require 18- to 24-month-long trials to determine if therapies are beneficial. Here we captured full-body movement kinematics from patients with wearable sensors, enabling us to define digital behavioral features based on the data from nine FA patients (six females and three males) and nine age- and sex-matched controls, who performed the 8-m walk (8-MW) test and 9-hole peg test (9 HPT). We used machine learning to combine these features to longitudinally predict the clinical scores of the FA patients, and compared these with two standard clinical assessments, Spinocerebellar Ataxia Functional Index (SCAFI) and Scale for the Assessment and Rating of Ataxia (SARA). The digital behavioral features enabled longitudinal predictions of personal SARA and SCAFI scores 9 months into the future and were 1.7 and 4 times more precise than longitudinal predictions using only SARA and SCAFI scores, respectively. Unlike the two clinical scales, the digital behavioral features accurately predicted FXN gene expression levels for each FA patient in a cross-sectional manner. Our work demonstrates how data-derived wearable biomarkers can track personal disease trajectories and indicates the potential of such biomarkers for substantially reducing the duration or size of clinical trials testing disease-modifying therapies and for enabling behavioral transcriptomics.
Different clinical characteristics of current smokers and former smokers with asthma: a cross-sectional study of adult asthma patients in China
Authors: Chen Zhifeng , Wasti Binaya , Shang Yulin , Ouyang Ruoyun , Yuan Yu , He Yi , Duan Wentao , Jia Jingsi , Xiao Bing , Zhang Dongshan , Liu Shaokun , Song Qing , Zeng Yuqin , Zeng Qingping , Zhang Xiufeng , Li Jianmin , Ji Xiaoying , Chen Ping , Ma Libing , Xiang Xudong
Published: January 2023

Smoking is a trigger for asthma, which has led to an increase in asthma incidence in China. In smokers, asthma management starts with smoking cessation. Data on predictors of smoking cessation in Chinese patients with asthma are scarce. The objective of this study was to find the differences in clinical characteristics between current smokers and former smokers with asthma in order to identify factors associated with smoking cessation. Eligible adults with diagnosed asthma and smoking from the hospital outpatient clinics (n = 2312) were enrolled and underwent a clinical evaluation, asthma control test (ACT), and pulmonary function test. Information on demographic and sociological data, lung function, laboratory tests, ACT and asthma control questionnaire (ACQ) scores was recorded. Patients were divided into a current smokers group and a former smokers group based on whether they had quit smoking. Logistic regression analysis was used to analyze the factors associated with smoking cessation. Of all patients with asthma, 34.6% were smokers and 65.4% were former smokers, and the mean age was 54.5 ± 11.5 years. Compared with current smokers, the former smokers were older, had longer duration of asthma, had higher ICS dose, had more partially controlled and uncontrolled asthma, had more pack-years, had smoked for longer, and had worse asthma control. The logistic regression model showed that smoking cessation was positively correlated with age, female sex, pack-years, years of smoking, partially controlled asthma, uncontrolled asthma, and body mass index (BMI), but was negatively correlated with ACT, FEV1, FEV1%predicted, and widowed status. More than 30% of asthma patients in the study were still smoking. Among those who quit smoking, many quit late, often not realizing they need to quit until they have significant breathing difficulties. The related factors of smoking cessation identified in this study indicate that there are still differences between continuing smokers and former smokers, and these factors should be focused on in asthma smoking cessation interventions to improve the prognosis of patients with asthma.
Properties of non-coding mutation hotspots as urinary biomarkers for bladder cancer detection
Authors: Baxter L. , Gordon N. S. , Ott S. , Wang J. , Patel P. , Goel A. , Piechocki K. , Silcock L. , Sale C. , Zeegers M. P. , Cheng K. K. , James N. D. ,   The BladderPath trial management group, Knight A. , Gallagher J. , Magwaro S. , Hughes A. , Pope A. , Tunariu N. , Doyle H. , Liu W. , Mintz H. , Nanton V. , James K. , Hafeez S. , Catto J. W. F. , Jefferson K. , Pirrie S. J. , Bryan R. T. , Ward D. G.
Published: January 2023

