bluuebunny/crossref_metadata_2025 huggingface dataset:
Was ist also Loben? Nietzsche on the Ethics of Praise
Authors: Lillehammer Hallvard
Published: September 2024

This paper explores the ethics of praise as discussed in the works of Friedrich Nietzsche. Nietzsche’s occasional remarks on praise are shown to be mainly critical, with his remarks falling into three broad categories, namely: i) metaphysical, ii) psychological, and iii) ethical. During the course of the paper, Nietzsche’s approach is located in the wider theoretical context of contemporary work on the ethics of praise and moral philosophy more generally.
Dionysian Religion and Socratic Philosophy in Nietzsche’s The Birth of Tragedy
Authors: Wood William
Published: September 2024

In The Birth of Tragedy, Nietzsche contrasts the rationalism and optimism of Socrates with the tragic outlook of the “Dionysian Greeks.” Most scholars read him as taking the side of the Dionysian Greeks against Socrates. I argue that Nietzsche presents the Dionysian as an essentially religious perspective, characterized by a proto-Christian need for redemption or “metaphysical solace” he implicitly disavows. Nietzsche himself occupies a perspective which incorporates elements of the Dionysian and the Socratic and gestures towards a higher synthesis, which like Socratic philosophy is reflective and contemplative, delighting in the pursuit and enjoyment of knowledge, but like Dionysian wisdom acknowledges the limits of rationalism. This new philosophy is neither tragic nor optimistic but playful and comic or, perhaps, tragicomic.
A case of eosinophilic granulomatosis with polyangiitis preceded by allergic bullous lesions
Authors: Hasegawa Eiko , Iijima Momoko , Sekine Akinari , Inoue Noriko , Tanaka Kiho , Suwabe Tatsuya , Yamanouchi Masayuki , Oba Yuki , Kume Ayako , Kono Kei , Kinowaki Keiichi , Ohashi Kenichi , Yamaguchi Yutaka , Suyama Yasuhiro , Wada Takehiko , Sawa Naoki , Takahashi Kotono , Ueki Shigeharu , Ubara Yoshifumi
Published: September 2024

A 62-year-old man with a history of diabetes mellitus was hospitalised with numbness of lower limbs, bullous lesions of the whole body, kidney dysfunction, presence of eosinophils, and elevated antineutrophil cytoplasmic antibodies to myeloperoxidase and anti-bullous pemphigoid 180 antibodies and was diagnosed with mononeuritis multiplex. Kidney and muscle biopsies showed vasculitis with fibrinoid necrosis, whereas skin biopsies showed only blister formation between the epidermis and dermis; a high eosinophilic infiltrate was present in all three tissues. These findings led to a diagnosis of eosinophilic granulomatosis with polyangiitis combined with allergic bullous lesions. Immunohistological examination indicated cytolytic eosinophils and extracellular traps, suggesting the presence of eosinophil extracellular trap cell death (eosinophil ETosis) in diseased tissue.
Plasma miR-122-5p and miR-142-5p and their role in chemoresistance of patients with colon cancer
Authors: Vokacova Klara , Landecka Aneta , Selvi Saba , Horak Josef , Novosadova Vendula , Manakova Katerina , Levy Miroslav , Vymetalkova Veronika
Published: September 2024

Chemoresistance represents a major issue affecting cancer therapy efficacy. Because microRNAs (miRNAs) regulate gene expression on multiple levels, their role in chemoresistance development is reasonably certain. In our previous study, miR-122-5p and miR-142-5p were identified as diagnostic, prognostic, and predictive biomarkers for primary and metastatic rectal cancer. The aim of the present study was to investigate whether these miRNAs can also reflect the disease course of patients with colon cancer (CC). Further, we focused on a deeper understanding of their involvement in 5-fluorouracil (5-FU) chemoresistance development.
Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs
Authors: Özden Furkan , Minary Peter
Published: September 2024

CRISPR-based genome editing technologies have revolutionised the field of molecular biology, offering unprecedented opportunities for precise genetic manipulation. However, off-target effects remain a significant challenge, potentially leading to unintended consequences and limiting the applicability of CRISPR-based genome editing technologies in clinical settings. Current literature predominantly focuses on point predictions for off-target activity, which may not fully capture the range of possible outcomes and associated risks. Here, we present crispAI, a neural network architecture-based approach for predicting uncertainty estimates for off-target cleavage activity, providing a more comprehensive risk assessment and facilitating improved decision-making in single guide RNA (sgRNA) design. Our approach makes use of the count noise model Zero Inflated Negative Binomial (ZINB) to model the uncertainty in the off-target cleavage activity data. In addition, we present the first-of-its-kind genome-wide sgRNA efficiency score, crispAI-aggregate, enabling prioritization among sgRNAs with similar point aggregate predictions by providing richer information compared to existing aggregate scores. We show that uncertainty estimates of our approach are calibrated and its predictive performance is superior to the state-of-the-art in silico off-target cleavage activity prediction methods. The tool and the trained models are available at https://github.com/furkanozdenn/crispr-offtarget-uncertainty.
Striving for clarity in language about gene expression
Authors: Cunningham Ana S G , Gorospe Myriam
Published: September 2024

