bluuebunny/crossref_metadata_2025 huggingface dataset:
Peyote
Authors: Dawson Alexander
Published: January 2024

Indigenous peoples in Mexico and the United States have consumed peyote for millennia. It has also been the subject of interest and concern among Euro-Americans since the Spanish Conquest of Mexico. . Amid growing use by non-Native people, peyote was first banned by the Spanish Inquisition in 1620. While the historical record in the immediate period after the Inquisition left Mexico in 1824 is sparse, extant evidence suggests that peyote continued to circulate in herbal markets as a treatment for any number of maladies. Beginning in the late 19th century, peyote was the subject of significant scientific interest (mainly around the treatment of mental disorders), along with a growing fascination with and concern over its use in Indigenous communities in Mexico and the United States. Peyotism in Mexico at this point was a long-standing tradition among a limited number of communities, and it was linked to the evangelical cultural revivalist Native American Church in the United States. Use by non-Native persons (in both formally therapeutic settings and more informal settings) expanded considerably during the 1950s and 1960s. Peyote would ultimately be banned in the United States in 1965 and Mexico in 1971, although in both cases exceptions were made for Indigenous peyotists. Currently, peyote is the subject of a series of ecological concerns, as peyote habitats on both sides of the border have been threatened by climate change, economic development, and overharvesting.
Transcontinental Meteorology Infrastructures From Ancient Mesopotamia to the Early Modern Age
Authors: Wille Robert-Jan
Published: January 2024

The current global infrastructure of meteorology partly builds on older transcontinental structures of weather science and meteorological philosophy. For several millennia, the large belt stretching from East Asia, through mountains, silk roads, and the Indian Ocean, to the seas and river deltas where Western Eurasia and North Africa border on each other, has formed a key region. From Ancient Mesopotamia to the 16th century, a continuous and multi-site infrastructure emerged that was organized around meteorological texts, including not only scrolls, papyri, and manuscripts, but also ideas and concepts, as well as meteorological writers and readers traveling between institutions and storehouses.

Not considering the long history of orally transmitted pre-Mesopotamian weather knowledge, the first large-scale textual infrastructures were inseparable from astronomical tabulation and dynastical prognostication. In later millennia, in the city states and empires of Greece, Rome, China, and India, “meteorology” became a distinct subject, with its own language and concepts, even though it remained allied to agriculture and statecraft as knowledge practices. At the beginning of the Common Era, the first distinct meteorological instruments appeared, first in East Asia and later in the Near East and Greece.

In the 15th and 16th centuries, new regions were added to this knowledge infrastructure, with or without force, making it almost global: the Atlantic and Pacific Oceans, their Eurasian and African shores, and the Americas. This changed the power dynamics, with European empires controlling the transatlantic infrastructures of knowledge and labor. Ideas that were transcontinental in origin now became part of a Western European program to conquer the globe.
Basin Development Paths: Lessons From the Colorado and Nile River Basins
Authors: Wheeler Kevin
Published: January 2024

Complex societies have developed near rivers since antiquity. As populations have expanded, the need to exploit rivers has grown to supply water for agriculture, build cities, and produce electricity. Three key aspects help to characterize development pathways that societies have taken to expand their footprint in river basins including: (a) the evolution of the information systems used to collect knowledge about a river and make informed decisions regarding how it should be managed, (b) the major infrastructure constructed to manipulate the flows of water, and (c) the institutions that have emerged to decide how water is managed and governed. By reflecting on development pathways in well-documented transboundary river basins, one can extract lessons learned to help guide the future of those basins and the future of other developing basins around the world.
The Irony of British Human Rights Exceptionalism, 1948–1998
Authors: Kahn Jeffrey
Published: January 2024

Assessments of London’s relationship with Strasbourg tend to highlight recent discontent about perceived infringements of parliamentary sovereignty by the European Court of Human Rights. The British criticism is, in short, that this is not what we signed up for. But this complaint is not new. This Article argues against understanding this story as one in which this relationship only recently soured. A recurrent theme in the United Kingdom’s involvement with the institutions of the Council of Europe, especially its human rights commission and court, has been the dawning realization, again and again, that the treaties and institutions that the United Kingdom’s own lawyers and diplomats were so instrumental in devising for an emergent Council of Europe could and would be applied to its own foreign and domestic interests.

