bluuebunny/crossref_metadata_2025 huggingface dataset:
Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages
Authors: Huisjes Nadia M , Retzer Thomas M , Scherr Matthias J , Agarwal Rohit , Rajappa Lional , Safaric Barbara , Minnen Anita , Duderstadt Karl E
Published: September 2022

The rapid development of new imaging approaches is generating larger and more complex datasets, revealing the time evolution of individual cells and biomolecules. Single-molecule techniques, in particular, provide access to rare intermediates in complex, multistage molecular pathways. However, few standards exist for processing these information-rich datasets, posing challenges for wider dissemination. Here, we present Mars, an open-source platform for storing and processing image-derived properties of biomolecules. Mars provides Fiji/ImageJ2 commands written in Java for common single-molecule analysis tasks using a Molecule Archive architecture that is easily adapted to complex, multistep analysis workflows. Three diverse workflows involving molecule tracking, multichannel fluorescence imaging, and force spectroscopy, demonstrate the range of analysis applications. A comprehensive graphical user interface written in JavaFX enhances biomolecule feature exploration by providing charting, tagging, region highlighting, scriptable dashboards, and interactive image views. The interoperability of ImageJ2 ensures Molecule Archives can easily be opened in multiple environments, including those written in Python using PyImageJ, for interactive scripting and visualization. Mars provides a flexible solution for reproducible analysis of image-derived properties, facilitating the discovery and quantitative classification of new biological phenomena with an open data format accessible to everyone.
A unified view of low complexity regions (LCRs) across species
Authors: Lee Byron , Jaberi-Lashkari Nima , Calo Eliezer
Published: September 2022

Low complexity regions (LCRs) play a role in a variety of important biological processes, yet we lack a unified view of their sequences, features, relationships, and functions. Here, we use dotplots and dimensionality reduction to systematically define LCR type/copy relationships and create a map of LCR sequence space capable of integrating LCR features and functions. By defining LCR relationships across the proteome, we provide insight into how LCR type and copy number contribute to higher order assemblies, such as the importance of K-rich LCR copy number for assembly of the nucleolar protein RPA43 in vivo and in vitro. With LCR maps, we reveal the underlying structure of LCR sequence space, and relate differential occupancy in this space to the conservation and emergence of higher order assemblies, including the metazoan extracellular matrix and plant cell wall. Together, LCR relationships and maps uncover and identify scaffold-client relationships among E-rich LCR-containing proteins in the nucleolus, and revealed previously undescribed regions of LCR sequence space with signatures of higher order assemblies, including a teleost-specific T/H-rich sequence space. Thus, this unified view of LCRs enables discovery of how LCRs encode higher order assemblies of organisms.
Robust group- but limited individual-level (longitudinal) reliability and insights into cross-phases response prediction of conditioned fear
Authors: Klingelhöfer-Jens Maren , Ehlers Mana R , Kuhn Manuel , Keyaniyan Vincent , Lonsdorf Tina B
Published: September 2022

Here, we follow the call to target measurement reliability as a key prerequisite for individual-level predictions in translational neuroscience by investigating (1) longitudinal reliability at the individual and (2) group level, (3) internal consistency and (4) response predictability across experimental phases. One hundred and twenty individuals performed a fear conditioning paradigm twice 6 months apart. Analyses of skin conductance responses, fear ratings and blood oxygen level dependent functional magnetic resonance imaging (BOLD fMRI) with different data transformations and included numbers of trials were conducted. While longitudinal reliability was rather limited at the individual level, it was comparatively higher for acquisition but not extinction at the group level. Internal consistency was satisfactory. Higher responding in preceding phases predicted higher responding in subsequent experimental phases at a weak to moderate level depending on data specifications. In sum, the results suggest that while individual-level predictions are meaningful for (very) short time frames, they also call for more attention to measurement properties in the field.
BRCA2 BRC missense variants disrupt RAD51-dependent DNA repair
Authors: Jimenez-Sainz Judit , Mathew Joshua , Moore Gemma , Lahiri Sudipta , Garbarino Jennifer , Eder Joseph P , Rothenberg Eli , Jensen Ryan B
Published: September 2022

Pathogenic mutations in the BRCA2 tumor suppressor gene predispose to breast, ovarian, pancreatic, prostate, and other cancers. BRCA2 maintains genome stability through homology-directed repair (HDR) of DNA double-strand breaks (DSBs) and replication fork protection. Nonsense or frameshift mutations leading to truncation of the BRCA2 protein are typically considered pathogenic; however, missense mutations resulting in single amino acid substitutions can be challenging to functionally interpret. The majority of missense mutations in BRCA2 have been classified as Variants of Uncertain Significance (VUS) with unknown functional consequences. In this study, we identified three BRCA2 VUS located within the BRC repeat region to determine their impact on canonical HDR and fork protection functions. We provide evidence that S1221P and T1980I, which map to conserved residues in the BRC2 and BRC7 repeats, compromise the cellular response to chemotherapeutics and ionizing radiation, and display deficits in fork protection. We further demonstrate biochemically that S1221P and T1980I disrupt RAD51 binding and diminish the ability of BRCA2 to stabilize RAD51-ssDNA complexes. The third variant, T1346I, located within the spacer region between BRC2 and BRC3 repeats, is fully functional. We conclude that T1346I is a benign allele, whereas S1221P and T1980I are hypomorphic disrupting the ability of BRCA2 to fully engage and stabilize RAD51 nucleoprotein filaments. Our results underscore the importance of correctly classifying BRCA2 VUS as pathogenic variants can impact both future cancer risk and guide therapy selection during cancer treatment.
A global view of the aspiring physician-scientist
Authors: Williams Christopher S , Rathmell W Kimryn , Carethers John M , Harper Diane M , Lo YM Dennis , Ratcliffe Peter J , Zaidi Mone
Published: September 2022

