bluuebunny/crossref_metadata_2025 huggingface dataset:
Design, fabrication and clinical characterization of additively manufactured tantalum hip joint prosthesis
Authors: Zhao Dewei , Cheng Liangliang , Lu Faqiang , Zhang Xiuzhi , Ying Jiawei , Wei Xiaowei , Cao Fang , Ran Chunxiao , Zheng Guoshuang , Liu Ge , Yi Pinqiao , Wang Haiyao , Song Liqun , Wu Bin , Liu Lingpeng , Li Lu , Wang Xiaohu , Li Junlei
Published: June 2024

The joint prosthesis plays a vital role in the outcome of total hip arthroplasty. The key factors that determine the performance of joint prostheses are the materials used and the structural design of the prosthesis. This study aimed to fabricate a porous tantalum (Ta) hip prosthesis using selective laser melting (SLM) technology. The feasibility of SLM Ta use in hip prosthesis was verified by studying its chemical composition, metallographic structure and mechanical properties. In vitro experiments proved that SLM Ta exhibited better biological activities in promoting osteogenesis and inhibiting inflammation than SLM Ti6Al4V. Then, the topological optimization design of the femoral stem of the SLM Ta hip prosthesis was carried out by finite element simulation, and the fatigue performance of the optimized prosthesis was tested to verify the biomechanical safety of the prosthesis. A porous Ta acetabulum cup was also designed and fabricated using SLM. Its mechanical properties were then studied. Finally, clinical trials were conducted to verify the clinical efficacy of the SLM Ta hip prosthesis. The porous structure could reduce the weight of the prosthesis and stress shielding and avoid bone resorption around the prosthesis. In addition, anti-infection drugs can also be loaded into the pores for infection treatment. The acetabular cup can be custom-designed based on the severity of bone loss on the acetabular side, and the integrated acetabular cup can repair the acetabular bone defect while achieving the function of the acetabular cup.
Market Power and the Transmission of Loan Subsidies
Authors: Ornelas Jose Renato Haas , Pedraza Alvaro , Ruiz-Ortega Claudia , Silva Thiago Christiano
Published: June 2024

We study a large-scale Brazilian loan subsidy program to expand long-term credit. The government subsidizes banks’ funding costs for lenders, who then allocate credit to firms at regulated interest rates below a maximum ceiling. We propose and test a mechanism allowing banks to circumvent the rate caps and capture part of the subsidy. We show that when issuing a subsidized loan, lenders with market power use a cross-product pricing strategy, whereby they increase the price of other products to the same client. Our results have important policy implications for the design and effectiveness of government interventions in credit markets. (JEL G21, H81, E43)
Serum interleukin-34 levels in dermatomyositis: a potential biomarker for anti-MDA5-antibody-associated interstitial lung disease
Authors: Kuzumi Ai , Fukasawa Takemichi , Yamashita Takashi , Matsuda Kazuki M , Kotani Hirohito , Yoshizaki-Ogawa Asako , Sato Shinichi , Yoshizaki Ayumi
Published: June 2024

Objectives

IL-34 is a haematopoietic cytokine that promotes macrophage activation. Macrophage activation in interstitial lung disease (ILD) in patients with DM, especially in those with anti-melanoma differentiation-associated gene 5 (MDA5) antibody suggests the involvement of IL-34 in the disease. However, the association between IL-34 and DM is unknown. In this study, we aimed to determine serum IL-34 levels in DM patients and evaluate their association with DM-ILD.

Methods

We measured serum IL-34 levels in 56 DM patients and 14 age- and sex- matched healthy controls by ELISA, and examined their correlation with clinical parameters. In addition, pre- and post-treatment serum IL-34 levels were examined using serum samples from 7 anti-MDA5 antibody-positive DM patients.

Results

Serum IL-34 levels were significantly elevated in DM patients, especially in those with anti-MDA5 antibody, compared with healthy controls. In anti-MDA5-antibody-positive DM patients, serum IL-34 levels positively correlated with serum levels of ferritin and anti-MDA5 antibody, which are known biomarkers for rapidly progressive (RP)-ILD. Following combined immunosuppressive therapy, serum IL-34 levels decreased along with ferritin and anti-MDA5 antibody.

Conclusion

These data suggest that IL-34 may be involved in the development of RP-ILD in anti-MDA5 antibody-positive DM. Serum IL-34 levels can serve as a potential biomarker for RP-ILD in this clinical entity.
Are Invasive Group A Streptococcal Infections Preventable by Antibiotic Therapy?: A Collaborative Retrospective Study
Authors: Erlacher Rahel , Toepfner Nicole , Dressen Svenja , Berner Reinhard , Bösch Annemarie , Tenenbaum Tobias , Heininger Ulrich
Published: June 2024

Background:

In winter 2022/2023, a resurgence of invasive group A streptococcal (iGAS) infections in children was observed in Europe, including Germany and Switzerland. While a simultaneous increase in consultations for scarlet fever and pharyngitis was reported in England, leading to the recommendation to treat any suspected GAS disease with antibiotics, guidelines in Germany and Switzerland remained unchanged. We aimed to investigate whether this policy was appropriate.

Methods:

We conducted a retrospective multicenter study of children hospitalized for invasive GAS disease between September 2022 and March 2023 in pediatric departments in Dresden and Berlin (Germany) and Basel (Switzerland). We reviewed medical records and conducted structured telephone interviews to analyze whether suspected GAS infections with or without antibiotic treatment were reported prehospitalization.