Mutations at specific hotspots in non-coding regions of ADGRG6, PLEKHS1, WDR74, TBC1D12 and LEPROTL1 frequently occur in bladder cancer (BC). These mutations could function as biomarkers for the non-invasive detection of BC but this remains largely unexplored. Massively-parallel sequencing of non-coding hotspots was applied to 884 urine cell pellet DNAs: 591 from haematuria clinic patients (165 BCs, 426 non-BCs) and 293 from non-muscle invasive BC surveillance patients (29 with recurrence). Urine samples from 142 non-BC haematuria clinic patients were used to optimise variant calling. Non-coding mutations are readily detectable in the urine of BC patients and undetectable, or present at much lower frequencies, in the absence of BC. The mutations can be used to detect incident BC with 66% sensitivity (95% CI 58–75) at 92% specificity (95% CI 88–95) and recurrent disease with 55% sensitivity (95% CI 36–74) at 85% specificity (95% CI 80–89%) using a 2% variant allele frequency threshold. In the NMIBC surveillance setting, the detection of non-coding mutations in urine in the absence of clinically detectable disease was associated with an increased relative risk of future recurrence (RR = 4.62 (95% CI 3.75–5.48)). As urinary biomarkers, non-coding hotspot mutations behave similarly to driver mutations in BC-associated genes and could be included in biomarker panels for BC detection.
Thyroglobulin expression, Ki-67 index, and lymph node ratio in the prognostic assessment of papillary thyroid cancer
Authors: Lindfors Helene , Karlsen Marie , Karlton Ellinor , Zedenius Jan , Larsson Catharina , Ihre Lundgren Catharina , Juhlin C. Christofer , Shabo Ivan
Published: January 2023

The clinical significance of thyroglobulin (Tg) expression in papillary thyroid cancer (PTC) has not been systematically explored in relation to the Ki-67 index, lymph node ratio (LNR), or other conventional prognostic predictors. In this retrospective study of 327 patients with PTC, we investigated the immunohistochemical expression of Tg in both primary tumors and their matching lymph node metastases in relation to the Ki-67 index, LNR, and clinical data. Tumoral Tg immunoreactivity was inversely correlated to the Ki-67 index and tumor recurrence. The Ki-67 index was higher in lymph node metastases (mean 4%) than in the primary tumors (mean 3%). Reduced Tg expression, estimated as 0–25% Tg positive tumor cells, was more common in lymph node metastases compared to primary tumors. In addition to advanced metastatic burden (defined as N1b stage and LNR ≥ 21%), low Tg expression (0–25% positive tumor cells) in lymph node metastases had a significant prognostic impact with shorter recurrence-free survival. These findings support the potential value of histopathological assessment of Tg expression and Ki-67 index in lymph node metastases as complementary predictors to anticipate the prognosis of PTC patients better.
Elastic solution of surface loaded layer with couple and surface stress effects
Authors: Lawongkerd Jintara , Le Toan Minh , Wongviboonsin Wipavee , Keawsawasvong Suraparb , Limkatanyu Suchart , Van Chung Nguyen , Rungamornrat Jaroon
Published: January 2023

In this study, an elastic solution of an axisymmetrically surface-loaded thin layer resting on a rigid substrate is established by taking the surface stress and material microstructural effects into account. Derived solutions provide not only a means to investigate the size effects on the mechanical response but also a set of fundamental solutions essential for tackling contact problems in a micro/nano scale. In the formulation, the couple stress and surface elasticity theories are adopted to simulate the microstructured bulk layer and the surface material, respectively. A general solution of an elastic field within the bulk layer is obtained first by Hankel transform method and subsequently used together with the surface equations and boundary conditions to form a set of conditions essential for determining all unknown constants. After being fully tested with available benchmark solutions, results are used to study the role of surface and couple stresses on the load transferring mechanism to the substrate and its size-dependent characteristic for a wide range of external length scales relative to the internal length scales.
Strain-specific alterations in gut microbiome and host immune responses elicited by tolerogenic Bifidobacterium pseudolongum
Authors: Ma Bing , Gavzy Samuel J. , Saxena Vikas , Song Yang , Piao Wenji , Lwin Hnin Wai , Lakhan Ram , Iyyathurai Jegan , Li Lushen , France Michael , Paluskievicz Christina , Shirkey Marina W. , Hittle Lauren , Munawwar Arshi , Mongodin Emmanuel F. , Bromberg Jonathan S.
Published: January 2023