Physician-scientists have epitomized the blending of deep, rigorous impactful curiosity with broad attention to human health for centuries. While we aspire to prepare all physicians with an appreciation for these skills, those who apply them to push the understanding of the boundaries of human physiology and disease, to advance treatments, and to increase our knowledge base in the arena of human health can fulfill an essential space for our society, economies, and overall well-being. Working arm in arm with basic and translational scientists as well as expert clinicians, as peers in both groups, this career additionally serves as a bridge to facilitate the pace and direction of research that ultimately impacts health. Globally, there are remarkable similarities in challenges in this career path, and in the approaches employed to overcome them. Herein, we review how different countries train physician-scientists and suggest strategies to further bolster this career path.
Isometric spiracular scaling in scarab beetles—implications for diffusive and advective oxygen transport
Authors: Wagner Julian M , Klok C Jaco , Duell Meghan E , Socha John J , Cao Guohua , Gong Hao , Harrison Jon F
Published: September 2022

The scaling of respiratory structures has been hypothesized to be a major driving factor in the evolution of many aspects of animal physiology. Here, we provide the first assessment of the scaling of the spiracles in insects using 10 scarab beetle species differing 180× in mass, including some of the most massive extant insect species. Using X-ray microtomography, we measured the cross-sectional area and depth of all eight spiracles, enabling the calculation of their diffusive and advective capacities. Each of these metrics scaled with geometric isometry. Because diffusive capacities scale with lower slopes than metabolic rates, the largest beetles measured require 10-fold higher PO2 gradients across the spiracles to sustain metabolism by diffusion compared to the smallest species. Large beetles can exchange sufficient oxygen for resting metabolism by diffusion across the spiracles, but not during flight. In contrast, spiracular advective capacities scale similarly or more steeply than metabolic rates, so spiracular advective capacities should match or exceed respiratory demands in the largest beetles. These data illustrate a general principle of gas exchange: scaling of respiratory transport structures with geometric isometry diminishes the potential for diffusive gas exchange but enhances advective capacities; combining such structural scaling with muscle-driven ventilation allows larger animals to achieve high metabolic rates when active.
High temperature mortality of Wolbachia impacts the sex ratio of the parasitoid Ooencyrtus mirus (Hymenoptera: Encyrtidae)
Authors: Power Nancy R. , Rugman-Jones Paul F. , Stouthamer Richard , Ganjisaffar Fatemeh , Perring Thomas M.
Published: September 2022

Background

Wolbachia bacteria are estimated to occur in more than half of all insect species. In Hymenoptera, Wolbachia often manipulates its host’s reproduction to its own advantage. Wolbachia is likely the reason that males are rare in the uniparental Ooencyrtus mirus Triapitsyn & Power (Hymenoptera: Encyrtidae). The likelihood of producing male offspring can be increased by giving mothers a continuous supply of Bagrada hilaris (Burmeister) (Heteroptera: Pentatomidae) host eggs to parasitize for 2–3 weeks, by feeding the parents antibiotics, or by rearing parent wasps at high temperatures; all variables that have been shown to correlate with depleting Wolbachia titers in other organisms. The purpose of the current study was to determine whether thelytoky in O. mirus is due to Wolbachia, and if so, at what time in development the sex change occurs. We also wished to determine if Wolbachia removal results in the production of intersexes, as in some other hymenopterans. Finally, mating behavior was observed to see if and where it breaks down as a result of the species becoming thelytokous.

Methods

Females were collected from parental lines of O. mirus reared at 26, 30, 31, 32, 33, 34, and 36 °C. The offspring of these females were reared at 26 °C, and their sex-ratio was determined. In a subsequent experiment, the parental generation was switched between 26 °C and 36 °C during development to narrow down the critical period at which changes occurred that subsequently affected the sex-ratio of their offspring.

Results

The sex ratio was male biased in the offspring of O. mirus parents reared at 34 °C and 36 °C (high temperatures), even if the offspring themselves were reared at 26 °C. The constant temperature at which the percentage of males started to increase after two generations was 31 °C (10% males), rising to 39% males at 33 °C, and 100% males at 34 °C and 36 °C. Lasting more than 2 days, the critical period for the change toward a male biased sex ratio was during the second half of the parent’s development. Molecular diagnostic assays confirmed that O. mirus females contain Wolbachia and males do not. Examination of preserved males and male-female pairs under a dissecting microscope showed no signs of intersex characters. Observation of the mating behavior of live O. mirus showed that males initiate courtship by drumming their antennae on a female’s antennae, but after a few seconds, the females typically turn and walk away. However, a few instances of possible copulation were noted.

