bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of SnO Composition in SnO/SnO2 Nanocomposites on the Photocatalytic Degradation of Malachite Green under Visible Light
Authors: Phuong Pham Hoai , Hoa Huynh Tran My , Hung Nguyen Hoang , Thuy Thanh Giang Le , Tran Quang Trung , Tin Tran Trung , Dinh Duc Anh , Cuong Tran Viet
Published: November 2021

Three types of SnO/SnO2 nanocomposites with different component ratios were synthesized using a simple hydrothermal process. Three samples, S1, S2, and S3, were produced by optimizing the occupied volume inside the Teflon flask, and are referred to as SnO2 rich, intermediate level, and SnO rich, respectively. In terms of degradation of malachite green under visible light, the photocatalytic activity of the S2 sample outperforms the other two samples and pure SnO by 30 %. It is attributed to the fact that the S2 sample has the most heterojunction between p‐type SnO and n‐type SnO2 of the three samples because the formation of p‐type SnO and n‐type SnO2 heterojunction in S2 prevents photogenerated electron‐hole recombination. By comparing S1 and S3 samples, we figured out that Sn2+ doped into the SnO2 lattice acts as an electron trap, slowing the recombination process and increasing photocatalytic activity.
Phenol Formaldehyde Resole/Nanosilver Colloid Immobilized Polyester Textile Composite for Antibacterial Applications
Authors: Pullichola Abdul H. , Varghese Lity A. , Unnikrishnan Gopalakrishna P. , Manaf Olongal , Das Kottotil M. , Jowhar Ameen
Published: November 2021

This work reports the fabrication of an antibacterial phenol formaldehyde (PF)/silver (Ag) nanocomposite coated polyester fabric material for industrial coating applications. Spherical Ag nanoparticles (NPs), with an average particle size of 20 nm were uniformly distributed in the PF resole resin. The polymer nanocomposites with different percentages of Ag NPs (0.2 %, 0.4 %, and 0.6 %) have been coated on polyester fabric by a hand layup procedure. The fabric samples were characterized by scanning electron microscopy (SEM), energy dispersive X‐ray analysis (EDAX) and X‐ray diffraction analysis. The thermal properties of samples have been investigated by differential scanning calorimetry and thermo‐ gravimetric analysis. The effect of Ag NPs on the adhesion features of resole resin coated polyester fabric was evaluated by the peel strength measurement. The optimized composite showed excellent antibacterial properties against Staphylococcus aureus and Escherichia coli bacteria. All the resole PF/Ag nanocomposite coated polyester fabrics are biocompatible. It has been proposed for a variety of applications in the fields of apparel, architecture and construction, insulation, automotive and chemical processing.
Analysis and control of a Stewart platform as base motion compensators - Part I: Kinematics using moving frames
Authors: Ono Takeyuki , Eto Ryosuke , Yamakawa Junya , Murakami Hidenori
Published: November 2021

Kinematics and its control application are presented for a Stewart platform whose base plate is installed on a floor in a moving ship or a vehicle. With a manipulator or a sensitive equipment mounted on the top plate, a Stewart platform is utilized to mitigate the undesirable motion of its base plate by controlling actuated translational joints on six legs. To reveal closed loops, a directed graph is utilized to express the joint connections. Then, kinematics begins by attaching an orthonormal coordinate system to each body at its center of mass and to each joint to define moving coordinate frames. Using the moving frames, each body in the configuration space is represented by an inertial position vector of its center of mass in the three-dimensional vector space ℝ3, and a rotation matrix of the body-attached coordinate axes. The set of differentiable rotation matrices forms a Lie group: the special orthogonal group, SO(3). The connections of body-attached moving frames are mathematically expressed by using frame connection matrices, which belong to another Lie group: the special Euclidean group, SE(3). The employment of SO(3) and SE(3) facilitates effective matrix computations of velocities of body-attached coordinate frames. Loop closure constrains are expressed in matrix form and solved analytically for inverse kinematics. Finally, experimental results of an inverse kinematics control are presented for a scale model of a base-moving Stewart platform. Dynamics and a control application of inverse dynamics are presented in the part II-paper.
Redistribution of tax resources: a cooperative game theory approach
Authors: Calvo Emilio
Published: November 2021

We consider the problem of how to distribute public expenditure among the different regions of an economic entity after all taxes have been collected. Typical examples are: the regions that make up a country, the states of a federal country, or the countries of a confederation of countries. We model the problem as a cooperative game in coalitional form, called the tax game. This game estimates the fiscal resources collected in each region, or coalition of regions, by differentiating between what comes from economic activity within each region and what comes from trade with the other regions. This methodology provides a measure of the disagreement within a region, or coalitions of regions, with respect to the budget received. Similarly, the stability of a budget allocation can be inferred by its situation within the core of the corresponding tax game. We consider the Spanish case as an example and show that the current regional financial system has a moderate degree of instability. We introduce two budget allocation rules, both borrowed from the cooperative games literature: the balanced allocation, which coincides with the nucleolus and with the Shapley value of the tax game, and the weighted balanced allocation, which coincides with the weighted Shapley value. We compare both budget allocation rules with the current Spanish financial system.
Negotiating Authenticity in Technological Environments
Authors: Beerends Siri , Aydin Ciano
Published: November 2021

