bluuebunny/crossref_metadata_2025 huggingface dataset:
The Australian Biosecurity Genomic Database: a new resource for high-throughput sequencing analysis based on the National Notifiable Disease List of Terrestrial Animals
Authors: Batovska Jana , Brohier Natasha D , Mee Peter T , Constable Fiona E , Rodoni Brendan C , Lynch Stacey E
Published: August 2024

The Australian Biosecurity Genomic Database (ABGD) is a curated collection of reference viral genome sequences based on the Australian National Notifiable Disease List of Terrestrial Animals. It was created to facilitate the screening of high-throughput sequencing (HTS) data for the potential presence of viruses associated with notifiable disease. The database includes a single verified sequence (the exemplar species sequence, where relevant) for each of the 60 virus species across 21 viral families that are associated with or cause these notifiable diseases, as recognized by the World Organisation for Animal Health. The open-source ABGD on GitHub provides usage guidance documents and is intended to support building a culture in Australian HTS communities that promotes the use of quality-assured, standardized, and verified databases for Australia’s national biosecurity interests. Future expansion of the database will include the addition of more strains or subtypes for highly variable viruses, viruses causing diseases of aquatic animals, and genomes of other types of pathogens associated with notifiable diseases, such as bacteria.

Database URL: https://github.com/ausbiopathgenDB/AustralianBiosecurityGenomicDatabase
Autoinhibited Protein Database: a curated database of autoinhibitory domains and their autoinhibition mechanisms
Authors: Cho Daeahn , Lee Hyang-Mi , Kim Ji Ah , Song Jae Gwang , Hwang Su-hee , Lee Bomi , Park Jinsil , Tran Kha Mong , Kim Jiwon , Vo Phuong Ngoc Lam , Bae Jooeun , Pimt Teerapat , Lee Kangseok , Gsponer Jörg , Kim Hyung Wook , Na Dokyun
Published: August 2024

Autoinhibition, a crucial allosteric self-regulation mechanism in cell signaling, ensures signal propagation exclusively in the presence of specific molecular inputs. The heightened focus on autoinhibited proteins stems from their implication in human diseases, positioning them as potential causal factors or therapeutic targets. However, the absence of a comprehensive knowledgebase impedes a thorough understanding of their roles and applications in drug discovery. Addressing this gap, we introduce Autoinhibited Protein Database (AiPD), a curated database standardizing information on autoinhibited proteins. AiPD encompasses details on autoinhibitory domains (AIDs), their targets, regulatory mechanisms, experimental validation methods, and implications in diseases, including associated mutations and post-translational modifications. AiPD comprises 698 AIDs from 532 experimentally characterized autoinhibited proteins and 2695 AIDs from their 2096 homologs, which were retrieved from 864 published articles. AiPD also includes 42 520 AIDs of computationally predicted autoinhibited proteins. In addition, AiPD facilitates users in investigating potential AIDs within a query sequence through comparisons with documented autoinhibited proteins. As the inaugural autoinhibited protein repository, AiPD significantly aids researchers studying autoinhibition mechanisms and their alterations in human diseases. It is equally valuable for developing computational models, analyzing allosteric protein regulation, predicting new drug targets, and understanding intervention mechanisms AiPD serves as a valuable resource for diverse researchers, contributing to the understanding and manipulation of autoinhibition in cellular processes.

Database URL: http://ssbio.cau.ac.kr/databases/AiPD.
Pharmacological Inhibition of N-Acylethanolamine Acid Amidase (NAAA) Mitigates Intestinal Fibrosis Through Modulation of Macrophage Activity
Authors: Nanì Maria Francesca , Pagano Ester , De Cicco Paola , Lucariello Giuseppe , Cattaneo Fabio , Tropeano Francesca Paola , Cicia Donatella , Amico Rebecca , Raucci Federica , Ercolano Giuseppe , Maione Francesco , Rinaldi Maria Michela , Esposito Fabiana , Ammendola Rosario , Luglio Gaetano , Capasso Raffaele , Makriyannis Alexandros , Petrosino Stefania , Borrelli Francesca , Romano Barbara , Izzo Angelo A
Published: August 2024

Background and Aims

Intestinal fibrosis, a frequent complication of inflammatory bowel disease, is characterized by stricture formation with no pharmacological treatment to date. N-acylethanolamine acid amidase (NAAA) is responsible for the hydrolysis of acylethanolamides (AEs, eg, palmitoylethanolamide and oleoylethanolamide). Here, we investigated NAAA and AE signaling in gut fibrosis.

Methods

NAAA and AE signaling were evaluated in human intestinal specimens from patients with stenotic Crohn’s disease (CD). Gut fibrosis was induced by 2,4,6-trinitrobenzenesulfonic acid, monitored by colonoscopy, and assessed by qRT-PCR, histological analyses, and confocal microscopy. Immune cells in mesenteric lymph nodes were analyzed by FACS. Colonic fibroblasts were cultured in conditioned media derived from polarized or non-polarized bone marrow-derived macrophages (BMDMs). IL-23 signaling was evaluated by qRT-PCR, ELISA, FACS, and western blot in BMDMs and in lamina propria CX3CR1+ cells.