Conclusions

As hypothesized, the results indicated that thelytoky in O. mirus is likely mediated by Wolbachia bacteria. To maximize the population growth rate without generating males, the best temperature for mass rearing this species is 30 °C.
PTC2 region genotypes counteract Biomphalaria glabrata population differences between M-line and BS90 in resistance to infection by Schistosoma mansoni
Authors: Blouin Michael S. , Bollmann Stephanie R. , Tennessen Jacob A.
Published: September 2022

Background

Biomphalaria glabrata is a snail intermediate host for Schistosoma mansoni, a trematode responsible for human schistosomiasis. BS90 is one of the most well studied strains of B. glabrata owing to its high resistance to infection by most strains of S. mansoni. An F2 mapping study from 1999 identified two RAPD markers that associated with what appeared to be single-locus, dominant resistance by the BS90 population relative to the susceptible M-line population. One marker cannot be mapped, but the other, OPM-04, maps to within 5 Mb of PTC2, a region we recently showed has a very large effect on resistance within another snail population challenged by the same strain of parasite (PR1). Here we tested the hypothesis that the PTC2 region contains the causal gene/s that explain the iconic resistance of BS90 snails.

Methods

We used marker-assisted backcrossing to drive the BS90 version of the PTC2 region (+/−~1 Mb on either side) into an M-line (susceptible strain) genetic background, and the M-line version into a BS90 genetic background. We challenged the offspring with PR1-strain schistosomes and tested for effects of allelic variation in the PTC2 region in a common genetic background.

Results

Relative to M-line haplotypes, the BS90 haplotype actually confers enhanced susceptibility. So we reject our original hypothesis. One possible explanation for our result was that the causal gene linked to OPM-04 is near, but not in the PTC2 block that we introgressed into each line. So we used an F2 cross to independently test the effects of the PTC2 and OPM-04 regions in a randomized genetic background. We confirmed that the BS90 haplotype confers increased susceptibility, and we see a similar, although non-significant effect at OPM-04. We discuss possible reasons why our results differed so dramatically from those of the 1999 study. We also present Pacbio assemblies of the PTC2 and flanking region in BS90 and M-line, compare with previously published PTC2 haplotypes, and discuss candidate genes that might be behind the enhanced susceptibility of the BS90 haplotype.
Screening of potential key ferroptosis-related genes in sepsis
Authors: Cui Shunan , Niu Kun , Xie Yining , Li Shuo , Zhu Wenzhi , Yu Ling , Tan Hongyu
Published: September 2022

Background

Sepsis leads to multiple organ dysfunction caused by a dysregulated host response to infection with a high incidence and mortality. The effect of ferroptosis on the development of sepsis remains unclear. In this study, we aimed to identify the key ferroptosis-related genes involved in sepsis and further explore the potential biological functions of these ferroptosis-related genes in sepsis using bioinformatics analysis.

Methods

The GSE13904 (from children) and GSE28750 (from adults) datasets were downloaded from the Gene Expression Omnibus (GEO). The ferroptosis-related genes were obtained from the FerrDb database. The ferroptosis-related differentially expressed genes (DEGs) were screened by the limma R package. The DAVID online database or clusterProfiler R package was used for the functional enrichment analysis. Then, the STRING database was used to predict the interactions of proteins, and the CytoHubba plugin of Cytoscape was used to confirm key clustering modules. Then, the miRNAs and lncRNAs associated with the key clustering modules were predicted by miRWalk 2.0 and LncBase v.2 respectively. Finally, we generated a cecal ligation and puncture (CLP) polymicrobial sepsis model in C57 male mice and examined the expression of the mRNAs and noncoding RNAs of interest in peripheral blood leukocytes by PCR during the acute inflammation phase.

Results

In total, 34 ferroptosis-related DEGs were identified in both adult and pediatric septic patients. These ferroptosis-related DEGs were mainly enriched in inflammatory pathways. Then, a significant clustering module containing eight genes was identified. Among them, the following five genes were closely associated with the MAPK signaling pathway: MAPK14, MAPK8, DUSP1, MAP3K5 and MAPK1. Then, crucial miRNAs and lncRNAs associated with biomarker MAPK-related genes were also identified. In particular, let-7b-5p and NEAT1 were selected as noncoding RNAs of interest because of their correlation with ferroptosis in previous studies. Finally, we examined the mRNAs, miRNAs and lncRNAs of interest using CLP-induced sepsis in peripheral blood leukocytes of mice. The results showed that MAPK14, MAPK8, MAP3K5, MAPK1 and NEAT1 were upregulated, while DUSP1 and let-7b-5p were downregulated in the CLP group compared with the sham group.

Conclusions

The MAPK signaling pathway may play a key role in regulating ferroptosis during sepsis. This study provides a valuable resource for future studies investigating the mechanism of MAPK-related ferroptosis in sepsis.
Moonlighting proteins in medically relevant fungi
Authors: Arvizu-Rubio Verania J. , García-Carnero Laura C. , Mora-Montes Héctor Manuel
Published: September 2022