It is ironic that the United Kingdom should have been so central to crafting human rights instruments from which it later sought to exempt itself. The irony is heightened by the frequency with which this founding member state realized, opposed, and then accepted the implications of its actions. An unexpected consequence of this ironic refrain of exceptionalism may be to reinforce the objective legitimacy of the system’s most challenged institutions. After all, it is hard to allege an infringement of parliamentary sovereignty if the state’s ministers repeatedly choose to abide by the (sometimes changing) treaty obligations they helped establish. On the other hand, when ministers in high dudgeon declare their outrage at the latest Strasbourg ruling, the erosion they facilitate to popular legitimacy may ultimately reduce overall respect for the European Convention. Ironically, we become the masks we wear.
The landscape of the methodology in drug repurposing using human genomic data: a systematic review
Authors: Wang Lijuan , Lu Ying , Li Doudou , Zhou Yajing , Yu Lili , Mesa Eguiagaray Ines , Campbell Harry , Li Xue , Theodoratou Evropi
Published: January 2024

The process of drug development is expensive and time-consuming. In contrast, drug repurposing can be introduced to clinical practice more quickly and at a reduced cost. Over the last decade, there has been a significant expansion of large biobanks that link genomic data to electronic health record data, public availability of various databases containing biological and clinical information and rapid development of novel methodologies and algorithms in integrating different sources of data. This review aims to provide a thorough summary of different strategies that utilize genomic data to seek drug-repositioning opportunities. We searched MEDLINE and EMBASE databases to identify eligible studies up until 1 May 2023, with a total of 102 studies finally included after two-step parallel screening. We summarized commonly used strategies for drug repurposing, including Mendelian randomization, multi-omic-based and network-based studies and illustrated each strategy with examples, as well as the data sources implemented. By leveraging existing knowledge and infrastructure to expedite the drug discovery process and reduce costs, drug repurposing potentially identifies new therapeutic uses for approved drugs in a more efficient and targeted manner. However, technical challenges when integrating different types of data and biased or incomplete understanding of drug interactions are important hindrances that cannot be disregarded in the pursuit of identifying novel therapeutic applications. This review offers an overview of drug repurposing methodologies, providing valuable insights and guiding future directions for advancing drug repurposing studies.
Recognition of rare antinuclear antibody patterns based on a novel attention-based enhancement framework
Authors: Zeng Junxiang , Gao Xiupan , Gao Limei , Yu Youyou , Shen Lisong , Pan Xiujun
Published: January 2024

Rare antinuclear antibody (ANA) pattern recognition has been a widely applied technology for routine ANA screening in clinical laboratories. In recent years, the application of deep learning methods in recognizing ANA patterns has witnessed remarkable advancements. However, the majority of studies in this field have primarily focused on the classification of the most common ANA patterns, while another subset has concentrated on the detection of mitotic metaphase cells. To date, no prior research has been specifically dedicated to the identification of rare ANA patterns. In the present paper, we introduce a novel attention-based enhancement framework, which was designed for the recognition of rare ANA patterns in ANA-indirect immunofluorescence images. More specifically, we selected the algorithm with the best performance as our target detection network by conducting comparative experiments. We then further developed and enhanced the chosen algorithm through a series of optimizations. Then, attention mechanism was introduced to facilitate neural networks in expediting the learning process, extracting more essential and distinctive features for the target features that belong to the specific patterns. The proposed approach has helped to obtained high precision rate of 86.40%, 82.75% recall, 84.24% F1 score and 84.64% mean average precision for a 9-category rare ANA pattern detection task on our dataset. Finally, we evaluated the potential of the model as medical technologist assistant and observed that the technologist’s performance improved after referring to the results of the model prediction. These promising results highlighted its potential as an efficient and reliable tool to assist medical technologists in their clinical practice.
Interpretable feature extraction and dimensionality reduction in ESM2 for protein localization prediction
Authors: Luo Zeyu , Wang Rui , Sun Yawen , Liu Junhao , Chen Zongqing , Zhang Yu-Juan
Published: January 2024

As the application of large language models (LLMs) has broadened into the realm of biological predictions, leveraging their capacity for self-supervised learning to create feature representations of amino acid sequences, these models have set a new benchmark in tackling downstream challenges, such as subcellular localization. However, previous studies have primarily focused on either the structural design of models or differing strategies for fine-tuning, largely overlooking investigations into the nature of the features derived from LLMs. In this research, we propose different ESM2 representation extraction strategies, considering both the character type and position within the ESM2 input sequence. Using model dimensionality reduction, predictive analysis and interpretability techniques, we have illuminated potential associations between diverse feature types and specific subcellular localizations. Particularly, the prediction of Mitochondrion and Golgi apparatus prefer segments feature closer to the N-terminal, and phosphorylation site-based features could mirror phosphorylation properties. We also evaluate the prediction performance and interpretability robustness of Random Forest and Deep Neural Networks with varied feature inputs. This work offers novel insights into maximizing LLMs’ utility, understanding their mechanisms, and extracting biological domain knowledge. Furthermore, we have made the code, feature extraction API, and all relevant materials available at https://github.com/yujuan-zhang/feature-representation-for-LLMs.
CAP-RNAseq: an integrated pipeline for functional annotation and prioritization of co-expression clusters
Authors: Vural-Ozdeniz Merve , Calisir Kubra , Acar Rana , Yavuz Aysenur , Ozgur Mustafa M , Dalgıc Ertugrul , Konu Ozlen
Published: January 2024