Results:

In total, 63 patients met the inclusion criteria (median age 4.2 years, 57% males); however, clinical information was not complete for all analyzed characteristics; 32/54 (59%) had ≥1 physician visit ≤4 weeks prehospitalization. In 4/32 (13%) patients, GAS disease, that is, tonsillitis or scarlet fever, was suspected; 2/4 of them received antibiotics, and a positive rapid antigen test for GAS was documented in 1 of them.

Conclusions:

A small minority of patients had suspected GAS infection within 4 weeks before iGAS disease. These data suggest that there is little opportunity to prevent iGAS disease by antibiotic therapy, because in most patients—even if seen by a physician—there was either no evidence of GAS disease or when GAS disease was suspected and treated with antibiotics, consecutive invasive GAS disease was not prevented.
Twenty-four Month Outcomes of Extended- Versus Standard-course Antibiotic Therapy in Children Hospitalized With Pneumonia in High-risk Settings: A Randomized Controlled Trial
Authors: Kok Hing C. , McCallum Gabrielle B. , Yerkovich Stephanie T. , Grimwood Keith , Fong Siew M. , Nathan Anna M. , Byrnes Catherine A. , Ware Robert S. , Nachiappan Nachal , Saari Noorazlina , Morris Peter S. , Yeo Tsin W. , Oguoma Victor M. , Masters I. Brent , de Bruyne Jessie A. , Eg Kah P. , Lee Bilawara , Ooi Mong H. , Upham John W. , Torzillo Paul J. , Chang Anne B.
Published: June 2024

Background:

Pediatric community-acquired pneumonia (CAP) can lead to long-term respiratory sequelae, including bronchiectasis. We determined if an extended (13–14 days) versus standard (5–6 days) antibiotic course improves long-term outcomes in children hospitalized with CAP from populations at high risk of chronic respiratory disease.

Methods:

We undertook a multicenter, double-blind, superiority, randomized controlled trial involving 7 Australian, New Zealand, and Malaysian hospitals. Children aged 3 months to ≤5 years hospitalized with radiographic-confirmed CAP who received 1–3 days of intravenous antibiotics, then 3 days of oral amoxicillin-clavulanate, were randomized to either extended-course (8-day oral amoxicillin-clavulanate) or standard-course (8-day oral placebo) arms. Children were reviewed at 12 and 24 months. The primary outcome was children with the composite endpoint of chronic respiratory symptoms/signs (chronic cough at 12 and 24 months; ≥1 subsequent hospitalized acute lower respiratory infection by 24 months; or persistent and/or new chest radiographic signs at 12-months) at 24-months postdischarge, analyzed by intention-to-treat, where children with incomplete follow-up were assumed to have chronic respiratory symptoms/signs (“worst-case” scenario).

Results:

A total of 324 children were randomized [extended-course (n = 163), standard-course (n = 161)]. For our primary outcome, chronic respiratory symptoms/signs occurred in 97/163 (60%) and 94/161 (58%) children in the extended-courses and standard-courses, respectively [relative risk (RR) = 1.02, 95% confidence interval (CI): 0.85–1.22]. Among children where all sub-composite outcomes were known, chronic respiratory symptoms/signs between groups, RR = 1.10, 95% CI: 0.69–1.76 [extended-course = 27/93 (29%) and standard-course = 24/91 (26%)]. Additional sensitivity analyses also revealed no between-group differences.

Conclusion:

Among children from high-risk populations hospitalized with CAP, 13–14 days of antibiotics (versus 5–6 days), did not improve long-term respiratory outcomes.
Analysis of Antipsychotic Dosage in Patients With Tardive Dyskinesia: A Case-Control Study Using the Claims Database of the Corporate Health Insurance Association
Authors: Gouda Maki , Abe Michikazu , Watanabe Yumi , Kato Takahiro A.
Published: June 2024

Purpose

This study aimed to assess the association between antipsychotic doses and the risk of tardive dyskinesia (TD) in clinical practice using a Japanese claims database from 2010 to 2020.

Methods

The study population included patients 15 years or older with a diagnosis record of schizophrenia, depression, or bipolar disorder who were prescribed antipsychotics. Using a case-control design, we categorized patients newly diagnosed with TD as cases, with corresponding 1:10 matching in the control group. The primary endpoint was the relative risk of TD in the >median dose and ≤median dose groups, as determined using conditional logistic regression analysis adjusted for age.

Results

The analysis population included 58,452 patients, and the median daily antipsychotic dose was 75 mg/d of chlorpromazine equivalent (CPZE). Of these, 80 were identified as TD cases, and doses >75 mg/d were associated with a significantly increased risk of TD at the last prescription and the maximum dose, respectively, before the date of the first diagnosis of TD. Post-hoc analysis further showed a significant association between doses ≥300 mg/d and the risk of TD compared to doses ≤75 mg/d and doses >75 to <300 mg/d. Comparing ≥300 mg/d versus >75 to <300 mg/d, the odd ratios at the last prescription and maximum dose before the first diagnosis of TD were 3.40 and 3.50, respectively.