Essentialists understand authenticity as an inherent quality of a person, object, artifact, or place, whereas constructionists consider authenticity as a social creation without any pre-given essence, factuality, or reality. In this paper, we move beyond the essentialist-constructionist dichotomy. Rather than focusing on the question whether authenticity can be found or needs to be constructed, we hook into the idea that authenticity is an interactive, culturally informed process of negotiation. In addition to essentialist and constructionist approaches, we discuss a third, less well-known approach that cannot be reduced to any of the two forms. This approach celebrates the authenticity of inauthenticity by amplifying the made. We argue that the value of (in)authenticity lies not in choosing for one of these approaches, but in the degree to which the process of negotiating authenticity enables a critical formation of selves and societies. Authenticity is often invoked as a method of social control or a mark of power relations: once something is defined as authentic, it is no longer questioned. Emerging technologies—especially data-driven technologies—have the capacity to conceal these power relations, propel a shift in power, and dominate authentication processes. This raises the question how processes of authentication can contribute to a critical formation of selves and societies, against the backdrop of emerging technologies. We argue in favor of an interactionist approach of authenticity and discuss the importance of creating space in authentication processes that are increasingly influenced by technology as an invisible actor.
Life cycle assessment of opencast lignite mining
Authors: Lelek Lukasz , Kulczycka Joanna
Published: November 2021

The life cycle phase of fossil fuel extraction is mainly considered in the life cycle assessment (LCA) when evaluating the energy production processes. It is then only one of many unit processes, which contribute to the blurring of mining-relevant results. There are few items in the literature focusing exclusively on the lignite mining phase and analysing the specific mining conditions and associated environmental impacts. The article focuses on the LCA of lignite mining processes on the basis of data coming from a Polish mine. The technology for opencast lignite mining is noted for its high production efficiency, high level of recovery and lower risk as regards the safety of workers when compared with underground mining systems. However, the need to remove large amounts of overburden to uncover the deposit contributes to a much greater degradation of the landscape. Analysing the results obtained, several key (hot spot) elements of the lignite mining operations were distinguished for modelling the environmental impact, i.e.: calorific value, the amount of electricity consumption, the manner in which waste and overburden are managed. As a result there is a high sensitivity of the final indicator to changes in these impacts.
Community membership consistency applied to corporate board interlock networks
Authors: Kuppevelt Dafne E. van , Bakhshi Rena , Heemskerk Eelke M. , Takes Frank W.
Published: November 2021

Community detection is a well-established method for studying the meso-scale structure of social networks. Applying a community detection algorithm results in a division of a network into communities that is often used to inspect and reason about community membership of specific nodes. This micro-level interpretation step of community structure is a crucial step in typical social science research. However, the methodological caveat in this step is that virtually all modern community detection methods are non-deterministic and based on randomization and approximated results. This needs to be explicitly taken into consideration when reasoning about community membership of individual nodes. To do so, we propose a metric of community membership consistency, that provides node-level insights in how reliable the placement of that node into a community really is. In addition, it enables us to distinguish the community core members of a community. The usefulness of the proposed metrics is demonstrated on corporate board interlock networks, in which weighted links represent shared senior level directors between firms. Results suggest that the community structure of global business groups is centered around persistent communities consisting of core countries tied by geographical and cultural proximity. In addition, we identify fringe countries that appear to associate with a number of different global business communities.
“What should be computed” for supporting post-pandemic recovery policymaking? A life-oriented perspective
Authors: Zhang Junyi , Feng Tao , Kang Jing , Li Shuangjin , Liu Rui , Ma Shuang , Zhai Baoxin , Zhang Runsen , Ding Hongxiang , Zhu Taoxing
Published: November 2021

The COVID-19 pandemic has caused various impacts on people’s lives, while changes in people’s lives have shown mixed effects on mitigating the spread of the SARS-CoV-2 virus. Understanding how to capture such two-way interactions is crucial, not only to control the pandemic but also to support post-pandemic urban recovery policies. As suggested by the life-oriented approach, the above interactions exist with respect to a variety of life domains, which form a complex behavior system. Through a review of the literature, this paper first points out inconsistent evidence about behavioral factors affecting the spread of COVID-19, and then argues that existing studies on the impacts of COVID-19 on people’s lives have ignored behavioral co-changes in multiple life domains. Furthermore, selected uncertain trends of people’s lives for the post-pandemic recovery are described. Finally, this paper concludes with a summary about “what should be computed?” in Computational Urban Science with respect to how to catch up with delays in the SDGs caused by the COVID-19 pandemic, how to address digital divides and dilemmas of e-society, how to capture behavioral co-changes during the post-pandemic recovery process, and how to better manage post-pandemic recovery policymaking processes.
Green anionic polymerization of vinyl acetate using Maghnite-Na+ (Algerian MMT): synthesis characterization and reactional mechanism
Authors: Cherifi Badia Imene , Belbachir Mohammed , Rahmouni Abdelkader
Published: November 2021

