bluuebunny/crossref_metadata_2025 huggingface dataset:
PSI-A-11 The Effect of Soybean Meal and Its Functional Compounds on Growth Performance, Fecal Scores, and Fecal Characteristics of Nursery Pigs
Authors: Self Rachel M , Bowen Brooke M , Miller Kade , Mitchell Ty M , Crome Thomas A , Miller Hannah , Legako Jerrad A , Petry Amy L
Published: October 2023

High levels of soybean meal (SBM) are deterred in nursery diets due to antinutritional factors and impacts on fecal consistency. However, SBM may improve performance in the presence of inflammatory stressors due to its functional compounds. The experimental objective was to evaluate the non-nutritive value of SBM and its functional compounds on growth performance and fecal characteristics of nursery pigs. A total of 408 newly weaned pigs with an initial BW of 5.43 ±0.77 kg were used for a 35-d study across three replications. Pigs were randomly assigned to 1 of 6 dietary treatments fed across 3 phases: d 0-7 (phase 1), d 7-21 (phase 2), and d 21-35 (phase 3). Dietary treatments consisted of a high SBM control (SBMC), a control void of SBM (SP), but included soy protein isolate and concentrate to provide amino acids similar to SBM in SBMC; SP formulated to equivalent contribution of isoflavones as SBMC (SP+ISO); SP diet fortified with soybean functional lipids to the level of SBMC (SP+LIP); SP formulated with a similar ratio of insoluble to soluble fiber as SBMC (SP+FIB); or SP diet fortified with lunasin (SP+LUN). There were 9 split-sex pens per treatment (7 or 8 pigs/pen). On d 7, 14, 21, and 35, pigs and feeders were weighed, pen fecal samples were collected, and fecal score was evaluated using a 4-point scale (1 = solid; 4 = liquid). Continuous data were analyzed as a linear mixed model (PROC MIXED) with treatment and period as fixed effects, replicate as a random effect, and initial BW as a covariate where appropriate. Fecal scores were analyzed using a multinomial model in PROC FREQ. Compared with SP, on d 7 and 14 pigs fed SBMC and SP+FIB had reduced fecal dry matter (DM%), but on d 21 and 35, fecal DM% did not differ among treatments (time×treatment P = 0.016). There was a treatment×time interaction for fecal score, whereas on d 7, pigs fed SBMC had increased proportion of semi-liquid feces and on d 14 pigs fed SP+FIB had increased abundance of semi-liquid feces, but fecal score distribution did not differ on d 21 or 35 (time×treatment P = 0.035). Fecal water binding capacity (WBC) did not differ across time (P=0.288) but relative to SP, SBMC had 30% less fecal WBC (P = 0.002). There was a treatment×time interaction for ADG and ADFI. Pigs fed SP+ISO had greater ADG in phase 2, but pigs fed SBMC gained more in phase 3 (time×treatment P = 0.044). Among treatments, ADFI did not differ in phase 1 and 2, but was increased in SBMC in phase 3 (time×treatment; P = 0.037). Pigs fed SBMC tended to have the greatest final BW (P = 0.071). Feeding SBM altered fecal characteristics in the early nursery period, but improved growth performance from d 21-35 post-weaning.
PSI-A-13 Changes in Daily Patterns of Physiological Measures of Heat Stress on Sows in Cool Room and in Heated Room with and without a Cooling Pad
Authors: Baributsa Jemima , Gonzalez Maria , Schinckel Allan P , Stwalley Robert M , Field Tyler C , Neeno Samantha , Paramba Sakkariya
Published: October 2023

Impacts of heat stress (HS) on lactating sows during the summer causes challenges in production. The study objective evaluated the daily patterns of common HS measures on late lactation sows. Sows in a HS environment, on and off electronic cooling pads (ECP), were compared with sows in a cool room (CR). From a sample of six sows, three sows were assigned to a HS environment, (31°C daytime for 6 h and 26°C nighttime for 5 h) with an ECP (n = 1) or without an ECP (nECP, n = 2). Three sows were placed in a CR (n = 3) with set temperature of 20°C. The ECP automatically flushed 2.0 L of cool water (18 to 19°C) when one of the three temperature sensors reached 26°C. Flushing occurred for 30 s replacing 1.73L of water in the ECP. All sows were in farrowing crates and provided ad libitum access to feed and water. Internal Temperature (TI) was measured in 10-minute intervals using vaginal implants. Skin temperature (TS) was measured hourly, using an infrared gun 10 cm behind the ear. Respiration rate (RR) was observed in 30-minute intervals from 0600 to 2200 h over 2 days. Mixed model periodic regressions were performed in R 4.2.2 using REML lme4, fitted to the RR, TS, and TI data. Significant treatment and treatment by periodic regression variables (P < 0.05) indicated the need for separate equations for each treatment. The final model for TI included the random effect of sow, effect of room, and single, double, and triple sine/cosine phase variables for each room. For TI, there were also significant (P < 0.001) interactions of the single-phase sine/cosine variables with the ECP treatment in the HS environment. The final model for TS included the random effect of sow, ECP treatment, single, double, and triple sine/cosine and their interactions with room, and the interaction of the single phase with ECP treatment in the HS environment. The final model for RR included the effects of room and ECP within the HS environment (P < 0.001), the single-phase sine/cosine variables, and their interactions of ECP within the HS environment and CR. Daily increases in RR and TI were much greater for sows in the HS environment compared with the CR, or the sow on the ECP. The RR for the ECP sow increased from 18 to 24 bpm from 6000 h to mid-afternoon (1500 to 1700 h), versus 65 to 108 bpm for the nECP sows. Overall, the ECP reduced TI on average by 0.39°C with the greatest impact of 0.8 to 0.9°C from 1500 to 1900 h. As in previous experiments, the sow on the ECP had greater relative reductions in RR and smaller differences in TI.
Implementing Nexobrid for Burn Debridement in a Major Italian Burn Center: A Retrospective Review of Patient Outcomes
Authors: Lombardo Giuseppe A G , Ciancio Francesco , Violini Hillary , Sapuppo Claudia , Zagami Santo , Vena Adelina , Giardina Maria , Donia Claudio , Ranno Rosario
Published: October 2023