What do we mean when we say ‘gene expression’? In the decades following Crick's 1958 central dogma of molecular biology, whereby genetic information flows from DNA (genes) to RNA (transcripts) to protein (products), we have learned a great deal about DNA, RNA, proteins, and the ensuing phenotypic changes. With the advent of high-throughput technologies (1990s), molecular biologists and computer scientists forged critical collaborations to understand the vast amount of data being generated, rapidly escalating gene expression research to the ‘omics’ level: entire sets of genes (genomes), transcribed RNAs (transcriptomes), and synthesized proteins (proteomes). However, some concessions came to be made for molecular biologists and computer scientists to understand each other—one of the most prevalent being the increasingly widespread use of ‘gene’ to mean ‘RNAs originating from a DNA segment’. This loosening of terminology, we will argue, creates ambiguity and confusion. We propose guidelines to increase precision and clarity when communicating about gene expression, most notably to reserve ‘gene’ for the DNA template and ‘transcript’ for the RNA transcribed from that gene. Striving to use perspicuous terminology will promote rigorous gene expression science and accelerate discovery in this highly promising area of biology.
CRISETR: an efficient technology for multiplexed refactoring of biosynthetic gene clusters
Authors: He Fuqiang , Liu Xinpeng , Tang Min , Wang Haiyi , Wu Yun , Liang Shufang
Published: September 2024

The efficient refactoring of natural product biosynthetic gene clusters (BGCs) for activating silent BGCs is a central challenge for the discovery of new bioactive natural products. Herein, we have developed a simple and robust CRISETR (CRISPR/Cas9 and RecET-mediated Refactoring) technique, combining clustered regulatory interspaced short palindromic repeats (CRISPR)/Cas9 and RecET, for the multiplexed refactoring of natural product BGCs. By this approach, natural product BGCs can be refactored through the synergistic interaction between RecET-mediated efficient homologous recombination and the CRISPR/Cas9 system. We first performed a proof-of-concept validation of the ability of CRISETR, and CRISETR can achieve simultaneous replacement of four promoter sites and marker-free replacement of single promoter site in natural product BGCs. Subsequently, we applied CRISETR to the promoter engineering of the 74-kb daptomycin BGC containing a large number of direct repeat sequences for enhancing the heterologous production of daptomycin. We used combinatorial design to build multiple refactored daptomycin BGCs with diverse combinations of promoters different in transcriptional strengths, and the yield of daptomycin was improved 20.4-fold in heterologous host Streptomyces coelicolor A3(2). In general, CRISETR exhibits enhanced tolerance to repetitive sequences within gene clusters, enabling efficient refactoring of diverse and complex BGCs, which would greatly accelerate discovery of novel bioactive metabolites present in microorganism.
Advancing microRNA target site prediction with transformer and base-pairing patterns
Authors: Bi Yue , Li Fuyi , Wang Cong , Pan Tong , Davidovich Chen , Webb Geoffrey I , Song Jiangning
Published: September 2024

MicroRNAs (miRNAs) are short non-coding RNAs involved in various cellular processes, playing a crucial role in gene regulation. Identifying miRNA targets remains a central challenge and is pivotal for elucidating the complex gene regulatory networks. Traditional computational approaches have predominantly focused on identifying miRNA targets through perfect Watson–Crick base pairings within the seed region, referred to as canonical sites. However, emerging evidence suggests that perfect seed matches are not a prerequisite for miRNA-mediated regulation, underscoring the importance of also recognizing imperfect, or non-canonical, sites. To address this challenge, we propose Mimosa, a new computational approach that employs the Transformer framework to enhance the prediction of miRNA targets. Mimosa distinguishes itself by integrating contextual, positional and base-pairing information to capture in-depth attributes, thereby improving its predictive capabilities. Its unique ability to identify non-canonical base-pairing patterns makes Mimosa a standout model, reducing the reliance on pre-selecting candidate targets. Mimosa achieves superior performance in gene-level predictions and also shows impressive performance in site-level predictions across various non-human species through extensive benchmarking tests. To facilitate research efforts in miRNA targeting, we have developed an easy-to-use web server for comprehensive end-to-end predictions, which is publicly available at http://monash.bioweb.cloud.edu.au/Mimosa.
Accelerated discovery and miniaturization of novel single-stranded cytidine deaminases
Authors: Deng Jiacheng , Li Xueyuan , Yu Hao , Yang Lin , Wang Ziru , Yi Wenfeng , Liu Ying , Xiao Wenyu , Xiang Hongyong , Xie Zicong , Lv Dongmei , Ouyang Hongsheng , Pang Daxin , Yuan Hongming
Published: September 2024

Cytidine base editors (CBEs) hold significant potential in genetic disease treatment and in breeding superior traits into animals. However, their large protein sizes limit their delivery by adeno-associated virus (AAV), given its packing capacity of <4.7 kb. To overcome this, we employed a web-based fast generic discovery (WFG) strategy, identifying several small ssDNA deaminases (Sdds) and constructing multiple Sdd-CBE 1.0 versions. SflSdd-CBE 1.0 demonstrated high C-to-T editing efficiency, comparable to AncBE4max, while SviSdd-CBE 1.0 exhibited moderate C-to-T editing efficiency with a narrow editing window (C3 to C5). Utilizing AlphaFold2, we devised a one-step miniaturization strategy, reducing the size of Sdds while preserving their efficiency. Notably, we administered AAV8 expressing PCSK9 targeted sgRNA and SflSdd-CBEs (nSaCas9) 2.0 into mice, leading to gene-editing events (with editing efficiency up to 15%) and reduced serum cholesterol levels, underscoring the potential of Sdds in gene therapy. These findings offer new single-stranded editing tools for the treatment of rare genetic diseases.
Establishing Reference Intakes for Creatine in Infants Aged 0 to 12 Months
Authors: Ostojic Sergej M
Published: September 2024