Cluster analysis is one of the most widely used exploratory methods for visualization and grouping of gene expression patterns across multiple samples or treatment groups. Although several existing online tools can annotate clusters with functional terms, there is no all-in-one webserver to effectively prioritize genes/clusters using gene essentiality as well as congruency of mRNA-protein expression. Hence, we developed CAP-RNAseq that makes possible (1) upload and clustering of bulk RNA-seq data followed by identification, annotation and network visualization of all or selected clusters; and (2) prioritization using DepMap gene essentiality and/or dependency scores as well as the degree of correlation between mRNA and protein levels of genes within an expression cluster. In addition, CAP-RNAseq has an integrated primer design tool for the prioritized genes. Herein, we showed using comparisons with the existing tools and multiple case studies that CAP-RNAseq can uniquely aid in the discovery of co-expression clusters enriched with essential genes and prioritization of novel biomarker genes that exhibit high correlations between their mRNA and protein expression levels. CAP-RNAseq is applicable to RNA-seq data from different contexts including cancer and available at http://konulabapps.bilkent.edu.tr:3838/CAPRNAseq/ and the docker image is downloadable from https://hub.docker.com/r/konulab/caprnaseq.
The CUT&RUN greenlist: genomic regions of consistent noise are effective normalizing factors for quantitative epigenome mapping
Authors: de Mello Fabio N , Tahira Ana C , Berzoti-Coelho Maria Gabriela , Verjovski-Almeida Sergio
Published: January 2024

Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a recent development for epigenome mapping, but its unique methodology can hamper proper quantitative analyses. As traditional normalization approaches have been shown to be inaccurate, we sought to determine endogenous normalization factors based on the human genome regions of constant nonspecific signal. This constancy was determined by applying Shannon’s information entropy, and the set of normalizer regions, which we named the ‘Greenlist’, was extensively validated using publicly available datasets. We demonstrate here that the greenlist normalization outperforms the current top standards, and remains consistent across different experimental setups, cell lines and antibodies; the approach can even be applied to different species or to CUT&Tag. Requiring no additional experimental steps and no added cost, this approach can be universally applied to CUT&RUN experiments to greatly minimize the interference of technical variation over the biological epigenome changes of interest.
Multi-modal features-based human-herpesvirus protein–protein interaction prediction by using LightGBM
Authors: Yang Xiaodi , Wuchty Stefan , Liang Zeyin , Ji Li , Wang Bingjie , Zhu Jialin , Zhang Ziding , Dong Yujun
Published: January 2024

The identification of human-herpesvirus protein–protein interactions (PPIs) is an essential and important entry point to understand the mechanisms of viral infection, especially in malignant tumor patients with common herpesvirus infection. While natural language processing (NLP)-based embedding techniques have emerged as powerful approaches, the application of multi-modal embedding feature fusion to predict human-herpesvirus PPIs is still limited. Here, we established a multi-modal embedding feature fusion-based LightGBM method to predict human-herpesvirus PPIs. In particular, we applied document and graph embedding approaches to represent sequence, network and function modal features of human and herpesviral proteins. Training our LightGBM models through our compiled non-rigorous and rigorous benchmarking datasets, we obtained significantly better performance compared to individual-modal features. Furthermore, our model outperformed traditional feature encodings-based machine learning methods and state-of-the-art deep learning-based methods using various benchmarking datasets. In a transfer learning step, we show that our model that was trained on human-herpesvirus PPI dataset without cytomegalovirus data can reliably predict human-cytomegalovirus PPIs, indicating that our method can comprehensively capture multi-modal fusion features of protein interactions across various herpesvirus subtypes. The implementation of our method is available at https://github.com/XiaodiYangpku/MultimodalPPI/.
Sex and reproduction: a theoretical analysis
Authors: Xu Zhongneng
Published: January 2024

Sex in some organisms shows a continuous spectrum. Sometimes sexual differences in an individual’s organs are contradictory and determined by physiological, pathological and environmental factors, leading to debate over the definitions of sex in individuals. This study indicates that the essence of sex during reproduction distinguishes between reproductive subjects and that the unit of reproduction is not the individual but the reproductive cell. To properly supplement the existing definitions of sex, a definition of sex in reproduction in which only reproductive cells have sexes was herein addressed, focusing on material contributions to reproduction and the formation of zygotes by reproductive cells. Equations to describe sexes are proposed, as well as equations to make this only reproductive-cell sex definition compatible with the individual sex definition based on the quantitative proportions of different reproductive cells. The explanation of sex determination, sex differences and sex competition based on the definition of only reproductive-cell sex in reproduction is discussed.
The basal forebrain cholinergic system as target for cell replacement therapy in Parkinson’s disease
Authors: Björklund Anders , Barker Roger A
Published: January 2024

In recent years there has been a renewed interest in the basal forebrain cholinergic system as a target for the treatment of cognitive impairments in patients with Parkinson’s disease, due in part to the need to explore novel approaches to treat the cognitive symptoms of the disease and in part to the development of more refined imaging tools that have made it possible to monitor the progressive changes in the structure and function of the basal forebrain system as they evolve over time. In parallel, emerging technologies allowing the derivation of authentic basal forebrain cholinergic neurons from human pluripotent stem cells are providing new powerful tools for the exploration of cholinergic neuron replacement in animal models of Parkinson’s disease-like cognitive decline.