Moonlighting proteins represent an intriguing area of cell biology, due to their ability to perform two or more unrelated functions in one or many cellular compartments. These proteins have been described in all kingdoms of life and are usually constitutively expressed and conserved proteins with housekeeping functions. Although widely studied in pathogenic bacteria, the information about these proteins in pathogenic fungi is scarce, but there are some reports of their functions in the etiological agents of the main human mycoses, such as Candida spp., Paracoccidioides brasiliensis, Histoplasma capsulatum, Aspergillus fumigatus, Cryptococcus neoformans, and Sporothrix schenckii. In these fungi, most of the described moonlighting proteins are metabolic enzymes, such as enolase and glyceraldehyde-3-phosphate dehydrogenase; chaperones, transcription factors, and redox response proteins, such as peroxiredoxin and catalase, which moonlight at the cell surface and perform virulence-related processes, contributing to immune evasion, adhesions, invasion, and dissemination to host cells and tissues. All moonlighting proteins and their functions described in this review highlight the limited information about this biological aspect in pathogenic fungi, representing this a relevant opportunity area that will contribute to expanding our current knowledge of these organisms’ pathogenesis.
La producción de vida en América Latina y el Caribe y su relación con el diseño y otros campos afines: Sobre el desprendimiento, la desobediencia y la descolonización
Authors:   Universidade do Estado do Rio de Janeiro, Marques Correa Pamela Cordeiro , Carvalho Cardoso André Luiz ,   Universidade do Estado do Rio de Janeiro
Published: September 2022

Al trazar una breve genealogía del pensa­miento social latinoamericano, se advierte que en su esencia subyace la búsqueda por desprenderse de la modernidad occidental que impuso el proyecto colonial. Así, este artículo se propone, a través de la doble crítica de Laó-Montes y Vásquez, iniciar una crítica inmanente de la producción de vida en América Latina y el Caribe, así como de su relación con el Diseño y sus áreas afines, para lo cual se articulan ideas de los antro­pólogos Arturo Escobar y Tim Ingold. También se pretende desarrollar una crítica trascen­dente, una interpretación subalterna de esta producción a partir de la materialidad que se encuentra en el espacio urbano de la perife­ria capitalista; específicamente, en el diseño espontáneo periférico, o re-existencia del di­seño: la gambiarra brasileña y la desobedien­cia tecnológica cubana, entre otras, las que son consideradas como dispositivos para una “pedagogía encantada”. Como resulta­do, se señala que tanto el conocimiento de la realidad como el reconocimiento de la humanidad y la lucha por la emancipación, todos ellos presentes en la producción de vida a través de la historia subalterna, consti­tuyen, en conjunto, un camino para la desco­lonización.
Diálogos Sur-Sur en torno al diseño centrado en el buen vivir
Authors:   University of Auckland, Albarrán González Diana , Campbell Angus Donald ,   University of Auckland
Published: September 2022

Utilizando una metodología dialógica, en este artículo discutimos nuestras experien­cias de investigación doctoral y nuestros posicionamientos en dos contextos diferen­tes del Sur Global, en los que trabajamos con comunidades históricamente marginadas. La primera voz, originada en México, exploró la descolonización del diseño y los conoci­mientos textiles mayas en colaboración con un colectivo dirigido por mujeres en los Altos de Chiapas. La segunda voz, originada en Sudáfrica, exploró colaborativamente la in­novación tecnológica de los pequeños agri­cultores urbanos. El diálogo reflexiona sobre el “uno con el todo”, la colectividad, la condi­ción de resource(ful) o lleno de recursos, lo pluriversal y el equilibrio como principios rec­tores del diseño centrado en el buen vivir, lo que nos permite reflexionar sobre nuestros estudios. Discutimos los aprendizajes y las transformaciones en nuestra investigación en diseño, que transitó desde los enfoques dominantes hacia las formas indígenas y endógenas de conocer, ser y hacer.
Accesibilidad y movilidad en Milton Keynes: Una historia de diseño inclusivo en que los ideales de la planificación urbana y la intención de diseño se encuentran con las políticas de la discapacidad
Authors:   The Open University, Luck Rachael
Published: September 2022

Este documento ofrece la primera historia de diseño inclusivo de Milton Keynes, exami­nando cómo se concibió la accesibilidad de la ciudad en el momento en que fue planifi­cada y diseñada. A partir de testimonios de personas entrevistadas que recuerdan que se animó a las personas con discapacidad a vivir en Milton Keynes porque era accesible, se exploran los fundamentos de esta afirma­ción mediante recorridos, historias orales y pruebas documentales. El estudio revela que la “facilidad de movimiento y acceso” era uno de los objetivos de planificación de Milton Keynes y que la Open University era el lugar donde se desarrollaban los argu­mentos fundacionales que daban forma a la construcción social de la discapacidad. Resulta llamativo que el modelo social de la discapacidad y la injusticia de la inacce­sibilidad salieran a la luz en una ciudad que fue diseñada para permitir la movilidad y la accesibilidad, aun cuando el Milton Keynes de los setenta se recuerde como un lugar que atraía a diseñadores, académicos y activistas interesados en un futuro más equi­tativo.
Pattern of Non Motor Symptoms in Parkinson’s Disease: A Prospective Observational Study From a Tertiary Care Centre, Bihar, India
Authors: Rai Anand Kumar , Ranjan Abhay , Mudassir Sanaullah , Kumar Ashok
Published: September 2022

