bluuebunny/crossref_metadata_2025 huggingface dataset:
Feasibility validation of automatic diagnosis of mitral valve prolapse from multi-view echocardiographic sequences based on deep neural network
Authors: Wu Zijian , Ge Zhenyi , Ge Zhengdan , Xing Yumeng , Zhao Weipeng , Dong Lili , Wang Yongshi , Kong Dehong , Hu Chunqiang , Liang Yixiu , Chen Haiyan , Xue Wufeng , Pan Cuizhen , Ni Dong , Shu Xianhong
Published: October 2024

Aims

To address the limitations of traditional diagnostic methods for mitral valve prolapse (MVP), specifically fibroelastic deficiency (FED) and Barlow’s disease (BD), by introducing an automated diagnostic approach utilizing multi-view echocardiographic sequences and deep learning.

Methods and results

An echocardiographic data set, collected from Zhongshan Hospital, Fudan University, containing apical 2 chambers (A2C), apical 3 chambers (A3C), and apical 4 chambers (A4C) views, was employed to train the deep learning models. We separately trained view-specific and view-agnostic deep neural network models, which were denoted as MVP-VS and MVP view-agonistic (VA), for MVP diagnosis. Diagnostic accuracy, precision, sensitivity, F1-score, and specificity were evaluated for both BD and FED phenotypes. MVP-VS demonstrated an overall diagnostic accuracy of 0.94 for MVP. In the context of BD diagnosis, precision, sensitivity, F1-score, and specificity were 0.83, 1.00, 0.90, and 0.92, respectively. For FED diagnosis, the metrics were 1.00, 0.83, 0.91, and 1.00. MVP-VA exhibited an overall accuracy of 0.95, with BD-specific metrics of 0.85, 1.00, 0.92, and 0.94 and FED-specific metrics of 1.00, 0.83, 0.91, and 1.00. In particular, the MVP-VA model using mixed views for training demonstrated efficient diagnostic performance, eliminating the need for repeated development of MVP-VS models and improving the efficiency of the clinical pipeline by using arbitrary views in the deep learning model.

Conclusion

This study pioneers the integration of artificial intelligence into MVP diagnosis and demonstrates the effectiveness of deep neural networks in overcoming the challenges of traditional diagnostic methods. The efficiency and accuracy of the proposed automated approach suggest its potential for clinical applications in the diagnosis of valvular heart disease.
How to address the coronaries in TAVI candidates: can the need for revascularization be safely determined by CT angiography only?
Authors: Mascherbauer Katharina Theresa Julia , Lamm Gudrun , Kammerlander Andreas Anselm , Will Maximilian , Nitsche Christian , Mousavi Roya Anahita , Demirel Caglayan , Bartko Philipp Emanuel , Schwarz Konstantin , Hengstenberg Christian , Mascherbauer Julia
Published: October 2024

Coronary artery disease (CAD) remains one of the most frequent comorbidities among transcatheter aortic valve implantation (TAVI) candidates. Whether routine assessment of CAD by invasive coronary angiography (CA) and eventual peri-procedural percutaneous coronary intervention (PCI) is generally beneficial in TAVI patients has recently been heavily questioned. CA carries significant risks, such as kidney injury, bleeding, and prolonged hospital stay, and may frequently be unnecessary if significant stenoses of the proximal coronary segments can be ruled out on computed tomography angiography. Moreover, the benefits of pre-emptive coronary revascularization at the time of TAVI are not well defined. Despite these facts and weak guideline recommendations, CA and eventual PCI of stable significant coronary lesions at the time of TAVI remain common practice. However, ongoing randomized trials currently challenge the efficacy of such strategies to enable a more streamlined, individualized, and resource-sparing treatment with TAVI.
No Refuge from Childhood: How Child Protection Harms Refugees
Authors: Viterbo Hedi , Ioffe Yulia
Published: October 2024

This article sheds new and critical light on the notion, enshrined in international law, that child refugees are a uniquely vulnerable and dependent age group requiring special protection. Although protection is not inherently detrimental, this conception of child protection often ends up harming refugees of all ages. It casts adult refugees as less vulnerable, less dependent and less deserving of protection than their younger counterparts. It downplays the contextual, relational and socially constructed nature of vulnerability, dependence and childhood. It potentially contributes to the disregard for the capacity and wishes of child refugees. It usually affords these children only temporary protection, thereby increasing their uncertainty, driving them to disengage from welfare services and incentivizing the state to delay decisions about their entitlements. Meanwhile, international law not only places great value on children’s relationships with their parents but also authorizes the punishment of supposedly unfit parents, and this ambivalence helps states weaponize legal principles of child protection against refugee families. What is needed, however, is not for child refugees to be denied protection. Rather, a fundamental reimagining of protection is in order: a shift from hierarchies of vulnerability, dependence and deservingness towards free global movement based on solidarity and equity.
A New Moral World Order: Carl Alexander Simon and the German Colonization of Southern Chile
Authors: Gaete C. Miguel
Published: October 2024