Creatine is recognized as a conditionally essential nutrient in certain populations; however, there is a lack of established reference values across different life stages. Infants rely exclusively on dietary creatine from human milk for their first 6 months; evaluating creatine adequacy in this population can be estimated based on preliminary data regarding the intake needed to promote optimal growth. This special article explores creatine requirements for infants aged 0 to 12 months, presents a summary of creatine content in human milk, and proposes reference intakes for creatine in this population.
Rediscovering a Forgotten Link: TSPO and RIM-BP1 in Appetite Regulation
Authors: Wang Joshua , Moody Hayley , Beecher Kate , Chehrehasa Fatemeh
Published: September 2024

The translocator protein of 18 kDa (TSPO) and RIM binding protein 1 (RIM-BP1) are both heavily expressed in neurons at the olfactory bulb. These proteins have overlapping functional profiles and are both implicated in the development of obesity. Over 20 years ago, a yeast 2-hybrid experiment discovered that RIM-BP1 interacts with a peptide constructed from a fraction of the TSPO sequence. Considering these data, the authors predict that the interaction between RIM-BP1 and TSPO could alter the olfactory system’s mediation of appetite. Despite the therapeutic potential of this interaction, it has never been confirmed if the full TSPO protein and RIM-BP1 interact. The interaction is instead often cited as physiologically irrelevant. This commentary revisits the forgotten interaction between TSPO and RIM-BP1, reviewing all relevant literature discussing their relationship. Contrary to common discourse that the RIM-BP1 and TSPO are potential binding partners, while the interaction may regulate many neurological functions, existing evidence suggests that the interaction would have a specific role in odor-guided appetite. Further research into the nutritional neuroscientific consequences of TSPO/RIM-BP1 interactions should therefore be conducted.
A better approach to mitigate the risk of airborne infections in workplaces
Authors: Agius Raymond M
Published: September 2024

Although the worst of the coronavirus disease 2019 pandemic appears to be over, the burden of airborne infection in workplaces remains unacceptably high, leaving society vulnerable, and harming workers and others. A better approach is needed to mitigate the risk of infection as actively as other multifactorial ubiquitous risks such as workplace stress. Sources and pathways of transmission need much improved control, with special emphasis on ensuring the protection of the vulnerable and susceptible.
90 years SOM then and now
Authors: Nicholson Paul J , Greenberg Neil
Published: September 2024

A past and the current President of the Society of Occupational Medicine describe the socio-political conditions that led to the formation of the Association of Industrial Medical Officers in 1935. They discuss milestones in its development—the formation of regional groups, the publication of a journal, the change of name and the Society’s status today as a multidisciplinary learned society of health professionals from different backgrounds who have an interest in occupational health/medicine.
Economic impact of large earthquakes: lessons from residential property values
Authors: Paudel Jayash
Published: September 2024

Understanding how economic agents respond to seismic shocks in a developing country setting is crucial to evaluating the economic costs of natural disasters. This article makes use of the quasi-random spatial and temporal nature of ground tremors to estimate the economic impact of the April 2015 earthquake on residential property values in Nepal. Regression estimates from the difference-in-differences research design show that residential property values declined by about 40.52 percentage points in areas with high seismic intensity. The event study model illustrates that these negative economic effects are more pronounced between 12 and 24 months after the incidence of the earthquake. Findings further underscore the underlying mechanism of physical damage and indicate that residential properties with weaker outer walls, foundations and roof materials became more susceptible to the earthquake.
Evaluation of Turnaround Times for Antigen Testing in Hospitalized Patients With Histoplasmosis and Blastomycosis
Authors: Dalton Liam M , Kauffman Carol A , Richards Blair , Miceli Marisa H
Published: September 2024

Review of histoplasmosis and blastomycosis antigen testing for 39 patients hospitalized with these diseases found that there were significantly longer turnaround times between the time of specimen collection and receipt of positive test results among those patients who had worse outcomes.
Optimization of the Diagnosis of Central Nervous System Infections in Vietnamese Hospitals: Results From a Retrospective Multicenter Study
Authors: Dong Do Van , Boutin Sébastien , Sang Vu Viet , Manh Nguyen Dang , Hoan Nghiem Xuan , Quang Hoang Xuan , Lien Tran Thi , Trang Van Dinh , The Nguyen Trong , Linh Le Thi Kieu , Schmauder Kristina , Ueltzhöffer Viola , Hafza Nourhane , Hauswaldt Susanne , Rupp Jan , Kremsner Peter G , Song Le Huu , Nurjadi Dennis , Peter Silke , Velavan Thirumalaisamy P
Published: September 2024

Introduction

Central nervous system infections pose significant health challenges, particularly in low- and middle-income countries, because of high morbidity and mortality rates. Rapid and accurate diagnosis is essential for effective treatment to prevent adverse outcomes. Traditional culture-based diagnostics are often slow and lack specificity. This study evaluates the BioFire FilmArray Meningitis/Encephalitis (FAME) Panel against standard diagnostics in Vietnam to assess its clinical impact and suitability for local epidemiology.