In this review, we discuss the rationale for cholinergic cell replacement as a potential therapeutic strategy in Parkinson’s disease and how this approach can be explored in rodent models of Parkinson’s disease-like cognitive decline, building on insights gained from the extensive animal experimental work that was performed in rodent and primate models in the 1980s and 90s. Although therapies targeting the cholinergic system have so far been focused mainly on patients with Alzheimer’s disease, Parkinson’s disease with dementia may be a more relevant condition. In Parkinson’s disease with dementia, the basal forebrain system undergoes progressive degeneration and the magnitude of cholinergic cell loss has been shown to correlate with the level of cognitive impairment. Thus, cell therapy aimed to replace the lost basal forebrain cholinergic neurons represents an interesting strategy to combat some of the major cognitive impairments in patients with Parkinson’s disease dementia.
Digest: The detrimental effects of abrupt environmental stress on diversity and fitness
Authors: Dela Cruz Gio Randon , Talukdar Jishnu Pathak
Published: January 2024

Does the rate of environmental deterioration influence diversity and fitness in a population? Zhou and Zhang 2024 found that, compared with gradual stress, abrupt stress led to a larger decrease in fitness and diversity in the bacterium, Pseudomonas fluorescens. These findings help explain the relationship between species evolution and antimicrobial resistance.
Impact of Residential Area Characteristics and Political Group Participation on Depression Among Middle-Aged and Older Adults: Results of an 11-Year Longitudinal Study
Authors: Lin Yu-Chun , Yan Huang-Ting
Published: January 2024

Background and Objectives

The claim that political group attendance is associated with poor mental health among older adults may be conditioned on geographic conditions. This study examined the geographical context in which political group participation may be associated with depression.

Research Design and Methods

The 11-year follow-up data from the Taiwan Longitudinal Study on Aging, covering 5,334 persons aged ≥50 years, were analyzed using random-effects panel logit models. Depression was assessed using 10 items on the Centre for Epidemiologic Studies Depression scale. Participants were asked to indicate whether they belonged to different social groups. We modeled depression as a function of political group participation (the independent variable) and geographical region (moderators), adjusting for individual-level characteristics.

Results

Respondents in political groups were more likely to report depression than those in nonpolitical groups (adjusted odds ratio [AOR] = 1.90, 95% confidence interval [CI] = 1.34–2.68). Between urban and rural settlements, there were no statistically significant differences in mental health outcomes among older adults engaged in political groups (AOR = 1.72, 95% CI = 0.81–3.67). For those who remained politically engaged, living in areas with lower levels of electoral competition was associated with a lower likelihood of depression (AOR = 0.92, 95% CI = 0.86–0.98); this conditional effect was not prevalent among those who were solely engaged in nonpolitical groups (AOR = 1.02, 95% CI = 0.99–1.03).

Discussion and Implications

Political group participation is associated with poor mental health among older adults living in politically competitive regions.
MMV_Im2Im: an open-source microscopy machine vision toolbox for image-to-image transformation
Authors: Sonneck Justin , Zhou Yu , Chen Jianxu
Published: January 2024

Over the past decade, deep learning (DL) research in computer vision has been growing rapidly, with many advances in DL-based image analysis methods for biomedical problems. In this work, we introduce MMV_Im2Im, a new open-source Python package for image-to-image transformation in bioimaging applications. MMV_Im2Im is designed with a generic image-to-image transformation framework that can be used for a wide range of tasks, including semantic segmentation, instance segmentation, image restoration, image generation, and so on. Our implementation takes advantage of state-of-the-art machine learning engineering techniques, allowing researchers to focus on their research without worrying about engineering details. We demonstrate the effectiveness of MMV_Im2Im on more than 10 different biomedical problems, showcasing its general potentials and applicabilities. For computational biomedical researchers, MMV_Im2Im provides a starting point for developing new biomedical image analysis or machine learning algorithms, where they can either reuse the code in this package or fork and extend this package to facilitate the development of new methods. Experimental biomedical researchers can benefit from this work by gaining a comprehensive view of the image-to-image transformation concept through diversified examples and use cases. We hope this work can give the community inspirations on how DL-based image-to-image transformation can be integrated into the assay development process, enabling new biomedical studies that cannot be done only with traditional experimental assays. To help researchers get started, we have provided source code, documentation, and tutorials for MMV_Im2Im at [https://github.com/MMV-Lab/mmv_im2im] under MIT license.
Unveiling Colitis: A Journey through the Dextran Sodium Sulfate-induced Model
Authors: Yang Chunhua , Merlin Didier
Published: January 2024

