bluuebunny/crossref_metadata_2025 huggingface dataset:
Objectivity and Intellectual Humility in Scientific Research: They’re Harder Than You Think
Authors: Cartwright Nancy , Ray Faron
Published: July 2023

We begin from the assumption that where scientific research will predictably be used to affect things of moral significance in the world, you have a special duty, a duty of care, to ‘get it right’. This, we argue, requires a special kind of objectivity, ‘objectivity to be found’. What is it that’s to be found? In any kind of scientific endeavour, you should make all reasonable efforts to find the right methods to get the right results to serve the purposes at stake and neither exaggerate nor underestimate the credibility of what you have done. That, we take it, is what in this context constitutes objectivity and intellectual humility. But where your results will affect the world, you have a more demanding duty: a duty to ‘get it right’ about the purposes the endeavour should serve. Often the most morally significant purposes are those that ‘go without saying’ and because they are not said, we can too easily overlook them, sometimes at the cost even of human lives. We illustrate this with the example of the Vajont dam design and the flawed modelling that resulted in the Hillsborough football disaster.
Canopy Structure and Air Temperature Inversions Impact Simulation of Sub‐Canopy Longwave Radiation in Snow‐Covered Boreal Forests
Authors: Rutter Nick , Essery Richard , Baxter Robert , Hancock Steven , Horton Maya , Huntley Brian , Reid Tim , Woodward John
Published: July 2023

Longwave radiation is often the dominant source of energy for snowmelt in forests. Measurements at forest sites of varying density in Sweden and Finland show that downwelling longwave radiation is enhanced under forest canopies, even for sparse canopies and particularly for clear skies. Canopy density must be estimated accurately to predict this enhancement. Linear regression with above‐canopy longwave radiation and air temperature as predictors of sub‐canopy radiation gives good predictions of sub‐canopy longwave radiation with weightings for transmission through canopy gaps that are close to measured sky view fractions. Air temperature serves here as a proxy for effective canopy radiative temperature. Adding above‐canopy shortwave radiation as a predictor gives little improvement in the predictions, suggesting that daytime heating of trunks above the air temperature (“hot trees”) has limited influence on longwave radiation under these continuous canopies. The influence of canopy temperatures falling below the above‐canopy air temperature (“cold trees”) on calm, clear nights, however, is apparent. Decoupling of canopy and above‐canopy air temperatures in an energy balance model of the type used in large‐scale land surface modeling allows this cooling.
Nicotinamide enhances osteoblast differentiation through activation of the mitochondrial antioxidant defense system
Authors: Yoon Heein , Park Seung Gwa , Kim Hyun-Jung , Shin Hye-Rim , Kim Ki-Tae , Cho Young-Dan , Moon Jae-I , Park Min-Sang , Kim Woo-Jin , Ryoo Hyun-Mo
Published: July 2023

Although the normal physiological level of oxidative stress is beneficial for maintaining bone homeostasis, imbalance between reactive oxygen species (ROS) production and antioxidant defense can cause various bone diseases. The purpose of this study was to determine whether nicotinamide (NAM), an NAD+ precursor, can support the maintenance of bone homeostasis by regulating osteoblasts. Here, we found that NAM enhances osteoblast differentiation and mitochondrial metabolism. NAM increases the expression of antioxidant enzymes, which is due to increased FOXO3A transcriptional activity via SIRT3 activation. NAM has not only a preventive effect against weak and chronic oxidative stress but also a therapeutic effect against strong and acute exposure to H2O2 in osteoblast differentiation. Collectively, the results indicate that NAM increases mitochondrial biogenesis and antioxidant enzyme expression through activation of the SIRT3-FOXO3A axis, which consequently enhances osteoblast differentiation. These results suggest that NAM could be a potential preventive or therapeutic agent for bone diseases caused by ROS.
Distinct B cell profiles characterise healthy weight and obesity pre- and post-bariatric surgery
Authors: Šlisere B. , Arisova M. , Aizbalte O. , Salmiņa M. M. , Zolovs M. , Levenšteins M. , Mukāns M. , Troickis I. , Meija L. , Lejnieks A. , Bīlande G. , Rosser E. C. , Oļeiņika K.
Published: July 2023

Background/Objectives

Obesity-associated metabolic dysfunction and inflammation can be ameliorated by bariatric surgery. While obesity is also linked to impaired B cell activation, differentiation, and persistence in response to infection and vaccination little is known about post-operative immune B cell compartment and to what extent dysregulation in B cell pathways can be reversed. To bridge this gap in knowledge, we carried out in-depth evaluation of B cell composition in individuals with obesity prior to and following bariatric surgery compared to lean controls.

Subjects/Methods

We recruited individuals with obesity (BMI at least 35 kg/m2) before bariatric surgery (n = 21) and followed them up 6 months post-operatively (n = 17). As controls we recruited age- and sex-matched lean (BMI < 25) individuals (n = 18). We carried out comprehensive immunophenotyping of peripheral blood B cells as well as interrogated their association with inflammatory and metabolic parameters.

Results

In obesity the balance of antigen-inexperienced and memory B cells in the peripheral blood is altered, with an expansion of naïve and a reduction in total memory B cells. 6 months following bariatric surgery this balance is restored. However, post-operative patients are uniquely characterised by an increase in B cell subsets associated with chronic inflammation – CD11c+CXCR5-IgD-CD27- double negative 2 (DN2) B cells and CD27+CD38++ plasmablasts. Correlations between B cells subsets, inflammatory and metabolic parameters were distinct in lean people and individuals with obesity pre- and post-bariatric surgery.

