bluuebunny/crossref_metadata_2025 huggingface dataset:
Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference
Authors: Dong Xiaoru , Leary Jack R , Yang Chuanhao , Brusko Maigan A , Brusko Todd M , Bacher Rhonda
Published: May 2024

Single-cell RNA sequencing (scRNA-seq) experiments have become instrumental in developmental and differentiation studies, enabling the profiling of cells at a single or multiple time-points to uncover subtle variations in expression profiles reflecting underlying biological processes. Benchmarking studies have compared many of the computational methods used to reconstruct cellular dynamics; however, researchers still encounter challenges in their analysis due to uncertainty with respect to selecting the most appropriate methods and parameters. Even among universal data processing steps used by trajectory inference methods such as feature selection and dimension reduction, trajectory methods’ performances are highly dataset-specific. To address these challenges, we developed Escort, a novel framework for evaluating a dataset’s suitability for trajectory inference and quantifying trajectory properties influenced by analysis decisions. Escort evaluates the suitability of trajectory analysis and the combined effects of processing choices using trajectory-specific metrics. Escort navigates single-cell trajectory analysis through these data-driven assessments, reducing uncertainty and much of the decision burden inherent to trajectory inference analyses. Escort is implemented in an accessible R package and R/Shiny application, providing researchers with the necessary tools to make informed decisions during trajectory analysis and enabling new insights into dynamic biological processes at single-cell resolution.
TransPTM: a transformer-based model for non-histone acetylation site prediction
Authors: Meng Lingkuan , Chen Xingjian , Cheng Ke , Chen Nanjun , Zheng Zetian , Wang Fuzhou , Sun Hongyan , Wong Ka-Chun
Published: May 2024

Protein acetylation is one of the extensively studied post-translational modifications (PTMs) due to its significant roles across a myriad of biological processes. Although many computational tools for acetylation site identification have been developed, there is a lack of benchmark dataset and bespoke predictors for non-histone acetylation site prediction. To address these problems, we have contributed to both dataset creation and predictor benchmark in this study. First, we construct a non-histone acetylation site benchmark dataset, namely NHAC, which includes 11 subsets according to the sequence length ranging from 11 to 61 amino acids. There are totally 886 positive samples and 4707 negative samples for each sequence length. Secondly, we propose TransPTM, a transformer-based neural network model for non-histone acetylation site predication. During the data representation phase, per-residue contextualized embeddings are extracted using ProtT5 (an existing pre-trained protein language model). This is followed by the implementation of a graph neural network framework, which consists of three TransformerConv layers for feature extraction and a multilayer perceptron module for classification. The benchmark results reflect that TransPTM has the competitive performance for non-histone acetylation site prediction over three state-of-the-art tools. It improves our comprehension on the PTM mechanism and provides a theoretical basis for developing drug targets for diseases. Moreover, the created PTM datasets fills the gap in non-histone acetylation site datasets and is beneficial to the related communities. The related source code and data utilized by TransPTM are accessible at https://www.github.com/TransPTM/TransPTM.
Treating epidermolytic ichthyosis and ichthyosis with confetti with epidermal autografts cultured from revertant skin
Authors: Tanahashi Kana , Kono Michihiro , Yoshikawa Takenori , Suzuki Yuika , Inoie Masukazu , Kuwatsuka Yachiyo , Kinoshita Fumie , Takeichi Takuya , Akiyama Masashi
Published: May 2024

Background

No efficient treatment has yet been established for epidermolytic ichthyosis (EI), which is caused by pathogenic variants of KRT1 or KRT10. Patients with ichthyosis with confetti (IWC) have multiple normal-appearing spots, caused by the revertant somatic recombination of pathogenic variants that occurs at each spot independently. Additionally, some patients with EI have large areas of normal skin due to revertant postzygotic mosaicism.