Conclusions

In the Japanese medical claims database of patients receiving relatively low doses of antipsychotics, doses >75 mg/d were associated with an increased risk of TD in a dose-dependent manner.
Low-value care: an evolutionary concept analysis
Authors: Guan Yushan , Song Suhang , Wu Huazhang , Meng Zhaolin
Published: June 2024

Background:

Low-value care is a significant contributor to health care waste and a threat to the viability and sustainability of health care systems. Low-value care has attracted increasing international attention in the last decade, but its precise conception remains elusive.

Objective:

To clarify the concept of low-value care.

Methods:

A systematic search was conducted of the Medline, Cochrane Central Register of Controlled Trials, NHS Economic Evaluation Database, Health Technology Assessment, Web of Science, and Cumulative Index to Nursing and Allied Health Literature databases from their inception to July 22, 2023 for articles written in English. Rodgers’ evolutionary method guided the narrative analysis. The attributes of low-value care, as well as its antecedents, consequences, and related terms were extracted and synthesized.

Results:

A total of 53 articles were included in this concept analysis. Defining attributes included being of little to no benefit or potentially harmful, not being cost-effective, occurring along a continuum, being relative, ignoring or disregarding patient wishes in certain circumstances, and involving multiple types of care. Low-value care antecedents were classified into 4 categories: demand-side factors, supply-side factors, social factors, and health care system factors, while consequences of low-value care were categorized into patient harms and health care system-related consequences.

Conclusions:

This in-depth analysis of attributes, antecedents, and consequences of low-value care promotes a better understanding of low-value care among health care providers, thus contributing to the identification and deimplementation of low-value care in practice and eventually contributing to reducing waste in health care spending and improving patient outcomes.
State Laws Governing the Hiring of Public Health Government Employees, 2023
Authors: Yeager Valerie A. , Demosthenidy Mollye , Burns Ashlyn
Published: June 2024

Objective:

Governmental public health agencies have experienced longstanding challenges in recruiting individuals at the state and local level. Understanding civil service laws as they relate to the hiring processes is an important component of recruitment and increasing public health workforce capacity. This study presents state hiring laws and regulations governing the public health government workforce.

Methods:

Legal mapping techniques were employed to collect and code data on current hiring laws governing governmental public health employees across all 50 states. The review of laws included constitutions, statutes and regulations, and searches of administrative code.

Results:

In 12 states, the laws do not specify civil service exam criteria or they have no mention of civil service exams in the law. Almost a third of states have laws that establish civil service exam requirements without specifying conditions for when exams must be required, or which positions allow which types of exam/criteria. Similarly, almost all of the states that have civil service exams denoted in their laws have unspecified language about whether there are exam fees. Requirements for the maintenance/use of state hiring lists are in place in 36 states and 26 states have a non-public health agency managing this process. Nearly all states (n = 48, 96%) require hiring preferences for certain types of individuals, most commonly veterans (n = 48, 96%) and family members of veterans (n = 30, 60%). No state laws provide hiring preferences for individuals from public health fellowships or special training programs.

Conclusion:

Key findings suggest that the laws governing the merit system and civil service vary and often lack clarity, which may be difficult for public health agencies and for potential employees to understand, navigate, and successfully recruit key employees. The recruitment and hiring of new governmental public health staff are complicated by the management of hiring by other state agencies and the vague civil service exam requirements and process. Developing preferences for hiring individuals who have additional practical training in public health (eg, public health fellowships and AmeriCorps) should be considered.
scRNA-seq revealed the rules for CDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains in human and mice
Authors: Xiao Jiaping , Li Jun , Wu Yingjie , Zhu Lanwei , Peng Qi , Xu Yuanyuan , Yao Xinsheng
Published: June 2024

The binding of T cell receptor (TCR)/B cell receptor (BCR) CDR3 with linear or conformational epitopes is a prerequisite for the adaptive immune response. The rules for CDR3 length pairing and the amino acid (AA) distributions in the prioritized rearrangement of the β chain (or heavy chain) and subsequent rearrangement of the α chain (or light chain) during the process of germline V(D)J gene rearrangement and self-tolerance selection to form the T- or B-cell CDR3 repertoire are currently unknown. Single-cell VDJ sequencing can provide abundant information on CDR3 sequences in paired chains. In this study, the paired-chain CDR3 sequences of central and peripheral T and B cells in humans and mice were analyzed according to single-cell VDJ sequencing data. This is the first study to find that T cells with β chains longer than paired α chains and B cells with heavy chains longer than paired light chains have absolute advantages. The proportion of T cells with length differences of three or more AAs between paired chains in CDR3 in humans was significantly higher than that in mice, and the proportion of B cells with length differences of six or more AAs between paired chains in CDR3 in humans was significantly higher than that in mice. The CDR3 length range of the β chain was narrower than that of the α chain, while the heavy chain had a much wider range than the light chain. The CDR3 length in human TCRs and BCRs was greater than that in mice. Extreme length differences were found between paired chains in both human and mouse T and B cells. There were significant differences in the range of pairing length, AA distribution, hydrophobicity, and polarity of the paired-chain CDR3 region in 5 chains (β, α, H, κ, and λ). Human TCR and BCR paired CDR3 sequences exhibited greater plasticity than those of mice. This study reveals new ideas about the molecular mechanisms of TCR and BCR responses to different antigenic epitopes. Our innovative findings offer novel perspectives and techniques for examining V(D)J rearrangement and selection mechanisms in T and B cells. These advancements enable us to analyze antigenic epitopes targeted by TCRs and BCRs, and further, to explore the genetic evolution of T and B cell responses across diverse animal species.