Conclusions

Bariatric surgery patients display a unique B cell profile 6 months post-operatively; this bears minimal resemblance to that of pre-operative patients and only partially overlaps with that of lean controls. Post-operative differences in the B cell compartment compared to lean controls are detected despite global amelioration of inflammation and restoration of metabolic health. Collectively, this indicates that bariatric surgery creates a specific immunometabolic state with potential implications for health outcomes.
The potential preventive effect of dietary phytochemicals In Vivo
Authors: Saleh Mai M. , Darwish Zeinab E. , El Nouaem Manal I. , Fayed Nesrin A. , Mourad Ghada M. , Ramadan Omneya R.
Published: July 2023

Introduction

Chemoprevention refers to using specific substances during oncogenesis. Curcumin and catechins are both polyphenol types of phytochemicals present in curcuma longa and green tea. The effect of curcumin is synergistic with epigallocatechin gallate, the most abundant polyphenol in tea.

Aim

To evaluate and compares the chemopreventive effect of both green tea and curcumin (each individually and in combination) through induction of hamster buccal pouch carcinoma.

Materials and methods

Squamous cell carcinoma was chemically induced in fifty Syrian golden hamsters divided into 5 groups (10 each). The first group was used as a normal control group. The second group received the carcinogenic agent only. The other three groups received green tea, curcumin, and a combination of both, respectively. Flow cytometry, immunofluorescence, and immunohistochemical assays were used to evaluate apoptosis, proliferation, and angiogenesis. ANOVA test was used to analyze the results between the study groups.

Results

The cells of the positive control group (B) resulted in 11.57% apoptosis. In the study groups, treatment of the cells with green tea (C), and curcumin (D) and both of them (E) showed increased apoptosis. The fluorescent image in group B showed an increase of the red fluorescence in the nucleus and cytoplasm of the squamous cell carcinoma cells while groups C, D, and E showed a decrease of the red fluorescence in the nuclei of the squamous cell carcinoma cells. The microvessel density was higher in the positive control group as compared to the treated groups.

Conclusions

The combination of green tea and curcumin has a significant chemopreventive effect against oral carcinogenesis.
Evolutionary history of the Arctic flora
Authors: Zhang Jun , Li Xiao-Qian , Peng Huan-Wen , Hai Lisi , Erst Andrey S. , Jabbour Florian , Ortiz Rosa del C. , Xia Fu-Cai , Soltis Pamela S. , Soltis Douglas E. , Wang Wei
Published: July 2023

The Arctic tundra is a relatively young and new type of biome and is especially sensitive to the impacts of global warming. However, little is known about how the Arctic flora was shaped over time. Here we investigate the origin and evolutionary dynamics of the Arctic flora by sampling 32 angiosperm clades that together encompass 3626 species. We show that dispersal into the Arctic and in situ diversification within the Arctic have similar trends through time, initiating at approximately 10–9 Ma, increasing sharply around 2.6 Ma, and peaking around 1.0–0.7 Ma. Additionally, we discover the existence of a long-term dispersal corridor between the Arctic and western North America. Our results suggest that the initiation and diversification of the Arctic flora might have been jointly driven by progressive landscape and climate changes and sea-level fluctuations since the early Late Miocene. These findings have important conservation implications given rapidly changing climate conditions in the Arctic.
Allosteric activation of vinculin by talin
Authors: Franz Florian , Tapia-Rojo Rafael , Winograd-Katz Sabina , Boujemaa-Paterski Rajaa , Li Wenhong , Unger Tamar , Albeck Shira , Aponte-Santamaria Camilo , Garcia-Manyes Sergi , Medalia Ohad , Geiger Benjamin , Gräter Frauke
Published: July 2023

The talin-vinculin axis is a key mechanosensing component of cellular focal adhesions. How talin and vinculin respond to forces and regulate one another remains unclear. By combining single-molecule magnetic tweezers experiments, Molecular Dynamics simulations, actin-bundling assays, and adhesion assembly experiments in live cells, we here describe a two-ways allosteric network within vinculin as a regulator of the talin-vinculin interaction. We directly observe a maturation process of vinculin upon talin binding, which reinforces the binding to talin at a rate of 0.03 s−1. This allosteric transition can compete with force-induced dissociation of vinculin from talin only at forces up to 10 pN. Mimicking the allosteric activation by mutation yields a vinculin molecule that bundles actin and localizes to focal adhesions in a force-independent manner. Hence, the allosteric switch confines talin-vinculin interactions and focal adhesion build-up to intermediate force levels. The ‘allosteric vinculin mutant’ is a valuable molecular tool to further dissect the mechanical and biochemical signalling circuits at focal adhesions and elsewhere.
Cancer-associated fibroblast classification in single-cell and spatial proteomics data
Authors: Cords Lena , Tietscher Sandra , Anzeneder Tobias , Langwieder Claus , Rees Martin , de Souza Natalie , Bodenmiller Bernd
Published: July 2023