Results

In ileocolonic human CD strictures, increased transcript expression of NAAA was observed with a decrease in its substrates oleoylethanolamide and palmitoylethanolamide. NAAA inhibition reduced intestinal fibrosis in vivo, as indicated by a decrease in inflammatory parameters, collagen deposition, and fibrosis-related genes, including those involved in epithelial-to-mesenchymal transition. More in-depth studies revealed modulation of the immune response related to IL-23 following NAAA inhibition. The antifibrotic actions of NAAA inhibition are mediated by Mφ and M2 macrophages that indirectly affect fibroblast collagenogenesis. NAAA inhibitor AM9053 normalized IL-23 signaling in BMDMs and in lamina propria CX3CR1+ cells.

Conclusions

Our findings provide new insights into the pathophysiological mechanism of intestinal fibrosis and identify NAAA as a promising target for the development of therapeutic treatments to alleviate CD-related fibrosis.
Association of vessel fractional flow reserve (vFFR) with luminal obstruction and plaque characteristics as detected by optical coherence tomography (OCT) in patients with NSTE-ACS: the FAST OCT study
Authors: Ziedses des Plantes Annemieke C , Scoccia Alessandra , Groenland Frederik T W , Tovar Forero Maria N , Tomaniak Mariusz , Kochman Janusz , Wojakowski Wojciech , Roleder-Dylewska Magda , Ameloot Koen , Adriaenssens Tom , den Dekker Wijnand K , Nuis Rutger-Jan , Kardys Isabella , Van Mieghem Nicolas M , Spitzer Ernest , Daemen Joost
Published: August 2024

Aims

There is a paucity of data on the performance of angiography-derived vessel fractional flow reserve (vFFR) in coronary artery lesions of patients presenting with non-ST-segment elevation acute coronary syndrome (NSTE-ACS). Optical coherence tomography (OCT) allows for visualization of lumen dimensions and plaque integrity with high resolution. The aim of this study was to define the association between vFFR and OCT findings in intermediate coronary artery lesions in patients presenting with NSTE-ACS.

Methods and results

The FAST OCT study was a prospective, multicenter, single-arm study. Patients presenting with NSTE-ACS with intermediate to severe coronary artery stenosis in one or multiple vessels with TIMI 3 flow suitable for OCT imaging were eligible. Complete pre-procedural vFFR and OCT data were available in 226 vessels (in 188 patients). A significant association between vFFR and minimal lumen area (MLA) was observed, showing an average decrease of 20.4% (95% CI −23.9% to −16.7%) in MLA per 0.10 decrease in vFFR (adjusted P < 0.001). vFFR ≤ 0.80 showed a sensitivity of 56.7% and specificity of 92.5% to detect MLA ≤ 2.5 mm2. Conversely, vFFR had a poor to moderate discriminative ability to detect plaque instability (sensitivity, 46.9%; specificity, 71.6%).

Conclusion

In patients with NSTE-ACS, vFFR is significantly associated with OCT-detected MLA, and vFFR ≤ 0.80 is highly predictive of the presence of significant disease based on OCT. Conversely, the sensitivity of vFFR ≤ 0.80 to detect OCT-assessed significant disease was low, indicating that the presence of significant OCT findings cannot be ruled out based on a negative vFFR.
Comparative Population Genomics of Arctic Sled Dogs Reveals a Deep and Complex History
Authors: Smith Tracy A , Srikanth Krishnamoorthy , Huson Heather Jay
Published: August 2024

Recent evidence demonstrates genomic and morphological continuity in the Arctic ancestral lineage of dogs. Here, we use the Siberian Husky to investigate the genomic legacy of the northeast Eurasian Arctic lineage and model the deep population history using genome-wide single nucleotide polymorphisms. Utilizing ancient dog-calibrated molecular clocks, we found that at least two distinct lineages of Arctic dogs existed in ancient Eurasia at the end of the Pleistocene. This pushes back the origin of sled dogs in the northeast Siberian Arctic with humans likely intentionally selecting dogs to perform different functions and keeping breeding populations that overlap in time and space relatively reproductively isolated. In modern Siberian Huskies, we found significant population structure based on how they are used by humans, recent European breed introgression in about half of the dogs that participate in races, moderate levels of inbreeding, and fewer potentially harmful variants in populations under strong selection for form and function (show, sled show, and racing populations of Siberian Huskies). As the struggle to preserve unique evolutionary lineages while maintaining genetic health intensifies across pedigreed dogs, understanding the genomic history to guide policies and best practices for breed management is crucial to sustain these ancient lineages and their unique evolutionary identity.
Network Analysis of Brain and Bone Tissue Transcripts Reveals Shared Molecular Mechanisms Underlying Alzheimer’s Disease and Related Dementias and Osteoporosis
Authors: Nagarajan Archana , Laird Jason , Ugochukwu Obiadada , Reppe Sjur , Gautvik Kaare , Ross Ryan D , Bennett David A , Rosen Clifford , Kiel Douglas P , Higginbotham Lenora A , Seyfried Nicholas T , Lary Christine W
Published: August 2024

Background

Alzheimer’s disease and related dementias (ADRD) and osteoporosis (OP) are 2 prevalent diseases of aging with demonstrated epidemiological association, but the underlying molecular mechanisms contributing to this association are unknown.