This retrospective study examines the implementation of Nexobrid, an enzymatic debriding agent developed from bromelain, for burn debridement in a major Italian burn center. With previous research showing encouraging results for Nexobrid in terms of reducing the need for surgical intervention and faster eschar removal, the current study aims to add to the growing body of evidence regarding its potential benefits and limitations. The patient database was utilized to identify patients who received Nexobrid treatment between October 2019 and June 2023. A retrospective analysis was conducted to gather demographic information, burn causes, procedural details, and patient outcomes. Of the 30 patients treated with Nexobrid, 10% did not require further surgical intervention, showcasing Nexobrid’s potential to improve patient outcomes. However, over 80% of patients still required additional surgical intervention, demonstrating that Nexobrid’s effectiveness varies across patients and should be considered a tool rather than a definitive solution in burn wound management. A few patients developed complications, and about 10% of patients succumbed to systemic complications. The study results reveal both the potential benefits and limitations of using Nexobrid in burn debridement. While it successfully eliminated the need for further surgical intervention in a small percentage of patients, the majority still required additional surgical procedures. These findings not only highlight Nexobrid’s role as a tool in burn wound management but also point toward the discrepancies with previous studies. The authors suggest future research should include randomized controlled trials, direct comparisons between Nexobrid and traditional debridement methods, and studies incorporating larger and more diverse patient groups.
Garden catalogues as sources for studying the collection and transmission of plants
Authors: Mesquita Sandra , Capelo Jorge , Menezes de Sequeira Miguel , Espírito-Santo Dalila
Published: October 2023

This paper considers the use of plant lists and related documents in addressing questions about the collection and circulation of plants and plant knowledge. The focus is on plants cultivated in Lisbon’s Ajuda botanical garden up to the mid-nineteenth century, and additionally on plants from the island of Madeira. Three plant catalogues, prepared between the early 1770s and mid-1840s, are analysed, together with register books and documents that habitually accompanied plant shipments sent to the garden. The study shows which plants were present in the garden and how the collection evolved, as well as which world regions were represented. In comparing Madeiran plants listed as present in the garden with those documented as being shipped from the island in the late 1790s, the paucity of shared names is striking. On the one hand, this may reflect document loss, while on the other it suggests that Madeiran plants may have been transported from their native range to other European locations by means of complex exchange networks.
Proactive Prevention: Denmark’s Domestic Practices of Human Rights Compliance
Authors: Küçüksu Aysel
Published: October 2023

Fuelled by an ambition to solve the puzzle of the stark contrast between Denmark’s increasingly negative presence in the international press and its leading performance in European Court of Human Rights (ECtHR) compliance statistics, this article presents the results of a mixed-method study of the country’s domestic human rights’ protection and implementation practices. The story that emerges is not one of compliance, but of proactive prevention with a tinge of strategic risk-taking and prompt implementation. The majority of the Danish action within the compliance sphere takes place before one can even talk about compliance—domestically before the international spotlight is prompted to shine on Denmark by an adverse judgment against it. The article shows how each branch of power has an idiosyncratic way of working towards the prevention of human rights’ breaches. Yet, domestic prevention and international statistics say little about the quality of implementation and human rights’ protection. The article offers a concrete illustration of the blind spots of compliance data in the absence of qualitative research related to domestic practices and proves that there are lessons to be learned from studying even the most exemplary compliers. This makes the Danish case study an important contribution to the broader literature on the ways in which the ECtHR influences states other than through the implementation of judgments. Importantly, it also shows that while the proactive prevention of adverse ECtHR judgments can mean the same as the proactive prevention of human rights’ breaches, this is not always the case.
The new EC proposal for a regulation on the production and marketing of plant reproductive material: upgrade or regression? An intellectual property perspective
Authors: Vives Vallés Juan Antonio
Published: October 2023

With the proposed EC reform, Value for Cultivation and Use (VCU) trials will include sustainability as a driver, broadening their scope from agricultural varieties to horticultural and fruit ones, and a plethora of derogations to variety registration and seed certification standards will be added or deepened; however, it is unlikely that the EU and Member States’ plant variety protection schemes, farmers, or end consumers will truly benefit from it.
Criminal enforcement of intellectual property rights: an overview and comparative analysis of the Balkans
Authors: Peppo Etlon , Bode Jola
Published: October 2023