Cancer-associated fibroblasts (CAFs) are a diverse cell population within the tumour microenvironment, where they have critical effects on tumour evolution and patient prognosis. To define CAF phenotypes, we analyse a single-cell RNA sequencing (scRNA-seq) dataset of over 16,000 stromal cells from tumours of 14 breast cancer patients, based on which we define and functionally annotate nine CAF phenotypes and one class of pericytes. We validate this classification system in four additional cancer types and use highly multiplexed imaging mass cytometry on matched breast cancer samples to confirm our defined CAF phenotypes at the protein level and to analyse their spatial distribution within tumours. This general CAF classification scheme will allow comparison of CAF phenotypes across studies, facilitate analysis of their functional roles, and potentially guide development of new treatment strategies in the future.
Manipulating microRNA miR408 enhances both biomass yield and saccharification efficiency in poplar
Authors: Guo Yayu , Wang Shufang , Yu Keji , Wang Hou-Ling , Xu Huimin , Song Chengwei , Zhao Yuanyuan , Wen Jialong , Fu Chunxiang , Li Yu , Wang Shuizhong , Zhang Xi , Zhang Yan , Cao Yuan , Shao Fenjuan , Wang Xiaohua , Deng Xin , Chen Tong , Zhao Qiao , Li Lei , Wang Guodong , Grünhofer Paul , Schreiber Lukas , Li Yue , Song Guoyong , Dixon Richard A. , Lin Jinxing
Published: July 2023

The conversion of lignocellulosic feedstocks to fermentable sugar for biofuel production is inefficient, and most strategies to enhance efficiency directly target lignin biosynthesis, with associated negative growth impacts. Here we demonstrate, for both laboratory- and field-grown plants, that expression of Pag-miR408 in poplar (Populus alba × P. glandulosa) significantly enhances saccharification, with no requirement for acid-pretreatment, while promoting plant growth. The overexpression plants show increased accessibility of cell walls to cellulase and scaffoldin cellulose-binding modules. Conversely, Pag-miR408 loss-of-function poplar shows decreased cell wall accessibility. Overexpression of Pag-miR408 targets three Pag-LACCASES, delays lignification, and modestly reduces lignin content, S/G ratio and degree of lignin polymerization. Meanwhile, the LACCASE loss of function mutants exhibit significantly increased growth and cell wall accessibility in xylem. Our study shows how Pag-miR408 regulates lignification and secondary growth, and suggest an effective approach towards enhancing biomass yield and saccharification efficiency in a major bioenergy crop.
Regulation of Rad52-dependent replication fork recovery through serine ADP-ribosylation of PolD3
Authors: Richards Frederick , Llorca-Cardenosa Marta J. , Langton Jamie , Buch-Larsen Sara C. , Shamkhi Noor F. , Sharma Abhishek Bharadwaj , Nielsen Michael L. , Lakin Nicholas D.
Published: July 2023

Although Poly(ADP-ribose)-polymerases (PARPs) are key regulators of genome stability, how site-specific ADP-ribosylation regulates DNA repair is unclear. Here, we describe a novel role for PARP1 and PARP2 in regulating Rad52-dependent replication fork repair to maintain cell viability when homologous recombination is dysfunctional, suppress replication-associated DNA damage, and maintain genome stability. Mechanistically, Mre11 and ATM are required for induction of PARP activity in response to replication stress that in turn promotes break-induced replication (BIR) through assembly of Rad52 at stalled/damaged replication forks. Further, by mapping ADP-ribosylation sites induced upon replication stress, we identify that PolD3 is a target for PARP1/PARP2 and that its site-specific ADP-ribosylation is required for BIR activity, replication fork recovery and genome stability. Overall, these data identify a critical role for Mre11-dependent PARP activation and site-specific ADP-ribosylation in regulating BIR to maintain genome integrity during DNA synthesis.
HCK induces macrophage activation to promote renal inflammation and fibrosis via suppression of autophagy
Authors: Chen Man , Menon Madhav C. , Wang Wenlin , Fu Jia , Yi Zhengzi , Sun Zeguo , Liu Jessica , Li Zhengzhe , Mou Lingyun , Banu Khadija , Lee Sui-Wan , Dai Ying , Anandakrishnan Nanditha , Azeloglu Evren U. , Lee Kyung , Zhang Weijia , Das Bhaskar , He John Cijiang , Wei Chengguo
Published: July 2023

Renal inflammation and fibrosis are the common pathways leading to progressive chronic kidney disease (CKD). We previously identified hematopoietic cell kinase (HCK) as upregulated in human chronic allograft injury promoting kidney fibrosis; however, the cellular source and molecular mechanisms are unclear. Here, using immunostaining and single cell sequencing data, we show that HCK expression is highly enriched in pro-inflammatory macrophages in diseased kidneys. HCK-knockout (KO) or HCK-inhibitor decreases macrophage M1-like pro-inflammatory polarization, proliferation, and migration in RAW264.7 cells and bone marrow-derived macrophages (BMDM). We identify an interaction between HCK and ATG2A and CBL, two autophagy-related proteins, inhibiting autophagy flux in macrophages. In vivo, both global or myeloid cell specific HCK-KO attenuates renal inflammation and fibrosis with reduces macrophage numbers, pro-inflammatory polarization and migration into unilateral ureteral obstruction (UUO) kidneys and unilateral ischemia reperfusion injury (IRI) models. Finally, we developed a selective boron containing HCK inhibitor which can reduce macrophage pro-inflammatory activity, proliferation, and migration in vitro, and attenuate kidney fibrosis in the UUO mice. The current study elucidates mechanisms downstream of HCK regulating macrophage activation and polarization via autophagy in CKD and identifies that selective HCK inhibitors could be potentially developed as a new therapy for renal fibrosis.
Structures of p53/BCL-2 complex suggest a mechanism for p53 to antagonize BCL-2 activity
Authors: Wei Hudie , Wang Haolan , Wang Genxin , Qu Lingzhi , Jiang Longying , Dai Shuyan , Chen Xiaojuan , Zhang Ye , Chen Zhuchu , Li Youjun , Guo Ming , Chen Yongheng
Published: July 2023