Graphical Abstract

scRNA-seq the TCR and BCR CDR3 repertoires of 35 samples from the central and peripheral tissues of humans and mice. It provides an opportunity to reveal the rules for CDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains.
Beyond variability: a novel gene expression stability metric to unveil homeostasis and regulation
Authors: Chen Mengjie
Published: June 2024

The concept of gene expression stability within a homeostatic cell is explored through the gene homeostasis Z-index, a measure that highlights genes under active regulation in response to internal and external stimuli. This index reveals distinct regulatory activities and patterns in different organs, such as enhanced synaptic transmission in pancreatic islets. The research indicates that traditional mean-based methods may miss these nuances, underlining the significance of new metrics in identifying gene regulation specifics in cellular adaptation.
A PHOX2B+ PONTINE NUCLEUS ESSENTIAL FOR INGESTION
Authors: Sungeelee Selvee , Mailhes-Hamon Caroline , Chettouh Zoubida , Bokiniec Philip , Eymael Annaliese , Dempsey Bowen , Brunet Jean-François
Published: June 2024

The first phase of feeding consists in acquiring solid foods from the environment by biting, and their preparation for swallowing by chewing. These actions require the precise coordination of tens of orofacial muscles for the jaw and tongue. The siege for this motor patterning is known to be in the reticular formation, a complex and poorly mapped region of the hindbrain, but the neuron groups involved are still elusive. Here, we characterize a group of reticular interneurons located in the supratrigeminal area that express the homeodomain transcription factorPhox2b. This nucleus — Sup5Phox2b— is premotor to both jaw-closing and jaw-opener motoneurons and receives direct input from cranial sensory afferents, motor cortex and satiation related nuclei. Its activity differentially tracks lapping, biting and chewing movements, suggesting its involvement in the elaboration of distinct orofacial motor patterns in vivo. Acute global activation or inhibition of Sup5Phox2bby optogenetics both interrupt volitional feeding sequences. Thus, Sup5Phox2bis an obligatory subcortical node, topologically and genetically defined, in the neural circuits that control the oral phase of feeding.

Teaser

A genetically defined cluster of neurons in the hindbrain is an essential relay for biting and chewing food.
Adaptive Cell Size, Merging, Tilting, and Layering in Honeybee Comb Construction
Authors: Gharooni-Fard Golnar , Prasanna Chethan Kavaraganahalli , Peleg Orit , Jiménez Francisco López
Published: June 2024

Honeybees are renowned for their skills in building intricate and adaptive hives that display notable variation in cell size. However, the extent of their adaptability in constructing honeycombs with varied cell sizes has not been in-vestigated thoroughly. We use 3D-printing and X-ray Microscopy to quantify honeybees’ capacity in adjusting the comb to different initial conditions. Using the average area of natural worker cells as a reference, our findings suggest three distinct construction modes when faced with foundations of varying cell sizes. For smaller cell size, bees occasionally merge cells to compensate for the reduced space. However, for larger cell sizes, the hive uses adaptive strategies like tilting for cells up to twice the reference size, and layering for cells that are three times larger than the reference cell. Our findings shed light on honey-bees’ adaptive comb construction strategies with potential to find applications in additive manufacturing, bio-inspired materials, and entomology.
CytoBatchNorm: an R package with graphical interface for batch effects correction of cytometry data
Authors: Granjeaud Samuel , Abdellaoui Naoill , Chrétien Anne-Sophie , Woitrain Eloise , Pineau Laurent , Ninni Sandro , Harari Alexandre , Arnaud Marion , Montaigne David , Staels Bart , Dombrowicz David , Molendi-Coste Olivier
Published: June 2024

Innovation in cytometry propelled it to an almost “omic” dimension technique during the last decade. The application fields concomitantly enlarged, resulting in generation of high-dimensional high-content data sets which have to be adequately designed, handled and analyzed. Experimental solutions and detailed data processing pipelines were developed to reduce both the staining conditions variability between samples and the number of tubes to handle. However, an unavoidable variability appears between samples, barcodes, series and instruments (in multicenter studies) contributing to “batch effects” that must be properly controlled. Computer aid to this aim is necessary, and several methods have been published so far, but configuring and carrying out batch normalization remains unintuitive for scientists with “pure” academic backgrounds in biology. To address this challenge, we developed an R package called CytoBatchNorm that offers an intuitive and user-friendly graphical interface. Although the processing is based on the script by Schuyler et al., the graphical interface revolutionizes its use. CytoBatchNorm enables users to define a specific correction for each marker in a single run. It provides a graph that guides you through quickly setting the correction for each marker. It allows corrections to be previewed and inter-marker effects to be checked as the settings are made. CytoBatchNorm will help the cytometry community to adequately scale data between batches, reliably reducing batch effects and improving subsequent dimension reduction and clustering.