Animal models of inflammatory bowel disease (IBD) are valuable tools for investigating the factors involved in IBD pathogenesis and evaluating new therapeutic options. The dextran sodium sulfate (DSS)-induced model of colitis is arguably the most widely used animal model for studying the pathogenesis of and potential treatments for ulcerative colitis (UC), which is a primary form of IBD. This model offers several advantages as a research tool: it is highly reproducible, relatively easy to generate and maintain, and mimics many critical features of human IBD. Recently, it has also been used to study the role of gut microbiota in the development and progression of IBD and to investigate the effects of other factors, such as diet and genetics, on colitis severity. However, although DSS-induced colitis is the most popular and flexible model for preclinical IBD research, it is not an exact replica of human colitis, and some results obtained from this model cannot be directly applied to humans. This review aims to comprehensively discuss different factors that may be involved in the pathogenesis of DSS-induced colitis and the issues that should be considered when using this model for translational purposes.
Emergent Normativity: Communities of Practice, Technology, and Lethal Autonomous Weapon Systems
Authors: Bode Ingvild
Published: January 2024

Lethal autonomous weapon systems (LAWS) are the subject of considerable international debate turning around the extent to which humans remain in control over using force. But what is precisely at stake is less clear as stakeholders have different perspectives on the technologies that animate LAWS. Such differences matter because they shape the substance of the debate, which regulatory options are put on the table, and also normativity on LAWS in the sense of understandings of appropriateness. To understand this process, I draw on practice theories, science and technology studies (STS), and critical norm research. I argue that a constellation of communities of practice (CoPs) shapes the public debate about LAWS and focus on three of these CoPs: diplomats, weapon manufacturers, and journalists. Actors in these CoPs discursively perform practices of boundary-work, in the STS sense, to shape understandings of technologies at the heart of LAWS: automation, autonomy, and AI. I analyze these dynamics empirically in two steps: first, by offering a general-level analysis of practices of boundary-work performed by diplomats at the Group of Governmental Experts on LAWS from 2017 to 2022; and second, through examining such practices performed by weapon manufacturers and journalists in relation to the use of loitering munitions, a particular type of LAWS, in the Second Libyan Civil War (2014–2020).
Exploring Communities of Practice from an Informality Perspective: Insights from the AU, ECOWAS, and UN in West African Mediation Theaters
Authors: Tieku Thomas Kwasi , Yakohene Afua Boatemaa
Published: January 2024

The article explores how and why communities of practice (CoPs) of international organizations (IOs) work together effectively despite the rigid formal bureaucratic and institutional borders they inhabit. The manuscript explains how four informal mechanisms combined to enable CoPs embedded in the African Union (AU), the Economic Community of West African States (ECOWAS), and the United Nations (UN) Organization to resolve political crises in Burkina Faso, Gambia, Ghana, Guinea, Mali, and Togo between 2016 and 2022. The informal mechanisms allowed CoPs to overcome their institutional limitations, cross rigid organizational borders, and work together to resolve different political crises in the six countries. Some of the informal mechanisms were cultivated by CoPs, while others emerged organically from activities and interactions of these like-minded professionals. The informal instruments that were developed and used to resolve the crises provide a telling illustration of how CoPs create global governance norms, practices, processes, rules, and structures from below. The enabling role that informality played in the six conflict theaters suggests that paying close attention to the informal dimensions of CoPs has enormous analytical benefits.
Constructions of quorum sensing signaling network for activated sludge microbial community
Authors: Jin Ying , Chen Wenkang , Hu Jie , Wang Jinfeng , Ren Hongqiang
Published: January 2024

In wastewater treatment systems, the interactions among various microbes based on chemical signals, namely quorum sensing (QS), play critical roles in influencing microbial structure and function. However, it is challenging to understand the QS-controlled behaviors and the underlying mechanisms in complex microbial communities. In this study, we constructed a QS signaling network, providing insights into the intra- and interspecies interactions of activated sludge microbial communities based on diverse QS signal molecules. Our research underscores the role of diffusible signal factors in both intra- and interspecies communication among activated sludge microorganisms, and signal molecules commonly considered to mediate intraspecies communication may also participate in interspecies communication. QS signaling molecules play an important role as communal resources among the entire microbial group. The communication network within the microbial community is highly redundant, significantly contributing to the stability of natural microbial systems. This work contributes to the establishment of QS signaling network for activated sludge microbial communities, which may complement metabolic exchanges in explaining activated sludge microbial community structure and may help with a variety of future applications, such as making the dynamics and resilience of highly complex ecosystems more predictable.
Acceptability Study of Emotional Expressions of In-Vehicle Virtual Assistant
Authors: Kim Youngsang , Yoo Hoonsik
Published: January 2024

We analyzed the differences in drivers’ preferences for emotional expressions from an in-vehicle virtual assistant based on data collected from 823 respondents in five countries categorized into three different cultural settings: collectivism (Korea, China and Brazil), individualism (USA) and a mixture of both (Russia). To quantify the degree of acceptance, we used a 5-point Likert scale (1 = strongly disagree; 5 = strongly agree) on four emotion types categorized based on Thayer’s two-dimensional emotion model. Analysis revealed that respondents in all five countries preferred emotion type 1 (pleased, happy, excited) and emotion type 4 (calm, peaceful, relaxed), that is, positive emotions under Thayer’s two-dimensional emotion model expressions, and they showed low acceptance for emotion type 2 (nervous, angry, annoying) and emotion type 3 (sad, bored, sleepy), negative emotional expressions. In a cross-cultural comparative analysis, Brazil and China ranked highest in both positive emotion types (1 and 4), and Korea ranked highest in negative emotion types.
Effects of dietary xylanase supplementation on growth performance, intestinal health, and immune response of nursery pigs fed diets with reduced metabolizable energy
Authors: Baker Jonathan T , Duarte Marcos Elias , Kim Sung Woo
Published: January 2024