Mitochondrial apoptosis is strictly controlled by BCL-2 family proteins through a subtle network of protein interactions. The tumor suppressor protein p53 triggers transcription-independent apoptosis through direct interactions with BCL-2 family proteins, but the molecular mechanism is not well understood. In this study, we present three crystal structures of p53-DBD in complex with the anti-apoptotic protein BCL-2 at resolutions of 2.3–2.7 Å. The structures show that two loops of p53-DBD penetrate directly into the BH3-binding pocket of BCL-2. Structure-based mutations at the interface impair the p53/BCL-2 interaction. Specifically, the binding sites for p53 and the pro-apoptotic protein Bax in the BCL-2 pocket are mostly identical. In addition, formation of the p53/BCL-2 complex is negatively correlated with the formation of BCL-2 complexes with pro-apoptotic BCL-2 family members. Defects in the p53/BCL-2 interaction attenuate p53-mediated cell apoptosis. Overall, our study provides a structural basis for the interaction between p53 and BCL-2, and suggests a molecular mechanism by which p53 regulates transcription-independent apoptosis by antagonizing the interaction of BCL-2 with pro-apoptotic BCL-2 family members.
Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution
Authors: Ramos-Barbero María Dolores , Gómez-Gómez Clara , Sala-Comorera Laura , Rodríguez-Rubio Lorena , Morales-Cortes Sara , Mendoza-Barberá Elena , Vique Gloria , Toribio-Avedillo Daniel , Blanch Anicet R. , Ballesté Elisenda , Garcia-Aljaro Cristina , Muniesa Maite
Published: July 2023

Crassvirales (crAss-like phages) are an abundant group of human gut-specific bacteriophages discovered in silico. The use of crAss-like phages as human fecal indicators is proposed but the isolation of only seven cultured strains of crAss-like phages to date has greatly hindered their study. Here, we report the isolation and genetic characterization of 25 new crAss-like phages (termed crAssBcn) infecting Bacteroides intestinalis, belonging to the order Crassvirales, genus Kehishuvirus and, based on their genomic variability, classified into six species. CrAssBcn phage genomes are similar to ΦCrAss001 but show genomic and aminoacidic differences when compared to other crAss-like phages of the same family. CrAssBcn phages are detected in fecal metagenomes around the world at a higher frequency than ΦCrAss001. This study increases the known crAss-like phage isolates and their abundance and heterogeneity open the question of what member of the Crassvirales group should be selected as human fecal marker.
Multi-reward reinforcement learning based development of inter-atomic potential models for silica
Authors: Koneru Aditya , Chan Henry , Manna Sukriti , Loeffler Troy D. , Dhabal Debdas , Bertolazzo Andressa A. , Molinero Valeria , Sankaranarayanan Subramanian K. R. S.
Published: July 2023

Silica is an abundant and technologically attractive material. Due to the structural complexities of silica polymorphs coupled with subtle differences in Si–O bonding characteristics, the development of accurate models to predict the structure, energetics and properties of silica polymorphs remain challenging. Current models for silica range from computationally efficient Buckingham formalisms (BKS, CHIK, Soules) to reactive (ReaxFF) and more recent machine-learned potentials that are flexible but computationally costly. Here, we introduce an improved formalism and parameterization of BKS model via a multireward reinforcement learning (RL) using an experimental training dataset. Our model concurrently captures the structure, energetics, density, equation of state, and elastic constants of quartz (equilibrium) as well as 20 other metastable silica polymorphs. We also assess its ability in capturing amorphous properties and highlight the limitations of the BKS-type functional forms in simultaneously capturing crystal and amorphous properties. We demonstrate ways to improve model flexibility and introduce a flexible formalism, machine-learned ML-BKS, that outperforms existing empirical models and is on-par with the recently developed 50 to 100 times more expensive Gaussian approximation potential (GAP) in capturing the experimental structure and properties of silica polymorphs and amorphous silica.
Mechanism and therapeutic implications of pomalidomide-induced immune surface marker upregulation in EBV-positive lymphomas
Authors: Jaeger Hannah K. , Davis David A. , Nair Ashwin , Shrestha Prabha , Stream Alexandra , Yaparla Amulya , Yarchoan Robert
Published: July 2023

Epstein-Barr virus (EBV) downregulates immune surface markers to avoid immune recognition. Pomalidomide (Pom) was previously shown to increase immune surface marker expression in EBV-infected tumor cells. We explored the mechanism by which Pom leads to these effects in EBV-infected cells. Pom increased B7-2/CD86 mRNA, protein, and surface expression in EBV-infected cells but this was virtually eliminated in EBV-infected cells made resistant to Pom-induced cytostatic effects. This indicates that Pom initiates the upregulation of these markers by interacting with its target, cereblon. Interestingly, Pom increased the proinflammatory cytokines IP-10 and MIP-1∝/β in EBV infected cells, supporting a possible role for the phosphoinositide 3-kinase (PI3K)/AKT pathway in Pom’s effects. Idelalisib, an inhibitor of the delta subunit of PI3 Kinase, blocked AKT-Ser phosphorylation and Pom-induced B7-2 surface expression. PU.1 is a downstream target for AKT that is expressed in EBV-infected cells. Pom treatment led to an increase in PU.1 binding to the B7-2 promoter based on ChIP analysis. Thus, our data indicates Pom acts through cereblon leading to degradation of Ikaros and activation of the PI3K/AKT/PU.1 pathway resulting in upregulation of B7-2 mRNA and protein expression. The increased immune recognition in addition to the increases in proinflammatory cytokines upon Pom treatment suggests Pom may be useful in the treatment of EBV-positive lymphomas.
Selective isotropic etching of SiO2 over Si3N4 using NF3/H2 remote plasma and methanol vapor
Authors: Gil Hong Seong , Kim Doo San , Jang Yun Jong , Kim Dea Whan , Kwon Hea In , Kim Gyoung Chan , Kim Dong Woo , Yeom Geun Young
Published: July 2023