Methods

We used network analysis of bone and brain transcriptomes to discover common molecular mechanisms underlying these 2 diseases. Our study included RNA-sequencing data from the dorsolateral prefrontal cortex tissue of autopsied brains in 629 participants from ROSMAP (Religious Orders Study and the Rush Memory and Aging Project), with a subgroup of 298 meeting criteria for inclusion in 5 ADRD categories, and RNA array data from transiliac bone biopsies in 84 participants from the Oslo study of postmenopausal women. After developing each network within each tissue, we analyzed associations between modules (groups of coexpressed genes) with multiple bone and neurological traits, examined overlap in modules between networks, and performed pathway enrichment analysis to discover conserved mechanisms.

Results

We discovered 3 modules in ROSMAP that showed significant associations with ADRD and bone-related traits and 4 modules in Oslo that showed significant associations with multiple bone outcomes. We found significant module overlap between the 2 networks in modules linked to signaling, tissue homeostasis, and development, and Wingless-related integration site (Wnt) signaling was found to be highly enriched in OP and ADRD modules of interest.

Conclusions

These results provide translational opportunities in the development of treatments and biomarkers for ADRD and OP.
The Causal Effect of Adult Height on Late-Life Handgrip Strength: The Singapore Chinese Health Study
Authors: Chang Xuling , Chua Kevin Yiqiang , Shih Chih Chuan , Chen Jieqi , Lee Ai Shan , Tan Patrick , Wang Ling , Liu Jianjun , Heng Chew-Kiat , Yuan Jian-Min , Khor Chiea Chuen , Dorajoo Rajkumar , Koh Woon-Puay
Published: August 2024

Background

Adult height has been associated with handgrip strength, which is a surrogate marker of physical frailty. However, it is uncertain if this association is causative or due to confounding bias.

Methods

We evaluated pairwise associations among handgrip strength, adult height, and genetically determined height (using a polygenic score [PGS] for height in a mediation framework and a 2-sample Mendelian randomization approach) by means of a multivariable regression model using a prospective cohort of Chinese living in Singapore. We additionally evaluated pathway enrichments of height-related genes in relation to increased handgrip strength to discover common biological mechanisms underlying associations of genetically determined height with handgrip strength.

Results

Height PGS exhibited a positive association with handgrip strength at late life after adjusting for midlife body weight and other baseline exposures (cigarette smoking, education, and physical activity status, p = 1.2 × 10−9). Approximately 66.4% of the total effect of height PGS on handgrip strength was mediated through adult height (βindirect-effect = 0.034, pindirect-effect = 1.4 × 10−40). Two-sample Mendelian randomization evaluations showed a consistent causal relationship between increased height and increased handgrip strength in late life (p between 6.6 × 10−4 and 3.9 × 10−18), with insignificant horizontal pleiotropic effects (pMR-Egger intercept = 0.853). Pathway analyses of genes related to both increased adult height and handgrip strength revealed enrichment in ossification and adipogenesis pathways (padj between .034 and 6.8 × 10−4).

Conclusions

The study highlights a potentially causal effect between increased adult height and increased handgrip strength in late life, which may be explained by related biological processes underlying the preservation of muscle mass and strength in aging.
Antimicrobial Peptides From the Gut Microbiome of the Centenarians: Diversification of Biosynthesis and Youthful Development of Resistance Genes
Authors: Lu Chunrong , Wang Xiaojun , Ye Pengpeng , Lu Zhilong , Ma Jie , Luo Weifei , Wang Shuai , Chen Xiaochun
Published: August 2024

Antimicrobial peptides (AMPs) offer a potential solution to the antibiotic crisis owing to their antimicrobial properties, and the human gut biome may be a source of these peptides. However, the potential AMPs and AMP resistance genes (AMPRGs) of gut microbes in different age groups have not been thoroughly assessed. Here, we investigated the potential development of AMPs and the distribution pattern of AMPRGs in the gut microbiome at different ages by analyzing the intestinal metagenomic data of healthy individuals at different life stages (CG: centenarians group n = 20; OAG: older adults group: n = 15; YG: young group: n = 15). Age-related increases were observed in the potential AMPs within the gut microbiome, with centenarians showing a greater diversity of these peptides. However, the gut microbiome of the CG group had a lower level of AMPRGs compared to that of the OAG group, and it was similar to the level found in the YG group. Additionally, conventional probiotic strains showed a significant positive correlation with certain potential AMPs and were associated with a lower detection of resistance genes. Furthermore, comparing potential AMPs with existing libraries revealed limited similarity, indicating that current machine learning models can identify novel peptides in the gut microbiota. These results indicate that longevity may benefit from the diversity of AMPs and lower resistance genes. Our findings help explain the age advantage of the centenarians and identify the potential for antimicrobial peptide biosynthesis in the human gut microbiome, offering insights into the development of antimicrobial peptide resistance and the screening of probiotic strains.
Does Pain Explain Trends in Disability? An Analysis of Middle-Aged and Older U.S. Adults, 2002–2018
Authors: Ruan Hangqing , Zajacova Anna , Zimmer Zachary , Grol-Prokopczyk Hanna
Published: August 2024

Objectives

This article investigates the role of pain in disability trends in the United States, within the context of recent unfavorable disability trends and the concurrent rise in pain.