This study aimed to investigate the effects of xylanase on growth performance and intestinal health of nursery pigs fed diets with reduced metabolizable energy (ME). One hundred ninety-two pigs at 8.7 kg ± 0.7 body weight (BW) after 7 d of weaning were allotted in a randomized complete block design with initial BW and sex as blocks. Eight dietary treatments consisted of 5 ME levels (3,400, 3,375, 3,350, 3,325, and 3,300 kcal ME/kg) below the NRC (2012) requirement and 4 levels of xylanase (0, 1,200, 2,400, and 3,600 XU/kg) to a diet with 3,300 kcal ME/kg. All pigs received their respective treatments for 35 d in 2 phases, pre-starter (14 d) and starter (21 d). On day 35, eight pigs in 3,400 kcal/kg (CON), 3,300 kcal/kg (LE), and 3,300 kcal/kg + 3,600 XU xylanase/kg (LEX) were euthanized to collect jejunal tissues and digesta for the evaluation of mucosa-associated microbiota, intestinal immune response, oxidative stress status, intestinal morphology, crypt cell proliferation, and digesta viscosity as well as ileal digesta to measure apparent ileal digestibility. Data were analyzed using the MIXED procedure on SAS 9.4. The LE increased (P < 0.05) jejunal digesta viscosity, tended to have decreased (P = 0.053) relative abundance of Prevotella, and tended to increase (P = 0.055) Lactobacillus. The LE also increased (P < 0.05) the concentration of protein carbonyl whereas malondialdehyde, villus height (VH), villus height to crypt depth ratio (VH:CD), apparent ileal digestibility (AID) of nutrients, and finally average daily feed intake were decreased (P < 0.05). The LE did not affect average daily gain (ADG). The LEX decreased (P < 0.05) digesta viscosity, increased (P < 0.05) the relative abundance of Prevotella, decreased (P < 0.05) Helicobacter, decreased (P < 0.05) the concentration of protein carbonyl, tended to increase (P = 0.065) VH, and decreased (P < 0.05) VH:CD and crypt cell proliferation. Moreover, LEX increased (P < 0.05) the AID of dry matter and gross energy and tended to increase (P = 0.099; P = 0.076) AID of crude protein, and ether extract. The LEX did not affect ADG but did tend to decrease (P = 0.070) fecal score during the starter phase. Overall, reducing ME negatively affected intestinal health parameters and nutrient digestibility without affecting growth. Supplementation of xylanase mitigated some of the negative effects observed by ME reduction on intestinal health and digestibility of nutrients without affecting growth.
Chronic exposure to polytetrafluoroethylene microplastics caused sex-specific effects in the model insect, Drosophila melanogaster (Diptera: Drosophilidae)
Authors: Jin Hui , Xu Yifan , Kong Fanhao , Shen Jie
Published: January 2024

Microplastics (MPs) have become a prominent environmental concern due to their ubiquity in various ecosystems and widespread distribution through multiple channels. In this study, the oral effects of 2,000 mesh polytetrafluoroethylene (PTFE) microplastics were tested against Drosophila melanogaster (Meigen), at concentrations of 0, 0.1, 1, 10, and 20. After exposure to a microplastic-containing medium for 20 days, energy metabolism, fecundity, spontaneous movement, and sleeping time were measured. The study results showed that glucose levels in male flies were significantly reduced after exposure to PTFE-MPs. Measurement of lipid and protein levels indicated an increase in males but decrease in females, whereas these changes were not statistically significant. Reduction in sleep time was also observed, especially in males at the concentration of 20 g/l. Our study indicates that chronic exposure of PTFE-MPs can change energy metabolism and the amount of sleep on D. melanogaster in a sex dependent and dose dependent way. The results of our study are hoped to contribute to a better understanding of the effects of microplastics as new pollutants on insects.
Exploring Institutional Barriers to Effective Human Rights-Based Climate Litigation in Latin American Courts—Lessons from Chile and Ecuador
Authors: Zenteno Villa Lorena
Published: January 2024