Introduction: Non motor symptoms are highly prevalent in Parkinson’s Disease (PD) but are often overshadowed by the dominance of motor symptoms. Aim: To assess non motor symptoms in patients with Parkinson’s disease. Materials and Methods: In this prospective observational study, patients of PD fulfilling United Kingdom Parkinson's Disease Society Brain Bank (UKPDSBB) criteria were recruited, between August 2019 to July 2021, in the Neurology Department of Indira Gandhi Institute of Medical Sciences, Patna, Bihar, India. The pattern of Non Motor Symptoms (NMS) in PD was studied using detailed questionnaire and association of NMS with age, gender and modified Hoehn and Yahr stage were assessed. Chi-square test and Student's t-test was calculated where required. Results: Total 102 patients were included, with male constituting 73.5% patients. The mean age was 60.14±13.55 years. Constipation (74, 72.55%) was the most common non motor symptom. Most of the patients belonged to mild stage (52.94%) followed by moderate (40.20%) and severe (6.86%) stages, according to modified Hoehn and Yahr classification. Rapid eye movement sleep behaviour disorder (n=15) and sexual dysfunction (n=28) were significantly more prevalent in male patients. Depression, REM sleep behaviour disorder, olfactory disturbance, visual disturbance, urinary urgency, sweating abnormality, constipation, vomiting and visual blurring were significantly common in patients with earlier disease stages while psychosis in patients with advanced stage. Conclusion: This study showed the high prevalence of non motor symptoms in PD patient which is consistent with other studies, but there are differences in the frequency of individual symptoms which may relate to cultural and geographic differences.
Nucleic Acid Test versus Enzyme Linked Section Immunosorbent Assay for Screening of Human Immunodeficiency Virus in Donated Blood Units: A Comparative Study at a Blood Centre in Western Rajasthan, India
Authors: Mathur Rishi , Mahawar NL , Arya DR , Bharti Arun
Published: September 2022

Introduction: With a population of 1.3 billion people and a frequency of Human Immunodeficiency Virus (HIV) (0.17-0.29%), Hepatitis B Virus (3-4%), and Hepatitis C Virus (0.09-15%) in the general population, maintaining blood safety is a difficult undertaking in India. The fourth-generation Enzyme Linked Immunosorbent Assay (ELISA), which can be used in place of Nucleic Acid Amplification Test (NAT) testing in situations with limited resources, has been recommended as the minimal HIV test to increase the safety of blood transfusions. Aim: To compare the fourth generation ELISA with NAT in the screening of transfusion transmissible HIV infection in blood donors. Materials and Methods: A cross-sectional study was carried out at the Blood Centre, Department of Immuno-Haematology and Transfusion Medicine, Sardar Patel Medical College and Associated Groups of Hospitals, in Bikaner, Rajasthan, India. A total of 2000 voluntary and replacement blood donors were recruited consecutively between January 2020 to December 2021 (two years), and their samples were screened using fourthgeneration ELISA. All of these samples were sent to AIIMS in Jodhpur for NAT to identify HIV RNA, HCV RNA and HBV DNA. Results: In this study, when the fourth generation ELISA negative samples were subjected to NAT, no sample was found to be reactive for HIV in NAT, i.e. there was no NAT yield for HIV. Conclusion: As a bare minimum, the fourth-generation ELISA test should be used for blood donor screening and can be considered a cost-effective and reliable test in a resource limited setting. However, additional tests can be advocated for an additional layer of blood safety.
Effect of Major Nutrients (N:P:K) on Plant Growth and Flower Yield of Jasmine (Jasminum auriculatum)
Authors: Bilji V. S. , Prasad Vipin M. , Topno Samir E.
Published: September 2022

The present investigation entitled, “Effect of major nutrients (N:P:K) on Plant growth and Flower yield of Jasmine (Jasminum auriculatum)” was under taken in the Department of Horticulture, Naini Agricultural Institute, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj (Allahabad) during 2021-2022. The experiment was layout in Randomized Block Design (RBD) with 09 treatments and each treatment replicated thrice. The treatments consist of different combinations of Chemical fertilizers (N, P and K). The treatment T8 (120:120:120g N:P:K/plant) was found the statistically significant compared to other treatment combination, which recorded highest plant height (92.44 cm), plant spread (61.82 cm), Number of leaves (142.77), Number of branches (16.29), followed by T6 (90:180:180g N:P:K/plant) and lowest growth by T2 (30:60:60g N:P:K/plant). The treatment T9 (120:240:240g N:P:K/plant) was found the statistically significant compared to other treatment combination, which recorded least days for flower bud development (14.25 days), days to first flower bud initiation (219.92 days), duration of flower (5.56 days), flower bud diameter (26.20 mm), flower bud length (2.16 cm), weight of single flower bud (0.198 g), flower yield per ha. (2.54 tons.) followed by T7 (105:210:210g N:P:K/plant).
Quasi‐Two‐Dimensional Ferromagnetic SrRuO3 Grown by Pulsed Laser Deposition with Layer‐by‐Layer Growth Fashion
Authors: Deng Zhixiong , Liu Junhua , Hong Yuhao , Wei Long , Hu Shilin , Xiao Wen , Li Lin , Wang Lingfei , Chen Kai , Liao Zhaoliang
Published: September 2022

One of the keys to the construction of metal oxide heterostructures is the short characteristic length scale, which requires controlled growth and interface engineering on an atomic level. At present, the growth mode of SrRuO3 (SRO) thin films grown on TiO2‐terminated (001) SrTiO3 (STO) substrates usually transitions from 2D layer‐by‐layer to step‐flow at the first few growth periods, which is not conducive to the construction of superlattices or multilayer films. In this paper, persistent layer‐by‐layer growth of SRO thin films is demonstrated by regulating the growth conditions. As a result, the thickness can be precisely controlled down to a single unit cell (u.c.) and achieve precise regulation of superlattices. Interestingly, the physical properties are well comparable to that of traditional step‐flow mode and the critical thickness (tc) for the dead layer is only 3 u.c. Through constructing SRO/STO superlattices, the SRO layers become more conductive and a quasi‐2D ferromagnetic monolayer film is achieved. The results pave a path toward SRO heterostructure synthesis and properties control at an atomic scale.
Age differences in expenditure responses to Supplemental Nutrition Assistance Program benefits
Authors: Waehrer Geetha M.
Published: September 2022