In this work, the green polymerization of vinyl acetate is carried out by a new method which consists in the use of clay called Maghnite-Na+ as an ecological catalyst, non-toxic, inexpensive and recyclable by simple filtration. X-ray diffraction (XRD) showed that Maghnite-Na+ is successfully obtained after cationic treatment (sodium) on raw Maghnite. It is an effective alternative to replace toxic catalysts such as benzoyl peroxide (BPO) and Azobisisobutyronitrile (AIBN) which are mostly used during the synthesis of polyvinyl acetate (PVAc) making the polymerization reaction less problematic for the environment. The synthesis reaction is less energetic by the use of recycled polyurethane as container for the reaction mixture and which is considered as a renewable material and a good thermal insulator which maintains the temperature at 0 °C for 6 h. The reaction in bulk is also preferred to avoid the use of a solvent and therefore to stay in the context of green chemistry. In these conditions, the structure of obtained polymer is established by Nuclear Magnetic Resonance Spectroscopy 1H NMR and 13C NMR. Infrared spectroscopy (FT-IR) is also used to confirm the structure of PVAc. Thermogravimetric analysis (TGA) showed that it is thermally stable and it starts to degrade from 330 °C while Differential Scanning calorimetry (DSC) shows that this polymer has a glass transition temperature (Tg  = 50 °C). The composition in PVAc/Maghnite-Na+ (7 wt% of catalyst) is the most tensile resistant with a force of 182 N and a maximum stress of 73.16 MPa, the most flexible (E  = 955 MPa) and the most ductile (εr  = 768%).
Recent progress in the treatment of women with diminished ovarian reserve
Authors: Yin Jingwen , Chang Hsun-Ming , Li Rong , Leung Peter C.K.
Published: November 2021

Diminished ovarian reserve (DOR) refers to a decrease in the number and/or quality of oocytes in the ovary, accompanied by a decline in reproductive potential, which is generally related to advanced age or ovarian disease. In in vitro fertilization (IVF) clinical practice, managing patients with DOR remains one of the most challenging tasks. In recent years, increased research on improving ovarian function has provided us with new insights into treating patients with DOR. Many therapeutic options have been proposed to improve the ovarian function of patients with DOR, yet they are not widely utilized in clinical practice because of limited evidence of safety and effectiveness. In this review, we focus on the mechanisms from animal models and clinical trials that have been applied to the treatment of DOR in recent years, intending to improve IVF outcomes in patients with DOR. Furthermore, new insights and perspectives on the molecular and cellular regulation of follicular development and ovarian reserve are emphasized to provide more clues for research on the treatment of DOR.
Planning Community-Centered Inquiries: (Re)Imagining K-8 Civics Teacher Education With/In Rural and Indigenous Communities
Authors: Stanton Christine Rogers , Morrison Danielle , Hancock Hailey
Published: November 2021

This phenomenological case study investigates how planning community-centered civics inquiries can prepare elementary pre-service teachers to better address inequities facing rural communities, including those located on Indigenous reservations. Specifically, the study addresses this research question: How does community-centered planning inform pre-service teacher readiness to support place-conscious and anti-colonial civics education within elementary contexts? Findings suggest that guided, community-centered planning leads to enhanced pre-service teacher confidence in preparing to facilitate equity-oriented elementary education, particularly as related to evolving understandings of civics content competence, relational commitments, and responsibilities of rural teachers.
A weight-homogenous condition to the real Jacobian conjecture in
Authors: Braun Francisco , Valls Claudia
Published: November 2021

It is known that a polynomial local diffeomorphism $(f,\, g): {\mathbb {R}}^{2} \to {\mathbb {R}}^{2}$ is a global diffeomorphism provided the higher homogeneous terms of $f f_x+g g_x$ and $f f_y+g g_y$ do not have real linear factors in common. Here, we give a weight-homogeneous framework of this result. Our approach uses qualitative theory of differential equations. In our reasoning, we obtain a result on polynomial Hamiltonian vector fields in the plane, generalization of a known fact.
Knowledge, belief, and moral psychology
Authors: Mikhail John
Published: November 2021

Phillips et al. make a strong case that knowledge representations should play a larger role in cognitive science. Their arguments are reinforced by comparable efforts to place moral knowledge, rather than moral beliefs, at the heart of a naturalistic moral psychology. Conscience, Kant's synthetic a priori, and knowledge attributions in the law all point in a similar direction.
Are knowledge- and belief-reasoning automatic, and is this the right question?
Authors: Surtees Andrew D. R. , Todd Andrew R.
Published: November 2021

Phillips et al. conclude that current evidence supports knowledge-, but not belief-reasoning as being automatic. We suggest four reasons why this is an oversimplified answer to a question that might not have a clear-cut answer: (1) knowledge and beliefs can be incompletely equated to perceptual states, (2) sensitivity to mental states does not necessitate representation, (3) automaticity is not a single categorical feature, and (4) how we represent others' minds is dependent on social context.
Clathrin adapters AP-1 and GGA2 support expression of epidermal growth factor receptor for cell growth
Authors: Uemura Takefumi , Suzuki Takehiro , Dohmae Naoshi , Waguri Satoshi
Published: November 2021