Methods

We conducted a prospective study involving 330 patients with suspected central nervous system infections at 4 hospitals in northern Vietnam from July 2022 to April 2023. Cerebrospinal fluid samples were analyzed using routine culture methods and FAME. We compared pathogen detection rates and assessed the potential clinical impact of FAME results on patient management.

Results

Of the 330 cerebrospinal fluid specimens, 64 (19%) were positive by either conventional diagnostics (n = 48) and/or FAME (n = 33). The agreement between FAME and conventional diagnostics was 87%. Key pathogens Mycobacterium tuberculosis (n = 7), Klebsiella pneumoniae (n = 5), Streptococcus suis (n = 5), Epstein-Barr virus (n = 3), Acinetobacter baumannii (n = 1), and Trichosporon asahii (n = 1) were not detected by FAME. Classical meningitis parameter clinical symptoms, altered glucose, protein, and pleocytosis were good predictors of FAME positivity, indicating their utility in optimizing local diagnostic algorithms.

Conclusions

FAME complements traditional diagnostics by offering rapid and broad pathogen detection, crucial for timely and appropriate therapy. However, its effectiveness varies with local epidemiology, and it should not replace conventional methods entirely. Tailoring diagnostic panels to regional pathogen prevalence is recommended to enhance diagnostic accuracy and clinical outcomes in low- and middle-income countries.
Gene-based drug therapy for children and youth treated with psychoactive medications
Authors: Verstegen Ruud H J , Cohn Iris , Feldman Mark E , Gorman Daniel , Ito Shinya
Published: September 2024

Psychoactive medications are increasingly used to treat children and youth with mental health conditions, but individual variations in response highlight the need for precision medicine. Pharmacogenetic (PGx) testing is a key component of precision medicine. The number of commercial pharmacogenetic testing companies promoting PGx, with the promise of achieving individualized and effective treatment of mental health conditions, has grown exponentially in recent years. Scientific evidence supporting the use of PGx to manage mental health conditions is limited, especially for paediatric populations. This practice point outlines steps guiding the use and interpretation of PGx testing for psychoactive medications in clinical settings, along with key supportive resources. Practice guidelines have been developed for variants in pharmacogenes encoding cytochrome P450 drug-metabolizing enzymes (e.g., CYP2C19, CYP2D6, CYP2C9) as one determinant of drug concentrations in blood, which can support both drug choice and dosing strategy for certain anti-psychotics, anti-depressants, and anti-epileptics. Adverse drug reactions to some anti-epileptic drugs (e.g., carbamazepine and phenytoin) have been associated with certain human leukocyte antigen types and variants in DNA polymerase gamma (POLG; valproic acid). Evidence remains limited for genetic variants of drug target proteins, making it challenging to identify patients with altered treatment responses at a therapeutic blood concentration.
Improving cycling safety for children and youth
Authors: Rosenfield Daniel , Fuselli Pamela , Beno Suzanne
Published: September 2024

Cycling remains a popular activity for children and youth around the world, combining the fun of moving at speed with numerous health and societal benefits. However, cycling is also associated with risk for serious injury and death. Over the past decade, research has increasingly shown that improving safety for cyclists depends, in large part, on the environment they are cycling in as well as on individual safety measures such as helmet use. The pandemic provided greater opportunity for many children and youth to engage in cycling, and refocused public attention on safer cycling infrastructure such as protected bike lanes. This statement reviews the evidence supporting safer cycling infrastructure for children and youth along with the physical and mental health benefits of cycling. The advantages of active transportation for young people, and how the built environment influences their cycling safety and uptake, are discussed. An overview of measures individuals can take to improve cycling safety is followed by recommendations for clinicians, the cycling community, parents, and policy-makers.
At2-MMP Is Required for Attenuation of Cell Proliferation during Wound Healing in Incised Arabidopsis Inflorescence Stems
Authors: Machfuudzoh Afiifah , Pitaksaringkarn Weerasak , Koshiba Ryo , Higaki Takumi , Rakwal Randeep , Ohba Yusuke , Asahina Masashi , Satoh Shinobu , Iwai Hiroaki
Published: September 2024

Wound healing of partially incised Arabidopsis inflorescence stems constitutes cell proliferation that initiates mainly in pith tissues about 3 d after incision and the healing process that completes in about 7 d. Although the initiation mechanisms of cell proliferation have been well documented, the suppression mechanisms remain elusive. Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases well known as proteolytic enzymes in animal system functioning in extracellular matrix remodeling during physiological and pathological processes, including tissue differentiation, growth, defense, wound healing and control of cancer growth. In this study, we report that At2-MMP might contribute to the suppression mechanism for cell proliferation during the tissue-repair process of incised inflorescence stems. At2-MMP transcript was gradually upregulated from day 0 to 5 after incision and slightly decreased on day 7. Morphological analysis of incised stem of defected mutant at2-mmp revealed significantly enhanced cell proliferation around the incision site. Consistent with this, semi-quantitative analysis of dividing cells displayed a significant increment in the number of dividing cells in at2-mmp as compared to wild type. These results showed that the upregulation of At2-MMP at a later stage of the wound-healing process is likely to be involved in the completion of the process by attenuating cell proliferation.
Dominant-Negative KAI2d Paralogs Putatively Attenuate Strigolactone Responses in Root Parasitic Plants
Authors: White Alexandra R F , Kane Annalise , Ogawa Satoshi , Shirasu Ken , Nelson David C
Published: September 2024