Using data from the 2007–2011 and 2012–2014 Consumer Expenditure Surveys, this study finds that unlike younger adults, senior Supplemental Nutrition Assistance Program (SNAP) participants' food‐at‐home expenditures did not respond to the 2009 increase in SNAP benefits. Higher benefits did not shift seniors' Engel curve for food‐at‐home spending suggesting that in‐kind SNAP benefits are equivalent to cash income for seniors, unlike younger adults. The 2013 decrease in SNAP benefits had no effect on senior or younger adult food spending. Changes in benefits also resulted in spillover effects on non‐food spending for seniors and younger adults including spending on transportation, utilities, health services, and other expenditures.
Atomically precise copper nanoclusters as ultrasmall molecular aggregates: Appealing compositions, structures, properties, and applications
Authors: Zhang Leon Li‐Min , Wong Wai‐Yeung
Published: September 2022

Metal nanoclusters (NCs) are ultrasmall molecular aggregates consisting of dozens to hundreds of metal atoms consolidated by organic ligands, which represent an emerging area of nanoscience. Amide a myriad of metal NCs, copper NCs (CuNCs) comprise a low‐cost, high‐value subclass that has attracted great attention. The variable copper cores and diversity of protecting ligands have rendered CuNCs interesting molecular aggregates featuring structural and compositional versatility, hence showing distinctive properties and potential applications. In the present review, we have summarized the progress on atomically precise CuNCs that exhibit a range of appealing properties and applications in different fields. This review is expected to provide not only an overview of the current development on atomically precise CuNCs, but also possible directions for the future design of novel CuNCs for fundamental studies and practical applications.
Evaluating perceptual and semantic interpretability of saliency methods: A case study of melanoma
Authors: Bokadia Harshit , Yang Scott Cheng‐Hsin , Li Zhaobin , Folke Tomas , Shafto Patrick
Published: September 2022

In order to be useful, XAI explanations have to be faithful to the AI system they seek to elucidate and also interpretable to the people that engage with them. There exist multiple algorithmic methods for assessing faithfulness, but this is not so for interpretability, which is typically only assessed through expensive user studies. Here we propose two complementary metrics to algorithmically evaluate the interpretability of saliency map explanations. One metric assesses perceptual interpretability by quantifying the visual coherence of the saliency map. The second metric assesses semantic interpretability by capturing the degree of overlap between the saliency map and textbook features—features human experts use to make a classification. We use a melanoma dataset and a deep‐neural network classifier as a case‐study to explore how our two interpretability metrics relate to each other and a faithfulness metric. Across six commonly used saliency methods, we find that none achieves high scores across all three metrics for all test images, but that different methods perform well in different regions of the data distribution. This variation between methods can be leveraged to consistently achieve high interpretability and faithfulness by using our metrics to inform saliency mask selection on a case‐by‐case basis. Our interpretability metrics provide a new way to evaluate saliency‐based explanations and allow for the adaptive combination of saliency‐based explanation methods.
Neuroprotection of Low‐Frequency Repetitive Transcranial Magnetic Stimulation after Ischemic Stroke in Rats
Authors: Buetefisch Cathrin M. , Wei Ling , Gu Xiaohuan , Epstein Charles M. , Yu Shan P.
Published: September 2022

Objective

Stroke is a leading cause of human death and disability. Effective early treatments with reasonable therapeutic windows remain critically important to improve the outcomes of stroke. Transcranial magnetic stimulation (TMS) is an established noninvasive technique that has been applied clinically and in animal research for multiple brain disorders, but few studies have examined acute neuroprotection against ischemic stroke. The present investigation tested the novel approach of low‐frequency repetitive TMS (rTMS) as an acute treatment after ischemic stroke.

Methods

Adult male rats received focal ischemic surgery through occlusion of the right middle cerebral artery for 60 minutes. The rats received either rTMS or sham treatment with 1.5‐, 3‐, 4‐, or 7‐hour delay after the onset of stroke. Low‐frequency and low‐intensity rTMS was applied to the rat brain for two 30‐minute episodes separated by a 1‐hour interval.

Results

Three days after stroke, compared to stroke controls, rats receiving rTMS treatment with a 1.5‐hour delay showed a 35% reduction of infarct volume. Protective effects were also seen with 3‐ or 4‐hour‐delayed treatments by rTMS, shown as reduced infarct volume and cell death. rTMS treatment upregulated the antiapoptotic factor Bcl‐2 and downregulated the proapoptotic caspase‐3 cleavage, expressions of Bax and matrix metallopeptidase‐9. In sensorimotor functional assessments 3 to 21 days after stroke, rats receiving rTMS treatment with a 1.5‐ or 3‐hour delay showed significantly better performance compared to stroke controls.