This article focuses on overlooked aspects of German colonization in southern Chile by examining the treatise Auswanderung und deutsch-nationale Kolonisation von Süd-Amerika mit besonderer Berücksichtigung des Freistaates Chile (Emigration and German National Colonization of South America with Special Attention to the Free State of Chile) by Carl Alexander Simon. Simon was a Romantic artist who advocated for overseas colonization and settled in Chile to promote his ideas. His treatise, which blended poetry and Romantic rhetoric with political ideas, aimed to encourage German occupation of Chile and South America based on the supposed physical and intellectual superiority of the Germans. This article argues that Simon’s work is integral to understanding the intersection of Romanticism and German colonialism in the nineteenth century and how racial and nationalistic sentiments fuelled German colonialism in remote corners of the world. Furthermore, it contributes to discussions on German nation-building overseas and the connections between German colonialism and race, the legacies of German colonialism, German colonial fantasies, and indigeneity and Germanness. Finally, this study of Simon’s work complements existing research on German settlements in Africa, Asia and the Pacific from 1850 onwards, highlighting the importance of considering the role of Germany in the global colonial project.
Multiome-wide Association Studies: Novel Approaches for Understanding Diseases
Authors: Shao Mengting , Chen Kaiyang , Zhang Shuting , Tian Min , Shen Yan , Cao Chen , Gu Ning
Published: October 2024

The rapid development of multiome (transcriptome, proteome, cistrome, imaging, and regulome)-wide association study methods have opened new avenues for biologists to understand the susceptibility genes underlying complex diseases. Thorough comparisons of these methods are essential for selecting the most appropriate tool for a given research objective. This review provides a detailed categorization and summary of the statistical models, use cases, and advantages of recent multiome-wide association studies. In addition, to illustrate gene–disease association studies based on transcriptome-wide association study (TWAS), we collected 478 disease entries across 22 categories from 235 manually reviewed publications. Our analysis reveals that mental disorders are the most frequently studied diseases by TWAS, indicating its potential to deepen our understanding of the genetic architecture of complex diseases. In summary, this review underscores the importance of multiome-wide association studies in elucidating complex diseases and highlights the significance of selecting the appropriate method for each study.
X Factors and Tipping Points in Eviction Cases: A Statistical Analysis of Eviction Litigation of the European Court of Human Rights
Authors: Bruijn Michelle
Published: October 2024

This study is the first to statistically analyse all eviction case law of the European Court of Human Rights up to 2024. It examines the impact of various case characteristics, such as the type of tenure, the reason for eviction and the involvement of vulnerable people, with a specific focus on the role of ownership and property rights. The study evaluates whether evicted homeowners have a higher success rate compared to non-owners, as they can invoke both Article 8 and Article 1 of Protocol No. 1. Additionally, it investigates whether landmark cases like McCann v the United Kingdom and F.J.M. v the United Kingdom serve as ‘tipping points’ that significantly altered the Court’s jurisprudence. The findings highlight the substantial influence of the McCann case on subsequent eviction rulings and reveal that being a tenant in the public rental sector significantly increases the likelihood of the Court finding a violation of Article 8.
Treatment of concomitant persistent chylothorax and superior vena cava syndrome through innominate vein-right atrial bypass
Authors: Şişli Emrah , Tarhan Arzu Funda , Kıral Eylem , Bozan Gürkan
Published: October 2024

Persistent chylothorax is a major challenge in paediatric patients. We present a case of a 6.5 kg, 1-year-old boy with superior vena cava syndrome and persistent chylothorax who underwent successful surgery without cardiopulmonary bypass. His medical history included multiple comorbidities such as myeloproliferative disease, short bowel syndrome and central vein catheterizations. The patient also had innominate vein thrombosis, progressing to superior vena cava, and was on anticoagulants. Despite dietary changes and somatostatin, his high-output chylous pleural effusion persisted. He was treated with innominate vein-to-right atrial bypass using a 6-mm Dacron graft. Postoperatively, there was a significant reduction in effusion and accelerated recovery. Somatostatin failure was likely due to mechanical obstruction of the thoracic duct.
Methodology Matters: Emplotting Interpretivism in Contemporary Political Science and International Studies
Authors: Harris Christina V , Radomski Julie
Published: October 2024

The visibility and adoption of interpretive research approaches in the post-Perestroika period have increased in the United States, yet common knowledge within political science (PS) and international studies (IS) departments still signals their marginality. This paper stems from the observation that interpretive scholars often share autobiographical narratives or “journey stories” describing how they came to embrace interpretive research despite socio-institutional obstacles. Based on semi-structured interviews and participant observation, it asks: What do the journey stories of both new and established scholars engaged in interpretivism reveal about the sociology of PS and IS academies? Our findings reveal a widespread perception that interpretivism is gaining a foothold in the United States while intimating the spread of neopositivist hegemony, to some degree, to academies abroad. We show how scholars make use of the label “interpretivism” and identify key diffusion pathways responsible for interpretivism’s wider recognition today. In addition, we find that despite shared assumptions of neopositivist hegemony, our interlocutors pursue interpretive research because it provides them with epistemological and experiential congruence. Their journey stories, we argue, point toward an evolving methodological landscape in PS and IS, which in turn shapes what forms of knowledge production are considered legitimate and valuable.
Gene editing technology combined with response surface optimization to improve the synthesis ability of lycopene in Pantoea dispersa MSC14
Authors: Lai La , Xin Run , Cui Tangbing
Published: October 2024

Aim

The aim of this study is to engineer Pantoea dispersa MSC14 into a strain capable of producing lycopene and to enhance its lycopene content.