Many root parasitic plants in the Orobanchaceae use host-derived strigolactones (SLs) as germination cues. This adaptation facilitates attachment to a host and is particularly important for the success of obligate parasitic weeds that cause substantial crop losses globally. Parasite seeds sense SLs through ‘divergent’ KARRIKIN INSENSITIVE2 (KAI2d)/HYPOSENSITIVE TO LIGHT α/β-hydrolases that have undergone substantial duplication and diversification in Orobanchaceae genomes. After germination, chemotropic growth of parasite roots toward a SL source also occurs in some species. We investigated which of the seven KAI2d genes found in a facultative hemiparasite, Phtheirospermum japonicum, may enable chemotropic responses to SLs. To do so, we developed a triple mutant Nbd14a,b kai2i line of Nicotiana benthamiana in which SL-induced degradation of SUPPRESSOR OF MORE AXILLARY GROWTH2 (MAX2) 1 (SMAX1), an immediate downstream target of KAI2 signaling, is disrupted. In combination with a transiently expressed, ratiometric reporter of SMAX1 protein abundance, this mutant forms a system for the functional analysis of parasite KAI2d proteins in a plant cellular context. Using this system, we unexpectedly found three PjKAI2d proteins that do not trigger SMAX1 degradation in the presence of SLs. Instead, these PjKAI2d proteins inhibit the perception of low SL concentrations by SL-responsive PjKAI2d in a dominant-negative manner that depends upon an active catalytic triad. Similar dominant-negative KAI2d paralogs were identified in an obligate hemiparasitic weed, Striga hermonthica. These proteins suggest a mechanism for attenuating SL signaling in parasites, which might be used to enhance the perception of shallow SL gradients during root growth toward a host or to restrict germination responses to specific SLs.
Unraveling the Magmatic-to-Carbothermal Processes in the Ba–Sr–REE Mineralization of the Sevattur Carbonatites, India
Authors: Dey Monojit , Chakrabarty Aniket , Mitchell Roger H , Bhattacharjee Sourav , Pal Supratim , Kynicky Jindrich , Drüppel Kirsten
Published: September 2024

The Neoproterozoic Sevattur carbonatite complex (India) consists of calcite carbonatite, silicate-poor- and silicate-rich (banded and blue) dolomite carbonatite. The trace element composition of the calcite and ferroan dolomite shows that most of them have magmatic characteristics. The predominance of dolomite carbonatite over calcite carbonatite and the absence of a genetically related silicate suite at Sevattur suggest a dolomitic parental magma derived by the direct melting of the mantle. Regardless of the prevalent magmatic character of the Sevattur carbonatites they host a plethora of Ba–Sr–REE minerals formed throughout the orthomagmatic-to-carbothermal stages under varying activities of ${\mathrm{F}}^{-}$,${\mathrm{CO}}_3^{2-}$, ${\mathrm{PO}}_4^{3-},\kern0.5em$and ${\mathrm{SO}}_4^{2-}$. The orthomagmatic stage begins with the crystallization of calcite carbonatite containing xenocrystic diopside, antecrystic Y-bearing calcite (Cal-I), and primary benstonite, apatite, and richterite in a Sr–Mg-rich calcite (Cal-II) matrix. Fractionation of apatite, carbocernaite, and cordylite-(Ce) together with the enrichment of Mg, Fe, Na, and F in late-magmatic stages, forms the dolomite carbonatite. The decomposition of benstonite to norsethite, Ba–Ca carbonate, and strontianite occurs within dolomite carbonatite at the same stage with minimal wall-rock assimilation. Interaction between the xenocrystal clinopyroxenite and the primary magma during late-magmatic stages has resulted in the formation of aegirine and phlogopite in calcite carbonatite. Similarly, the prolonged assimilation of clinopyroxenite by the evolving magma leads to the formation of magnesio-riebeckite and magnesio-arfvedsonite within the banded- and blue carbonatites. The increasing activities of ${\mathrm{PO}}_4^{3-},{\mathrm{SO}}_4^{2-}$, and H2O during the carbothermal stage, destabilizes precursor carbocernaite and cordylite-(Ce), resulting in an assemblage consisting of synchysite-(Ce), ancylite-(Ce), daqingshanite, hydroxylbastnäsite-(Ce), ferriallanite-(Ce), monazite-(Ce), and baryte in dolomite carbonatite. In the banded carbonatite, the carbothermal stage is characterized by ferri-winchite, tremolite-actinolite, and phlogopite crystallization. Further contamination and differentiation of the carbothermal fluid have resulted in the crystallization of quartz and albite in blue carbonatite. Phlogopitization within the blue carbonatite and clinopyroxenite results from late K enrichment in the carbothermal fluids.
High prey capture efficiencies of oceanic epipelagic lobate and cestid ctenophores
Authors: Child Taylor , Costello John H , Gemmell Brad J , Sutherland Kelly R , Colin Sean P
Published: September 2024