Criminal enforcement plays an important role to safeguard both the private rights and the public interests against counterfeiting, piracy and other unlawful activities related to the infringement of intellectual property rights (IPRs). Owing to the international obligations outlined in the Agreement on Trade-Related Aspects of Intellectual Property Rights (the TRIPS Agreement), infringement of IPRs has been criminalized by all member states and criminal procedures shall apply accordingly under the conditions determined in their national laws. This article aims to present an overview and comparative analysis of the criminal law protection of IPRs in the Balkans to point out the main difficulties faced by the criminal courts in their practice. In particular, attention focuses on trade mark rights as a case study. The article examines the relevance of criminal law within the context of international obligations and domestic legal frameworks by providing a detailed legal analysis of the corresponding criminal law provisions in the Balkan countries. In this regard, the article identifies the elements required for the investigation and prosecution of such type of offences by evidencing the practical issues and difficulties of law enforcement agencies where they need to prove the intention of deceiving consumers as a necessary element to hold a person criminally responsible. Overall, the article explores the practical significance of criminal law in the enforcement of IPRs as an effective tool in deterring and prosecuting IP crimes, as well as provides some important steps to improve criminal law tools in the Balkans.
Supplemental magnetic resonance imaging plus mammography compared with magnetic resonance imaging or mammography by extent of breast density
Authors: Kerlikowske Karla , Zhu Weiwei , Su Yu-Ru , Sprague Brian L , Stout Natasha K , Onega Tracy , O’Meara Ellen S , Henderson Louise M , Tosteson Anna N A , Wernli Karen , Miglioretti Diana L
Published: October 2023

Background

Examining screening outcomes by breast density for breast magnetic resonance imaging (MRI) with or without mammography could inform discussions about supplemental MRI in women with dense breasts.

Methods

We evaluated 52 237 women aged 40-79 years who underwent 2611 screening MRIs alone and 6518 supplemental MRI plus mammography pairs propensity score–matched to 65 810 screening mammograms. Rates per 1000 examinations of interval, advanced, and screen-detected early stage invasive cancers and false-positive recall and biopsy recommendation were estimated by breast density (nondense = almost entirely fatty or scattered fibroglandular densities; dense = heterogeneously/extremely dense) adjusting for registry, examination year, age, race and ethnicity, family history of breast cancer, and prior breast biopsy.

Results

Screen-detected early stage cancer rates were statistically higher for MRI plus mammography vs mammography for nondense (9.3 vs 2.9; difference = 6.4, 95% confidence interval [CI] = 2.5 to 10.3) and dense (7.5 vs 3.5; difference = 4.0, 95% CI = 1.4 to 6.7) breasts and for MRI vs MRI plus mammography for dense breasts (19.2 vs 7.5; difference = 11.7, 95% CI = 4.6 to 18.8). Interval rates were not statistically different for MRI plus mammography vs mammography for nondense (0.8 vs 0.5; difference = 0.4, 95% CI = -0.8 to 1.6) or dense breasts (1.5 vs 1.4; difference = 0.0, 95% CI = -1.2 to 1.3), nor were advanced cancer rates. Interval rates were not statistically different for MRI vs MRI plus mammography for nondense (2.6 vs 0.8; difference = 1.8 (95% CI = -2.0 to 5.5) or dense breasts (0.6 vs 1.5; difference = -0.9, 95% CI = -2.5 to 0.7), nor were advanced cancer rates. False-positive recall and biopsy recommendation rates were statistically higher for MRI groups than mammography alone.

Conclusion

MRI screening with or without mammography increased rates of screen-detected early stage cancer and false-positives for women with dense breasts without a concomitant decrease in advanced or interval cancers.
Adverse Childhood Experiences and Positive Childhood Experiences Among United States Military Children
Authors: Crouch Elizabeth , Andersen Tia S , Smith Hayden P
Published: October 2023

Introduction

Many facets of military life are contributors to child health including frequent mobility, family separation, and increased risk to parental physical and mental health, as well as strong social networks and military support systems; yet, there has not been an examination of adverse childhood experiences (ACEs) and positive childhood experiences (PCEs) among military children.

Materials and methods

This study used the 2020–2021 National Survey of Children’s Health, limited to children aged 6 to 17 years of age, to examine the association between a child who has ever had a caregiver on active duty and their exposure to ACEs and PCEs (n = 54,256 children). Bivariate analyses used Pearson’s chi-squared tests and were weighted to be nationally representative. Multivariable regression models were used to examine the association between military status and selected ACEs.

Results

There were no statistically significant differences in PCEs between military and civilian children. Compared to children with a civilian caregiver, children who had a caregiver who had ever served on active duty had a higher odds of experiencing domestic violence (adjusted Odds Ratio (aOR), 1.61; 95% CI 1.23–2.11), mental health issues or depression in the household (aOR 1.28; 95% CI 1.07–1.52), and substance use (aOR 1.28; 95% CI 1.06–1.55).