Methods and results

Our laboratory isolated the strain P. dispersa MSC14 from petroleum-contaminated soil in a mining area. Whole-genome sequencing confirmed the existence of a carotenoid synthesis pathway in this strain. This study employed an optimized CRISPR/Cas9 system to perform a traceless gene knockout of the lycopene cyclase gene crtY and to overexpress the octahydrolycopene dehydrogenase gene crtI in the P. dispersa MSC14. This strategic genetic modification successfully constructed the lycopene-producing strain MSC14-LY, which exhibited a notable lycopene content with a biomass productivity of 553 μg of lycopene per gram dry cell weight (DCW). Additionally, the components of the lycopene fermentation medium were optimized using Plackett–Burman design and response surface methodology. The average lycopene content was increased to 5.13 mg g −1 DCW in the optimized LY fermentation medium. Through genetic engineering, P. dispersa MSC14 was transformed into a strain capable of producing lycopene, achieving a yield of 5.13 mg g−1 DCW after medium optimization.

Conclusions

Genetic engineering successfully transformed P. dispersa MSC14 into a strain capable of producing lycopene, achieving a yield of 5.13 mg g−1 DCW after medium optimization.
Decoding disparities: evaluating automatic speech recognition system performance in transcribing Black and White patient verbal communication with nurses in home healthcare
Authors: Zolnoori Maryam , Vergez Sasha , Xu Zidu , Esmaeili Elyas , Zolnour Ali , Anne Briggs Krystal , Scroggins Jihye Kim , Hosseini Ebrahimabad Seyed Farid , Noble James M , Topaz Maxim , Bakken Suzanne , Bowles Kathryn H , Spens Ian , Onorato Nicole , Sridharan Sridevi , McDonald Margaret V
Published: October 2024

Objectives

As artificial intelligence evolves, integrating speech processing into home healthcare (HHC) workflows is increasingly feasible. Audio-recorded communications enhance risk identification models, with automatic speech recognition (ASR) systems as a key component. This study evaluates the transcription accuracy and equity of 4 ASR systems—Amazon Web Services (AWS) General, AWS Medical, Whisper, and Wave2Vec—in transcribing patient-nurse communication in US HHC, focusing on their ability in accurate transcription of speech from Black and White English-speaking patients.

Materials and Methods

We analyzed audio recordings of patient-nurse encounters from 35 patients (16 Black and 19 White) in a New York City-based HHC service. Overall, 860 utterances were available for study, including 475 drawn from Black patients and 385 from White patients. Automatic speech recognition performance was measured using word error rate (WER), benchmarked against a manual gold standard. Disparities were assessed by comparing ASR performance across racial groups using the linguistic inquiry and word count (LIWC) tool, focusing on 10 linguistic dimensions, as well as specific speech elements including repetition, filler words, and proper nouns (medical and nonmedical terms).

Results

The average age of participants was 67.8 years (SD = 14.4). Communication lasted an average of 15 minutes (range: 11-21 minutes) with a median of 1186 words per patient. Of 860 total utterances, 475 were from Black patients and 385 from White patients. Amazon Web Services General had the highest accuracy, with a median WER of 39%. However, all systems showed reduced accuracy for Black patients, with significant discrepancies in LIWC dimensions such as “Affect,” “Social,” and “Drives.” Amazon Web Services Medical performed best for medical terms, though all systems have difficulties with filler words, repetition, and nonmedical terms, with AWS General showing the lowest error rates at 65%, 64%, and 53%, respectively.

Discussion

While AWS systems demonstrated superior accuracy, significant disparities by race highlight the need for more diverse training datasets and improved dialect sensitivity. Addressing these disparities is critical for ensuring equitable ASR performance in HHC settings and enhancing risk prediction models through audio-recorded communication.
Chromosome-level genome of Osmia excavata (Hymenoptera: Megachilidae) provides insights into low-temperature tolerance of Osmia pollinator
Authors: Ouyang Fang , Guo Honggang , Xie Wen , Song Yingying , Yan Zhuo , Peng Zhenqing , Zhang Yongsheng , Qu Ritao , Xin Huaigen , Yuan Zheming , Xiao Zhishu , Men Xingyuan
Published: October 2024

The solitary bee Osmia excavata (Hymenoptera: Megachilidae) is a key pollinator managed on a large scale. It has been widely used for commercial pollination of fruit trees, vegetables, and other crops with high efficiency in increasing the crop seeding rate, yield, and seed quality in Northern hemisphere. Here, a high-quality chromosome-level genome of O. excavata was generated using PacBio sequencing along with Hi-C technology. The genome size was 207.02 Mb, of which 90.25% of assembled sequences were anchored to 16 chromosomes with a contig N50 of 9,485 kb. Approximately 186.83 Mb, accounting for 27.93% of the genome, was identified as repeat sequences. The genome comprises 12,259 protein-coding genes, 96.24% of which were functionally annotated. Comparative genomics analysis suggested that the common ancestor of O. excavata and Osmia bicornis (Hymenoptera: Megachilidae) lived 8.54 million years ago. Furthermore, cytochrome P450 family might be involved in the responses of O. excavata to low-temperature stress. Taken together, the chromosome-level genome assembly of O. excavata provides in-depth knowledge and will be a helpful resource for the pollination biology research.
Subterranean termites (Coptotermes formosanus [Blattodea: Rhinotermitidae]) colonies can readily intercept commercial inground bait stations placed at label-prescribed distance
Authors: Gazdick Kaitlin , Lee Sang-Bin , Mizumoto Nobuaki , Chouvenc Thomas , Su Nan-Yao
Published: October 2024