Objectives

To assess the feasibility of transplanting cultured epidermal autografts (CEAs) produced from revertant epidermal keratinocytes in patients with EI and IWC.

Methods

We performed a clinical trial of treatment with CEAs produced from each patient’s own revertant epidermal keratinocytes as a proof-of-concept study. This was a single-arm, open, unmasked, uncontrolled, single-assignment, treatment-purpose study. The primary outcome was the percentage area that lacked recurrence of ichthyosis lesions 4 weeks after the final transplant. The secondary outcome was the percentage area lacking recurrence of ichthyosis lesions 24 weeks after the initial transplantation. The trial was registered with the Japan Registry of Clinical Trials (jRCTb041190097).

Results

We successfully produced CEAs from genetically confirmed revertant skin from two patients with mosaic EI and from one patient with IWC and confirmed by amplicon sequencing and droplet digital polymerase chain reaction analysis that the CEAs mainly consisted of revertant wild-type cells. Single-cell RNA sequencing analysis confirmed the normal proliferation and safety profiling of CEAs. CEAs were transplanted onto desquamated lesional sites in the patients. Four weeks post-transplantation, the percentage area lacking recurrence of ichthyosis lesions in the three patients was 40%, 100% and 100% respectively, although recurrence of ichthyosis lesions was seen at the site of CEA transplantation in all three patients at 24 weeks post-transplantation.

Conclusions

CEAs from normal skin have the potential to be a safe and local treatment option for EI and IWC.
Stability-Indicating HPLC Method for Determination of Ibuprofen and Famotidine Degradation Products
Authors: Atilgan Nurdan , Tabansiz Gizem , Turkes Ezgi , Sarracoglu Nagehan , Doganay Asuman Aybey , Pinarbasli Onur
Published: May 2024

A new stability-indicating high-performance liquid chromatographic method for the quantitative determination of ibuprofen and famotidine degradation products in combined pharmaceutical products was developed and validated. The current aim of this study is to develop a rapid, accurate and robust analytical stability indicating impurity method that can separate ibuprofen, famotidine and their related impurities by using a reversed-phase high-performance liquid chromatography. A Zorbax SB-Phenyl column (4.6 × 150 mm2, 5-μm particle size) with mobile phase containing phosphate buffer solution with a pH value of 3.0 and acetonitrile was used. The flow rate was 0.8 mL/min and the analytes were detected by UV detector at 265 nm. The retention times of ibuprofen and famotidine were 18.43 and 5.14 min, respectively. This method was validated to confirm specificity, linearity, sensitivity (limit of detection and limit of quantitation), precision, accuracy, robustness and sample stability according to the International Conference on Harmonization guidelines. Studies have been completed and reported with two active substances in the combined dosage form and seven impurities in total. There is no method in the literature that simultaneously distinguishes and quantitatively analyzes both active substances and degradation products.
Empagliflozin inhibits increased Na influx in atrial cardiomyocytes of patients with HFpEF
Authors: Trum Maximilian , Riechel Johannes , Schollmeier Elisa , Lebek Simon , Hegner Philipp , Reuthner Kathrin , Heers Silvia , Keller Karoline , Wester Michael , Klatt Susanne , Hamdani Nazha , Provaznik Zdenek , Schmid Christof , Maier Lars , Arzt Michael , Wagner Stefan
Published: May 2024

Aims

Heart failure with preserved ejection fraction (HFpEF) causes substantial morbidity and mortality. Importantly, atrial remodelling and atrial fibrillation are frequently observed in HFpEF. Sodium–glucose cotransporter 2 inhibitors (SGLT2i) have recently been shown to improve clinical outcomes in HFpEF, and post-hoc analyses suggest atrial anti-arrhythmic effects. We tested if isolated human atrial cardiomyocytes from patients with HFpEF exhibit an increased Na influx, which is known to cause atrial arrhythmias, and if that is responsive to treatment with the SGTL2i empagliflozin.