Conclusions

This study complements and extends previous research that has taken a deficit approach and focused exclusively on the hardships faced by children in military families. The findings from this study may be instructive for child welfare advocates and policymakers as they intervene in communities with programming that promotes PCEs among children and adolescents.
StORF-Reporter: finding genes between genes
Authors: Dimonaco Nicholas J , Clare Amanda , Kenobi Kim , Aubrey Wayne , Creevey Christopher J
Published: October 2023

Large regions of prokaryotic genomes are currently without any annotation, in part due to well-established limitations of annotation tools. For example, it is routine for genes using alternative start codons to be misreported or completely omitted. Therefore, we present StORF-Reporter, a tool that takes an annotated genome and returns regions that may contain missing CDS genes from unannotated regions. StORF-Reporter consists of two parts. The first begins with the extraction of unannotated regions from an annotated genome. Next, Stop-ORFs (StORFs) are identified in these unannotated regions. StORFs are open reading frames that are delimited by stop codons and thus can capture those genes most often missing in genome annotations. We show this methodology recovers genes missing from canonical genome annotations. We inspect the results of the genomes of model organisms, the pangenome of Escherichia coli, and a set of 5109 prokaryotic genomes of 247 genera from the Ensembl Bacteria database. StORF-Reporter extended the core, soft-core and accessory gene collections, identified novel gene families and extended families into additional genera. The high levels of sequence conservation observed between genera suggest that many of these StORFs are likely to be functional genes that should now be considered for inclusion in canonical annotations.
scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species
Authors: Qian Feng-Cui , Zhou Li-Wei , Zhu Yan-Bing , Li Yan-Yu , Yu Zheng-Min , Feng Chen-Chen , Fang Qiao-Li , Zhao Yu , Cai Fu-Hong , Wang Qiu-Yu , Tang Hui-Fang , Li Chun-Quan
Published: October 2023

Chromatin accessibility profiles at single cell resolution can reveal cell type-specific regulatory programs, help dissect highly specialized cell functions and trace cell origin and evolution. Accurate cell type assignment is critical for effectively gaining biological and pathological insights, but is difficult in scATAC-seq. Hence, by extensively reviewing the literature, we designed scATAC-Ref (https://bio.liclab.net/scATAC-Ref/), a manually curated scATAC-seq database aimed at providing a comprehensive, high-quality source of chromatin accessibility profiles with known cell labels across broad cell types. Currently, scATAC-Ref comprises 1 694 372 cells with known cell labels, across various biological conditions, >400 cell/tissue types and five species. We used uniform system environment and software parameters to perform comprehensive downstream analysis on these chromatin accessibility profiles with known labels, including gene activity score, TF enrichment score, differential chromatin accessibility regions, pathway/GO term enrichment analysis and co-accessibility interactions. The scATAC-Ref also provided a user-friendly interface to query, browse and visualize cell types of interest, thereby providing a valuable resource for exploring epigenetic regulation in different tissues and cell types.
The IUPHAR/BPS Guide to PHARMACOLOGY in 2024
Authors: Harding Simon D , Armstrong Jane F , Faccenda Elena , Southan Christopher , Alexander Stephen P H , Davenport Anthony P , Spedding Michael , Davies Jamie A
Published: October 2023

The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb; https://www.guidetopharmacology.org) is an open-access, expert-curated, online database that provides succinct overviews and key references for pharmacological targets and their recommended experimental ligands. It includes over 3039 protein targets and 12 163 ligand molecules, including approved drugs, small molecules, peptides and antibodies. Here, we report recent developments to the resource and describe expansion in content over the six database releases made during the last two years. The database update section of this paper focuses on two areas relating to important global health challenges. The first, SARS-CoV-2 COVID-19, remains a major concern and we describe our efforts to expand the database to include a new family of coronavirus proteins. The second area is antimicrobial resistance, for which we have extended our coverage of antibacterials in partnership with AntibioticDB, a collaboration that has continued through support from GARDP. We discuss other areas of curation and also focus on our external links to resources such as PubChem that bring important synergies to the resources.
PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters
Authors: Chow Chi-Nga , Yang Chien-Wen , Wu Nai-Yun , Wang Hung-Teng , Tseng Kuan-Chieh , Chiu Yu-Hsuan , Lee Tzong-Yi , Chang Wen-Chi
Published: October 2023

PlantPAN 4.0 (http://PlantPAN.itps.ncku.edu.tw/) is an integrative resource for constructing transcriptional regulatory networks for diverse plant species. In this release, the gene annotation and promoter sequences were expanded to cover 115 species. PlantPAN 4.0 can help users characterize the evolutionary differences and similarities among cis-regulatory elements; furthermore, this system can now help in identification of conserved non-coding sequences among homologous genes. The updated transcription factor binding site repository contains 3428 nonredundant matrices for 18305 transcription factors; this expansion helps in exploration of combinational and nucleotide variants of cis-regulatory elements in conserved non-coding sequences. Additionally, the genomic landscapes of regulatory factors were manually updated, and ChIP-seq data sets derived from a single-cell green alga (Chlamydomonas reinhardtii) were added. Furthermore, the statistical review and graphical analysis components were improved to offer intelligible information through ChIP-seq data analysis. These improvements included easy-to-read experimental condition clusters, searchable gene-centered interfaces for the identification of promoter regions’ binding preferences by considering experimental condition clusters and peak visualization for all regulatory factors, and the 20 most significantly enriched gene ontology functions for regulatory factors. Thus, PlantPAN 4.0 can effectively reconstruct gene regulatory networks and help compare genomic cis-regulatory elements across plant species and experiments.
ViralZone 2024 provides higher-resolution images and advanced virus-specific resources
Authors: De Castro Edouard , Hulo Chantal , Masson Patrick , Auchincloss Andrea , Bridge Alan , Le Mercier Philippe
Published: October 2023