The Formosan subterranean termite, Coptotermes formosanus Shiraki, is both an economically impactful pest and a successful invader. One method of subterranean termite control is baiting. According to the label, baits are installed surrounding the structure at a uniform interval distance of ≈3 m. However, homeowners and pest control professionals are often concerned that termites may bypass bait stations and have access to the structure. To address this concern, we experimentally duplicated field conditions using a large planar arena (3.6 m × 1.1 m) to study the optimal distribution of bait stations based on colony-wide foraging activity. We installed 2 bait stations 3 m apart as per label instructions and introduced C. formosanus colonies to allow them to explore the arena by tunneling through the sand. In this real-scale arena, all termite colonies intercepted a bait station in an average of 21 (± 8 SD) days. We assumed that termites could find bait faster if there were more bait stations by overlaying additional hypothetical baits closer than per label instruction, but the improvement was incremental, requiring 4 times more stations (0.45 m interval) to obtain a significant difference. We also revealed the characteristic behavior after intercepting bait stations, termites created a burst of tunnels that radiated from the bait station. These branching tunnels averaged 16 cm in length, suggesting immediate interceptions of additional auxiliary stations placed within 16 cm of an active station. These findings contribute to our understanding on how subterranean termites intercept inground bait stations.
Combination therapy with immune agonists and senescence-inducing agents delivers promise for immunotherapeutic success in pancreatic cancer
Authors: Anderko Renee R , Zureikat Amer H , Bruno Tullia C
Published: October 2024

Reprogramming the PDAC tumor microenvironment via nanoparticles may help to induce tertiary lymphoid structures that support antitumor immunity.
Focal granule cell bilamination of the dentate gyrus—its prevalence across the human age spectrum and review of the literature
Authors: Machaalani Rita , Rodriguez Michael , Vivekanandarajah Arunnjah
Published: October 2024

The prevalence of focal granule cell bilamination (FGCB) in the hippocampal dentate gyrus varies from 0% to 44%, depending on age and study population. FGCB is commonly thought to be a specific feature of temporal lobe epilepsy (TLE) but its prevalence in cases without TLE is unclear. Using formalin-fixed, paraffin-embedded hippocampal sections, this retrospective postmortem study evaluated the prevalence of FGCB and other granule cell pathologies in infants (1-12 months of age, n = 16), children (4-10 years, n = 6), and adults (28-91 years, n = 15) with no known history of epilepsy or seizures. We found FGCB in 6% of infants, 17% of children, and 27% of adults. We then compared our findings with those in published reports of sudden unexpected deaths in infancy (SUDI), childhood (SUDC), and epilepsy (SUDEP), and in surgical specimens from patients with TLE. The reported prevalence of FGCB in those studies was 6%-19% in infants, 0%-17% in children, and 0%-2% in adults in non-seizure-related cases and 9% in children and 3%-25% in adults with TLE. Our findings highlight the presence of FGCB in individuals with no known epilepsy/seizure-related histories in proportions similar to those reported in individuals with clinical epilepsy.
Elevated α/β ratio after hypofractionated radiotherapy correlated with DNA damage repairment in an experimental model of prostate cancer
Authors: Cui Ming , Li Yuexian , Liu Ji , Sun Deyu
Published: October 2024

Our previous study demonstrated that the linear quadratic model appeared to be not well-suited for high dose per fraction due to an observed increase in α/β ratio as the dose per fraction increased. To further validate this conclusion, we draw the cell survival curve to calculate the α/β ratio by the clone formation experiment and then convert the fractionated radiation dose into an equivalent single hypofractionated radiation dose comparing with that on the survival curve. Western Blot and laser confocal immunofluorescence were used to detect the expression of γ-H2AX and RAD51 after different fractionated modes of radiation. We constructed a murine xenograft model, and changes in transplanted tumor volume were used to evaluate the biological effects after different fractionated radiation. The results demonstrated that when fractionated radiation dose was converted into equivalent single hypofractionated radiation dose, the effectiveness of hypofractionated radiation was overestimated. If a larger α/β ratio was used, the discrepancy tended to become smaller. γ-H2AX was higher in 24 h after a single high dose radiation than the continuous expression of the DNA repair marker RAD51. This implies more irreparable damage in a single high dose radiation compared with fractionated radiation. In the murine xenograft model, the effectiveness of hypofractionated radiation was also overestimated, and additional fractions of irradiation may be required. The conclusion is that after single hypofractionated radiation, the irreparable damage in cells increased (α value increased) and some repairable sublethal damage (β value) was converted into irreparable damage (α value). When α value increased and β value decreased, the ratio increased.
Incidental aortic valve papillary fibroelastoma diagnosed by transesophageal echocardiography in a patient undergoing coronary artery bypass surgery: a case report
Authors: Al-Sarraf Nael , Maher Adel , Agzamov Yuldash , Hasan Mohammed , Alhumaidan Ali
Published: October 2024