The beneficial effects attributed to Bifidobacterium are largely attributed to their immunomodulatory capabilities, which are likely to be species- and even strain-specific. However, their strain-specificity in direct and indirect immune modulation remain largely uncharacterized. We have shown that B. pseudolongum UMB-MBP-01, a murine isolate strain, is capable of suppressing inflammation and reducing fibrosis in vivo. To ascertain the mechanism driving this activity and to determine if it is specific to UMB-MBP-01, we compared it to a porcine tropic strain B. pseudolongum ATCC25526 using a combination of cell culture and in vivo experimentation and comparative genomics approaches. Despite many shared features, we demonstrate that these two strains possess distinct genetic repertoires in carbohydrate assimilation, differential activation signatures and cytokine responses signatures in innate immune cells, and differential effects on lymph node morphology with unique local and systemic leukocyte distribution. Importantly, the administration of each B. pseudolongum strain resulted in major divergence in the structure, composition, and function of gut microbiota. This was accompanied by markedly different changes in intestinal transcriptional activities, suggesting strain-specific modulation of the endogenous gut microbiota as a key to immune modulatory host responses. Our study demonstrated a single probiotic strain can influence local, regional, and systemic immunity through both innate and adaptive pathways in a strain-specific manner. It highlights the importance to investigate both the endogenous gut microbiome and the intestinal responses in response to probiotic supplementation, which underpins the mechanisms through which the probiotic strains drive the strain-specific effect to impact health outcomes.
An earphone fit deviation analysis algorithm
Authors: Yan Yan , Liu Yonghong , Wang Haining
Published: January 2023

This study provides an accurate method for evaluating the fit of earphones, which could be used for establishing a linkage between interference/gap values with human perception. Seven commercial CAD software tools stood out and were explored for the analysis of the deviation between earphone and ear. However, the current deviation analysis method remains to be improved for earphone fit evaluation due to excessive points in the calculation (Geomagic Wrap and Siemens NX), lack of value on interference (Geomagic Control X), computation boundary required (Rapidform XOR/Redesign), repetitive computation with same points and inclined calculation line segment or even invalid calculation (Solidworks, Creo). Therefore, an accurate deviation analysis algorithm was promoted, which calculated the deviation between earphone and ear exactly and classified the interference set and gap set precisely. There are five main procedures of this algorithm, which are point cloud model pre-processing, the generation of distance vectors, the discrimination of interference set and gap set, the discrimination of validity, and statistical analysis and visualization. Furthermore, the usability and validity of the deviation analysis algorithm were verified through statistical analysis and comparing visual effects based on the earphone-wearing experiment. It is certified that the deviation analysis algorithm is appropriate for earphone fit evaluation and the eight indexes of this algorithm were proved to be related to subjective comfort scores. It is meaningful for ear-worn product fit analysis, design, and development phases.
Stabilization through self-coupling in networks of small-world and scale-free topology
Authors: Luboeinski Jannik , Claro Luis , Pomi Andrés , Mizraji Eduardo
Published: January 2023

Mechanisms that ensure the stability of dynamical systems are of vital importance, in particular in our globalized and increasingly interconnected world. The so-called connectivity-stability dilemma denotes the theoretical finding that increased connectivity between the components of a large dynamical system drastically reduces its stability. This result has promoted controversies within ecology and other fields of biology, especially, because organisms as well as ecosystems constitute systems that are both highly connected and stable. Hence, it has been a major challenge to find ways to stabilize complex systems while preserving high connectivity at the same time. Investigating the stability of networks that exhibit small-world or scale-free topology is of particular interest, since these topologies have been found in many different types of real-world networks. Here, we use an approach to stabilize recurrent networks of small-world and scale-free topology by increasing the average self-coupling strength of the units of a network. For both topologies, we find that there is a sharp transition from instability to asymptotic stability. Then, most importantly, we find that the average self-coupling strength needed to stabilize a system increases much slower than its size. It appears that the qualitative shape of this relationship is the same for small-world and scale-free networks, while scale-free networks can require higher magnitudes of self-coupling. We further explore the stabilization of networks with Kronecker-Leskovec topology. Finally, we argue that our findings, in particular the stabilization of large recurrent networks through small increases in the unit self-regulation, are of practical importance for the stabilization of diverse types of complex systems.
Rapid photonic curing effects of xenon flash lamp on ITO–Ag–ITO multilayer electrodes for high throughput transparent electronics
Authors: Zhao Zhenqian , Rose Alex , Kwon Sang Jik , Jeon Yongmin , Cho Eou-Sik
Published: January 2023