The role of Golgi/endosome-localized clathrin adapters in the maintenance of steady-state cell surface epidermal growth factor receptor (EGFR) is not well known. Here, we show that EGFR associates preferentially with both AP-1 and GGA2 in vitro. AP-1 depletion caused a reduction in the EGFR protein by promoting its lysosomal degradation. Triple immunofluorescence microscopy and proximity ligation assays demonstrated that the interaction of EGFR with AP-1 or GGA2 occurred more frequently in Rab11-positive recycling endosomes than in Rab5-positive early endosomes. Biochemical recycling assay revealed that the depletion of AP-1 or GGA2 significantly suppressed EGFR recycling to the plasma membrane regardless of the EGF stimulation. Depletion of AP-1 or GGA2 also reduced cell contents of other tyrosine kinases, MET and ErbB4, and therefore, suppressed the growth of H1975 cancer cells in culture and xenograft model. Moreover, AP-1 was expressed in endosomes at higher levels in some cancer tissues. Collectively, these results suggest that AP-1 and GGA2 function in recycling endosomes to retrieve endocytosed EGFR, thereby sustaining its cell surface expression and, consequently, cancer cell growth.
Disordered photonics behavior from terahertz to ultraviolet of a three-dimensional graphene network
Authors: Tomarchio Luca , Macis Salvatore , D’Arco Annalisa , Mou Sen , Grilli Antonio , Romani Martina , Guidi Mariangela Cestelli , Hu Kailong , Kukunuri Suresh , Jeong Samuel , Marcelli Augusto , Ito Yoshikazu , Lupi Stefano
Published: November 2021

The diffusion of light by random materials is a general phenomenon that appears in many different systems, spanning from colloidal suspension in liquid crystals to disordered metal sponges and paper composed of random fibers. Random scattering is also a key element behind mimicry of several animals, such as white beetles and chameleons. Here, random scattering is related to micro and nanosized spatial structures affecting a broad electromagnetic region. In this work, we have investigated how random scattering modulates the optical properties, from terahertz to ultraviolet light, of a novel functional material, i.e., a three-dimensional graphene (3D Graphene) network based on interconnected high-quality two-dimensional graphene layers. Here, random scattering generates a high-frequency pass-filter behavior. The optical properties of these graphene structures bridge the nanoworld into the macroscopic world, paving the way for their use in novel optoelectronic devices.
Self-organization of human dorsal-ventral forebrain structures by light induced SHH
Authors: De Santis Riccardo , Etoc Fred , Rosado-Olivieri Edwin A. , Brivanlou Ali H.
Published: November 2021

Organizing centers secrete morphogens that specify the emergence of germ layers and the establishment of the body’s axes during embryogenesis. While traditional experimental embryology tools have been instrumental in dissecting the molecular aspects of organizers in model systems, they are impractical in human in-vitro model systems to dissect the relationships between signaling and fate along embryonic coordinates. To systematically study human embryonic organizer centers, we devised a collection of optogenetic ePiggyBac vectors to express a photoactivatable Cre-loxP recombinase, that allows the systematic induction of organizer structures by shining blue-light on human embryonic stem cells (hESCs). We used a light stimulus to geometrically confine SHH expression in neuralizing hESCs. This led to the self-organization of mediolateral neural patterns. scRNA-seq analysis established that these structures represent the dorsal-ventral forebrain, at the end of the first month of development. Here, we show that morphogen light-stimulation is a scalable tool that induces self-organizing centers.
Resolving sub-angstrom ambient motion through reconstruction from vibrational spectra
Authors: Griffiths Jack , Földes Tamás , de Nijs Bart , Chikkaraddy Rohit , Wright Demelza , Deacon William M. , Berta Dénes , Readman Charlie , Grys David-Benjamin , Rosta Edina , Baumberg Jeremy J.
Published: November 2021

Metal/organic-molecule interactions underpin many key chemistries but occur on sub-nm scales where nanoscale visualisation techniques tend to average over heterogeneous distributions. Single molecule imaging techniques at the atomic scale have found it challenging to track chemical behaviour under ambient conditions. Surface-enhanced Raman spectroscopy can optically monitor the vibrations of single molecules but understanding is limited by the complexity of spectra and mismatch between theory and experiment. We demonstrate that spectra from an optically generated metallic adatom near a molecule of interest can be inverted into dynamic sub-Å metal-molecule interactions using a comprehensive model, revealing anomalous diffusion of a single atom. Transient metal-organic coordination bonds chemically perturb molecular functional groups > 10 bonds away. With continuous improvements in computational methods for modelling large and complex molecular systems, this technique will become increasingly applicable to accurately tracking more complex chemistries.
The autophagy protein ATG9A enables lipid mobilization from lipid droplets
Authors: Mailler Elodie , Guardia Carlos M. , Bai Xiaofei , Jarnik Michal , Williamson Chad D. , Li Yan , Maio Nunziata , Golden Andy , Bonifacino Juan S.
Published: November 2021

The multispanning membrane protein ATG9A is a scramblase that flips phospholipids between the two membrane leaflets, thus contributing to the expansion of the phagophore membrane in the early stages of autophagy. Herein, we show that depletion of ATG9A does not only inhibit autophagy but also increases the size and/or number of lipid droplets in human cell lines andC. elegans. Moreover, ATG9A depletion blocks transfer of fatty acids from lipid droplets to mitochondria and, consequently, utilization of fatty acids in mitochondrial respiration. ATG9A localizes to vesicular-tubular clusters (VTCs) that are tightly associated with an ER subdomain enriched in another multispanning membrane scramblase, TMEM41B, and also in close proximity to phagophores, lipid droplets and mitochondria. These findings indicate that ATG9A plays a critical role in lipid mobilization from lipid droplets to autophagosomes and mitochondria, highlighting the importance of ATG9A in both autophagic and non-autophagic processes.
A national cohort study (2000–2018) of long-term air pollution exposure and incident dementia in older adults in the United States
Authors: Shi Liuhua , Steenland Kyle , Li Haomin , Liu Pengfei , Zhang Yuhan , Lyles Robert H. , Requia Weeberb J. , Ilango Sindana D. , Chang Howard H. , Wingo Thomas , Weber Rodney J. , Schwartz Joel
Published: November 2021