Methods

We conducted a 2-part analysis using National Health Interview Survey data from 2002 to 2018 for U.S. adults aged 45–84. First, we assessed how changes in the prevalence of 5 site-specific types of pain (headaches/migraines, joint, low back, neck, and facial/jaw pain) associated with disability trends. Second, we used self-reported causes of disability and examined whether there has been a change in the proportion of individuals who attribute their disability to 1 of 5 chronic or acute painful conditions.

Results

The 5 site-specific types of pain, individually and collectively, were significantly associated with increases in disability. If site-specific chronic pain had not increased during the study period, the trend for functional limitations would have been 40% lower, and that for activity limitations would have shown a slight decline instead of an increase. Attributions of functional limitations to painful conditions increased by 23% during the 2002–2018 period, representing an additional 9.82 million Americans experiencing pain-attributable disability. Arthritis/rheumatism, back/neck problems, and other musculoskeletal/connective conditions were the primary sources of pain-related disability.

Discussion

Our research provides the first systematic, national examination of how pain is contributing to disability trends in the United States. The findings have implications for disability reduction policies and shed light on the far-reaching consequences of pain for overall population health.
A Polysocial Approach in Exploring Racial and Ethnic Differences in Dementia and Cognitive Decline Among U.S. Older Adults: Health and Retirement Study
Authors: Ping Yongjing , Odden Michelle C , Chen Xi , Prina Matthew , Xu Hanzhang , Xiang Hao , Wu Chenkai
Published: August 2024

Background and Objectives

The racial or ethnic disparity in the burden of dementia exists among older adults in the United States, whereas gaps remain in understanding the synergic effect of multiple social determinants of health on diminishing this disparity. We aim to build a polysocial score for dementia and investigate the racial or ethnic difference in dementia risk among older persons with different polysocial score categories.

Research Design and Methods

In this prospective cohort study, we utilized longitudinal data from the Health and Retirement Study in the United States recruiting 6 945 participants aged ≥65 years who had data on 24 social determinants of health in 2006/2008. The dementia status of participants was measured by a modified version of the Telephone Interview of Cognitive Status. The stepwise Cox regression was applied to select social determinants of health associated with incident dementia to construct a polysocial score. The multivariable Poisson model and linear mixed model were utilized to investigate the associations between polysocial score and incident dementia and cognitive decline, respectively.

Results

Eight social determinants of health were used to build the polysocial score. Non-Hispanic Black older participants had a higher incidence rate (incidence rate difference [IRD] = 22.7; 95% confident interval [95% CI] = 12.7–32.8) than non-Hispanic White older adults in the low polysocial score, while this difference was substantially attenuated in the high polysocial score category (IRD = 0.5; 95% CI = −6.4 to −7.5). The cognitive decline of non-Hispanic older Black adults with high polysocial score was 84.6% slower (averaged cognitive decline: non-Hispanic White: −2.4 [95% CI = −2.5 to −2.3] vs non-Hispanic Black: −1.3 [95% CI = −1.9 to −0.8]) than that of non-Hispanic older White persons.

Discussion and Implications

These findings may help comprehensively understand and address racial and ethnic disparities in dementia risk and may be integrated into existing dementia prevention programs to provide targeted interventions for community-dwelling older adults with differentiated social disadvantages.
Older Adults in Administrative Quagmire: A Scoping Review of Policy and Program Coordination Across Six Marginalized Older Adult Populations
Authors: Marier Patrik , Joy Meghan , Smele Sandra , Zakaria Rym , Beauchamp Julie , Bourgeois-Guérin Valérie , Lupien Pierre-Luc , Sussman Tamara
Published: August 2024

Background and Objectives

Coordination of governmental action is crowded with policies and programs that are highly interdependent, sometimes operating in silos if not contradicting each other. These dilemmas, or administrative quagmires, are heightened for older adults in general, but they are particularly problematic for marginalized older adults because these groups often require public assistance and support. This scoping review studies the coordination of governmental action on aging published in social science journals, focusing on 6 groups of marginalized older adults: those with histories of immigration, individuals with severe mental health problems, those who have had experiences of homelessness, formerly incarcerated individuals, members of the LGBT (lesbian, gay, bisexual, and transgender) community, and individuals living in a rural area.

Research Design and Methods

A 5-stage scoping review methodology was followed, and 53 articles (published between 2000 and 2022) from 5 social science databases were analyzed.

Results

The analysis revealed a limited number of contributions with coordination as a primary focus. Understandings of coordination varied but tended to examine structure, organization, and relationships between sectors. When coordination was the primary object of a study, it was often analyzed in 1 specific policy area or within a clinical setting along the lines of facilitating care coordination.