ViralZone (http://viralzone.expasy.org) is a knowledge repository for viruses that links biological knowledge and databases. It contains data on virion structure, genome, proteome, replication cycle and host-virus interactions. The new update provides better access to the data through contextual popups and higher resolution images in Scalable Vector Graphics (SVG) format. These images are designed to be dynamic and interactive with human viruses to give users better access to the data. In addition, a new coronavirus-specific resource provides regularly updated data on variants and molecular biology of SARS-CoV-2. Other virus-specific resources have been added to the database, particularly for HIV, herpesviruses and poxviruses.
COV2Var, a function annotation database of SARS-CoV-2 genetic variation
Authors: Feng Yuzhou , Yi Jiahao , Yang Lin , Wang Yanfei , Wen Jianguo , Zhao Weiling , Kim Pora , Zhou Xiaobo
Published: October 2023

The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has resulted in the loss of millions of lives and severe global economic consequences. Every time SARS-CoV-2 replicates, the viruses acquire new mutations in their genomes. Mutations in SARS-CoV-2 genomes led to increased transmissibility, severe disease outcomes, evasion of the immune response, changes in clinical manifestations and reducing the efficacy of vaccines or treatments. To date, the multiple resources provide lists of detected mutations without key functional annotations. There is a lack of research examining the relationship between mutations and various factors such as disease severity, pathogenicity, patient age, patient gender, cross-species transmission, viral immune escape, immune response level, viral transmission capability, viral evolution, host adaptability, viral protein structure, viral protein function, viral protein stability and concurrent mutations. Deep understanding the relationship between mutation sites and these factors is crucial for advancing our knowledge of SARS-CoV-2 and for developing effective responses. To fill this gap, we built COV2Var, a function annotation database of SARS-CoV-2 genetic variation, available at http://biomedbdc.wchscu.cn/COV2Var/. COV2Var aims to identify common mutations in SARS-CoV-2 variants and assess their effects, providing a valuable resource for intensive functional annotations of common mutations among SARS-CoV-2 variants.
TADB 3.0: an updated database of bacterial toxin–antitoxin loci and associated mobile genetic elements
Authors: Guan Jiahao , Chen Yongkui , Goh Ying-Xian , Wang Meng , Tai Cui , Deng Zixin , Song Jiangning , Ou Hong-Yu
Published: October 2023

TADB 3.0 (https://bioinfo-mml.sjtu.edu.cn/TADB3/) is an updated database that provides comprehensive information on bacterial types I to VIII toxin–antitoxin (TA) loci. Compared with the previous version, three major improvements are introduced: First, with the aid of text mining and manual curation, it records the details of 536 TA loci with experimental support, including 102, 403, 8, 14, 1, 1, 3 and 4 TA loci of types I to VIII, respectively; Second, by leveraging the upgraded TA prediction tool TAfinder 2.0 with a stringent strategy, TADB 3.0 collects 211 697 putative types I to VIII TA loci predicted in 34 789 completely sequenced prokaryotic genomes, providing researchers with a large-scale dataset for further follow-up analysis and characterization; Third, based on their genomic locations, relationships of 69 019 TA loci and 60 898 mobile genetic elements (MGEs) are visualized by interactive networks accessible through the user-friendly web page. With the recent updates, TADB 3.0 may provide improved in silico support for comprehending the biological roles of TA pairs in prokaryotes and their functional associations with MGEs.
The greenhouse gas budget for China's terrestrial ecosystems
Authors: Wang Xuhui , Gao Yuanyi , Wang Kai , Sang Yuxing , Wang Yilong , Zhang Yuzhong , Hong Songbai , Zhang Yao , Yuan Wenping
Published: October 2023

The first greenhouse gas (GHG) budget accounting over China shows that China's land ecosystems is close to GHG neutral, in contrast to the net GHG source of global land ecosystems.
Risks and benefits of salicylates in food: a narrative review
Authors: Suliburska Joanna , Cholik Rafsan Syabani
Published: October 2023

Salicylates are generally present in plants as part of their defense system against pathogens and environmental stress. Major dietary sources of salicylates were found in spices and herbs, such as curry and paprika (hot powder). Several studies suggest that these natural salicylates offer health benefits in the human body, such as antidiabetic, anticancer, antiviral, and anti-inflammatory properties. However, despite their advantages, salicylates can be harmful to people with allergies, and high doses of salicylates may cause respiratory alkalosis and gastrointestinal bleeding. Additionally, salicylates can interact with certain drugs, such as nonsteroidal anti-inflammatory drugs and warfarin. This narrative review aimed to consolidate recent information on the content of salicylates in food based on the literature, while also highlighting the benefits and risks associated with salicylate consumption in humans. Based on the literature review and analysis of results, it can be concluded that the dietary intake of salicylates in vegetarians can be relatively high, resulting in concentrations of salicylic acid in the blood and urine that are comparable to those observed in patients taking a low dose of aspirin (75 mg). This suggests that a diet rich in salicylates may have potential benefits in preventing and treating some diseases that require low doses of aspirin.
Diet quality indexes for use during pregnancy: a scoping review
Authors: Robb Liska , Joubert Gina , Walsh Corinna May
Published: October 2023