Air pollution may increase risk of Alzheimer’s disease and related dementias (ADRD) in the U.S., but the extent of this relationship is unclear. Here, we constructed two national U.S. population-based cohorts of those aged ≥65 from the Medicare Chronic Conditions Warehouse (2000–2018), combined with high-resolution air pollution datasets, to investigate the association of long-term exposure to ambient fine particulate matter (PM2.5), nitrogen dioxide (NO2), and ozone (O3) with dementia and AD incidence, respectively. We identified ~2.0 million incident dementia cases (N = 12,233,371; dementia cohort) and ~0.8 million incident AD cases (N = 12,456,447; AD cohort). Per interquartile range (IQR) increase in the 5-year average PM2.5 (3.2 µg/m3), NO2 (11.6 ppb), and warm-season O3 (5.3 ppb) over the past 5 years prior to diagnosis, the hazard ratios (HRs) were 1.060 (95% confidence interval [CI]: 1.054, 1.066), 1.019 (95% CI: 1.012, 1.026), and 0.990 (95% CI: 0.987, 0.993) for incident dementias, and 1.078 (95% CI: 1.070, 1.086), 1.031 (95% CI: 1.023, 1.039), and 0.982 (95%CI: 0.977, 0.986) for incident AD, respectively, for the three pollutants. For both outcomes, concentration-response relationships for PM2.5 and NO2 were approximately linear. Our study suggests that exposures to PM2.5 and NO2 are associated with incidence of dementia and AD.
BST1 regulates nicotinamide riboside metabolism via its glycohydrolase and base-exchange activities
Authors: Yaku Keisuke , Palikhe Sailesh , Izumi Hironori , Yoshida Tomoyuki , Hikosaka Keisuke , Hayat Faisal , Karim Mariam , Iqbal Tooba , Nitta Yasuhito , Sato Atsushi , Migaud Marie E. , Ishihara Katsuhiko , Mori Hisashi , Nakagawa Takashi
Published: November 2021

Nicotinamide riboside (NR) is one of the orally bioavailable NAD+ precursors and has been demonstrated to exhibit beneficial effects against aging and aging-associated diseases. However, the metabolic pathway of NR in vivo is not yet fully understood. Here, we demonstrate that orally administered NR increases NAD+ level via two different pathways. In the early phase, NR was directly absorbed and contributed to NAD+ generation through the NR salvage pathway, while in the late phase, NR was hydrolyzed to nicotinamide (NAM) by bone marrow stromal cell antigen 1 (BST1), and was further metabolized by the gut microbiota to nicotinic acid, contributing to generate NAD+ through the Preiss–Handler pathway. Furthermore, we report BST1 has a base-exchange activity against both NR and nicotinic acid riboside (NAR) to generate NAR and NR, respectively, connecting amidated and deamidated pathways. Thus, we conclude that BST1 plays a dual role as glycohydrolase and base-exchange enzyme during oral NR supplementation.
Dysbiosis of human gut microbiome in young-onset colorectal cancer
Authors: Yang Yongzhi , Du Lutao , Shi Debing , Kong Cheng , Liu Jianqiang , Liu Guang , Li Xinxiang , Ma Yanlei
Published: November 2021

The incidence of sporadic young-onset colorectal cancer (yCRC) is increasing. A significant knowledge gap exists in the gut microbiota and its diagnostic value for yCRC patients. Through 16S rRNA gene sequencing, 728 samples are collected to identify microbial markers, and an independent cohort of 310 samples is used to validate the results. Furthermore, species-level and functional analysis are performed by metagenome sequencing using 200 samples. Gut microbial diversity is increased in yCRC. Flavonifractor plautii is an important bacterial species in yCRC, while genus Streptococcus contains the key phylotype in the old-onset colorectal cancer. Functional analysis reveals that yCRC has unique characteristics of bacterial metabolism characterized by the dominance of DNA binding and RNA-dependent DNA biosynthetic process. The random forest classifier model achieves a powerful classification potential. This study highlights the potential of the gut microbiota biomarkers as a promising non-invasive tool for the accurate detection and distinction of individuals with yCRC.
Moving beyond bimetallic-alloy to single-atom dimer atomic-interface for all-pH hydrogen evolution
Authors: Kumar Ashwani , Bui Viet Q. , Lee Jinsun , Wang Lingling , Jadhav Amol R. , Liu Xinghui , Shao Xiaodong , Liu Yang , Yu Jianmin , Hwang Yosep , Bui Huong T. D. , Ajmal Sara , Kim Min Gyu , Kim Seong-Gon , Park Gyeong-Su , Kawazoe Yoshiyuki , Lee Hyoyoung
Published: November 2021