Papillary fibroelastoma of aortic valve is a rare benign tumor that can present with symptoms of obstruction or embolization and can be asymptomatic. The main stay of diagnosis is echocardiography. The size of the tumor affects the sensitivity of transthoracic echocardiography which can miss small size tumors. The treatment is surgical resection. Here, we report a case of papillary fibroelastoma of aortic valve that was detected intraoperatively by transesophageal echocardiography and was missed by transthoracic echocardiography in a patient undergoing coronary artery surgery. The tumor was resected successfully with preservation of aortic valve with no complication. This case highlights importance of intraoperative transesophageal echocardiography in making the diagnosis.
No free entry: stomatal state as decision maker in defining stress response strategies
Authors: Tarkowski Łukasz P , Signorelli Santiago
Published: October 2024

This article comments on:

Maleki FA, Seidl-Adams I, Felton GW, Kersch-Becker MF, Tumlinson JH. 2024. Stomata: gatekeepers of uptake and defense signaling by green leaf volatiles in maize. Journal of Experimental Botany 75, 6872–6887. https://doi.org/10.1093/jxb/erae401.
Thoracic Epidural and Analgesic Options After Failed Transversus Abdominus Plane Block With Liposomal Bupivacaine
Authors: Cohen Kevin T , Lee Matthew I
Published: October 2024

A 39 year-old female with a history of Roux-en-Y gastric bypass underwent emergent partial colectomy. Her postoperative analgesic management of a transversus abdominus plane block administered with a combination of bupivacaine and liposomal bupivacaine was ineffective. A bupivacaine thoracic epidural was then placed, which provided significant pain relief. This use of a bupivacaine thoracic epidural infusion following liposomal bupivacaine regional anesthesia demonstrated a case of effective analgesia without the development of local anesthetic systemic toxicity symptoms in a remote hospital setting, where certain laboratory analyses were not readily available.
Transposable Element Diversity and Activity Patterns in Neotropical Salamanders
Authors: Decena-Segarra Louis Paul , Rovito Sean M
Published: October 2024

Transposable elements (TEs) compose a substantial proportion of the largest eukaryotic genomes. TE diversity has been hypothesized to be negatively correlated with genome size, yet empirical demonstrations of such a relationship in a phylogenetic context are largely lacking. Furthermore, the most abundant type of TEs in genomes varies across groups, and it is not clear if there are patterns of TE activity consistent with genome size among different taxa with large genome sizes. We use low-coverage sequencing of 16 species of Neotropical salamanders, which vary ∼7-fold in genome size, to estimate TE relative abundance and diversity for each species. We also compare the divergence of copies of each TE superfamily to estimate patterns of TE activity in each species. We find a negative relationship between TE diversity and genome size, which is consistent with the hypothesis that either competition among TEs or reduced selection against ectopic recombination may result in lower diversity in the largest genomes. We also find divergent activity patterns in the largest versus the smallest genomes, suggesting that the history of TE activity may explain differences in genome size. Our results suggest that both TE diversity and relative abundance may be predictable, at least within taxonomic groups.
χ-Conotoxins are an Evolutionary Innovation of Mollusk-Hunting Cone Snails as a Counter-Adaptation to Prey Defense
Authors: Espino Samuel , Watkins Maren , Probst Rodolfo , Koch Thomas Lund , Chase Kevin , Imperial Julita , Robinson Samuel D , Flórez Salcedo Paula , Taylor Dylan , Gajewiak Joanna , Yandell Mark , Safavi-Hemami Helena , Olivera Baldomero M
Published: October 2024

Mollusk-hunting (molluscivorous) cone snails belong to a monophyletic group in Conus, a genus of venomous marine snails. The molluscivorous lineage evolved from ancestral worm-hunting (vermivorous) snails ∼18 Ma. To enable the shift to a molluscivorous lifestyle, molluscivorous cone snails must solve biological problems encountered when hunting other gastropods, namely: (i) preventing prey escape and (ii) overcoming the formidable defense of the prey in the form of the molluscan shell, a problem unique to molluscivorous Conus. Here, we show that χ-conotoxins, peptides exclusively expressed in the venoms of molluscivorous Conus, provide solutions to the above problems. Injecting χ-conotoxins into the gastropod mollusk Aplysia californica results in impaired locomotion and uncoordinated hyperactivity. Impaired locomotion impedes escape, and a hyperactive snail will likely emerge from its shell, negating the protection the shell provides. Thus, χ-conotoxins are an evolutionary innovation that accompanied the emergence of molluscivory in Conus and provide solutions to problems posed by hunting other snails.
NCBI Taxonomy: enhanced access via NCBI Datasets
Authors: Cox Eric , Tsuchiya Mirian T N , Ciufo Stacy , Torcivia John , Falk Robert , Anderson W Ray , Holmes J Bradley , Hem Vichet , Breen Laurie , Davis Emily , Ketter Anne , Zhang Peifen , Soussov Vladimir , Schoch Conrad L , O’Leary Nuala A
Published: October 2024