Aims

High diet quality is related to better health outcomes in general. During pregnancy, a high-quality diet is of paramount importance to promote optimal maternal and neonatal outcomes. This is a scoping review of research available on diet quality indexes (DQIs) for use during pregnancy that summarizes the DQIs in terms of development, country of origin, population used, components, scoring and weighting of components, and evaluation. Furthermore, the DQIs are discussed narratively to inform and direct the development of improved and country-specific DQIs for pregnancy.

Methods

The EBSCOhost database was used to identify English-language, peer-reviewed articles published between 2000 and 2023, from which 11 publications were identified that describe the development of pregnancy-specific DQIs. This review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews model.

Results

Almost all DQIs (n = 9 of 11) were developed in high-income countries, using dietary intake data from food frequency questionnaires. Several DQIs (n = 5 of 11) used the US Healthy Eating Index as basis and modified it in various ways. Almost all DQIs included both foods and nutrients as components (n = 9 of 11), with vegetables being the most commonly included component alone (n = 8 of 11) or combined with fruit (n = 2 of 11).

Conclusion

Because most DQIs were developed using dietary guidelines, recommendations, and dietary intake data from high-income countries, it is recommended that pregnancy-specific DQIs be developed and validated to reflect the nutrition guidelines for lower-income and culturally diverse countries.
A version of Kalton’s theorem for the space of regular homogeneous polynomials on Banach lattices
Authors: Bu Qingying
Published: October 2023

We give a version of Kalton’s theorem for the space of regular homogeneous polynomials on Banach lattices. As applications, we obtain sufficient conditions for the reflexivity of ${\mathcal P}^r(^nE;F)$, the space of regular n-homogeneous polynomials from a Banach lattice E to a Banach lattice F, and sufficient conditions for the positive Grothendieck property of $\hat{\otimes}_{n,s,|\pi|}E$, the n-fold positive projective symmetric tensor product of a Banach lattice E. Moreover, we also prove that these sufficient conditions are also necessary under the bounded regular approximation property.
Up-regulation of the Trace Amine Receptor, TAAR-1, in the Prefrontal Cortex of Individuals Affected by Schizophrenia
Authors: Imbriglio Tiziana , Alborghetti Marika , Bruno Valeria , Battaglia Giuseppe , Nicoletti Ferdinando , Cannella Milena
Published: October 2023

Background and Hypothesis

Type-1 trace amine-associated receptors (TAAR1) modulate dopaminergic and glutamatergic neurotransmission and are targeted by novel antipsychotic drugs. We hypothesized that schizophrenia (SCZ) causes adaptive changes in TAAR1 expression in the prefrontal cortex.

Study Design

We measured TAAR1 mRNA and protein levels by quantitative PCR and immunoblotting in post-mortem prefrontal cortical samples obtained from 23 individuals affected by SCZ and 23 non-schizophrenic controls (CTRL). Data were correlated with a number of variables in both groups.

Study Results

TAAR1 mRNA levels were largely increased in the SCZ prefrontal cortex, and did not correlate with age, age at onset and duration of SCZ, or duration of antipsychotic treatment. For the analysis of TAAR1 protein levels, CTRL and SCZ were divided into 2 subgroups, distinguished by the extent of neuropathological burden. CTRL with low neuropathological burden (LNB) had lower TAAR1 protein levels than CTRL with high neuropathological burden (HNB), whereas no changes were found between LNB and HNB in the SCZ group. TAAR1 protein levels were lower in CTRL with LNB with respect to all SCZ samples or to SCZ samples with LNB. In the SCZ group, levels showed an inverse correlation with the duration of antipsychotic treatment and were higher in individuals treated with second-generation antipsychotics as compared with those treated with first-generation antipsychotics.

Conclusions

The up-regulation of TAAR1 observed in the SCZ prefrontal cortex supports the development of TAAR1 agonists as new promising drugs in the treatment of SCZ.
The urgency of restructuring the landscape of behavioral medicine: Commentary from early-career diversity institute scholars
Authors: Fowler Lauren A , Quiñones-Cordero Maria M , Sidani Jaime E , Bernhart John A , Mendoza-Vasconez Andrea S , Bannon Sarah M , Unni Elizabeth J
Published: October 2023