VISUAL ABSTRACT
A Novel Approach for Accurate Sequence Assembly Using de Bruijn graphs
Authors: Prybol Cameron J. , Hammack Aeron T. , Ashley Euan A. , Snyder Michael P.
Published: June 2024

Sequence assembly methods are valuable for reconstructing genomes from shorter read fragments. Modern nucleic acid sequencing instruments produce quality scores associated with each reported base; however, these quality scores are not generally used as a core part of sequence assembly or alignment algorithms. Here, we leverage weighted de Bruijn graphs as graphical probability models representing the relative abundances and qualities of kmers within FASTQ-encoded observations. We then utilize these weighted de Bruijn graphs to identify alternate, higher-likelihood candidate sequences compared to the original observations, which are known to contain errors. By improving the original observations with these resampled paths, iteratively across increasing k-lengths, we can use this expectation-maximization approach to “polish” read sets from any sequencing technology according to the mutual information shared in the reads. We use this polishing approach to probabilistically correct simulated short- and long-read datasets of lower coverages and higher error rates than some algorithms can produce satisfactory assemblies for. We find that this approach corrects sequencing errors at rates that are able to produce error-free and nearly-error-free de Bruijn assembly graphs for simulated read-set challenges.
Adeno-associated viral delivery of Env-specific antibodies prevents SIV rebound after discontinuing antiretroviral therapy
Authors: Klenchin Vadim A. , Clark Natasha M. , Keles Nida K. , Capuano Saverio , Mason Rosemarie , Gao Guangping , Broman Aimee , Kose Emek , Immonen Taina T. , Fennessey Christine M. , Keele Brandon F. , Lifson Jeffrey D. , Roederer Mario , Gardner Matthew R. , Evans David T.
Published: June 2024

An alternative to lifelong antiretroviral therapy (ART) is needed to achieve durable control of HIV-1. Here we show that adeno-associated virus (AAV)-delivery of two rhesus macaque antibodies to the SIV envelope glycoprotein (Env) with potent neutralization and antibody-dependent cellular cytotoxicity can prevent viral rebound in macaques infected with barcoded SIVmac239M after discontinuing suppressive ART. Following AAV administration, sustained antibody expression with minimal anti-drug antibody responses was achieved in all but one animal. After ART withdrawal, SIV replication rebounded within two weeks in all of the control animals but remained below the threshold of detection in plasma (<15 copies/mL) for more than a year in four of the eight animals that received AAV vectors encoding Env-specific antibodies. Viral sequences from animals with delayed rebound exhibited restricted barcode diversity and antibody escape. Thus, sustained expression of antibodies with potent antiviral activity can afford durable, ART-free containment of pathogenic SIV infection.
Mutation Reporter: fast identification of mutations in NGS files
Authors: Teodoro Mikaela , Chagas Rosana V. das , Yunes José A. , Migita Natacha A. , Meidanis Joaõ
Published: June 2024

Next-generation sequencing (NGS) has accelerated precision medicine by enabling analysis of multiple genes at once and detection of low-frequency mutations. Nevertheless, there is a paucity of software applications enabling users not trained in bioinformatics to discern and adjust the quality parameters employed for analyzing sequencing data, which yield the output containing detected mutations alongside their corresponding variant allele frequency (VAF). Mutation Reporter was developed to identify point mutations, offering users the ability to adjust parameters including alignment e-value, minimum read size, minimum read depth, and minimum reported VAF.

Availability and implementation

Mutation Reporter is available to users through a free GNU software license and can be accessed on GitHub (https://github.com/meidanis-lab/mutation-reporter) and as a Code Ocean capsule (https://codeocean.com/capsule/4682823/tree/v1).
The genomic signature and transcriptional response of metal tolerance in brown trout inhabiting metal-polluted rivers
Authors: Paris Josephine R , King R Andrew , Ferrer Obiol Joan , Shaw Sophie , Lange Anke , Bourret Vincent , Hamilton Patrick B , Rowe Darren , Laing Lauren V , Farbos Audrey , Moore Karen A , Urbina Mauricio A , van Aerle Ronny , Catchen Julian M , Wilson Rod W , Bury Nicolas R , Santos Eduarda M , Stevens Jamie R
Published: June 2024

Industrial pollution is a major driver of ecosystem degradation, but it can also act as a driver of contemporary evolution. As a result of intense mining activity during the Industrial Revolution, several rivers across the southwest of England are polluted with high concentrations of metals. Despite the documented negative impacts of ongoing metal pollution, brown trout (Salmo truttaL.) survive and thrive in many of these metal-impacted rivers. We used population genomics, transcriptomics, and metal burdens to investigate the genomic and transcriptomic signatures of potential metal tolerance. RADseq analysis of six populations (originating from three metal-impacted and three control rivers) revealed strong genetic substructuring between impacted and control populations. We identified selection signatures at 122 loci, including genes related to metal homeostasis and oxidative stress. Trout sampled from metal-impacted rivers exhibited significantly higher tissue concentrations of cadmium, copper, nickel, and zinc, which remained elevated after 11 days in metal-free water. After depuration, we used RNAseq to quantify gene expression differences between metal-impacted and control trout, identifying 2,042 differentially expressed genes (DEGs) in the gill, and 311 DEGs in the liver. Transcriptomic signatures in the gill were enriched for genes involved in ion transport processes, metal homeostasis, oxidative stress, hypoxia and response to xenobiotics. Our findings reveal shared genomic and transcriptomic pathways involved in detoxification, oxidative stress responses, and ion regulation. Overall, our results demonstrate the diverse effects of metal pollution in shaping both neutral and adaptive genetic variation, whilst also highlighting the potential role of constitutive gene expression in promoting metal tolerance.
Haploid-phased chromosomal telomere to telomere genome assembly of Uncaria rhynchophylla accelerating gene mining on the biosynthesis of medicinal alkaloids
Authors: Hu Tao , Duan Lei , Shangguan Liyang , Zhao Qingshi , Hang Ye , Li Xue , Yang Nngxian , Yan Fulin , Lv Qiuyu , Tang Liu , Liu Miao , Qiang Wei , Wang Xincun , Wang Xuewen , Zhang Mingsheng
Published: June 2024