High-throughput transparent and flexible electronics are essential technologies for next-generation displays, semiconductors, and wearable bio-medical applications. However, to manufacture a high-quality transparent and flexible electrode, conventional annealing processes generally require 5 min or more at a high temperature condition of 300 °C or higher. This high thermal budget condition is not only difficult to apply to general polymer-based flexible substrates, but also results in low-throughput. Here, we report a high-quality transparent electrode produced with an extremely low thermal budget using Xe-flash lamp rapid photonic curing. Photonic curing is an extremely short time (~ μs) process, making it possible to induce an annealing effect of over 800 °C. The photonic curing effect was optimized by selecting the appropriate power density, the irradiation energy of the Xe-flash lamp, and Ag layer thickness. Rapid photonic curing produced an ITO–Ag–ITO electrode with a low sheet resistance of 6.5 ohm/sq, with a high luminous transmittance of 92.34%. The low thermal budget characteristics of the rapid photonic curing technology make it suitable for high-quality transparent electronics and high-throughput processes such as roll-to-roll.
Demulsification of asphaltene stabilized crude oil emulsions by biodegradable ethylcellulose polymers with varying viscosities
Authors: Husain Arafat , Adewunmi Ahmad A. , Gbadamosi Afeez , Al-Harthi Mamdouh A. , Patil Shirish , Kamal Muhammad Shahzad
Published: January 2023

Efficient demulsifiers for fast demulsification of asphaltene stabilized crude oil emulsions are currently in high demand. In this work, we evaluated the demulsification potential of ethyl cellulose (EC) demulsifiers with varying viscosities—4 cp, 22 cp, and 100 cp, designated as EC-4, EC-22, and EC-100. Demulsifcation efficiency (DE) of these demulsifiers to remove water from emulsions produced from distilled water, seawater, and different salts (NaCl, MgCl2, and CaCl2) solution were assessed using the bottle test technique at ambient and elevated temperatures (25 °C and 90 °C). The bottle test outcomes showed that EC-4 and EC-22 had better performance at the ambient conditions to demulsify the emulsions formed from distilled water with %DE of 85.71% and 28.57%, respectively, while EC-100 achieved 3.9% water removal owing to its high viscosity which inhibited its adsorption at the oil–water interface. At demulsification temperature (90 °C) under the emulsions from distilled water, the %DE of EC-4, EC-22, and EC-100 was 99.23%, 58.57%, and 42.85%, respectively. Seawater hastened the demulsification activities of these demulsifiers. Also, these demulsifiers demonstrated excellent demulsification in emulsions from various salts. The demulsification performance of the EC-4 demulsifier in the presence of any of these salts was approximately 98% while MgCl2 and CaCl2 accelerated the water/oil separation performance of EC-22 and EC-100 by promoting their diffusion and adsorption at the interface. Viscosity and shear stress measurements corroborated the results obtained from the bottle tests. Injection of EC demulsifiers led to a reduction in the viscosity and shear stress of the formed emulsion. Reduction in the shear stress and viscosity were highest in EC-4 and lowest in EC-100. Optical microscopic images of emulsion injected with EC-4 demulsifier were analyzed at various periods during viscosity measurements. Based on the optical images obtained at different durations, a demulsification mechanism describing the activity of the EC demulsifier was proposed.
Numerical modelling of soldered superconducting REBCO stacks of tapes suggests strong reduction in cross-field demagnetization
Authors: Li Shuo , Pardo Enric
Published: January 2023