Structural and systemic barriers entrenched in academia have sustained for decades, and resulted in a lack of diversity in leadership positions, inequitable workloads for women and underrepresented racial/ethnic groups, and increasing issues with retention of faculty, particularly following the COVID-19 pandemic. Increasing opposition to diversity, equity, and inclusion (DEI) efforts in higher education via legislation, policies, and general anti-DEI sentiment contextualizes the importance of prioritizing DEI. The goal of this commentary is to open discussion among academic institutions regarding changes in DEI culture that will facilitate the growth of diverse early-career faculty (ECF). We use an adapted framework which incorporates DEI into a faculty competency model to (i) guide our discussion of the rationale for restructuring academic systems to promote DEI and (ii) recommend strategies for institutional progress for ECF that can translate across academic institutions. Implementing policies and practices that seek to recruit, retain, and support historically underrepresented ECF are needed, and may involve faculty mentorship programs, establishing equitable funding mechanisms, reforming faculty evaluation practices, and examining and correcting inequities in faculty workloads. The onus is on institutions to recognize and replace the exclusionary practices and biases that have existed within their walls, and continuously promote and monitor their DEI efforts and initiatives to ensure their efficacy. Inclusive academic cultures that demonstrate their value of diversity and commitment to equity promotion at all levels of the organization, including among ECF, are necessary for ensuring excellence in scholarship in academia.
Syndecan-1 levels predict septic shock in critically ill patients with COVID-19
Authors: Aragão Nilcyeli Linhares , Zaranza Marza de Sousa , Meneses Gdayllon Cavalcante , Lázaro Ana Paula Pires , Guimarães Álvaro Rolim , Martins Alice Maria Costa , Aragão Natalia Linhares Ponte , Beliero Andrea Mazza , da Silva Júnior Geraldo Bezerra , Mota Sandra Mara Brasileiro , Albuquerque Polianna Lemos Moura Moreira , Daher Elizabeth De Francesco , De Bruin Veralice Meireles Sales , de Bruin Pedro Felipe Carvalhedo
Published: October 2023

Background

The clinical picture of coronavirus disease 2019 (COVID-19)-associated sepsis is similar to that of sepsis of other aetiologies. The present study aims to analyse the role of syndecan-1 (SDC-1) as a potential predictor of septic shock in critically ill patients with COVID-19.

Methods

This is a prospective study of 86 critically ill patients due to COVID-19 infection. Patients were followed until day 28 of hospitalization. Vascular biomarkers, such as vascular cell adhesion protein-1, SDC-1, angiopoietin-1 and angiopoietin-2, were quantified upon admission and associated with the need for vasopressors in the first 7 d of hospitalization.

Results

A total of 86 patients with COVID-19 (mean age 60±16 y; 51 men [59%]) were evaluated. Thirty-six (42%) patients died during hospitalization and 50 (58%) survived. The group receiving vasopressors had higher levels of D-dimer (2.46 ng/ml [interquartile range {IQR} 0.6–6.1] vs 1.01 ng/ml [IQR 0.62–2.6], p=0.019) and lactate dehydrogenase (929±382 U/l vs 766±312 U/l, p=0.048). The frequency of deaths during hospitalization was higher in the group that received vasoactive amines in the first 24 h in the intensive care unit (70% vs 30%, p=0.002). SDC-1 levels were independently associated with the need for vasoactive amines, and admission values >269 ng/ml (95% CI 0.524 to 0.758, p=0.024) were able to predict the need for vasopressors during the 7 d following admission.

Conclusions

Syndecan-1 levels predict septic shock in critically ill patients with COVID-19.
Bioelectrical Synchronisation of Spruce Trees during a Solar Eclipse
Authors: Chiolerio Alessandro , Gagliano Monica , Pilia Silvio , Pilia Paolo , Vitiello Giuseppe , Dehshibi Mohammad Mahdi , Adamatzky Andrew
Published: October 2023

Regular light-dark cycles greatly affect organisms, and events like eclipses induce distinctive physiological and behavioural shifts. While well-documented in animals, plant behaviour during eclipses remains largely unexplored. Here we monitored multiple spruce trees to assess their individual and collective bioelectrical responses to a solar eclipse. Trees anticipated the eclipse, synchronising their individual bioelectrical behaviour hours in advance. Older trees displayed greater anticipatory behaviour with early time-asymmetry and entropy increases, characteristic of memory dynamics in open dissipative systems such as trees. These results reveal a complex relationship between individual and collective tree behaviour, shaped by individual age and physiology as well as collective history and memory. This highlights the adaptive significance of synchrony and collective memory in plants, offering new insights on coordinated behaviours in nature.

One Sentence Summary

Trees anticipate and respond collectively to a solar eclipse.
The Hill-type equation reveals the regulatory principle of target protein expression led by p53 pulsing
Authors: Shi Xiaomin
Published: October 2023

The central dogma indicates the basic direction of gene expression pathways. For activated gene expression, the quantitative relationship between various links from the binding of transcription factors (TFs) to DNA to protein synthesis remains unclear and debated. There is consensus that at a steady state, protein levels are largely determined by the mRNA level. How can we find this steady state? Taking p53 as an example, based on the previously discovered Hill-type equation that characterizes mRNA expression under p53 pulsing, I proved that the same equation can be used to describe the average steady state of target protein expression. Therefore, at steady state, the average fold changes in mRNA and protein expression under TFs pulsing were the same. This consensus has been successfully demonstrated. For the p53 target geneBAX, the observed fold changes in mRNA and protein expression were 1.40 and 1.28, respectively; the fold changes in mRNA and protein expression calculated using the Hill-type equation were both 1.35. Therefore, using this equation, we can not only fine-tune gene expression, but also predict the proteome from the transcriptome. Furthermore, by introducing two quantitative indicators, we can determine the degree of accumulation and stability of protein expression.
Molecular control of the lymphocyte death timer
Authors: Ruhle Michelle , Thomas Evan , Dann Edward , Gottscheber Nicole , Teh Charis E. , Gray Daniel H.D. , Dowling Mark R. , Heinzel Susanne , Hodgkin Philip D.
Published: October 2023