Methods and results

Cardiomyocytes were isolated from atrial biopsies of 124 patients (82 with HFpEF) undergoing elective cardiac surgery. Na influx was measured with the Na-dye Asante Natrium Green–2 AM (ANG-2). Compared to patients without heart failure (NF), Na influx was doubled in HFpEF patients (NF vs. HFpEF: 0.21 ± 0.02 vs. 0.38 ± 0.04 mmol/L/min (N = 7 vs. 18); P = 0.0078). Moreover, late INa (measured via whole-cell patch clamp) was significantly increased in HFpEF compared to NF. Western blot and HDAC4 pulldown assay indicated a significant increase in CaMKII expression, CaMKII autophosphorylation, CaMKII activity, and CaMKII-dependent NaV1.5 phosphorylation in HFpEF compared to NF, whereas NaV1.5 protein and mRNA abundance remained unchanged. Consistently, increased Na influx was significantly reduced by treatment not only with the CaMKII inhibitor autocamtide-2-related inhibitory peptide (AIP), late INa inhibitor tetrodotoxin (TTX) but also with sodium/hydrogen exchanger 1 (NHE1) inhibitor cariporide. Importantly, empagliflozin abolished both increased Na influx and late INa in HFpEF. Multivariate linear regression analysis, adjusting for important clinical confounders, revealed HFpEF to be an independent predictor for changes in Na handling in atrial cardiomyocytes.

Conclusion

We show for the first time increased Na influx in human atrial cardiomyocytes from HFpEF patients, partly due to increased late INa and enhanced NHE1-mediated Na influx. Empagliflozin inhibits Na influx and late INa, which could contribute to anti-arrhythmic effects in patients with HFpEF.
Influence of prey availability on the movement pattern of breeding saker falcons (Falco cherrug) in Mongolia
Authors: Bold Batbayar , Rahman Lutfor , Purev-Ochir Gankhuyag , Saruul Amarsaikhan , Zhan Xiangjiang , Dixon Andrew
Published: May 2024

As an apex predator in arid steppe, saker falcon plays a crucial role in maintaining ecosystem balance. Understanding their movement patterns concerning conspecific competition and prey availability is important for their conservation. We aim to understand how movement pattern of breeding saker falcons relates to prey availability. Twelve adult sakers were tracked during the breeding seasons, using satellite transmitters. Throughout the breeding season, sakers exhibited territorial behavior, with minimal overlap in range use among neighboring conspecifics. Males occupied larger areas (mean = 2,397 ha, median = 1,221 ha), compared to females (mean = 1,241 ha, median = 554 ha), and it remained consistent throughout breeding season. Female home range size increased notably during a late nestling stage and post-fledging dependence periods, indicating release from brooding constraints. Notably, we found a negative relationship between male home range size and prey availability. In high rodent density areas, males occupied smaller areas (mean = 1,135 ha, median = 1,034 ha), contrasting with low rodent density areas (mean = 6,815 ha, median = 6,516 ha). However, no significant relationship was observed between female home range size and prey availability. We also noted instances of nest abandonment and early dispersal behavior in some females, potentially influenced by a handicapping effect of tagging. Our findings offer valuable insight into how prey availability shapes saker falcon space use and defines their spatial requirements for successful breeding. This knowledge is crucial for the conservation and management of globally endangered saker falcons, informing targeted habitat protection and resource management strategies.
Racial/Ethnic Disparities in Hospital Readmission and Frequent Hospitalizations Among Medicare Beneficiaries With Alzheimer’s Disease and Related Dementia: Traditional Medicare Versus Medicare Advantage
Authors: Mahmoudi Elham , Margosian Sara , Lin Paul
Published: May 2024

Objectives

Examine racial/ethnic disparities in 30-day readmission and frequent hospitalizations among Medicare beneficiaries with dementia in traditional Medicare (TM) versus Medicare Advantage (MA).