In this study, an isotropic etching process of SiO2 selective to Si3N4 using NF3/H2/methanol chemistry was investigated. HF was formed using a NF3/H2 remote plasma, and in order to remove the F radicals, which induces spontaneous etching of Si-base material, methanol was injected outside the plasma discharge region. Through this process, etch products were formed on the surface of SiO2, and then the (NH4)2SiF6 was removed by following heating process. When the H and F radicals were abundant, the highest SiO2 etch per cycle (EPC) was obtained. And, the increase of H2 and methanol percentage in the gas chemistry increased the etch selectivity by decreasing the F radicals. The etch products such as (NH4)2SiF6 were formed on the surfaces of SiO2 and Si3N4 during the reaction step and no noticeable spontaneous etching by formation of SiF4 was observed. By optimized conditions, the etch selectivity of SiO2 over Si3N4 and poly Si higher than 50 and 20, respectively, was obtained while having SiO2 EPC of ~ 13 nm/cycle. It is believed that the cyclic process using NF3/H2 remote plasma and methanol followed by heating can be applied to the selective isotropic SiO2 etching of next generation 3D device fabrication.
Sensitive and selective detection of p-nitroaniline with the assistance of a fluorescence capillary imprinted sensor
Authors: Xiao Huiwen , Zhang Zhaohui
Published: July 2023

A novel fluorescence capillary imprinted sensor was prepared firstly with high selectivity and sensitivity for the detection of p-nitroaniline.
Disulfide re-bridging reagents for single-payload antibody-drug conjugates
Authors: King Thomas A. , Walsh Stephen J. , Kapun Mia , Wharton Thomas , Krajcovicova Sona , Glossop Melanie S. , Spring David R.
Published: July 2023

A tetra-reactive disulfide re-bridging reagent, TetraDVP, enables the efficient synthesis of antibody-drug conjugates (ADCs) bearing a single payload.
Prediction of metastable phase of the Sc–N system in the N-rich region under high pressure
Authors: Niu Shifeng , Liu Yuanyuan , Yang Zhenxing , Liu Shijie , Yao Zhen
Published: July 2023

Three metastable phase structures (P1̄-ScN8, P1-ScN9 and P1-ScN11) are proposed in the N-rich region (ScNx; x ≥ 8), which have excellent physical and chemical properties, and also enrich the structural evolution behavior of the Sc and N atom under pressure.
Temperature dependence of O solubility in liquid Na by atomistic simulation of Na(l)–Na2O(s) interfaces using corrected machine learning potential: a step towards simulating Na combustion
Authors: Kim Chaeyeong , Oda Takuji
Published: July 2023

Na(l)–Na2O(s) interfaces were successfully described by corrected machine-learning potential and temperature dependence of O solubility was revealed.
Physical mechanism on the linear spectrum and nonlinear spectrum in a twist bilayer graphdiyne nanodisk
Authors: Gai Xinwen , Sheng Hao , Wang Jingang
Published: July 2023

The OPA, TPA, ECD spectra and PDOS of a twist bilayer graphdiyne nanodisk (TwBLGDY-ND) were investigated by using a variety of quantum chemistry and wave function analyses.
Effect of bromine substitution on blue phosphorescent trans-(N-heterocyclic carbene)Pt(ii) acetylide complexes
Authors: Khan Amran A. T. , Gobeze Habtom B. , Islam Tanjila , Arman Hadi D. , Schanze Kirk S.
Published: July 2023

N-heterocyclic carbene complexes of the type trans-(NHC)2PtII(CC–Ar)2 (where Ar = phenyl or substituted phenyl) are of interest as violet and blue phosphors.
From Cu(i) and Cu(i)–Cu(ii) mixed-valence clusters to 2D Cu(ii) and Cu(i) coordination polymers supported by a flexible bis-tetrazole organosulfur ligand
Authors: Gómez-Paz Olaya , Carballo Rosa , Lago Ana B. , Prieto Inmaculada , Vázquez-López Ezequiel M.
Published: July 2023

Study of the Cu(i) and Cu(i)–Cu(ii) mixed-valence clusters and Cu(i) and Cu(ii) coordination polymers obtained with a flexible bis-tetrazole organosulfur ligand.
Efficient synthesis of symmetrically substituted pyridines and substituted alkenes through green and heterogeneous catalysis with zinc phosphate
Authors: El Hallaoui Achraf , Merroun Youssef , Chehab Soukaina , Boukhris Said , Hassoune Hicham , Ghailane Rachida , Souizi Abedelaziz
Published: July 2023

A novel, green, and more efficient method for synthesizing substituted alkene derivatives and symmetrically substituted pyridine derivatives using zinc phosphate (Zn3(PO4)2·4H2O) as a highly effective and eco-friendly heterogeneous catalyst.
S-Alkylation of dithiocarbamates via a hydrogen borrowing reaction strategy using alcohols as alkylating agents
Authors: P Hima , Hati Spandan , Dey Raju
Published: July 2023