The global climate crisis demands that all branches of government play a role in tackling climate change, including the judiciary. One important mechanism is climate litigation. In the adjudication of climate litigation, courts can advance the protection of human rights, promote environmental values, assist in developing climate change law and policy, and uphold the rule of law. However, some Latin American countries are facing several constitutional and legal barriers to adequately protecting environmental and human rights enshrined in their constitutions. Through analysis of the Chilean and Ecuadorian contexts, this note identifies obstacles and barriers that might prevent human rights’ protection in each jurisdiction when adjudicating climate cases and proposes reforms that may strengthen courts’ performance. Among the options are strengthening existing environmental and human rights provisions, developing new legal frameworks addressing climate change, and enhancing the capacity of courts to hear and decide climate change cases. Furthermore, these reforms must be accompanied by adequate resources, training, and support for the judiciary effectively to advance climate justice through human rights.
Traditional uses, hepatoprotective potential, and phytopharmacology of Tinospora cordifolia: a narrative review
Authors: Balkrishna Acharya , Kumar Ashwani , Rohela Akansha , Arya Vedpriya , Gautam Ajay Kumar , Sharma Hemant , Rai Priyanka , Kumari Amita , Amarowicz Ryszard
Published: January 2024

Objectives

Despite significant advancements in modern medicine, effective hepatoprotective medication with minimal side effects is still lacking. In this context. Tinospora cordifolia, an Indian Ayurvedic liana, has attracted much attention.

Key findings

Traditionally, T. cordifolia has been found to be effective in the treatment of jaundice; according to the literature, T. cordifolia is a hepatoprotective agent, and the CCl4 model is the most frequently used to evaluate its potential. Its hepatoprotective effects might be attributed to alkaloids (berberine, palmatine, and jatrorrhizine) and sinapic acid. Berberine decreases inflammation by inhibiting the proinflammatory cascade triggered by TNF-α and reduces nitrosative stress by inhibiting iNOS. T. cordifolia also exhibits anticancer, anti-inflammatory, antimicrobial, antioxidant, and other activities; it is safe at concentrations up to 2000 mg/kg. Its biological action can be attributed to polyphenols, alkaloids, steroids, terpenoids, and glycosides. T. cordifolia has also been found to be an active ingredient in several polyherbal formulations used to treat chemical-mediated hepatotoxicity.

Conclusion

T. cordifolia’s hepatoprotective effects are mediated by the inhibition of lipid peroxidation, the management of oxidative stress, and other factors. T. cordifolia can be used to manage liver disorders and as a hepatoprotective supplement in the food industry. The bioprospecting of its alkaloids can lead to the development of novel formulations against hepatic ailments.
Intestinal intussusception—not just for kids
Authors: Lynch Paul , Feeney Gerard , Ali Nisar , Hussein Akthar , Cury Jorge
Published: January 2024

Intussusception is a phenomenon commonly associated with the paediatric population. In adults, intussusception is frequently a result of a neoplastic process. We present the case of a 56-year-old gentleman who was diagnosed to the local Emergency Department with a 4-day history of worsening severe, left sided lower abdominal pain. The pain was colicky in nature. Computed tomography identified a long-segment intussusception involving distal small bowel, caecum, ascending colon, the entirety of transverse colon and its associated mesentery. The patient proceeded to theatre where a laparotomy and right hemicolectomy was performed. Histopathological analysis of the specimen identified an ileal myxoma as the lead-point of the intussusception. This report emphasises the value of prompt investigation in atypical clinical presentations.
ABA INSENSITIVE 2 promotes flowering by inhibiting OST1/ABI5-dependent FLOWERING LOCUS C transcription in Arabidopsis
Authors: Ali Akhtar , Zareen Shah , Park Junghoon , Khan Haris Ali , Lim Chae Jin , Bader Zein Eddin , Hussain Shah , Chung Woo Sik , Gechev Tsanko , Pardo Jose M , Yun Dae-Jin
Published: January 2024

The plant hormone abscisic acid (ABA) is an important regulator of plant growth and development and plays a crucial role in both biotic and abiotic stress responses. ABA modulates flowering time, but the precise molecular mechanism remains poorly understood. Here we report that ABA INSENSITIVE 2 (ABI2) is the only phosphatase from the ABA-signaling core that positively regulates the transition to flowering in Arabidopsis. Loss-of-function abi2-2 mutant shows significantly delayed flowering both under long day and short day conditions. Expression of floral repressor genes such as FLOWERING LOCUS C (FLC) and CYCLING DOF FACTOR 1 (CDF1) was significantly up-regulated in abi2-2 plants while expression of the flowering promoting genes FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was down-regulated. Through genetic interactions we further found that ost1-3 and abi5-1 mutations are epistatic to abi2-2, as both of them individually rescued the late flowering phenotype of abi2-2. Interestingly, phosphorylation and protein stability of ABA INSENSITIVE 5 (ABI5) were enhanced in abi2-2 plants suggesting that ABI2 dephosphorylates ABI5, thereby reducing protein stability and the capacity to induce FLC expression. Our findings uncovered the unexpected role of ABI2 in promoting flowering by inhibiting ABI5-mediated FLC expression in Arabidopsis.
Functional characterization of calmodulin-like proteins, CML13 and CML14, as novel light chains of Arabidopsis class VIII myosins
Authors: Symonds Kyle , Teresinski Howard J , Hau Bryan , Dwivedi Vikas , Belausov Eduard , Bar-Sinai Sefi , Tominaga Motoki , Haraguchi Takeshi , Sadot Einat , Ito Kohji , Snedden Wayne A
Published: January 2024