Methods

In this case-control study, we used 2018–2019 TM and MA claims data. Participants included individuals 65+ with 2 years of continuous enrollment, diagnosis of dementia, a minimum of 4 office visits in 2018, and at least 1 hospitalization in 2019, (cases: TM [n = 36,656]; controls: MA [n = 29,366]). We conducted matching based on health-need variables and applied generalized linear models adjusting for demographics, health-related variables, and healthcare encounters.

Results

TM was associated with higher odds of 30-day readmission (OR = 1.07 [CI: 1.02 to 1.12]) and frequent hospitalizations (OR = 1.10 [CI: 1.06 to 1.14]) compared to MA. Hispanic and Black enrollees in TM had higher odds of frequent hospitalizations compared with Hispanic and Black enrollees in MA, respectively (OR = 1.35 [CI: 1.19 to 1.54]) and (OR = 1.26 [CI: 1.13 to 1.40]). MA was associated with lower Hispanic–White and Black–White disparities in frequent hospitalizations by 5.8 (CI: −0.09 to −0.03) and 4.4 percentage points (PP; CI: −0.07 to −0.02), respectively. For 30-day readmission, there was no significant difference between Black enrollees in TM and MA (OR = 1.04 [CI: 0.92 to 1.18]), but Hispanic enrollees in TM had higher odds of readmission than Hispanics in MA (OR = 1.23 [CI: 1.06 to 1.43]). MA was associated with a lower Hispanic–White disparity in readmission by 1.9 PP (CI: −0.004 to −0.01).

Discussion

MA versus TM was associated with lower risks of 30-day readmission and frequent hospitalizations. Moreover, MA substantially reduced Hispanic–White and Black–White disparities in frequent hospitalizations compared with TM.
PE (Prickly Eggplant) encoding a cytokinin-activating enzyme responsible for the formation of prickles in eggplant
Authors: Zhang Lei , Zhang Runzhi , Yan Ping , Zeng Liqian , Zhao Weiwei , Feng Huiqian , Mu Ruyu , Hou Wenqian
Published: May 2024

Eggplant is one of the most important vegetables worldwide, with some varieties displaying prickles. These prickles, present on the leaves, stems, and fruit calyxes, posing challenges during cultivation, harvesting, and transportation, making them an undesirable agronomic trait. However, the genetic mechanisms underlying prickle morphogenesis in eggplant remain poorly understood, impeding genetic improvements. In this study, genetic analyses revealed that prickle morphogenesis is governed by a single dominant nuclear gene, termed PE (Prickly Eggplant). Subsequent bulk segregant RNA-sequencing (BSR-seq) and linkage analysis preliminarily mapped PE to chromosome 6. This locus was then fine mapped to a 9233 bp interval in a segregating population of 1109 plants, harboring only one candidate gene, SmLOG1, which encodes a LONELY GUY (LOG)-family cytokinin biosynthetic enzyme. Expression analyses via transcriptome and qRT-PCR demonstrate that SmLOG1 is predominantly expressed in immature prickles. CRISPR-Cas9 knockout experiments targeting SmLOG1 in prickly parental line ‘PI 381159’ abolished prickles across all tissues, confirming its critical role in prickle morphogenesis. Sequence analysis of SmLOG1 pinpointed variations solely within the non-coding region. We developed a cleaved amplified polymorphic sequences (CAPS) marker from a distinct SNP located at −735-bp within the SmLOG1 promoter, finding significant association with prickle variation in 190 eggplant germplasms. These findings enhance our understanding of the molecular mechanisms governing prickle development in eggplant and facilitate the use of marker-assisted selection (MAS) for breeding prickleless cultivars.
Phenotypic Convergence Is Stronger and More Frequent in Herbivorous Fishes
Authors: Kolmann M A , Poulin E , Rosen J , Hemraj-Naraine D , Burns M D
Published: May 2024