Discussion and Implications

This scoping review reveals a mutual neglect on the part of public administration and policy scholars toward marginalized older adults and a lack of public administration considerations on the part of scholars studying long-term care and social service programs for these marginalized older adults.
The effects of SNAP emergency allotments on state-level SNAP benefits and enrollment during the COVID-19 pandemic
Authors: Steffen David R , Kim David D
Published: August 2024

During the COVID-19 pandemic, all US states provided emergency allotments (EA) to enrollees of the Supplemental Nutrition Assistance Program (SNAP) to alleviate rising food insecurity. However, 18 states opted out of the SNAP-EA program before its official expiration in February 2023. Using a staggered difference-in-differences model to account for state-level variation in the timing of the SNAP-EA opt-out decisions, we analyzed SNAP and SNAP-EA data from the US Department of Agriculture Food and Nutrition Service to quantify the impact of state opt-out decisions on SNAP benefit size and enrollment. We found that the average SNAP monthly benefit among 18 SNAP opt-out states was reduced by $183 (95% confidence interval [CI]: −$214, −$152) per beneficiary. The percentage of the state population enrolled in the SNAP program among the opt-out states modestly decreased by 0.35 (95% CI: −0.61, −0.10) percentage points. Additionally, we employed logistic regression models to associate state opt-out decisions with state-level characteristics. We found that the state governor's political party being Republican was the only significant predictor for the state's opt-out decisions. Our findings help explain why opting out of SNAP-EA has been associated with higher food insufficiency and shed light on the impact of political decisions to opt out of SNAP-EA on the lives of millions of Americans.
Advancing artificial intelligence in fisheries requires novel cross-sector collaborations
Authors: Wing Kate , Woodward Benjamin
Published: August 2024

Artificial intelligence, or AI, has the potential to dramatically improve our understanding and management of the ocean. For fisheries, these benefits could include greater monitoring coverage at lower costs, improved estimates of catch and bycatch, identification of illegal fishing, and seafood traceability throughout the supply chain. However, fisheries AI innovation and adoption faces substantial barriers from the highly regulated nature of fisheries and the complex overlap of government policies, diverse user needs, and market pressures. We argue that needed advances in fisheries AI require novel collaborations to share data and methods, encourage new and diverse entrants to the field, and increase baseline technical literacy across the global fisheries community. Unlocking fisheries data to power AI, particularly image data, can only be achieved through partnerships across government managers, AI developers, fishers and vessel owners, and technology service providers, which, in turn, requires a common vocabulary for policy and technical concepts. With a greater shared understanding across the field, fisheries AI providers can deliver desired results, and users can have confidence that systems are performing as advertised, ultimately meeting monitoring demand and sustainability goals.
Computable error bounds for quasi-Monte Carlo using points with non-negative local discrepancy
Authors: Gnewuch Michael , Kritzer Peter , Owen Art B , Pan Zexin
Published: August 2024

Let $f:[0,1]^{d}\to{\mathbb{R}}$ be a completely monotone integrand as defined by Aistleitner and Dick (2015, Acta Arithmetica, 167, 143–171) and let points $\boldsymbol{x}_{0},\dots ,\boldsymbol{x}_{n-1}\in [0,1]^{d}$ have a non-negative local discrepancy (NNLD) everywhere in $[0,1]^{d}$. We show how to use these properties to get a non-asymptotic and computable upper bound for the integral of $f$ over $[0,1]^{d}$. An analogous non-positive local discrepancy property provides a computable lower bound. It has been known since Gabai (1967, Illinois J. Math., 11, 1–12) that the two-dimensional Hammersley points in any base $b\geqslant 2$ have NNLD. Using the probabilistic notion of associated random variables, we generalize Gabai’s finding to digital nets in any base $b\geqslant 2$ and any dimension $d\geqslant 1$ when the generator matrices are permutation matrices. We show that permutation matrices cannot attain the best values of the digital net quality parameter when $d\geqslant 3$. As a consequence the computable absolutely sure bounds we provide come with less accurate estimates than the usual digital net estimates do in high dimensions. We are also able to construct high-dimensional rank one lattice rules that are NNLD. We show that those lattices do not have good discrepancy properties: any lattice rule with the NNLD property in dimension $d\geqslant 2$ either fails to be projection regular or has all its points on the main diagonal. Complete monotonicity is a very strict requirement that for some integrands can be mitigated via a control variate.
A Trace Map on Higher Scissors Congruence Groups
Authors: Bohmann Anna Marie , Gerhardt Teena , Malkiewich Cary , Merling Mona , Zakharevich Inna
Published: August 2024

Cut-and-paste $K$-theory has recently emerged as an important variant of higher algebraic $K$-theory. However, many of the powerful tools used to study classical higher algebraic $K$-theory do not yet have analogues in the cut-and-paste setting. In particular, there does not yet exist a sensible notion of the Dennis trace for cut-and-paste $K$-theory. In this paper we address the particular case of the $K$-theory of polyhedra, also called scissors congruence $K$-theory. We introduce an explicit, computable trace map from the higher scissors congruence groups to group homology, and use this trace to prove the existence of some nonzero classes in the higher scissors congruence groups. We also show that the $K$-theory of polyhedra is a homotopy orbit spectrum. This fits into Thomason’s general framework of $K$-theory commuting with homotopy colimits, but we give a self-contained proof. We then use this result to re-interpret the trace map as a partial inverse to the map that commutes homotopy orbits with algebraic $K$-theory.
A Rapid Molecular Detection Tool for Toxigenic M1UK Streptococcus pyogenes
Authors: Brouwer Stephan , Das Swairindhree , Hayes Andrew J , Bertolla Olivia M , Davies Mark R , Walker Mark J , Whiley David M , Irwin Adam D , Tickner Jacob A
Published: August 2024

Background

The gradual replacement of the Streptococcus pyogenes M1global genotype by a newly emergent M1UK variant is a global public health threat warranting increased surveillance. M1UK differs from progenitor M1global genotype by 27 single-nucleotide polymorphisms and is characterized by increased speA superantigen expression in vitro.