Stacks of superconducting REBCO tapes (or “stacks”) can trap high magnetic fields, above 17 T. However, relatively low oscillating transverse magnetic fields can fully demagnetize the stacks. This is an issue if the stacks act as poles in the rotor of a superconducting motor, for instance. Here, we study the drastic suppression of cross-field demagnetization in stacks by soldering the tapes at the ends using a normal conductor. In particular, we analyzed by numerical modeling a stack of five REBCO thin films connected at the ends by resistances. The computed trapped field of a stack with zero solder resistance decays very fast at the beginning but then tends to stabilize to relatively high values, while the trapped field of an isolated stack (infinite resistance at the ends) decays further (it decays to zero if the transverse field is above the parallel penetration field). For intermediate solder resistances, the stable value of the trapped magnetic field is in between those of the isolated and zero-resistance configurations. Since the stable trapped field in soldered stacks increases with the number of tapes, stacks of sufficiently high number of soldered tapes could be immune to cross-field demagnetization. This opens the gate for a new kind of superconductors that mostly behave as bulks, especially if the stacks are made of delaminated tapes or it is possible to solder the tapes by very low resistance.
Design of highly nonlinear confusion component based on entangled points of quantum spin states
Authors: Muhammad Waseem Hafiz , Hwang Seong Oun
Published: January 2023

Cryptosystems are commonly deployed to secure data transmission over an insecure line of communication. To provide confusion in the data over insecure networks, substitution boxes are the solitary components for delivering a nonlinear mapping between inputs and outputs. A confusion component of a block cipher with high nonlinearity and low differential and linear approximation probabilities is considered secure against cryptanalysis. This study aims to design a highly nonlinear substitution-permutation network using the blotch symmetry of quantum spin states on the Galois field GF (28). To observe the efficiency of the proposed methodology, some common and advanced measures were evaluated for performance, randomness, and cryptanalytics. The outcomes of these analyses validate that the generated nonlinear confusion components are effective for block ciphers and attain better cryptographic strength with a high signal-to-noise ratio in comparison to state-of-the-art techniques.
3D metamaterial ultra-wideband absorber for curved surface
Authors: Norouzi Mahdi , Jarchi Saughar , Ghaffari-Miab Mohsen , Esfandiari Meisam , Lalbakhsh Ali , Koziel Slawomir , Reisenfeld Sam , Moloudian Gholamhosein
Published: January 2023

This paper proposes a three-dimensional metamaterial absorber based on a resistive film patch array to develop a low-cost, lightweight absorber for curved surfaces. An excellent absorption over a large frequency band is achieved through two different yet controllable mechanisms; in the first mechanism, a considerable attenuation in the wave power is achieved via graphite resistive films. The absorption is then intensified through magnetic dipoles created by the surface currents, leading to absorption peaks. The simulation results of the absorber show that a broadband absorption greater than 85% is achieved over 35–400 GHz for both TE and TM polarization waves at normal incidence. The structure has more than 167% and 80% absorption bandwidth above 85% and 90%, respectively. It is shown that the proposed metamaterial absorber is independent of incident wave polarization. In addition, the structure is insensitive to incident angles up to 60° for TE mode and full range angle 90° for TM mode. To describe the physical mechanism of the absorber, E-field, power loss density and surface current distributions on the structure are calculated and shown. Moreover, the oblique incidence absorption efficiency is also explained. This absorber paves the way for practical applications, such as sensing, imaging and stealth technology. In addition, the proposed structure can be extended to terahertz, infrared and optical regions.
Utilization of optimal antenatal care, institutional delivery, and associated factors in Northwest Ethiopia
Authors: Hailemariam Tesfahun , Atnafu Asmamaw , Gezie Lemma Derseh , Tilahun Binyam
Published: January 2023