The NCBI Taxonomy resource (https://www.ncbi.nlm.nih.gov/taxonomy) has long been a trusted, curated hub for organism names, classifications, and links to related data for all taxonomic nodes. NCBI Datasets (https://www.ncbi.nlm.nih.gov/datasets/) is an improved way to leverage the rich data available at NCBI so users can effectively browse, search, and download information. While taxonomy data has been a cornerstone of NCBI Datasets since its inception, we recently extended the taxonomy information available via NCBI Datasets by updating the existing NCBI Datasets taxonomy page, implementing a new taxonomy name details page, expanding programmatic access to taxonomic information via command-line tools and APIs and improving the way we handle taxonomic queries to connect users to gene and genome data. This paper highlights these improvements and provides examples to help users effectively harness these new features.
EVA1-antibody drug conjugate is a new therapeutic strategy for eliminating glioblastoma-initiating cells
Authors: Hou Jiahui , Uejima Tamami , Tanaka Miho , Son You Lee , Hanada Kazuharu , Kukimoto-Niino Mutsuko , Yamaguchi Shigeru , Hashimoto Shigeru , Yokoyama Shigeyuki , Takemori Toshitada , Saito Takashi , Shirouzu Mikako , Kondo Toru
Published: October 2024

Background

The discovery of glioblastoma (GBM)-initiating cells (GICs) has impacted GBM research. These cells are not only tumorigenic but also exhibit resistance to radiotherapy and chemotherapy. Therefore, it is crucial to characterize GICs thoroughly and identify new therapeutic targets. In a previous study, we successfully identified epithelial-V–like antigen 1 (EVA1) as a novel functional factor specific to GICs.

Methods

Hybridoma cells were generated by immunizing BALB/c mice with EVA1-Fc fusion protein. The reactivity of the supernatant from these hybridoma cells was examined using EVA1-overexpressing cells and GICs. Candidate antibodies were further selected using Biacore surface plasmon resonance analysis and 2 cytotoxicity assays—antibody-dependent cell cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC). Among the antibodies, the cytotoxicity of the B2E5-antibody drug conjugate (B2E5-ADC) was evaluated by both adding it to cultured GICs and injecting it into GIC tumor-bearing brains.

Results

B2E5 demonstrated a high affinity for human EVA1 and effectively killed both EVA1-expressing cell lines and GICs in culture through ADCC and CDC. B2E5-ADC also exhibited strong cytotoxicity to GICs in culture and prevented their tumorigenesis in the brain when administered intracranially to the tumor-bearing brain.

Conclusion

Our data indicate that B2E5-ADC is a new and promising therapeutic strategy for GBM.
A Case of Syphilis With Ocular Involvement: Persistent Negative Serology in a Patient With Multiple Sclerosis
Authors: Pipitò Luca , Ganci Irene , Cicero Andrea , Medaglia Alice Annalisa , D’Avenia Simona , Mandalà Edoardo , Calà Cinzia , Di Carlo Paola , Cascio Antonio
Published: October 2024

Diagnostic algorithms for syphilis are based on serology. However, with the advent of immunosuppressive therapies, these algorithms may fail. We report a case of an individual with multiple sclerosis on treatment with ofatumumab and secondary syphilis with visual and auditory systems involvement and persistent negative treponemal and nontreponemal tests.
Association of Neonatal and Maternal Nasal Microbiome Among Neonates in the Intensive Care Unit
Authors: Xiao Shaoming , Zhou Wei , Caldwell Ryan , Decker Slade , Oh Julia , Milstone Aaron M
Published: October 2024

The neonatal nasal microbiota may help protect neonates in the neonatal intensive care unit from pathogen colonization and infection. This preliminary study characterized the biodiversity of nasal microbiota comparing neonates in the neonatal intensive care unit and their mothers, highlighting the potential of strain sharing between mother–neonate pairs.
Phosphoketolase and KDPG aldolase metabolisms modulate photosynthetic carbon yield in cyanobacteria
Authors: Xie Ningdong , Sharma Chetna , Rusche Katherine , Wang Xin
Published: October 2024

Cyanobacteria contribute to roughly a quarter of global net carbon fixation. During diel light/dark growth, dark respiration substantially lowers the overall photosynthetic carbon yield in cyanobacteria and other phototrophs. How respiratory pathways participate in carbon resource allocation at night to optimize dark survival and support daytime photosynthesis remains unclear. Here, using the cyanobacterium Synechococcus elongatus PCC 7942, we show that phosphoketolase integrates into a respiratory network in the dark to best allocate carbon resources for amino acid biosynthesis and to prepare for photosynthesis reinitiation upon photoinduction. Moreover, we show that the respiratory Entner–Doudoroff pathway in S. elongatus is incomplete, with its key enzyme 2-keto-3-deoxy-6-phosphogluconate aldolase exhibiting alternative oxaloacetate decarboxylation activity that modulates daytime photosynthesis. This activity allows for the bypassing of the tricarboxylic acid cycle when ATP and NADPH consumption for biosynthesis is excessive and imbalanced relative to their production by the light reactions, thereby preventing relative NADPH accumulation and ensuring optimal photosynthetic carbon yield. Optimizing these metabolic processes offers opportunities to enhance photosynthetic carbon yield in cyanobacteria and other photosynthetic organisms under diel light/dark cycles.
Advances in seed hypoxia research
Authors: Rolletschek Hardy , Borisjuk Ljudmilla , Gómez-Álvarez Eva María , Pucciariello Chiara
Published: October 2024