Methods

An allele-specific real-time polymerase chain reaction assay was developed for the rapid detection of M1UK strains. The assay was used in combination with whole genome sequencing to determine emm (sub)type distribution for 51 invasive (n = 9) and noninvasive (n = 42) S pyogenes clinical isolates.

Results

Emm1 was the most prevalent S pyogenes emm serotype (n = 11) in this set of clinical isolates, with M1UK being the dominant emm1 genotype (4/5 invasive, 3/6 noninvasive isolates). The assay accurately detected M1UK strains. Whole genome sequencing revealed continued presence of Australian M1UK sublineages associated with epidemic scarlet fever–causing S pyogenes in Asia.

Conclusions

Our study establishes a suitable target for detection of the toxigenic M1UK and confirms the maintenance of M1UK strains in Queensland, Australia. This assay can be deployed in laboratories and provides a valuable, cost-effective tool to enhance surveillance of the expanding M1UK clone.
Phylogeny and diversification analyses of extant planthopper families (Hemiptera: Fulgoromorpha) based on a mitochondrial dataset reveal ancient lineages originating during the Jurassic and originally feeding on gymnosperms
Authors: Ai Deqiang , Bourgoin Thierry , Bucher Manon , Hu Yanhua , Zhang Yalin
Published: August 2024

Phylogenetic analyses of planthoppers were conducted using a mitogenome dataset to examine the evolutionary relationships of current families based on both maximum likelihood (ML) and Bayesian inference methods. Delphacoidea, including Cixiidae and Delphacidae, and Fulgoroidea, including all other families, were consistently identified as monophyletic groups. However, Nogodinidae displayed a polyphyletic pattern, with various lineages emerging sister to several issidoid families. Variations were observed across different analyses in the positioning of (Dictyopharidae + Fulgoridae) and the relationships of Ricaniidae sister either to Issidae or to (Flatidae + Acanaloniidae). Several statistical tests indicate that the ML topology has the highest level of statistical confidence. The (Dictyopharidae + Fulgoridae) clade is best positioned as sister to (Derbidae + (Achilidae + (Tropiduchidae + other “higher” planthoppers families))) and the Ricaniidae as sister to (Flatidae + Acanaloniidae). With 13 fossil calibration points, origin times for Delphacoidea and Fulgoroidea were dated back to the Late Permian, approximately 257.46 million years ago. Delphacidae and Cixiidae split during the Late Triassic, while Fulgoroidea diversified earlier during the Middle Triassic. Divergence and diversification times are also provided for all other extant planthopper families. These results suggest that Delphacoidea and Fulgoroidea likely diverged from the older planthopper fossil families prior to the emergence of angiosperms and may have initially fed on gymnosperms and ancient ferns. The diversification of extant planthopper families occurred during the Jurassic and Cretaceous periods, influenced by evolving climatic conditions, the decline in gymnosperms, and the increasing diversity of angiosperm plants.
Implementing virtual desktops for clinical research at an academic health center: a case report
Authors: Zai Adrian H , Wong Steven , Guilarte-Walker Yurima , Langlois Paul , Coleman Brian , Soni Apurv , McManus David D , Luzuriaga Katherine
Published: August 2024

Objectives

To address the challenges of sharing clinical research data through the implementation of cloud-based virtual desktops, enhancing collaboration among researchers while maintaining data security.

Materials and Methods

This case study details the deployment of virtual desktops at UMass Chan Medical School (UMass Chan). The process involved forming a Research Informatics Steering Executive workgroup, identifying key requirements, implementing Amazon WorkSpaces, and establishing configurable data management for research support.

Results

Key lessons include the significance of collaboration, balancing user-friendliness and functionality, flexibility in data management, maximizing virtual desktop efficiency within budget constraints, and continuous user feedback. The implementation of virtual desktops supports secure collaborative research, advancing medical knowledge and improving healthcare outcomes.

Discussion

The structured approach to implementing virtual desktops addresses data security, regulatory compliance, and real-time collaboration challenges. Continuous feedback and iterative improvements have enhanced the system’s effectiveness.

Conclusion

The successful implementation of virtual desktops at UMass Chan demonstrates the potential for such systems to support secure, collaborative research, offering insights for similar initiatives in other academic health centers.
Bromazolam in impaired driving investigations
Authors: Bierly Jolene J , Papsun Donna M , Logan Barry K
Published: August 2024

The designer benzodiazepine bromazolam is increasingly encountered in forensic casework, including impaired driving investigations. A series of suspected impaired driving cases that tested positive for bromazolam are described herein along with information about driving performance, driver appearance, and observed behavior. Bromazolam was indicated in casework either through screening by liquid chromatography–time of flight mass spectrometry (LC–TOF-MS) and/or a positive benzodiazepine immunoassay screen. Blood samples were forwarded for quantitative confirmatory analysis using a liquid chromatography–tandem mass spectrometry (LC–MS–MS) method with a reporting limit of 2.0 ng/mL. Bromazolam was reported in 98 impaired driving cases from samples reported between January 2021 and December 2023, with the earliest detection from September 2020. Mean and median blood concentrations were 125 ± 145 and 84 ng/mL respectively, with a range of 4.2–990 ng/mL. Additional positive findings were reported in almost all cases, with the highest result (990 ng/mL) being the only case in which bromazolam was the only finding. Fentanyl was the most frequent drug found in combination with bromazolam. Driving behaviors reported in these cases included erratic driving, errors in Standardized Field Sobriety Tests, and symptoms consistent with central nervous system depressants, including slurred speech, incoordination, and lethargic behavior. Based on its prevalence and demonstrated impairing effects, bromazolam should be included in the scope of impaired driving testing as long as it continues to be prevalent in the drug supply.
A traumatic arteriovenous fistula causing venous insufficiency
Authors: Shelton John , Marasinghe Amanthana
Published: August 2024