Single-atom-catalysts (SACs) afford a fascinating activity with respect to other nanomaterials for hydrogen evolution reaction (HER), yet the simplicity of single-atom center limits its further modification and utilization. Obtaining bimetallic single-atom-dimer (SAD) structures can reform the electronic structure of SACs with added atomic-level synergistic effect, further improving HER kinetics beyond SACs. However, the synthesis and identification of such SAD structure remains conceptually challenging. Herein, systematic first-principle screening reveals that the synergistic interaction at the NiCo-SAD atomic interface can upshift the d-band center, thereby, facilitate rapid water-dissociation and optimal proton adsorption, accelerating alkaline/acidic HER kinetics. Inspired by theoretical predictions, we develop a facile strategy to obtain NiCo-SAD on N-doped carbon (NiCo-SAD-NC) via in-situ trapping of metal ions followed by pyrolysis with precisely controlled N-moieties. X-ray absorption spectroscopy indicates the emergence of Ni-Co coordination at the atomic-level. The obtained NiCo-SAD-NC exhibits exceptional pH-universal HER-activity, demanding only 54.7 and 61 mV overpotentials at −10 mA cm−2 in acidic and alkaline media, respectively. This work provides a facile synthetic strategy for SAD catalysts and sheds light on the fundamentals of structure-activity relationships for future applications.
Transcriptomic evidence for versatile metabolic activities of mercury cycling microorganisms in brackish microbial mats
Authors: Vigneron Adrien , Cruaud Perrine , Aubé Johanne , Guyoneaud Rémy , Goñi-Urriza Marisol
Published: November 2021

Methylmercury, biomagnifying through food chains, is highly toxic for aquatic life. Its production and degradation are largely driven by microbial transformations; however, diversity and metabolic activity of mercury transformers, resulting in methylmercury concentrations in environments, remain poorly understood. Microbial mats are thick biofilms where oxic and anoxic metabolisms cooccur, providing opportunities to investigate the complexity of the microbial mercury transformations over contrasted redox conditions. Here, we conducted a genome-resolved metagenomic and metatranscriptomic analysis to identify putative activity of mercury reducers, methylators and demethylators in microbial mats strongly contaminated by mercury. Our transcriptomic results revealed the major role of rare microorganisms in mercury cycling. Mercury methylators, mainly related to Desulfobacterota, expressed a large panel of metabolic activities in sulfur, iron, nitrogen, and halogen compound transformations, extending known activities of mercury methylators under suboxic to anoxic conditions. Methylmercury detoxification processes were dissociated in the microbial mats with methylmercury cleavage being carried out by sulfide-oxidizing Thiotrichaceae and Rhodobacteraceae populations, whereas mercury reducers included members of the Verrucomicrobia, Bacteroidetes, Gammaproteobacteria, and different populations of Rhodobacteraceae. However most of the mercury reduction was potentially carried out anaerobically by sulfur- and iron-reducing Desulfuromonadaceae, revising our understanding of mercury transformers ecophysiology.
Interplay between copy number alterations and immune profiles in the early breast cancer Scandinavian Breast Group 2004-1 randomized phase II trial: results from a feasibility study
Authors: Zerdes Ioannis , Simonetti Michele , Matikas Alexios , Harbers Luuk , Acs Balazs , Boyaci Ceren , Zhang Ning , Salgkamis Dimitrios , Agartz Susanne , Moreno-Ruiz Pablo , Bai Yalai , Rimm David L. , Hartman Johan , Mezheyeuski Artur , Bergh Jonas , Crosetto Nicola , Foukakis Theodoros
Published: November 2021

Emerging data indicate that genomic alterations can shape immune cell composition in early breast cancer. However, there is a need for complementary imaging and sequencing methods for the quantitative assessment of combined somatic copy number alteration (SCNA) and immune profiling in pathological samples. Here, we tested the feasibility of three approaches—CUTseq, for high-throughput low-input SCNA profiling, multiplexed fluorescent immunohistochemistry (mfIHC) and digital-image analysis (DIA) for quantitative immuno-profiling- in archival formalin-fixed paraffin-embedded (FFPE) tissue samples from patients enrolled in the randomized SBG-2004-1 phase II trial. CUTseq was able to reproducibly identify amplification and deletion events with a resolution of 100 kb using only 6 ng of DNA extracted from FFPE tissue and pooling together 77 samples into the same sequencing library. In the same samples, mfIHC revealed that CD4 + T-cells and CD68 + macrophages were the most abundant immune cells and they mostly expressed PD-L1 and PD-1. Combined analysis showed that the SCNA burden was inversely associated with lymphocytic infiltration. Our results set the basis for further applications of CUTseq, mfIHC and DIA to larger cohorts of early breast cancer patients.
Identification of ligand binding sites in intrinsically disordered proteins with a differential binding score
Authors: Chen Qiao-Hong , Krishnan V. V.
Published: November 2021

Screening ligands directly binding to an ensemble of intrinsically disordered proteins (IDP) to discover potential hits or leads for new drugs is an emerging but challenging area as IDPs lack well-defined and ordered 3D-protein structures. To explore a new IDP-based rational drug discovery strategy, a differential binding score (DIBS) is defined. The basis of DIBS is to quantitatively determine the binding preference of a ligand to an ensemble of conformations specified by IDP versus such preferences to an ensemble of random coil conformations of the same protein. Ensemble docking procedures performed on repeated sampling of conformations, and the results tested for statistical significance determine the preferential ligand binding sites of the IDP. The results of this approach closely reproduce the experimental data from recent literature on the binding of the ligand epigallocatechin gallate (EGCG) to the intrinsically disordered N-terminal domain of the tumor suppressor p53. Combining established approaches in developing a new method to screen ligands against IDPs could be valuable as a screening tool for IDP-based drug discovery.
Interference of dissolved organic matter and its constituents on the accurate determination of hydrogen peroxide in water
Authors: Peng Jianbiao , Zhang Ya , Li Jianhua , Wu Xinan , Wang Mengjie , Gong Zhimin , Gao Shixiang
Published: November 2021