S-Alkylation of dithiocarbamates using alcohols as alkylating agents via a hydrogen borrowing strategy using hydroxyapatite-supported copper nanoparticles as a heterogeneous catalyst.
Base-mediated synthesis of cyclic dithiocarbamates from 1-amino-3-chloropropan-2-ol derivatives and carbon disulfide
Authors: Toda Yasunori , Iwasaki Masaya , Suga Hiroyuki
Published: July 2023

This paper describes the synthesis of six-membered cyclic dithiocarbamates from 1-amino-3-chloropropan-2-ol derivatives and carbon disulfide using triethylamine.
Interface passivation using choline acetate for efficient and stable planar perovskite solar cells
Authors: Thambidurai M. , Dewi Herlina Arianita , Xizu Wang , Mathews Nripan , Dang Cuong , Nguyen Hung D.
Published: July 2023

The choline acetate (ChAc) passivation improves both the device performance and long-term stability.
Modeling of the nebular-phase spectral evolution of stripped-envelope supernovae
Authors: Dessart L. , Hillier D. John , Woosley S. E. , Kuncarayakti H.
Published: July 2023

We present an extended grid of multi-epoch 1D nonlocal thermodynamic equilibrium radiative transfer calculations for nebular-phase Type Ibc supernovae (SNe) from He-star explosions. Compared to our previous work, which was focused on a post-explosion epoch of 200 days, here we study the spectral evolution from 100 to about 450 days. We also augment the model set with progenitors that evolved without wind mass loss. Models with the same final, pre-SN mass have similar yields and produce essentially the same emergent spectra. Hence, the uncertain progenitor mass loss history compromises the inference of the initial, main sequence mass. This shortcoming does not affect Type IIb SNe in which mass-loss has left a small residual H-rich envelope in the progenitor star at core collapse and, hence, an intact He core. However, our 1D models with a different pre-SN mass tend to yield widely different spectra, as seen through variations in the strong emission lines due to [N II] λλ 6548, 6583, [O I] λλ 6300, 6364, [Ca II] λλ 7291, 7323, [Ni II] λ 7378, and the forest of Fe II lines below 5500 Å. At the lower mass end, the ejecta are He-rich, and at 100 days, they cool through He I, N II, Ca II, and Fe II lines, with N II and Fe II dominating at 450 days. These models, associated with He giants, stand in conflict to observed SNe Ib, which typically lack strong N II emission. Instead, they may lead to SNe Ibn or, because of additional stripping by a companion star, ultra-stripped SNe Ic. In contrast, for higher pre-SN masses, the ejecta are progressively He poor and cool at 100 days through O I, Ca II, and Fe II lines, with O I and Ca II dominating at 450 days. Non-uniform, aspherical, large-scale mixing is more likely to determine the SN type at intermediate pre-SN masses, rather than any compositional differences. Variations in clumping and mixing, as well as departures from spherical symmetry would increase the spectral diversity, but also introduce additional degeneracies. More robust predictions from spectral modeling thus require that careful attention be paid to the initial conditions by incorporating the salient features of physically consistent 3D explosion models.
Effect of Y2O3 content on microstructure and properties of Ni-based self-lubricating composite coating
Authors: Huang Bensheng , Hong Xiaolong , Chen Peng , Li Tianning , Luo Xia , Chen Lingzhi , Liu Ge
Published: July 2023

In order to improve the wear resistance and corrosion resistance of sucker rod surface, Ni-based self-lubricating composite coating with Y2O3 was successfully prepared on 35CrMo steel substrate by high frequency induction heating cladding technology. The coating structure is uniform and dense, and there are no obvious defects such as pores and cracks. The microstructure of the coating layer was studied by means of metallographic microscope, scanning electron microscope and X-ray diffractometer. The hardness, wear resistance and corrosion resistance of the coating layer were tested by microhardness testers, friction and wear testers and electrochemical workstations. The results show that the main phases of the composite coating are γ- (Ni, Fe), Ni3Fe, CrB, TiC and Cr23C6. When the addition amount of Y2O3 is 2%, the average microhardness of the composite coating is the highest, which is 805.1 HV0.2; under the same wear conditions, the wear resistance of 2% Y2O3 composite coating is the best. The average friction coefficient and wear loss are reduced by 16.27% and 20.35% respectively compared with the composite coating without rare earth, and 37.55% and 48.02% respectively compared with the substrate. The wear mechanism of the composite coating is mainly severe adhesive wear, and there is a small amount of oxidation wear. With the increase of Y2O3 content, the self-corrosion potential of the composite coating fluctuates in a small range, and its self-corrosion current density decreases first and then increases. The self-corrosion potential of the composite coating containing 2% Y2O3 is more positive (–0.4316 V), and the self-corrosion current density is the smallest (3.9579 µA · cm−2), and its corrosion resistance is the best.
Sum-frequency generation at interfaces: A Fresnel story. II. Analytical expressions for multilayer systems
Authors: Busson Bertrand
Published: July 2023