Recorded traditionary medicinal plants contain important resources, including many natural medicinal alkaloids, for new medicine discovery and development. Uncaria genus is such a woody plant, with a high medicinal value in alkaloids, e.g. (iso)rhynchophylline. Natural alkaloids' contents usually vary between germplasms and are affected by the growth environment, which requires a genomics solution to understand the genetic and environmental factors that influence alkaloid production in more detail. Here, we have dissected the haploid-resolved chromosomal T2T genome assembly of Uncaria rhynchophylla with a size of ~634 Mb and contig N50 of 26 Mb using PacBio HiFi long-reads and Hi-C and anchored the contigs on 22 pairs of confirmed chromosomes. This genome contains 56% repeat sequences and ~2,9000 protein-encoding genes. U. rhynchophylla diverged from a common ancestor shared with Coffea around 20 million years ago and contains expanded and contracted gene families associated with secondary metabolites and plant-associated defenses. We constructed the pathway for (iso)rhynchophylline biosynthesis with genes mined from the genome and comparative transcriptomes. 53 alkaloids out of 2,578 metabolites were identified in (iso)rhynchophylline biosynthesis, where eight differentially expressed genes were the key for regulating the catalytic steps leading to alkaloid abundance difference between tissues. The chromosome-level genome and pathways of (iso)rhynchophylline constructed in this study provide a genetic basis and guidance for further breeding improvements and the development of pharmaceutical alkaloids.
Shiba: A versatile computational method for systematic identification of differential RNA splicing across platforms
Authors: Kubota Naoto , Chen Liang , Zheng Sika
Published: June 2024

Alternative pre-mRNA splicing (AS) is a fundamental regulatory process that generates transcript diversity and cell type variation. We developed Shiba, a comprehensive method that integrates transcript assembly, splicing event identification, read counting, and differential splicing analysis across RNA-seq platforms. Shiba excels in capturing annotated and unannotated AS events with superior accuracy, sensitivity, and reproducibility. It addresses the often-overlooked issue of junction read imbalance, significantly reducing false positives to aid target prioritization and downstream analyses. Unlike other tools that require large numbers of biological replicates or resulting in low sensitivity and high false positives, Shiba’s statistics framework is agnostic to sample size, as demonstrated by simulated data and its effective application to realn=1 RNA-seq datasets. To extend its utility to single-cell RNA-seq, we developed scShiba, which applies Shiba’s pseudobulk approach to analyze splicing at the cluster level. scShiba successfully revealed AS regulation in developmental dopaminergic neurons and differences between excitatory and inhibitory neurons. Both Shiba and scShiba are available in Docker/Singularity containers and Snakemake pipelines, ensuring reproducibility. With their comprehensive capabilities, Shiba and scShiba enable systematic quantification of alternative splicing events across various platforms, laying a solid foundation for mechanistic exploration of the functional complexity in RNA splicing.
Structures of PSI-FCPI fromThalassiosira pseudonanain high light provide convergent evolution and light-adaptive strategies in diatom FCPIs
Authors: Feng Yue , Li Zhenhua , Yang Yang , Shen Lili , Li Xiaoyi , Liu Xueyang , Zhang Xiaofei , Zhang Jinyang , Ren Fei , Wang Yuan , Liu Cheng , Han Guangye , Wang Xuchu , Kuang Tingyun , Shen Jian-Ren , Wang Wenda
Published: June 2024

Diatoms achieve great survival success in the fluctuating oceanic environment, rely on fucoxanthin chlorophylla/c-binding proteins (FCPs) to complete light harvesting and quenching, which provide about 20% primary productivity on earth. We report two cryo-electron microscopic structures of photosystem I (PSI) with 13 or 5 FCPIs respectively at 2.78 Å and 3.20 Å resolution fromThalassiosira pseudonanaunder high light conditions. 8 Lhcr FCPIs are found detached from the PSI-13FCPI supercomplex under high light conditions, remaining 5 FCPIs are stably combined with the PSI core including Lhcr3, RedCAP, Lhcq8, Lhcf10, and FCP3 subunits. The specific pigment network in this centric diatomT. pseudonanademonstrates a higher proportion of Chlorophyllsa, diadinoxanthins, and diatoxanthins but fewer fucoxanthins compared with the huge PSI-FCPI from another centric diatomChaetoceros gracilis, thus exhibiting more efficiency in energy transfer and dissipation among FCPI antennas. These results reveal the assembly mechanism of several types of peripheral FCPIs and corresponding light-adaptive strategies inT. pseudonana, as well as the convergent evolution of the diatoms PSI-FCPI structures.
Inhibition of Endothelial Lipase by MEDI5884 Normalizes Phosphatidylinositol Levels in Coronary Artery Disease Patients
Authors: Rosenbaum Anton I. , Huang Yue , Mu Ruipeng , Kovacina Kristina , Jin ChaoYu Denise , Hummer B. Timothy , Liang Meina , Grimsby Joseph S.
Published: June 2024