Optimal antenatal care visits (ANC4+) and institutional delivery are essentials to save lives of the women and the baby during pregnancy and delivery. Though focused antenatal care visits and institutional delivery is recommended by World Health Organization, Ethiopia has sub-optimal antenatal care and lagged facility delivery. A community-based cross-sectional study was conducted among 811 lactating women in Northwest Ethiopia. Multivariable logistic regression analysis was performed using 95% confidence level and p < 0.05. The prevalence of optimal antenatal care visits and institutional delivery were 39.6% (95%CI: 36.2–43) and 62.6% (95%CI: 59.2–66), respectively. Maternal education (AOR = 2.05; 95%CI: 1.14, 3.69), home visiting by health extension workers (AOR = 1.57; 95%CI: 1.01, 2.29), and early antenatal care booking (AOR = 11.92; 95%CI: 8.22, 17.31) were significant predictors of optimal antenatal care. Exposure to mass media (AOR = 1.65; 95% CI: 1.02, 2.65); intended pregnancy(AOR = 1.68; 95%CI:1.12, 3.63); parity of one (AO = 3.46; 95% CI: 1.73, 6.89); 1–3 antenatal care visits (AOR = 2.17; 95% CI: 1.29, 3.63); and ANC4 + (AOR = 3.57; 95% CI: 2.07, 6.14); history of pregnancy-related complications(AOR = 1.63; 95%CI: 1.04, 2.57), and access to transportation to reach a health facility(AOR = 1.58; 95%CI: 1.00, 2.45) were significant predictors of institutional delivery. Addressing the modifiable factors identified in this study could improve optimal antenatal care visit and institutional delivery.
Conditioning of microvascular venous flaps in rats
Authors: Heiliger Christian , Ritschl Lucas M. , Fichter Andreas M. , Postl Lukas K. , Kanatas Anastasios , Wolff Klaus Dietrich , Mücke Thomas
Published: January 2023

Venous-only perfusion flaps have not been used widely because of the associated high failure rate. Tissue conditioning offers a broad scope of techniques that can be applied pre-, peri-, or postoperatively to promote the adaptation of the affected tissue to any subsequent stress. This study aimed to assess the survival rates associated with a pure venous perfusion flap and investigate whether the timing of the vascular conditioning can affect free flap survival. Forty-four rats were included in the experiment. Group I underwent veno-arterial anastomoses with epigastric graft with pure venous perfusion without tissue conditioning. Groups II and III were pretreated for 7 or 14 days with ischemic conditioning. These groups were compared with a control group (group IV) of conventionally perfused flaps. After the initial surgery, all flaps were assessed clinically, photometrically, and by indocyanine green videoangiography. The flap success rates were 0% in group I, 49.97% ± 24.34% in group II, and 64.95% ± 20.36% in group III. The control group showed an overall survival of 89.3% ± 6.51%. With suitable conditioning, pure venous blood supply can provide adequate perfusion in the rat epigastric flap model. The timing of vascular conditioning appears to be critical for flap survival.
Sex-specific differences in the associations of metabolic syndrome or components with gallstone disease in Chinese euthyroid population
Authors: Jiang Li , Du Jinman , Wang Jufang , Ding Jinhua
Published: January 2023

In euthyroid population, it is uncertain whether there is sex-specific difference in the associations of metabolic syndrome (MetS) or its components with gallstone disease (GSD); in general population, MetS increases the risk of GSD. This was a cross-sectional study to investigate the sex-specific difference in the prevalence of MetS according to GSD status and the associations of MetS or its components with GSD in Chinese euthyroid population. The total prevalence of GSD was 8.1% (6.5% in men and 11.0% in women, with a significant difference (p < 0.001)). The total presence of MetS was 10.7% (12.1% in men and 8.2% in women,with a significant difference (p = 0.001)). The age-adjusted odds ratio of MetS for GSD was 2.775 in men (p < 0.001), 2.543 in women (p = 0.007) and 2.503 in the oveall samples (p < 0.001). Univariate analysis revealed that fasting plasma glucose (FPG), high-density lipoprotein cholesterol (HDL-C) and thyroid-stimulating hormone (TSH) were associated with the prevalence of GSD. After adjustment for age, multivariate logistic regression analysis demonstrated that above three parameters were still significantly associated with the risk of GSD in general population; FPG and HDL-C but not TSH levels were significantly associated with the risk of GSD in men; and FPG and TSH levels but not HDL-C in women. Our study demonstrated that in euthyroid population, MetS appeared to be strongly associated with GSD regardless of sex, and FPG and TSH were two independent risk factors for GSD in men, while FPG and HDL-C in women.