The well-known formalism for Sum-Frequency Generation (SFG) reflected or transmitted by a three-layer system involves three equations defining the emitted SFG intensity, the effective nonlinear susceptibility, and a set of Fresnel factors specific to the three-layer system. We generalize the equations to an N-layer system, where all media have non-vanishing thicknesses, by leaving the first two equations unchanged and modifying only the Fresnel factors. These universal Fresnel factors bear all the complexity of light propagation and interference in the system, in amplitude and phase. They are analytically known anywhere in the N-layer system, either at any interface or in any of the bulks, and share common expressions for the three beams, incoming or emitted, of the SFG process in reflection. Enclosing an ultrathin layer (e.g., a molecular monolayer) in the system does not modify the Fresnel factors except for boundary conditions at this layer, as in the three-layer case. Specific rules are elaborated to simplify systems containing macroscopic layers. Equations for the four- and five-layer systems are explicitly provided. Simulations in the four-layer system allow for the recovery of the results of the transfer matrix formalism at a lower complexity cost for SFG users. Finally, when several interfaces in the system produce SFG signals, we show that it is possible to probe only the most buried one by canceling all the SFG responses except at this last interface, generalizing the results of the three-layer system.
Polyadenine complexed to polyglutamine suggests the peptide backbone has a cis conformation
Authors: Bransgrove Anthony B. , Anderson Louise Amelia
Published: July 2023

The polyadenine (poly(A)) tail of mRNA is a homopolymer and as such is a potential H-bonding partner for other cellular homopolymers. The secondary structure of proteins and peptides employs the polar groups of the homopolymer backbone to bind with themselves or other polymers to respectively form an alpha helix or a beta sheet. These same backbone polar groups appear to be suitably positioned to bind with poly(A) but only when the backbone has rotated to the all-cis conformation. However the all-cis conformation of peptides or proteins is rarely encountered and so they would seem to be unlikely binding partners. Here we show that a homopolymer of glutamine (poly(Q)) may be an exception to this rarity because its default conformation seems to be all-cis. We found that exposure of poly(A) to increasing amounts of poly(Q) causes a progressive loss of soluble poly(A) migrating on gel electrophoresis, indicating binding between the two polymers. Stereochemical modelling of the likely complex has suggested the particular polar groups that are responsible for binding of the two polymers, along with an explanation for the all-cis conformation of poly(Q).
Tagasaste silvopastures in steep-hill country. 2. Effect of increasing proximity to tagasaste on growth and survival of companion pasture species
Authors: Tozer Katherine , Noakes Emma , Douglas Grant , Greenfield Rose , Cameron Catherine
Published: July 2023

Context Tagasaste (Cytisus proliferus), a fast-growing leguminous tree, has potential to supplement pasture production in steep-hill country and to increase pasture resilience. Aims In the companion paper, we quantified tagasaste production characteristics. Here, we determine the effect of proximity of 10-year-old tagasaste trees on productivity of eight pasture species including grasses (perennial ryegrass, Lolium perenne; cocksfoot, Dactylis glomerata; prairie grass, Bromus willdenowii; microlaena, Microlaena stipoides), perennial legumes (white clover, Trifolium repens; red clover, T. pratense; lotus, Lotus pedunculatus), and an annual legume (subterranean clover, T. subterraneum). Methods A site was established in the East Coast region of the North Island of New Zealand on steep-hill country (>20° slope). Herbage production, nutritive value and survival of pasture species established as spaced transplants were measured over 3 years. Results Cocksfoot had high survival, herbage production and metabolisable energy content but was negatively affected by proximity to tagasaste. Microlaena was not significantly affected by proximity to tagasaste; however, it was much less productive and had lower nutritive values than the other grasses. Only 40% of perennial ryegrass transplants survived 3 years, and survival of perennial legumes was negligible. Subterranean clover was able to set seed in the open and in shade. Conclusions Cocksfoot was the most productive grass species, and microlaena was least affected by proximity to tagasaste. Given the poor persistence of perennial clovers, annual clovers may be better suited to a tagasaste silvopasture on steep, dry hillsides. Implications Mixtures of cocksfoot and subterranean clover may be well suited to summer-dry hillsides, between and under trees in a tagasaste silvopasture. Microlaena may provide some forage and can maintain groundcover despite shade.
Stability and heterogeneity in the antimicrobiota reactivity of human milk-derived immunoglobulin A
Authors: Johnson-Hence Chelseá B. , Gopalakrishna Kathyayini P. , Bodkin Darren , Coffey Kara E. , Burr Ansen H.P. , Rahman Syed , Rai Ali T. , Abbott Darryl A. , Sosa Yelissa A. , Tometich Justin T. , Das Jishnu , Hand Timothy W.
Published: July 2023

Immunoglobulin A (IgA) is secreted into breast milk and is critical for both protecting against enteric pathogens and shaping the infant intestinal microbiota. The efficacy of breast milk–derived maternal IgA (BrmIgA) is dependent upon its specificity; however, heterogeneity in BrmIgA binding ability to the infant microbiota is not known. Using a flow cytometric array, we analyzed the reactivity of BrmIgA against bacteria common to the infant microbiota and discovered substantial heterogeneity between all donors, independent of preterm or term delivery. Surprisingly, we also observed intradonor variability in the BrmIgA response to closely related bacterial isolates. Conversely, longitudinal analysis showed that the antibacterial BrmIgA reactivity was relatively stable through time, even between sequential infants, indicating that mammary gland IgA responses are durable. Together, our study demonstrates that the antibacterial BrmIgA reactivity displays interindividual heterogeneity but intraindividual stability. These findings have important implications for how breast milk shapes the development of the preterm infant microbiota and protects against necrotizing enterocolitis.
Investigating DC and AC degradation behaviors to P-type low temperature polycrystalline silicon thin film transistor with fin-like structure
Authors: Chen Po-Hsun , Zheng Yu-Zhe , Yeh Tsung-Han , Nieh Tzu-Yun
Published: July 2023