Ctenophores are numerically dominant members of oceanic epipelagic communities around the world. The ctenophore community is often comprised of several common, co-occurring lobate and cestid genera. Previous quantifications of the amount of fluid that lobate ctenophores entrain in their feeding currents revealed that oceanic lobates have the potential for high feeding rates. In order to more directly examine the trophic role of oceanic lobate ctenophores, we quantified the encounter and retention efficiencies of several co-occurring species (Bolinopsis vitrea, Ocyropsis crystallina, Eurhamphea vexilligera and Cestum veneris) in their natural environments. Encounters and predator–prey interactions were video recorded in the field using specialized cameras and SCUBA techniques. The lobate species encountered, on average, 2.4 prey per minute and ingested 40% of these prey. This translated to an estimated ingestion rate of close to 1 prey per minute. Cestum veneris and most of the lobate species retained prey as efficiently as the voracious coastal lobate predator Mnemiopsis leidyi, suggesting that these oceanic species have a similar predation impact in their environments as M. leidyi does in coastal ecosystems. Hence, quantified in situ predatory-prey interactions indicate that epipelagic ctenophores have a significant impact on oceanic ecosystems worldwide.
Quantum efficiency of chloroplasts retained from food by the mixotrophic ciliate Strombidium rassoulzadegani
Authors: Grzywacz J , Gorbunov M , McManus G B
Published: September 2024

Strombidium rassoulzadegani is an oligotrich ciliate from coastal waters that retains functional chloroplasts from its algal diet. Using a Fluorescence Induction and Relaxation fluorometer, we measured the maximum quantum efficiency (QE) of Photosystem II in two algal foods, one chlorophyte and one cryptophyte, and in the chloroplasts retained by the ciliate. Within the ciliate, QE of the chloroplasts was about half the value (c. 0.3) of that in exponentially-growing, nutrient-replete algal cultures (0.5–0.6). Under starvation, when the ciliates were not able to replace aging chloroplasts, QE declined further, to values of 0.1–0.2. The rate of decline was similar at irradiances from 30–100 μmol m−2 s−1 and slightly faster in total darkness. Exposure of the ciliates to the Photosystem II inhibitor DCMU decreased growth rates much more strongly in chlorophyte-fed ciliates, compared to those fed the cryptophyte. The decline in the chlorophyte-fed ciliates was much greater than expected, given the small subsidy to growth provided by the retained chloroplasts, suggesting that their role in the ciliate’s metabolism may be more than just a photosynthetic boost.
Regulatory network of the late-recruited primary decarboxylase C4NADP-ME in sugarcane
Authors: Hua Xiuting , Shi Huihong , Zhuang Gui , Lan Yuhong , Zhou Shaoli , Zhao Dongxu , Lyu Ming-Ju Amy , Akbar Sehrish , Liu Jia , Yuan Yuan , Li Zhen , Jiang Qing , Huang Kaixin , Zhang Yating , Zhang Qing , Wang Gang , Wang Yu , Yu Xiaomin , Li Pinghua , Zhang Xingtan , Wang Jianping , Xiao Shenghua , Yao Wei , Ming Ray , Zhu Xin-Guang , Zhang Muqing , Tang Haibao , Zhang Jisen
Published: September 2024

In agronomically important C4 grasses, efficient CO2 delivery to Rubisco is facilitated by NADP-malic enzyme (C4NADP-ME), which decarboxylates malate in bundle sheath cells. However, understanding the molecular regulation of the C4NADP-ME gene in sugarcane (Saccharum spp.) is hindered by its complex genetic background. Enzymatic activity assays demonstrated that decarboxylation in sugarcane Saccharum spontaneum predominantly relies on the NADP-ME pathway, similar to sorghum (Sorghum bicolor) and maize (Zea mays). Comparative genomics analysis revealed the recruitment of 8 core C4 shuttle genes, including C4NADP-ME (SsC4NADP-ME2), in the C4 pathway of sugarcane. Contrasting to sorghum and maize, the expression of SsC4NADP-ME2 in sugarcane is regulated by different transcription factors (TFs). We propose a gene regulatory network for SsC4NADP-ME2, involving candidate TFs identified through gene coexpression analysis and yeast 1-hybrid experiment. Among these, ABA INSENSITIVE5 (ABI5) was validated as the predominant regulator of SsC4NADP-ME2 expression, binding to a G-box within its promoter region. Interestingly, the core element ACGT within the regulatory G-box was conserved in sugarcane, sorghum, maize, and rice (Oryza sativa), suggesting an ancient regulatory code utilized in C4 photosynthesis. This study offers insights into SsC4NADP-ME2 regulation, crucial for optimizing sugarcane as a bioenergy crop.
Histone deacetylase GhHDA5 negatively regulates Verticillium wilt resistance in cotton
Authors: Wei Chunyan , Wang Chaofan , Zhang Xin , Huang Weiyi , Xing Minghui , Han Chunyan , Lei Cangbao , Zhang Youpeng , Zhang Xiangyu , Cheng Kai , Zhang Xiao
Published: September 2024