Hydrogen peroxide (H2O2) is ubiquitous in natural waters, and plays an important role in both biological and chemical processes. This study investigated the influence of dissolved organic matter (DOM) and its substituents on the accurate measurement of H2O2 by peroxidase-mediated depletion of scopoletin fluorescence method which is one of the most widely used methods for the determination of low concentration H2O2 in water. Six DOM and its 24 substituents interfered the determination of H2O2 at environmentally relevant concentration of 200 nM with different levels except 2,6-dimethoxy-1,4-benzoquinone and benzoic acid, which may be associated with origin and types of DOM, and numbers and position of active functional groups in DOM constituents. Each substance concentration and the corresponding decreasing ratio to the measured H2O2 concentration was fitted well to the linear model (R2 > 0.9), and the obtained interfering ratios (k, (mgC L−1)−1), expressing the degree of DOM or its substituents per unit concentration to the measurement of H2O2, were approximate for DOM, but the order of magnitude of k values of DOM constituents took on a large span from 10–3 to 10–7. When DOM levels exceed 0.1 mgC L−1 or its substituent concentration is at nM level (low to 20 nM), the H2O2 content will be underestimated substantially. A quantitative structure–activity relationship model with remarkable stability and strong predictability for the k of DOM substituents to H2O2 measurement was established, and the k was related to the electron transfer capacity, hydrophobicity and stability of these compounds.
Trends, relationships and case attribution of antibiotic resistance between children and environmental sources in rural India
Authors: Mitchell Joseph , Purohit Manju , Jewell Chris P. , Read Jonathan M. , Marrone Gaetano , Diwan Vishal , Stålsby Lundborg Cecilia
Published: November 2021

Bacterial antibiotic resistance is an important global health threat and the interfaces of antibiotic resistance between humans, animals and the environment are complex. We aimed to determine the associations and overtime trends of antibiotic resistance between humans, animals and water sources from the same area and time and estimate attribution of the other sources to cases of human antibiotic resistance. A total of 125 children (aged 1–3 years old) had stool samples analysed for antibiotic-resistant bacteria at seven time points over two years, with simultaneous collection of samples of animal stools and water sources in a rural Indian community. Newey–West regression models were used to calculate temporal associations, the source with the most statistically significant relationships was household drinking water. This is supported by use of SourceR attribution modelling, that estimated the mean attribution of cases of antibiotic resistance in the children from animals, household drinking water and wastewater, at each time point and location, to be 12.6% (95% CI 4.4–20.9%), 12.1% (CI 3.4–20.7%) and 10.3% (CI 3.2–17.3%) respectively. This underlines the importance of the ‘one health’ concept and requires further research. Also, most of the significant trends over time were negative, suggesting a possible generalised improvement locally.
Impact of the definition of bronchopulmonary dysplasia on neurodevelopmental outcomes
Authors: Han Yea-Seul , Kim Sung-Ha , Sung Tae-Jung
Published: November 2021

Understanding the short and long-term pulmonary and neurologic outcomes of neonates with bronchopulmonary dysplasia (BPD) is important in neonatal care for low-birth-weight infants. Different criteria for BPD may have different associations with long-term outcomes. Currently, two criteria for diagnosing BPD have been proposed by the NIH (2001) and NRN (2019) for preterm infants at a postmenstrual age (PMA) of 36 weeks. We investigated which BPD definition best predicts long-term outcomes. Korean nationwide data for preterm infants born between 24+0 and < 32+0 weeks gestation from January 2013 to December 2015 were collected. For long-term outcomes, severity based on the NRN criteria was significantly related to neurodevelopmental impairment (NDI) in a univariate analysis after other risk factors were controlled. For the admission rate for respiratory disorder, grade 3 BPD of the NRN criteria had the highest specificity (96%), negative predictive value (86%), and accuracy (83%). For predicting NDI at the 18–24 month follow-up, grade 3 BPD of the NRN criteria had the best specificity (98%), positive (64%) and negative (79%) predictive values, and accuracy (78%) while NIH severe BPD had the highest sensitivity (60%). The NRN definition was more strongly associated with poor 2-year developmental outcomes. BPD diagnosed by NRN definitions might better identify infants at high risk for NDI.
Modeling optical design parameters for fine stimulation in sciatic nerve of optogenetic mice
Authors: Fritz Nicholas , Gulick Daniel , Bailly Mark , Blain Christen Jennifer M.
Published: November 2021

Optogenetics presents an alternative method for interfacing with the nervous system over the gold-standard of electrical stimulation. While electrical stimulation requires electrodes to be surgically embedded in tissue for in vivo studies, optical stimulation offers a less-invasive approach that may yield more specific, localized stimulation. The advent of optogenetic laboratory animals—whose motor neurons can be activated when illuminated with blue light—enables research into refining optical stimulation of the mammalian nervous system where subsets of nerve fibers within a nerve may be stimulated without embedding any device directly into the nerve itself. However, optical stimulation has a major drawback in that light is readily scattered and absorbed in tissue thereby limiting the depth with which a single emission source can penetrate. We hypothesize that the use of multiple, focused light emissions deployed around the circumference of a nerve can overcome these light-scattering limitations. To understand the physical parameters necessary to produce pinpointed light stimulation within a single nerve, we employed a simplified Monte Carlo simulation to estimate the size of nerves where this technique may be successful, as well as the necessary optical lens design for emitters to be used during future in vivo studies. By modeling multiple focused beams, we find that only fascicles within a nerve diameter less than 1 mm are fully accessible to focused optical stimulation; a minimum of 4 light sources is required to generate a photon intensity at a point in a nerve over the initial contact along its surface. To elicit the same effect in larger nerves, focusing lenses would require a numerical aperture $$> 1$$