Myosins are important motor proteins that associate with the actin cytoskeleton. Structurally, myosins function as heteromeric complexes where smaller light chains, such as calmodulin (CaM), bind to isoleucine–glutamine (IQ) domains in the neck region to facilitate mechano-enzymatic activity. We recently identified Arabidopsis CaM-like (CML) proteins CML13 and CML14 as interactors of proteins containing multiple IQ domains, including a myosin VIII. Here, we demonstrate that CaM, CML13, and CML14 bind the neck region of all four Arabidopsis myosin VIII isoforms. Among CMLs tested for binding to myosins VIIIs, CaM, CML13, and CML14 gave the strongest signals using in planta split-luciferase protein interaction assays. In vitro, recombinant CaM, CML13, and CML14 showed specific, high-affinity, calcium-independent binding to the IQ domains of myosin VIIIs. CaM, CML13, and CML14 co-localized to plasma membrane-bound puncta when co-expressed with red fluorescent protein–myosin fusion proteins containing IQ and tail domains of myosin VIIIs. In vitro actin motility assays using recombinant myosin VIIIs demonstrated that CaM, CML13, and CML14 function as light chains. Suppression of CML13 or CML14 expression using RNA silencing resulted in a shortened-hypocotyl phenotype, similar to that observed in a quadruple myosin mutant, myosin viii4KO. Collectively, our data indicate that Arabidopsis CML13 and CML14 are novel myosin VIII light chains.
A cooling flow around the low-redshift quasar H1821+643
Authors: Russell H R , Nulsen P E J , Fabian A C , Braben T E , Brandt W N , Clews L , McDonald M , Reynolds C S , Sanders J S , Veilleux S
Published: January 2024

H1821+643 is the nearest quasar hosted by a galaxy cluster. The energy output by the quasar, in the form of intense radiation and radio jets, is captured by the surrounding hot atmosphere. Here, we present a new deep Chandra observation of H1821+643 and extract the hot gas properties into the region where Compton cooling by the quasar radiation is expected to dominate. Using detailed simulations to subtract the quasar light, we show that the soft-band surface brightness of the hot atmosphere increases rapidly by a factor of ∼30 within the central $\sim\!{10}\ \rm kpc$. The gas temperature drops precipitously to $\lt 0.4\rm \,\, keV$ and the density increases by over an order of magnitude. The remarkably low metallicity here is likely due to photoionization by the quasar emission. The variations in temperature and density are consistent with hydrostatic compression of the hot atmosphere. The extended soft-band peak cannot be explained by an undersubtraction of the quasar or scattered quasar light and is instead due to thermal interstellar medium. The radiative cooling time of the gas falls to only $12\pm 1\rm \,\, Myr$, below the free fall time, and we resolve the sonic radius. H1821+643 is therefore embedded in a cooling flow with a mass deposition rate of up to $3000\ {\rm M}_{\odot}\,{\rm yr}^{-1}$. Multiwavelength observations probing the star-formation rate and cold gas mass are consistent with a cooling flow. We show that the cooling flow extends to much larger radii than can be explained by Compton cooling. Instead, the active galactic nucleus appears to be underheating the core of this cluster.
On reproduction in the Pacific boreal limpet Erginus (Problacmaea) puniceus Lindberg, 1988 (Patellogastropoda: Rhodopetalidae)
Authors: Buckland-Nicks John , Reunov Arkadiy , Yurchenko Olga
Published: January 2024

Fifty years ago, it was reported that individuals of the Pacific boreal limpet Problacmaea (= Erginus) bear a penis for copulation and brood their young in the pallial cavity. These observations were based on light microscopy, but now we reveal new details of the reproductive biology of Erginus (Problacmaea) puniceus with electron microscopy. Gametogenesis is fundamentally similar to other Patellogastropoda, but there are some key differences. Oocytes develop in the ovary, dorsal to the foot in the posterior half of the body, before passing through the oviduct to the pallial cavity, where they are fertilized and brooded. Development is direct with embryos being brooded to the crawl-away juvenile stage. However, sometimes fertilization occurs internally with embryos beginning development in or near the gonad. Free sperm, which were likely autosperm (self) but could have been allosperm (cross), were found near developing oocytes in the gonad. Spermiogenesis results in the formation of an enta-quasperm with a cap-like acrosome, a bullet-shaped nucleus and spherical mitochondria in the midpiece. Copulation was not observed, but we confirm the presence of a penis with a dorsal penial groove that lies below the right cephalic tentacle in males, which is typical of functional penises of some molluscs. Males were always smaller, but intermediate-sized individuals were hermaphroditic to different extents. The largest individuals were entirely female, and their penises were smaller and often lacked the penial groove. Thus, E. (Problacmaea) puniceus appears to be a protandrous hermaphrodite, passing from male to female phase. Remnants of the testis persist into the female phase, suggesting that they are protandrous hermaphrodites with overlap, possibly allowing for self-fertilization to occur on occasion. However, the largest females lacked any testis remnants, suggesting instead that the species may be protandrous sequential hermaphrodites.