Verticillium wilt (VW) caused by Verticillium dahliae (V. dahliae) is one of the most destructive diseases in cotton (Gossypium spp.). Histone acetylation plays critical roles in plant development and adaptive responses to biotic and abiotic stresses. However, the relevance of histone acetylation in cotton VW resistance remains largely unclear. Here, we identified histone deacetylase 5 (GhHDA5) from upland cotton (Gossypium hirsutum L.), as a negative regulator of VW resistance. GhHDA5 expression was responsive to V. dahliae infection. Silencing GhHDA5 in upland cotton led to improved resistance to V. dahliae, while heterologous expression of GhHDA5 in Arabidopsis (Arabidopsis thaliana) compromised V. dahliae tolerance. GhHDA5 repressed the expression of several lignin biosynthesis-related genes, such as 4-coumarate:CoA ligase gene Gh4CL3 and ferulate 5-hydroxylase gene GhF5H, through reducing the acetylation level of histone H3 lysine 9 and 14 (H3K9K14ac) at their promoter regions, thereby resulting in an increased deposition of lignin, especially S monomers, in the GhHDA5-silenced cotton plants. The silencing of GhF5H impaired cotton VW tolerance. Additionally, the silencing of GhHDA5 also promoted the production of reactive oxygen species (ROS), elevated the expression of several pathogenesis-related genes (PRs), and altered the content and signaling of the phytohormones salicylic acid (SA), jasmonic acid (JA), and strigolactones (SLs) after V. dahliae infection. Taken together, our findings suggest that GhHDA5 negatively regulates cotton VW resistance through modulating disease-induced lignification and the ROS- and phytohormone-mediated defense response.
Confidence and second-order errors in cortical circuits
Authors: Granier Arno , Petrovici Mihai A , Senn Walter , Wilmes Katharina A
Published: September 2024

Minimization of cortical prediction errors has been considered a key computational goal of the cerebral cortex underlying perception, action, and learning. However, it is still unclear how the cortex should form and use information about uncertainty in this process. Here, we formally derive neural dynamics that minimize prediction errors under the assumption that cortical areas must not only predict the activity in other areas and sensory streams but also jointly project their confidence (inverse expected uncertainty) in their predictions. In the resulting neuronal dynamics, the integration of bottom-up and top-down cortical streams is dynamically modulated based on confidence in accordance with the Bayesian principle. Moreover, the theory predicts the existence of cortical second-order errors, comparing confidence and actual performance. These errors are propagated through the cortical hierarchy alongside classical prediction errors and are used to learn the weights of synapses responsible for formulating confidence. We propose a detailed mapping of the theory to cortical circuitry, discuss entailed functional interpretations, and provide potential directions for experimental work.
The origin and function of arbitrary signals: Making false statements, having long hair, and smoking Virginia Slims
Authors: Wernerfelt Birger
Published: September 2024

We propose a model in which players take actions that run counter to social norms in part to announce their stand on a social controversy but also, and maybe mostly, to gain image benefits that allow them to join groups that are socially attractive to them. We give several examples, but the “election denial” debate is an important application: rather than assuming that proponents believe their claims to be true, it suggests that false statements can serve as symbolic actions and help them engage in self-branding for social and psychological gain. Specifically, the willingness to make a controversial statement can be a credible signal because untruth is ill-received by some members of society and therefore entails some costs. It is immaterial whether election deniers believe their claim to be true, but it is important that some members of society believe that it is false and therefore think poorly of those who make it: if there is social consensus about the truth of a statement, it cannot serve a signaling function. The same mechanism explains several other verbal and nonverbal signals associated with different sides of social controversies and analysis of those helps clarify the mechanism.
Association between neonatal mortality and births not weighed among 400 thousand institutional deliveries in 32 low- and middle-income countries
Authors: Karlsson Omar , Benski Caroline , Kapoor Mudit , Kim Rockli , Subramanian S V
Published: September 2024

Background

Low birthweight (LBW) children have a higher risk of neonatal mortality. All institutional deliveries, therefore, should be weighed to determine appropriate care. Mortality risk for newborns who are not weighed at birth (NWB) is unknown.

Methods

This paper used logit regression models to compare the odds of death for NWB neonates to that of other neonates using data on 401 712 institutional births collected in Demographic and Health Surveys from 32 low- and middle-income countries.

Results

In the pooled sample, 2.3% died in the neonatal period and 12% were NWB. NWB neonates had a high risk of mortality compared to normal birthweight children (Adjusted odds ratio [AOR] 5.8, 95% CI: 5.3, 6.5). The mortality risk associated with NWB was higher than for LBW. The neonatal mortality risk associated with NWB varied across countries from AOR of 2.1 (95% CI: 1.22, 3.8) in Afghanistan to 94 (95% CI: 22, 215) in Gabon. In the pooled sample, the 12% of children who were NWB accounted for 37% of all neonatal deaths.

Conclusions

The association between NWB and neonatal mortality may suggest a need to focus on the quality of institutions related to newborn care. However, further studies are needed to determine causality. A health emergency or death may also cause NWB.
The Brand Premium
Authors: Boustanifar Hamid , Kang Young Dae
Published: September 2024

We highlight the limitations of using cumulative advertising expenses as an input measure of brand value. Using two output measures—Interbrand’s data and a novel text-based measure—we find that an equal-weighted portfolio of top brands yields an annual abnormal return of 3%. The excess returns are driven by companies that develop their brands internally. Intangible factors proposed in the literature have no explanatory power for the premium. Analysts underestimate the future earnings of top brands, leading to significant excess returns following earnings announcements. We find no abnormal returns associated with the input measure of brand value. (JEL G4, G12, G14, M41)
Novel deep-learning analysis for connective tissue disease—related interstitial lung disease extent assessment on CT: a preliminary cross-sectional study
Authors: Ito Yuhei , Ichikawa Yasutaka , Murashima Shuichi , Sakuma Hajime , Iwasawa Tae , Arinuma Yoshiyuki , Nakajima Ayako
Published: September 2024

Objectives

Physician’s evaluation of interstitial lung disease (ILD) extension with high-resolution CT (HRCT) has limitations such as lack of objectivity and reproducibility. This study aimed to investigate the utility of computer-based deep-learning analysis using QZIP-ILD® software (DL-QZIP) compared with conventional approaches in CTD-related ILD.