Chronic leg ulcers are one of the clinical manifestations of untreated traumatic arteriovenous fistula (AVF). Ulcers due to secondary venous etiology like AVF are rare and easily missed. We present the case of a 31-year-old male who sustained a gunshot injury to the knee 12 years ago. Despite the absence of varicose veins, he presented with a neglected venous ulcer persisting for 2 years. A computed tomographic venogram revealed an AVF in the supra-genicular popliteal artery and vein. The patient subsequently underwent open surgical correction. Complete ulcer healing was achieved in 6 months. This case underscores the potential for a high-flow post-traumatic AVF to induce a non-healing venous ulcer even in the absence of apparent varicose veins. Secondary causes of chronic venous diseases are often overlooked, leading to complications. Early recognition is crucial to preventing further morbidity.
Antiretroviral Therapy and Cardiovascular Risk in People With HIV in the United States—An Updated Analysis
Authors: Parra-Rodriguez Luis , Sahrmann John M , Butler Anne M , Olsen Margaret A , Powderly William G , O’Halloran Jane A
Published: August 2024

Background

Several antiretroviral therapy (ART) medications have been associated with increased cardiovascular risk, but less is known about the safety of modern ART. We sought to compare the risk of major adverse cardiac events (MACEs) among different ART regimens.

Methods

Using insurance claims databases from 2008 to 2020, we identified adults aged <65 years who newly initiated ART. We compared non-nucleoside reverse transcriptase inhibitor (NNRTI)-based regimens to protease inhibitors (PI)- and integrase inhibitors (INSTI)-based regimens. We used propensity score-weighted Kaplan-Meier functions to estimate the 6, 12, 18, 24, 36, and 48 months’ risk and risk differences (RD) of MACE.

Results

Among 37 935 ART initiators (median age, 40 years; 23% female; 26% Medicaid-insured), 45% started INSTI-, 16% PI-, and 39% NNRTI-based regimens. MACE occurred in 418 individuals (1.1%) within 48 months after ART initiation. Compared to NNRTI initiators, the risk of MACE was higher at 12 months (RD, 0.50; 95% CI, 0.14–0.99), 18 months (RD, 0.53; 95% CI, 0.11–1.06), and 24 months (RD, 0.62; 95% CI, 0.04–1.29) for PI initiators, and at 12 (RD, 0.20; 95% CI, 0.03–0.37) and 18 months (RD, 0.31; 95% CI, 0.06–0.54) for INSTI initiators; the precision of estimates was limited for longer duration of follow-up.

Conclusions

Among ART initiators, PI-based and INSTI-based regimens were associated with higher short-term risk of MACE compared to NNRTI-based regimens. The pattern of association between INSTIs and PIs with excess risk of MACE was similar.
Evaluation of the Tuberculosis Infection Care Cascade Among Pregnant Individuals in a Low-Tuberculosis-Burden Setting
Authors: Campbell Jeffrey I , Lavache Dorine , Garing Ariane , Sabharwal Vishakha , Haberer Jessica E , Dubois Melanie , Jenkins Helen E , Brooks Meredith B , Joseph Naima T , Kissler Katherine , Horsburgh C Robert , Jacobson Karen R
Published: August 2024

In the United States, tuberculosis (TB) screening is recommended for pregnant individuals with TB risk factors. We conducted a retrospective study of perinatal TB infection testing and treatment in a tertiary health system. Of 165 pregnant individuals with positive TB infection tests, only 9% completed treatment within 4.6 years of follow-up.
Leaf Gas Film 1 promotes glycerol ester accumulation and formation of a tight root barrier to radial O2 loss in rice
Authors: Jiménez Juan de la Cruz , Noorrohmah Siti , Suresh Kiran , Zeisler-Diehl Viktoria V , Peralta Ogorek Lucas León , Herzog Max , Pellegrini Elisa , Nagai Keisuke , Ashikari Motoyuki , Takahashi Hirokazu , Pedersen Ole , Schreiber Lukas , Nakazono Mikio
Published: August 2024