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1

. These simulations inform on the design of instrumentation capable of stimulating disparate motor neurons in mouse sciatic nerve to control hindlimb movement.
Beneficial effects of end-ischemic oxygenated machine perfusion preservation for split-liver transplantation in recovering graft function and reducing ischemia–reperfusion injury
Authors: Ishii Daisuke , Matsuno Naoto , Gochi Mikako , Iwata Hiroyoshi , Shonaka Tatsuya , Nishikawa Yuji , Obara Hiromichi , Yokoo Hideki , Furukawa Hiroyuki
Published: November 2021

This study examined the efficacy of end-ischemic hypothermic oxygenated machine perfusion preservation (HOPE) using an originally developed machine perfusion system for split-liver transplantation. Porcine split-liver grafts were created via 75% liver resection after 10 min of warm ischemia. In Group 1, grafts were preserved by simple cold storage (CS) for 8 h (CS group; n = 4). In Group 2, grafts were preserved by simple CS for 6 h and end-ischemic HOPE for 2 h (HOPE group; n = 5). All grafts were evaluated using an isolated ex vivo reperfusion model with autologous blood for 2 h. Biochemical markers (aspartate aminotransferase and lactate dehydrogenase levels) were significantly better immediately after reperfusion in the HOPE group than in the CS group. Furthermore, the HOPE group had a better histological score. The levels of inflammatory cytokines (tumor necrosis factor-α, interferon-γ, interleukin-1β, and interleukin-10) were significantly lower after reperfusion in the HOPE group. Therefore, we concluded that end-ischemic HOPE for split-liver transplantation can aid in recovering the graft function and reducing ischemia–reperfusion injury. HOPE, using our originally developed machine perfusion system, is safe and can improve graft function while attenuating liver injury due to preservation.
Exploring the mechanism of Yixinyin for myocardial infarction by weighted co-expression network and molecular docking
Authors: Huo Mengqi , Ma Lina , Liu Guoguo
Published: November 2021

Yixinyin, the traditional Chinese medicine, has the effects of replenishing righteous qi, and promoting blood circulation to eliminate blood stagnation. It is often used to treat patients with acute myocardial infarction (MI). The purpose of our study is to explore the key components and targets of Yixinyin in the treatment of MI. In this study, we analyzed gene expression data and clinical information from 248 samples of MI patients with the GSE34198, GSE29111 and GSE66360 data sets. By constructing a weighted gene co-expression network, gene modules related to myocardial infarction are obtained. These modules can be mapped in Yixinyin PPI network. By integrating differential genes of healthy/MI and unstable angina/MI, key targets of Yixinyin for the treatment of myocardial infarction were screened. We validated the key objectives with external data sets. GSEA analysis is used to identify the biological processes involved in key targets. Through molecular docking screening, active components that can combine with key targets in Yixinyin were obtained. In the treatment of myocardial infarction, we have obtained key targets of Yixinyin, which are ALDH2, C5AR1, FOS, IL1B, TLR2, TXNRD1. External data sets prove that they behave differently in the healthy and MI (P < 0.05). GSEA enrichment analysis revealed that they are mainly involved in pathways associated with myocardial infarction, such as viral myocarditis, VEGF signaling pathway and type I diabetes mellitus. The docking results showed that the components that can be combined with key targets in YixinYin are Supraene, Prostaglandin B1, isomucronulatol-7,2′-di-O-glucosiole, angusifolin B, Linolenic acid ethyl ester, and Mandenol. For that matter, they may be active ingredients of Yixinyin in treating MI. These findings provide a basis for the preliminary research of myocardial infarction therapy in traditional Chinese medicine and provide ideas for the design of related drugs.
Protein innovation through template switching in the Saccharomyces cerevisiae lineage
Authors: Abraham May , Hazkani-Covo Einat
Published: November 2021

DNA polymerase template switching between short, non-identical inverted repeats (IRs) is a genetic mechanism that leads to the homogenization of IR arms and to IR spacer inversion, which cause multinucleotide mutations (MNMs). It is unknown if and how template switching affects gene evolution. In this study, we performed a phylogenetic analysis to determine the effect of template switching between IR arms on coding DNA of Saccharomyces cerevisiae. To achieve this, perfect IRs that co-occurred with MNMs between a strain and its parental node were identified in S. cerevisiae strains. We determined that template switching introduced MNMs into 39 protein-coding genes through S. cerevisiae evolution, resulting in both arm homogenization and inversion of the IR spacer. These events in turn resulted in nonsynonymous substitutions and up to five neighboring amino acid replacements in a single gene. The study demonstrates that template switching is a powerful generator of multiple substitutions within codons. Additionally, some template switching events occurred more than once during S. cerevisiae evolution. Our findings suggest that template switching constitutes a general mutagenic mechanism that results in both nonsynonymous substitutions and parallel evolution, which are traditionally considered as evidence for positive selection, without the need for adaptive explanations.