Methods

Patients with CTD–ILD visiting our Rheumatology Centre between December 2020 and April 2024 were recruited. Quantitative scores, including the percentage of lung involvement in ground-glass opacity (QGG), total fibrotic lesion (QFIB), and overall ILD extension encompassing both QGG and QFIB (QILD), calculated by DL-QZIP, were compared with semiquantitative visual method, employing intraclass correlation coefficients (ICC). We compared the capability of QILD scores to distinguish patients with forced vital capacity (FVC) % <70 in both methods determined by the area under the curve (AUC) by the receiver-operating characteristic curve analysis and DeLong’s test.

Results

Eighty patients (median age, 66 years; 14 men) were included. Median QGG, QFIB and QILD scores were 3.45%, 2.19% and 5.35% using DL-QZIP, and 3.25%, 4.06% and 8.48% using visual method, respectively. Correlations between DL-QZIP and visual method were 0.75 for QGG, 0.61 for QFIB and 0.75 for QILD. The AUC of QILD scores for FVC% <70 was significantly higher with DL-QZIP (0.833) compared with visual method (0.660) (P < 0.01).

Conclusion

QZIP-ILD® demonstrates superior capability in distinguishing patients with a radiological scenario correlated to severe physiological impairment, while showing relatively good correlations in quantifying the extent on HRCT compared with conventional method in CTD–ILD.
Imaging findings in cardiovascular involvements of IgG4-related disease: a systematic review study
Authors: Ghaffari Jolfayi Amir , Salmanipour Alireza , Heshmat-Ghahdarijani Kiyan , Meshgi Shahla , Dastmardi Maedeh , Salehabadi Ghazaleh , Azimi Amir , Bazargany Mohammad Hossein Mozafary , Roudsari Peyvand Parhizkar , Mahmoodiyeh Behnaz , Mohammadzadeh Ali
Published: September 2024

Background

Immunoglobulin G4-related disease (IgG4-RD) is a fibroinflammatory condition characterized by IgG4-positive plasma cell infiltration that can affect multiple organs, including the cardiovascular system. The diagnosis of IgG4-RD relies on a combination of clinical, serological, radiological and pathological findings. However, due to the varied and insidious clinical presentations, normal IgG4 levels in a significant percentage of patients and frequent multi-organ involvement, imaging plays a crucial role in the diagnosis of IgG4-RD. The aim of this study is to comprehensively examine the imaging findings in IgG4-related cardiovascular disease for accurate diagnosis and appropriate treatment.

Methods

A systematic search was conducted across the electronic databases PubMed, Scopus, Embase and Web of Science, to 1 September 2023, following PRISMA guidelines, searching for studies reporting detailed cardiovascular imaging findings in IgG4-RD.

Results

The search yielded 68 studies (60 case reports, 5 case series, 2 cross-sectional, 1 case–control) with 120 cases of cardiovascular IgG4-RD. Most of the cases were male, averaging 62.8 years. The common initial symptoms were dyspnoea and chest pain. The most common imaging finding was vasculopathy, including vessel wall thickening, periarteritits, periaortitis, aortitis, stenosis, ectasia, aneurysm formation, intramural haemorrhage, fistula formation and dissection, followed by pericardial involvement and mediastinal masses. Case series and cross-sectional studies also showed vasculopathy to be the most common finding on various imaging modalities, including angiography and PET/CT, highlighting the complex pathology of IgG4-RD.

Conclusion

This study evaluated current IgG4-RD articles, revealing a higher prevalence in men and vasculopathy as the most common cardiovascular complication.
Psychometric examination of the patient-reported outcome measurement information system parent proxy pediatric sleep measures from early childhood to adolescence in a nationally representative Spanish sample
Authors: Becker Stephen P , Burns G Leonard , Montaño Juan José , Servera Mateu
Published: September 2024

Study Objectives

To use a nationally representative sample to (1) evaluate the factor structure of the patient-reported outcome measurement information system (PROMIS) parent proxy pediatric sleep scales (Spanish translation), (2) examine the invariance of these scales across sex and across different developmental periods of childhood and adolescence, (3) confirm the information and precision of the scales using item response theory (IRT), and (4) provide age-based normative information.

Methods

Parents of a nationally representative sample of 5525 Spanish children and adolescents ages 5–16 years (56.1% boys) completed the Spanish translation parent proxy short versions of the sleep disturbance and sleep-related impairment scales. We conducted confirmatory factor analyses, invariance analyses, and graded-response IRT analyses.

Results

CFAs conducted separately on males and females within three age groups (early childhood: ages 5–8 years; middle childhood: ages 9–12 years; adolescence: ages 13–16 years) indicated all items had a substantial loading with one exception (the sleep continuity item [“my child slept through the night”] had a substantially lower loading and was removed for subsequent analyses). The scores on the two scales demonstrated invariance across sex within each age group. Using IRT analyses, both scales showed a high degree of information and precision from slightly below the trait means to slightly above two standard deviations above the trait means.

Conclusions

The strong psychometric properties of the short versions of the parent proxy PROMIS pediatric sleep disturbance and sleep-related impairment scales, coupled with age-based norms, suggest these scales are likely to be useful for research and clinical applications.