Seeds represent essential stages of the plant life cycle: embryogenesis, the intermittent quiescence phase, and germination. Each stage has its own physiological requirements, genetic program, and environmental challenges. Consequently, the effects of developmental and environmental hypoxia can vary from detrimental to beneficial. Past and recent evidence shows how low-oxygen signaling and metabolic adaptations to hypoxia affect seed development and germination. Here, we review the recent literature on seed biology in relation to hypoxia research and present our perspective on key challenges and opportunities for future investigations.
MYB30-INTERACTING E3 LIGASE 1 regulates LONELY GUY 5-mediated cytokinin metabolism to promote drought tolerance in cotton
Authors: Chen Chuan , Zhang Dayong , Niu Xin , Jin Xuanxiang , Xu Huijuan , Li Weixi , Guo Wangzhen
Published: October 2024

Ubiquitination plays important roles in modulating the abiotic stress tolerance of plants. Drought seriously restricts agricultural production, but how ubiquitination participates in regulating drought tolerance remains largely unknown. Here, we identified a drought-inducible gene, MYB30-INTERACTING E3 LIGASE 1 (GhMIEL1), which encodes a RING E3 ubiquitin ligase in cotton (Gossypium hirsutum). GhMIEL1 was strongly induced by polyethylene glycol (PEG-6000) and the phytohormone abscisic acid. Overexpression and knockdown of GhMIEL1 in cotton substantially enhanced and reduced drought tolerance, respectively. GhMIEL1 interacted with the MYB transcription factor GhMYB66 and could ubiquitinate and degrade it in vitro. GhMYB66 directly bound to the LONELY GUY 5 (GhLOG5) promoter, a gene encoding cytokinin riboside 5′-monophosphate phosphoribohydrolase, to repress its transcription. Overexpression of GhMIEL1 and silencing of GhMYB66 altered the homeostasis of cytokinin of plant roots, increased total root length and number of root tips, and enhanced plant drought tolerance. Conversely, silencing GhLOG5 decreased total root length and number of root tips and reduced plant drought tolerance. Our studies reveal that the GhMIEL1-GhMYB66-GhLOG5 module positively regulates drought tolerance in cotton, which deepens our understanding of plant ubiquitination-mediated drought tolerance and provides insights for improving drought tolerance.
Association between asthma and depression: results from the NHANES 2005–2018 and Mendelian randomization analysis
Authors: Guo Yikun , Yan Jun
Published: October 2024

Objective

Asthma is a common respiratory disease that is believed to be associated with mental disorders. This study aims to assess the correlation and causal relationship between asthma and depression by combining observational and Mendelian randomization (MR) approaches.

Methods

We collected relevant data from the National Health and Nutrition Examination Survey (NHANES) and employed multivariable logistic regression to evaluate the correlation between asthma and depression. Additionally, a two-sample MR analysis was conducted using inverse variance-weighted (IVW) method, along with multiple sensitivity analyses.

Results

The observational study included a total of 23 648 participants, and the results showed that asthma patients had an increased risk of developing depression compared to non-asthma individuals (OR 1.26; 95% CI 1.04–1.57; P < 0.01). The IVW-MR results from two datasets indicated a potential causal relationship between asthma and depression (EBI dataset: OR 1.141; 95% CI 1.051–1.239; P = 0.01; UKB dataset: OR 1.009; 95% CI 1.005–1.013; P < 0.01). These findings suggest that asthma may be a risk factor for the onset of depression, increasing the risk of developing depression.

Conclusion

There is a significant correlation and potential causal relationship between asthma and depression, with asthma being a risk factor for the onset of depression. These findings warrant further research for validation and exploration of preventive and therapeutic measures for depression in asthma patients.

Key messages What is already known on this topic—There are some potential associations between asthma and depression based on observational studies, but the results of observational studies are often biased. This study aims to further explore the relationship between asthma and depression through a combination of observational studies and Mendelian randomization (MR) analysis. What this study adds—The observational study results from the National Health and Nutrition Examination Survey database and MR analysis are consistent, indicating that after adjusting for multiple covariates and confounding factors, asthma increases the risk of depression and is a risk factor for depression, with similar results obtained at the genetic level. How this study might affect research, practice or policy—Asthma patients not only need active medication treatment, but also need timely psychological attention, and psychological treatment is more important to a certain extent.
Combined radiographic and US evaluations to decipher joint involvement in the hands of patients with SSc
Authors: Tas Marine , Lecigne Romain , Belhomme Nicolas , Robin François , Louis Thibaut , Perlat Antoinette , Cazalets Claire , Coiffier Guillaume , Lescoat Alain
Published: October 2024

Objective

The objective of this study was to explore the aetiologies and contributing factors of synovial and tenosynovial involvement in SSc, as well as to assess the phenotype of patients with these synovial and tenosynovial features.

Methods

One hundred and seventy-one SSc patients with hand manifestations (either vascular, skin or joint manifestations) who underwent standard X-rays of both hands and hand US, were included. Two independent evaluators recorded the presence or absence of acro-osteolysis, calcinosis, microcrystalline and degenerative rheumatisms, including osteophytosis on X-rays. The presence of synovitis and tenosynovitis (active or fibrotic) was assessed through US by a third evaluator, blinded for X-ray parameters.