Background

Endothelial lipase (EL) promotes high-density lipoproteins (HDL) phospholipid degradation, increases catabolism of HDL and is an attractive target for the potential treatment for cardiovascular disease. Inhibition of EL using a monoclonal neutralizing antibody, MEDI5884, demonstrated increased quantity and function of HDL. Determinants of anti-atherosclerotic function of HDL comprise the interplay of various components of HDL structure-activity relationship: size, shape and composition (lipid and protein). Previous studies have shown that single doses of MEDI5884 administered to healthy nonhuman primates (NHPs) and healthy subjects resulted in a dose- dependent increase in plasma phospholipids (PL) and that plasma PI levels in placebo treated healthy subjects are significantly increased relative to CAD subjects participating in clinical trialsNCT03001297andNCT03351738, respectively.

Methods

Herein, we characterized using LC-MS/MS the plasma lipidome of NHPs, heathy subjects and subjects with coronary artery disease (CAD) following MEDI5884 administration.

Results

MEDI5884 treated NHPs resulted in a prominent increase in phosphatidylinositols (PI) and cholesteryl esters (CE). Treatment with MEDI5884 restores near-normal levels of PI in CAD patients. PI increases in both healthy subjects and CAD patients were dose-dependent, correlated with exposure and saturated at approximately 200 mg MEDI5884 subcutaneous (SC) dose in CAD patients. Comparison of pharmacodynamic (PD) effects of repeat SC 200 mg doses of MEDI5884 in CAD patients revealed greater and more rapid increases in PI levels compared to HDL-C and HDL phospholipid (HDL-PL). The increase in PI species was inversely correlated with decreases in free EL mass levels.

Conclusions

PI has previously been shown to possess anti-atherosclerotic properties and led to increases in HDL cholesterol (HDL-C) and reverse cholesterol transport (RCT). The mechanism by which CE levels increase as the result of MEDI5884 administration can be attributed to the observed increase in both substrates of the lecithin-cholesterol acyltransferase (LCAT) reaction: phosphatidylcholine/phosphatidylethanolamine (PC/PE) and cholesterol as the consequence of EL inhibition. Further characterization of the underlying biological mechanisms responsible for the decrease of the PI biomarker in CAD patient population relative to healthy subjects as well as in conjunction with pharmacological intervention by MEDI5884 may reveal more information on this clinically-relevant biomarker and potential role in CAD.
A general approach to reduce off-target radioactivity in vivo via Tetrazine-Knock-Out (TKO)
Authors: Sarkar Swarbhanu , Pham Jonathan M. , Edwards Kimberly J. , Sharma Nitika , Xu Kexiang , King A. Paden , del Castillo Andres Fernandez , Farwell Michael D. , Pryma Daniel A. , Schuster Stephen J. , Sellmyer Mark A.
Published: June 2024

Monoclonal antibodies have had a remarkable impact on cancer therapy due to their high target specificity. However, their large molecular weight results in slow blood clearance, which can take weeks to clear from circulation. As companion nuclear imaging and diagnostic tools, these characteristics force delayed imaging and the use of isotopes with long half-lives such as89Zr. For optimal clinical application, it is desirable that radioimmunoconjugates remain in the blood for just enough time to accumulate adequately in target tissues, while non-targeted or circulating radioactivity is ideally rapidly excreted from the body to maximize imaging contrast and minimize radiation dose to healthy tissues. We addressed the current challenges of antibody-based imaging by developing rituximab radioimmunoconjugates that accumulate sufficient activity for tumor imaging within 24 h of administration, while clearing circulating radioactivity via administration of a small molecule clearing agent. Rituximab, an anti-CD20 monoclonal antibody, is used as standard first-line therapy for diffuse large B-cell lymphoma. CD20 is expressed by 95% of B-lymphocytes and their malignant counterparts, making it a therapeutic target for B-cell malignancies. We attached125I,68Ga, and89Zr to rituximab using a “clickable” linker containingtrans-cyclooctene and tested the ability of tetrazines to induce the inverse electron demand Diels-Alder reaction (iEDDA) after antibody administration. This “tetrazine-knock-out” (TKO) approach liberates the radioactivity from rituximab in the bloodstream, resulting in its rapid renal excretion which enhances target-to-background ratios, and minimizes off-target radiation exposure. Due to the internalization of the radioimmunoconjugate in CD20+tumor cells, no substantial clearance was observed from Raji xenografts. We characterized different leaving groups, several cellular models and antibodies with distinct internalizaing properties. The TKO approach opens opportunities to use radiolabeled antibodies for low-abundance or heterogeneously expressed biologic targets and may allow radioimmunotherapy (RIT) for targets traditionally untenable due to dose-limiting toxicities.