When stimulated, individual lymphocytes program times for division and death that are inherited within families, revealing a common timing mechanism transmitted over generations. Here we describe a threshold-based mechanism for the time to die. By comparing protein levels in control and apoptosis disabled cells, we show that death can be predicted by a cooperating ensemble of BCL-2 family proteins falling below a critical threshold. Single cell measurements predict the time of death with a simple formula, where an additional inhibition factor explains accelerated death induced by BH3 mimetic compounds. Thus, we identify the death timer as a protein-threshold device that underlies signal integration machinery. Together these results reveal that predicting lymphocyte behavior at single cell level, in complex environments, is possible with modular multiscale models that incorporate timers and heritability features of critical proteins.
Genome rearrangements drive evolution of ANK genes inWolbachia
Authors: Vostokova Ekaterina V. , Dranenko Natalia O. , Gelfand Mikhail S. , Bochkareva Olga O.
Published: October 2023

Introduction

GenusWolbachiacomprises endosymbionts infecting many arthropods and nematodes; it is a model for studying symbiosis as its members feature numerous, diverse mutualistic and parasitic adaptations to different hosts. In contrast to nematode-infectingWolbachia,genomes of arthropod-infecting strains contain a high fraction of repetitive elements creating possibilities for multiple recombination events and causing genome rearrangements. The mechanisms and role of these features are still not fully understood.

Results

Transposons cover up to 18% of an arthropod-infectingWolbachiagenome and drive numerous genome rearrangements including inversions and segmental amplifications. ANK (ankyrin-repeat domain family) genes are also often found at the breakpoints of rearrangements, while less than 7% of them were found within locally collinear blocks (LCBs). We observed a strong correlation between the number of ANK genes and the genome size as well as significant overrepresentation of transposons adjacent to these genes. We also revealed numerous cases of integration of transposases to the ANK genes affecting the sequences and putative products of the latter. Our results uncover the role of mobile elements in the amplification and diversification of ANK genes.

Conclusions

Evolution of arthropod-infectingWolbachiawas accompanied by diverse genome rearrangements driving the evolution of ANK genes important for bacteria-host interactions. This study demonstrates the effectiveness of our LCB-based approach to theWolbachiagenomics and provides a framework for understanding the impact of genome rearrangements on their rapid host adaptation.
Women’s representation in Indian academia and conferences
Authors: Muralidhar Shruti , Ananthanarayanan Vaishnavi
Published: October 2023

Abstract/Introduction

Indian science academia has a dearth of women researchers at all levels. Not only are they under-represented, but they are also under-highlighted, under-mentored and overlooked for awards, grants and other career-advancing steps. To effectively address this problem and devise a solution for the inequity, we need data on the proportion of women faculty across multiple STEM institutions. Such a database, currently, does not exist. To fill this gap, we formed BiasWatchIndia to (1) document the inequities, and (2) provide real-time actionable data as a basis for future remedial steps. Along with collecting data on women representation at the faculty level in Indian STEM (science, technology, engineering and mathematics) academia, BiasWatchIndia also helps highlight the lack of women representation and gender imbalance in Indian STEM talks, conferences, workshops and panels. Based on our findings, we recommend several measures that need to be implemented by universities and institutes to challenge thestatus quochanges for women in Indian academia.
Evaluation of short-term hair follicle storage conditions for maintenance of RNA integrity
Authors: Harkin Eilís E. , Browne John A. , Murphy Barbara A.
Published: October 2023

Hair follicles provide an easily accessible tissue for interrogating gene expression in mammals. RNAlater® is a liquid storage solution that stabilises and preserves cellular RNA, eliminating the need to immediately process or freeze tissue specimens. The manufacturer advises storage of samples at 2-8°C overnight before transfer to –20°C. This study aimed to evaluate RNA integrity in hair follicle samples collected from horses, stabilized in RNAlater®, and stored under three short-term storage conditions. Mane hair samples complete with follicles were collected from three horses at a single time point. Approximately 15 hairs were placed in each of three 2 mL tubes containing 0.75ml RNAlater® solution. Test group A was stored at 4°C for 24-h, then decanted and stored at -20°C. Test groups B and C were stored at 4°C and 19°C (room temperature) respectively for 7 days, then decanted and stored at -20°C. RNA was isolated from all samples and RNA quantity and quality were measured. One-way ANOVA revealed no difference in RNA concentration (A:516 +/-125 ng/ml, B:273+/-93 ng/ml, C:476+/-176 ng/ml;P = 0.4293) or quality (A:9.5 +/-0.19, B:9.8+/-0.09, C:9.2+/-0.35 RIN; P = 0.3193) between the test groups. There were no group differences in mean Cycle Threshold values from qPCR validation assays confirming high-quality template cDNA. The results suggest that storage of hair follicles for one week in RNAlater® at cool or room temperature conditions will not compromise RNA integrity and will permit extended transport times from remote sampling locations without the need for freezing.