Interpretation

These results support the inference that low‐frequency rTMS may be feasible as a neuroprotective acute treatment after ischemic stroke. ANN NEUROL 2023;93:336–347
Bi‐polaron Transport and Magnetic Field Induced Pauli Spin Blockade in Redox‐Active Molecular Junctions
Authors: Ding Xiaohai , Xue Junhong , Ding Shuaishuai , Chen Cong , Wang Xiaojing , Yu Xi , Hu Wenping
Published: September 2022

We report the bi‐polaron transport and magnetic field induced Pauli spin‐blockade in solid‐state molecular junctions (MJs) evidenced by a positive magnetoresistance (MR). The junction was made of thin layers of redox‐active ruthenium polypyridyl‐oligomers Ru(tpy)2 sandwiched between conducting amorphous carbon (a‐C) electrodes. The redox‐active Ru(tpy)2 molecule, which enables small polaron and deep traps in the charge transport of the Ru(tpy)2 MJ as revealed by the temperature‐dependent current–voltage response, leads to the formation of the bi‐polaron and magnetic field induced Pauli spin blockade, resulting into the MR. At the meantime, the reliable and controllable device performance renders a rigid thickness‐dependent MR evolution. The bi‐polaron transport revealed in our study underscores the importance of the multi‐particle transport by molecular design in MJs and laid the foundation for magnetic‐electronic function in molecular‐scale devices.
DNA‐Encoded Nanomaterials with Controllable Properties
Authors: Guo Yuchun , Ren Jiangtao , Wang Erkang
Published: September 2022

DNA as an attractive capping ligand or template has been extensively utilized for synthesizing nanomaterials, and fabricating nano‐systems with tuneable properties. This review aims to summarize related significant progress on DNA‐encoded nanomaterials and their controllable properties including catalysis, surface plasmon resonance, chirality, surface‐enhanced Raman scattering and fluorescence, moreover, to present the underlying clues to engineer nanomaterials with DNA on the basis of DNA‐metal ion and DNA‐nanomaterial interactions. The apparent utility of diverse DNA modules including DNA homopolymers (e. g., poly adenine), secondary structures (e. g., triplex) and DNA nanostructures (e. g., DNA origami), etc., is revealed, which is derived from their strong specific interactions, stimulus‐responsive features, or excellent addressable functions, etc. Accompanied by insight into the underlying mechanism of DNA‐participated interactions, it is anticipated that, new DNA‐encoded nanomaterials will be reported and contribute to exploration of intelligent nanocatalysts, nanoprobes and nanomedicines.
Synthesis and properties of environmentally friendly double‐network fire fighting gel: Based on natural polymer/industrial solid waste
Authors: Lu Wei , Zhang Huilin , Qi Guansheng , Hu Xiangming , Sun Lulu , Su Hao , Zhang Qian
Published: September 2022

In this paper, a new kind of environmental friendly double‐network gel material was prepared. The first network structure was formed by the graft copolymerization of sodium lignosulfonate (LS) and acrylic acid (AA), and the second network structure was formed by the chelation reaction of sodium alginate (SA) and carbide slag clarified solution (Ca2+). Through an orthogonal experiment, the effects of raw material addition on the compressive strength and apparent viscosity of the gel were analyzed. According to the analysis results, the optimal experimental ratio was obtained, i.e., 2 wt% of LS, 0.25 wt% of SA, 15 wt% of AA, 0.1 wt% of MBA and 0.3 wt% of APS. Furthermore, the structure of the gel are characterized by FTIR, XRD, SEM, XPS, and TG‐DTG, and the results prove that the gel successfully polymerized and a stable three‐dimensional network structure is formed. The results of water absorption experiment disclose that the gel is sensitive to ions and pH, and the water absorption rate reaches 121.25 times. In addition, the results of the air leakage experiment and fire extinguishing experiment show that the gel can effectively cover the surface of crushed coal and densely fill the gaps, demonstrating a good plugging capability and fire extinguishing capability.
Inhibitor of NF‐κB Kinase Subunit ε Contributes to Neuropsychiatric Manifestations in Lupus‐Prone Mice Through Microglial Activation
Authors: Karino Kohei , Kono Michihito , Takeyama Shuhei , Kudo Yuki , Kanda Masatoshi , Abe Nobuya , Aso Kuniyuki , Fujieda Yuichiro , Kato Masaru , Oku Kenji , Amengual Olga , Atsumi Tatsuya
Published: September 2022

Objective

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by multiorgan dysfunction. Neuropsychiatric SLE (NPSLE) occurs in 30–40% of lupus patients and is the most severe presentation of SLE, frequently resulting in limitation of daily life. Recent studies have shown that microglia, tissue‐resident macrophages in the central nervous system, are involved in the pathogenesis of NPSLE. This study was undertaken to explore new therapeutic targets for NPSLE focusing on microglia.

Methods

RNA sequencing of microglia in MRL/lpr, lupus‐prone mice, as well as that of microglia cultured in vitro with cytokines were performed. A candidate gene, which could be a therapeutic target for NPSLE, was identified, and its role in microglial activation and phagocytosis was investigated using specific inhibitors and small interfering RNA. The effect of intracerebroventricular administration of the inhibitor on the behavioral abnormalities of MRL/lpr was also evaluated.

Results

Transcriptome analysis revealed the up‐regulation of Ikbke, which encodes the inhibitor of NF‐κB kinase subunit ɛ (IKBKε) in both microglia from MRL/lpr mice and cytokine‐stimulated microglia in vitro. Intracerebroventricular administration of an IKBKε inhibitor ameliorated cognitive function and suppressed microglial activation in MRL/lpr mice. Mechanistically, IKBKε inhibition reduced glycolysis, which dampened microglial activation and phagocytosis.