Currently, thin film transistor (TFT) based on planar structure is widely used in the applications of display panels. However, when the device is scaling-down, new device structures or novel materials should be introduced. In this work, the low temperature polycrystalline silicon (LTPS) TFT with fin-like structure is investigated. On the basis of electrical measurements, the device features good switching characteristics with low operating voltages. However, the I
d–V
g sweeping result exhibits off-state leakage, which is known as the gate-induced drain leakage (GIDL) current. The GIDL current is increased with the drain bias and the temperature increasing. To observe the GIDL current degradations, different gate biases with negative bias stress and positive bias stress are applied. The results show different degradation behaviors. In addition, bias stresses with DC and AC methods are also applied to verify the device reliability. Both threshold voltage (V
t) shift and sub-threshold swing (S.S.) are also extracted to verify the degradations of the device. Finally, the physical models are also proposed to illustrate the degradation behaviors of the LTPS device with a fin-like structure, which can be beneficial to future related development of LTPS-based devices.
A comprehensive study on ZrO2-ZnO nanocomposites synthesized by the plant-mediated green method
Authors: Barman Subhodeep , Sikdar Suranjan , Das Rahul
Published: July 2023

Zirconia—zinc oxide (ZrO2-ZnO) nanocomposites with three different amounts of zirconia (ZrO2) contents (5%, 10%, and 15%) were successfully synthesized using the leaf extract of Azadirachta indica (also known as Neem). The prepared nanocomposites were examined from the microstructural and optical point of view. The existence of the mixed phase of hexagonal ZnO together with the tetragonal ZrO2 in each sample was confirmed by the X-ray diffraction data. Rietveld refinement was performed to determine the microstructural parameters. A significant morphological as well as microstructural change was also noticed from SEM and HRTEM images with the admixture of increasing quantities of zirconia. A characteristic metal oxide band within 1000 cm−1, was confirmed by the Fourier transform infrared spectroscopy. UV–visible spectra confirm the decrease in optical band gap energy values from 3.30 eV to 3.15 eV for the ZnO phase and from 3.93 eV to 3.73 eV for the tetragonal ZrO2 phase with the increasing amount of ZrO2 admixture into the ZnO host material. All of these findings would likely be useful not only in the manufacture of electronic and optical devices, but would also be useful for water purification through photocatalytic activities.
Microscopic thermal characteristics of parallelly arranged nanowires in a liquid: the role of interface thermal resistance, solid-like liquid layer, and the restricted phonon transport
Authors: Somarathna Chamara , Samaraweera Nalaka , Jayasekara Saliya , Perera Kapila
Published: July 2023

Nanofluids based on extended nanostructures, such as nanowires, have been demonstrated improved thermal conductivities (κ). However, the lack of a complete understanding at the microscopic level hinders the development of such nanofluids towards practical applications. We aim to provide it by investigating how the interface thermal resistance (R

b
), ballistic phonon transport, and the solid-like liquid layer affect the heat conduction in nanowire-based nanofluids. By employing Non-Equilibrium Molecular Dynamics (NEMD), it is found that the heat conduction in the parallelly arranged liquid and the nanowires exhibit a coupled thermal behavior owing to the R

b
. This contradicts the predictions of the classical parallel heat conduction model, therefore, a novel model is proposed taking this coupled behavior into account. Using this model, it is shown that the high κ of the solid phase has a limited contribution to the effective κ of nanofluids having short nanowires due to the dominant R

b
effect. For the case of long nanowires, however, the individual nanowire κ becomes a vital parameter defining the effective κ. Further, NEMD calculations reveal that the κ of suspended nanowires in a liquid is markedly reduced, questioning the validity of classical effective medium theories which use the bulk parameters. This reduction is attributed to surface atoms’ restricted vibrational freedom and the nanowire’s phonon-boundary scattering. By substituting this reduced κ of the solid phase into the new mathematical model, the theoretical predictions align closely with the NEMD calculations, exhibiting deviations below 10%. The sole contribution from the solid-like liquid layer to the κ enhancement lies between 20%–30% in the nanofluids presently considered. Therefore, the findings of this study highlight the important roles play by the identified microscopic thermal characteristics in defining the effective κ of nanofluids based on nanowires.
Distinct topological configurations of equatorial timelike circular orbit for spherically symmetric (hairy) black holes
Authors: Ye Xu , Wei Shao-Wen
Published: July 2023

Topology is a promising approach toward to the light ring in a generic black hole background, and equatorial timelike circular orbit in a stationary black hole background. In this paper, we consider the distinct topological configurations of the timelike circular orbits in static, spherically symmetric, and asymptotic flat black holes. By making use of the equation of motion of the massive particles, we construct a vector with its zero points exactly relating with the timelike circular orbits. Since each zero point of the vector can be endowed with a winding number, the topology of the timelike circular orbits is well established. Stable and unstable timelike circular orbits respectively have winding number +1 and -1. In particular, for given angular momentum, the topological number of the timelike circular orbits also vanishes whether they are rotating or not. Moreover, we apply the study to the Schwarzschild, scalarized Einstein-Maxwell, and dyonic black holes, which have three distinct topological configurations, representations of the radius and angular momentum relationship, with one or two pairs timelike circular orbits at most. It is shown that although the existence of scalar hair and quasi-topological term leads to richer topological configurations of the timelike circular orbits, they have no influence on the total topological number. These results indicate that the topological approach indeed provides us a novel way to understand the timelike circular orbits. Significantly, different topological configurations can share the same topology number, and hence belong to the same topological class. More information is expected to be disclosed when other different topological configurations are present.