Graphical abstract
Multiple mechanisms of aminoglycoside ototoxicity are distinguished by subcellular localization of action
Authors: Wu Patricia , Becker Francisco Barros , Ogelman Roberto , Camci Esra , Linbo Tor H , Simon Julian A. , Rubel Edwin W , Raible David
Published: June 2024

Mechanosensory hair cells of the inner ears and lateral line of vertebrates display heightened vulnerability to environmental insult, with damage resulting in hearing and balance disorders. An important example is hair cell loss due to exposure to toxic agents including therapeutic drugs such as the aminoglycoside antibiotics such as neomycin and gentamicin and antineoplastic agents. We describe two distinct cellular pathways for aminoglycoside-induced hair cell death in zebrafish lateral line hair cells. Neomycin exposure results in death from acute exposure with most cells dying within 1 hour of exposure. By contrast, exposure to gentamicin results primarily in delayed hair cell death, taking up to 24 hours for maximal effect. Washout experiments demonstrate that delayed death does not require continuous exposure, demonstrating two mechanisms where downstream responses differ in their timing. Acute damage is associated with mitochondrial calcium fluxes and can be alleviated by the mitochondrially-targeted antioxidant mitoTEMPO, while delayed death is independent of these factors. Conversely delayed death is associated with lysosomal accumulation and is reduced by altering endolysosomal function, while acute death is not sensitive to lysosomal manipulations. These experiments reveal the complexity of responses of hair cells to closely related compounds, suggesting that intervention focusing on early events rather than specific death pathways may be a successful therapeutic strategy.
Low T cell diversity is associated with poor outcome in bladder cancer: a comprehensive longitudinal analysis of the T cell receptor repertoire
Authors: Kjær Asbjørn , Kristjánsdóttir Nanna , Juul Randi Istrup , Nordentoft Iver , Birkenkamp-Demtröder Karin , Ahrenfeldt Johanne , Strandgaard Trine , Radif Deema , Hodgson Darren , Abbosh Christopher , Aerts Hugo JWL , Agerbæk Mads , Jensen Jørgen Bjerggaard , Birkbak Nicolai J , Dyrskjøt Lars
Published: June 2024

T cells are one of the primary effector cells in the endogenous defense against cancer, yet the clinical impact of their quantity, diversity, and dynamics remains underexplored. Here we investigated the clinical relevance of the T cell receptor (TCR) repertoire in patients with bladder cancer. In advanced-stage bladder cancer, low pre-treatment peripheral TCR diversity was associated with worse overall survival (p=0.024), particularly when it coincided with a low fraction of circulating T cells (p=0.00049). The low-diversity TCR repertoires were dominated by expanded clones that persisted throughout treatment and disproportionately targeted latent viral infections. Longitudinal analysis revealed a reduction in TCR diversity after treatment indicating an adverse effect on the immune system. In early-stage bladder cancer, we showed that immunotherapy had a stimulatory effect on TCR diversity in patients with good outcomes. Single-cell sequencing identified most expanded clones as cytotoxic T cells, while non-expanded clones were predominantly naive T cells. Overall, our findings suggest that TCR diversity is a promising new biomarker that may offer new avenues for tailored oncological treatment to enhance clinical outcomes for bladder cancer patients.
MULAN: Multimodal Protein Language Model for Sequence and Structure Encoding
Authors: Frolova Daria , Pak Marina A. , Litvin Anna , Sharov Ilya , Ivankov Dmitry N. , Oseledets Ivan
Published: June 2024

Most protein language models (PLMs), which are used to produce high-quality protein representations, use only protein sequences during training. However, the known protein structure is crucial in many protein property prediction tasks, so there is a growing interest in incorporating the knowledge about the protein structure into a PLM. In this study, we propose MULAN, a MULtimodal PLM for both sequence and ANgle-based structure encoding. MULAN has a pre-trained sequence encoder and an introduced Structure Adapter, which are then fused and trained together. According to the evaluation on 7 downstream tasks of various nature, both small and medium-sized MULAN models show consistent improvement in quality compared to both sequence-only ESM-2 and structure-aware SaProt. Importantly, our model offers a cheap increase in the structural awareness of the protein representations due to finetuning of existing PLMs instead of training from scratch. We perform a detailed analysis of the proposed model and demonstrate its awareness of the protein structure. The implementation, training data and model checkpoints are available athttps://github.com/DFrolova/MULAN.
Surforama: interactive exploration of volumetric data by leveraging 3D surfaces
Authors: Yamauchi Kevin A. , Lamm Lorenz , Gaifas Lorenzo , Righetto Ricardo D. , Litvinov Daniil , Engel Benjamin D. , Harrington Kyle
Published: June 2024

Motivation

Visualization and annotation of segmented surfaces is of paramount importance for studying membrane proteins in their native cellular environment by cryogenic electron tomography (cryo-ET). Yet, analyzing membrane proteins and their organization is challenging due to their small sizes and the need to consider local context constrained to the membrane surface.

Results

To interactively visualize, annotate, and analyze proteins in cellular context from cryo-ET data, we have developed Surforama, a Python package and napari plugin. For interactive visualization of membrane proteins in tomograms, Surforama renders the local densities projected on the surface of the segmentations. Suforama additionally provides tools to annotate and analyze particles on the membrane surfaces. Finally, for compatibility with other tools in the cryo-ET analysis ecosystem, results can be exported as RELION-formatted STAR files. As a demonstration, we performed subtomogram averaging and neighborhood analysis of photosystem II proteins in thylakoid membranes from the green algaChlamydomonas reinhardtii.

Availability and implementation

Python package, code and examples are available at:https://github.com/cellcanvas/surforama