Rice (Oryza sativa L.) and many other wetland plants form an apoplastic barrier in the outer parts of the roots to restrict radial O2 loss to the rhizosphere during soil flooding. This barrier facilitates longitudinal internal O2 diffusion via gas-filled tissues from shoot to root apices, enabling root growth in anoxic soils. We tested the hypothesis that Leaf Gas Film 1 (LGF1), which influences leaf hydrophobicity in rice, plays a crucial role in tight outer apoplastic barrier formation in rice roots. We examined the roots of a rice mutant (dripping wet leaf 7, drp7) lacking functional LGF1, its wild type, and an LGF1 overexpression line for their capacity to develop outer apoplastic barriers that restrict radial O2 loss. We quantified the chemical composition of the outer part of the root and measured radial O2 diffusion from intact roots. The drp7 mutant exhibited a weak barrier to radial O2 loss compared to the wild type. However, introducing functional LGF1 into the mutant fully restored tight barrier function. The formation of a tight barrier to radial O2 loss was associated with increased glycerol ester levels in exodermal cells, rather than differences in total root suberization or lignification. These results demonstrate that, in addition to its role in leaf hydrophobicity regulation, LGF1 plays an important role in controlling the function of the outer apoplastic barriers in roots. Our study suggests that increased deposition of glycerol esters in the suberized root exodermis establishes a tight barrier to radial O2 loss in rice roots.
Referring wisely: knowing when and how to make subspecialty consultations in hospital medicine
Authors: Ng Isaac K S , Lim Shir Lynn , Teo Kevin S H , Goh Wilson G W , Thong Christopher , Lee Joanne
Published: August 2024

Subspecialty consultations are becoming highly prevalent in hospital medicine, due to an ageing population with multimorbid conditions and increasingly complex care needs, as well as medicolegal fears that lead to widespread defensive medical practices. Although timely subspecialty consultations in the appropriate clinical context have been found to improve clinical outcomes, there remains a significant proportion of specialty referrals in hospital medicine which are inappropriate, excessive, or do not add value to patient care. In this article, we sought to provide an overview of the common problems pertaining to excessive quantity and suboptimal quality of inpatient subspecialty consultations made in real-world practice and highlight their implications for healthcare financing and patient care. In addition, we discuss the underlying contributing factors that predispose to inappropriate use of the specialist referral system. Finally, we offer a practical, multitiered approach to help rationalize subspecialty consultations, through (i) a systematic model (‘WISE’ template) for individual referral-making, (ii) development of standardized healthcare institutional referral guidelines with routine clinical audits for quality control, (iii) adopting an integrated generalist care model, and (iv) incorporating training on effective referral-making in medical education.
3D printing of recombinant collagen/chitosan methacrylate/nanoclay hydrogels loaded with Kartogenin nanoparticles for cartilage regeneration
Authors: Zhang Wanting , Shi Kejia , Yang Jianfeng , Li Wenjing , Yu Yang , Mi Yu , Yao Tianyu , Ma Pei , Fan Daidi
Published: August 2024

Cartilage defects are frequently caused by trauma, illness and degradation of the cartilage. If these defects are not sufficiently treated, the joints will degrade irreversibly, possibly resulting in disability. Articular cartilage lacks blood vessels and nerves and is unable to regenerate itself, so the repair of cartilage defects is extremely challenging in clinical treatment. Tissue engineering technology is an emerging technology in cartilage repair and cartilage regeneration. 3D-printed hydrogels show great potential in cartilage tissue engineering for the fabrication of 3D cell culture scaffolds to mimic extracellular matrix. In this study, we construct a 3D-printed hydrogel loaded with nanoparticles by electrostatic interaction and photo cross-linking for the regeneration of cartilage, which has adaptable and drug-continuous release behavior. A photopolymerizable bioink was prepared using recombinant collagen, chitosan, nanoclay Laponite-XLG and nanoparticles loaded with Kartogenin (KGN). This bioink was added with KGN, a small molecule drug that promotes cartilage differentiation, and as a result, the 3D-printed CF/CM/3%LAP/KGN scaffolds obtained by extrusion printing is expected to be used for cartilage repair. It was shown that the 3D-printed scaffolds had good cytocompatibility for human bone marrow mesenchymal stem cells (hBMSCs) and exhibited excellent antimicrobial properties, the continuous release of KGN in the scaffold induced the hBMSCs differentiation into chondrocytes, which significantly enhanced the expression of collagen II and glycosaminoglycan. In vivo studies have shown that implantation of KGN-loaded scaffolds into cartilage-injured tissues promoted cartilage tissue regeneration. This study demonstrated that 3D-printed CF/CM/3%LAP/KGN scaffolds can be used for cartilage repair, which is expected to lead to new healing opportunities for cartilage injury-based diseases.
Analysis of the impact of Arctic environment conditions on the psychophysical status of navigators and the safety of ice navigation
Authors: Goncharov Vadim K , Chugaeva Angelika E , Kviatkovskaia Elena S , Zueva Ekaterina S
Published: August 2024

The Arctic is a specific geographical region whose environment affects any person staying and working there, so it demands research on the practice of ice navigation. The most difficult period of navigation is the winter to spring time, when Arctic seas are covered by an ice cover. Ice navigation is always associated with many difficulties for a ship's crew, not only because of the geographical location of the water area but also because the climatic and environmental conditions impact their mental and physical state. These conditions, namely the length of the polar night and day, the extreme frosts, the maximum number of foggy days and the duration of the ice period on all the tracks of the cargo ships along the North Sea Route, were selected and analysed as the dominant factors that impact on crew members. The analysis was performed on the basis of the ‘Matrix of Arctic Impacts’, which summarizes data about the level of the selected factors in the local water areas along the North Sea Route and provides data on the local water areas with the most impacts of Arctic environment factors on the psychophysical status of crew members. In these water areas, accidents caused by the ‘human factor’ are most likely to occur. Therefore, special studies of the Arctic environment's impact on navigators is required in order to improve the safety of ice navigation.