Results

In multivariate analysis, the characteristics associated with active synovitis and tenosynovitis were CRP > 10 mg/l (P = 0.013), fibrotic tenosynovitis on US (P = 0.005), anti-RNA polymerase III antibodies (P = 0.043) and poly-osteophytosis on hand X-rays (P = 0.001). After exclusion of patients with RA (n = 5) and/or poly-osteophytosis (n = 53), 14 remaining patients (12.7%) had active synovitis and/or tenosynovitis on US. In multivariate analyses, parameters associated with active synovitis and/or tenosynovitis in this selected population were scleroderma renal crisis (P = 0.012) and fibrotic tenosynovitis on US (P < 0.001).

Conclusion

Our study confirms that osteophytosis is a significant contributor of joint involvement in SSc patients based on real life data. After exclusion of potential confounders, >10% of SSc patients still had active synovitis and/or tenosynovitis on US, providing indirect evidence for the existence of a specific SSc-related synovial and/or tenosynovial involvement.
Heterogeneous influences of specialization and diversification on regional R&D performance: a China, Europe, and US comparison
Authors: You Zhuoying , Teirlinck Peter
Published: October 2024

We study the impact of industrial specialization and diversification on regional R&D performance. We respond to a need to consider specialization and diversification as being complementary and to cover a broad geographical scope. Based on Malmquist-based data envelopment analysis, we disclose disparity in R&D productivity and underlying efficiency and technical change in regions in China, Europe, and in the USA in the period 2015–19. For provinces in China, industrial diversification affects regional R&D productivity growth and efficiency enhancement in a U-shape mode. For European countries, specialization has a U-shaped influence on R&D productivity change, and diversification has an inverted U-shaped influence on productivity and efficiency change. We find no significant influence of specialization and diversification on the improvement of R&D performance at the level of states in the USA. Our findings point to place-based specificities and complementarity between specialization and diversification and come with policy recommendations for enhancing regional R&D performance.
Double standards in status ascriptions? The role of gender, behaviors, and social networks in status orders among adolescents
Authors: Wittek Mark , Xu Xinwei
Published: October 2024

We examine the gendered distribution of peer-ascribed status in schools. Using network data from more than 14,000 students in 676 classrooms, we explore gender differences in the ascription of status and the types of behavior rewarded with status. On average, girls receive slightly fewer status ascriptions than boys, and students tend to grant status more frequently within the same gender. Contextual analyses show that classroom demographics can moderate some of these patterns. We also uncover gender-specific differences and similarities in status-related behaviors. Notably, girls engaging in substance use are awarded with slightly more status ascriptions than boys. However, network models reveal that most behaviors affect peer status similarly for both genders, suggesting that previous findings of gender-behavioral differences based on regression analysis may be conflated with network processes. Our study updates long-held notions regarding gendered status orders in schools and highlights the value of a multidimensional approach to status processes. We discuss implications for future social network research on status ascriptions and other relational cognitions and consider how school-based interventions might benefit from our findings.
Networks rewired: quota enforcement and the unintended mobilization of native place ties
Authors: Zheng Enying , Hong Wei , Huang Yasheng , Ke Rongzhu
Published: October 2024

We explore how institutional designs can have unintended consequences, especially by rewiring social networks. Using archival data on the civil-service examinations in historical China, we argue that the enforcement of a regional quota system in 1427 reshaped group boundaries along native place, turned emotional affinities for one’s hometown into political stakes, and reinforced the influence of native place ties among political elites. Analyzing approximately 30,000 individual records, we confirm this argument by documenting a macro-level shift from a highly unequal to a more balanced provincial distribution of students who passed the examinations following the enforcement of the quota system. As native place became a primary basis for network homophily, elites deliberately cultivated these connections, seizing the opportunity as ad hoc examiners to provide preferential treatment based on shared place of origin. Our micro-level analysis of 12,752 passing students between 1400 and 1580 identifies this in-group favoritism, with examiners often ranking students from their own provinces higher. A mechanism of safeguarding political stakes underscores this baseline effect, which became more pronounced during the quota stage, especially under weaker state capacity, among examiners from disadvantaged provinces, and when examiners had greater vested interest in their hometown. These findings enrich theories of group boundaries and categorization, network homophily and formation, and the unintended consequences of institutional designs while also providing policy insights for affirmative action.
Navigating Cumulative Disadvantages of Migration, Care, and Employment Regimes: Dependent Immigrants in Canada
Authors: Tanaka Yukiko , Cranford Cynthia J
Published: October 2024

This article uses interviews with dependent immigrant women and men in Canada to analyze immigrant disadvantage in the labor market and workplace. Synthesizing feminist social policy scholarship with sociological studies of gender, work, and migration, we develop a framework for analyzing how migration, care, and employment regimes intersect to generate disadvantages. We find that gendered disadvantages embedded in dependent migration policies accumulate through a family-market care regime and a racialized, precarious employment regime. Both women and men dependent immigrants are disadvantaged in the labor market and workplace through multiple, accumulating dynamics; yet we also find different degrees and pathways to disadvantage, and multiple strategies to navigate it, shaped by gender and class. We argue that analyzing both the structure of inequalities produced by intersecting regimes and the ways people navigate them over time is key to understanding the contradictory mechanisms that both produce disadvantage and provide openings for strategic maneuvering.