Conclusion

These findings suggest that IKBKε plays a vital role in the pathogenesis of NPSLE via microglial activation, and it could serve as a therapeutic target for NPSLE.
Interactions between hydroxylated polycyclic aromatic hydrocarbons and serum albumins: multispectral and molecular docking analyses
Authors: Li Meng‐shuo , Zhang Jing , Zhu Ya‐xian , Zhang Yong
Published: September 2022

Hydroxylated polycyclic aromatic hydrocarbons (OH‐PAHs) can bind to serum albumin and influence their distribution and elimination in organisms. Here, multispectral analysis and molecular docking methods were used to investigate the binding mechanism of two OH‐PAHs, 1‐hydroxyphenanthrene (1‐OHPhe) and 9‐hydroxyphenanthrene (9‐OHPhe), with two homologous serum albumins, human serum albumin (HSA) and bovine serum albumin (BSA). The quenching constants of HSA with 1‐OHPhe and 9‐OHPhe were much larger than those for BSA. Energy transfer from the tryptophan (Trp) residues in HSA to 1‐OHPhe and 9‐OHPhe was more probable than from Trp in BSA. The interactions of 1‐OHPhe and 9‐OHPhe with Trp in HSA and BSA altered the microenvironment of Trp. Molecular docking results revealed that the binding modes and binding forces of 1‐OHPhe and 9‐OHPhe with HSA and BSA were different. The two OH‐PAHs were used as fluorescent probes to analyze the microenvironmental hydrophobicities of HSA and BSA, which were distinctly different. The structural difference between HSA and BSA induced significant variations in their binding behaviour with 1‐OHPhe and 9‐OHPhe. Moreover, HSA was more susceptible to 1‐OHPhe and 9‐OHPhe than BSA. This work suggests that the differences between the two serum albumins should be considered in related studies.
Pharmacokinetics and tissue distribution of five bioactive components in the Corydalis yanhusuo total alkaloids transdermal patch following Shenque acupoint application in rats assessed by ultra‐performance liquid chromatography–tandem mass spectrometry
Authors: Wang Huinan , Wang Zhicheng , Jiang Mingrui , Yue Zhuzhu , Zhang Jingqiu , Chen Mengyu , Wang Menglin , Wei Xiaotong , Shi Shuanghui , Wang Yingzi
Published: September 2022

The purpose of this study was to evaluate the pharmacokinetics and tissue distribution of the Corydalis yanhusuo total alkaloids transdermal patch (CTTP) following Shenque acupoint application in rats. The concentrations of corydaline, tetrahydropalmatine, tetrahydrocolumbamine, protopine, and dehydrocorydaline in rat plasma and various tissues were simultaneously detected by ultra‐performance liquid chromatography–tandem mass spectrometry after Shenque acupoint administration of CTTP. Plasma, heart, liver, spleen, lung, and kidney tissue samples were collected at specific times and separated by gradient elution on an ACQUITY UPLC HSS T3 column (1.8 μm, 100 mm × 2.1 mm) with a mobile phase of 0.01% formic acid aqueous solution and acetonitrile–0.01% formic acid. The methodological results showed that the selectivity, linear range, accuracy, precision, stability, matrix effect, and extraction recovery of the established method met the requirements of biological sample analysis. The results indicated that CTTP following Shenque acupoint administration rapidly delivered adequate drug into rat blood and maintained an effective plasma level for a significantly longer time than non‐acupoint administration. Furthermore, CTTP effectively reached the liver through Shenque acupoint administration and showed tissue selectivity. The data obtained could provide a prospect for the treatment of chronic pain with CTTP following Shenque acupoint application.
Overall metabolic network analysis of urine in hyperlipidemic rats treated with Bidens bipinnata L.
Authors: Li Shu‐Jiao , Wang Yu‐Qing , Zhuang Guo , Jiang Xu , Shui Dong , Wang Xiao‐Yu
Published: September 2022

Hyperlipidemia has been highlighted as one of the most prominent and global chronic conditions nowadays. Bidens bipinnata L. (BBL), a folk medicine in contemporary China, has efficacy in the treatment of hyperlipidemia (HLP) in China. Although some physiological and pathological function parameters of hyperlipidemia have been investigated, little information about the changes in small metabolites in biofluids has been reported. In the present study, global metabolic profiling with high‐performance liquid chromatography–linear ion trap/Orbitrap high‐resolution mass spectrometry (HPLC–LTQ/Orbitrap MS) combined with a pattern recognition method was performed to discover the underlying lipid‐regulating mechanisms of BBL on hyperlipidemic rats induced by high‐fat diet (HFD). The total of four metabolites, up‐ or down‐regulated (p < 0.05 or 0.01), were identified and contributed to the progression of hyperlipidemia. These promising identified biomarkers underpin the metabolic pathway, including glyoxylate and dicarboxylate metabolism, the TCA cycle, sphingolipid metabolism and purine metabolism. They are disturbed in hyperlipidemic rats, and are identified using pathway analysis with MetPA. The altered metabolite indices could be regulated closer to normal levels after BBL intervention. The results demonstrated that urinary metabolomics is a powerful tool in the clinical diagnosis and treatment of hyperlipidemia to provide information on changes in metabolite pathways.