Synopsis

Constraints on phenotypic evolution can lead to patterns of convergent evolution, by limiting the “pool” of potential phenotypes in the face of endogenous (functional, developmental) or exogenous (competition, predation) selective pressures. Evaluation of convergence depends on integrating ecological and morphological data within a robust, comparative phylogenetic context. The staggering diversity of teleost fishes offers a multitude of lineages adapted for similar ecological roles and, therefore, offers numerous replicated evolutionary experiments for exploring phenotypic convergence. However, our understanding of fish feeding systems has been primarily shaped by marine species, with the monolithic exception of freshwater cichlids. Here we use piranhas and pacus (Serrasalmidae) to explore the evolution of different feeding ecologies and their morphological proxies in Neotropical freshwater environments. Specifically, we explore whether convergence is more widespread among plant-eating fishes, arising from strong constraints on phenotypic evolution in herbivores. Using osteological micro-computed tomographic imaging (μCT), we describe the major axes of morphological variation in pacus and piranhas, regarding their diet and feeding behaviors. Next, we evaluated whether herbivorous niches are less labile than other dietary guilds and whether herbivorous species’ phenotypes evolve at a slower evolutionary rate than other taxa. We then assess how convergent herbivorous taxa are, using three different suites of morphological characters (dental, jaw, and abdominal morphometrics). Ecologically, herbivory is not a dead end, exhibiting similar observed transition rates as those between carnivores and omnivores. However, we documented widespread convergence in herbivores and that herbivores have slower rates of phenotypic evolution than carnivores. Most instances of convergence are found in herbivorous taxa, specifically in frugivores and folivores. Moreover, instances of “complete” convergence, indicated by positive convergence metrics observed in more than one morphometric dataset, were only found in herbivores. Herbivores do appear to evolve under constrained circumstances, but this has not limited their ecological ability.
Extension of the geographical range of the primary burrowing crayfish Cambarus strigosus Hobbs, 1981 (Decapoda: Astacidea: Cambaridae) in South Carolina
Authors: Barnett Zanethia C , Bland Mickey R , Myers Gregory , Loughman Zachary J
Published: May 2024

Knowledge of the geographical distribution for many primary burrowing crayfishes is often limited to information presented in species descriptions or field notes associated with epigean crayfish surveys. Cambarus strigosusHobbs, 1981, a rare primary burrowing crayfish, was collected as part of a survey of the Sumter National Forest, South Carolina (SC), USA. Prior to this discovery, C. strigosus appeared to be endemic to mid-reaches of the Broad River Drainage in Georgia (GA). We conducted additional field sampling in SC and GA and used mitochondrial DNA (mtDNA) to compare the relative genetic distance between individuals across all populations in an effort to determine the identity of the specimens collected. Genetic data indicated that the crayfish collected in SC was C. strigosus, with one shared haplotype between SC and GA populations. Our genetic results exhibited geographic structuring and indicated that SC populations have a specific haplotype unique to them, providing strong evidence that SC populations are not introduced. Two additional SC records of C. strigosus from 1983 housed in the US National Museum were examined and determined to be C. strigosus. With these records, we hypothesized that like in GA, the distribution of C. strigosus in SC is limited to riparian habitats associated with the Savannah River Drainage. While the range of this species has been extended, it is still limited to small portions of this drainage. Thus, further sampling to determine the true extent of C. strigosus distribution within SC along with conservation efforts are needed to protect this globally rare species.
Development of a sterile insect technique as a control strategy for the Asian citrus psyllid: establishing the effect of sterilizing X-rays on fecundity, fertility, and survival
Authors: Ferrater Jedeliza B , Gómez-Marco Francesc , Yoshimoto Andrew K , Greene Thomas D , Simmons Gregory S , Daugherty Matthew P , Rugman-Jones Paul F
Published: May 2024

The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama (Hemiptera: Psyllidae), is a major pest of citrus due to its role as the vector of the bacterium that causes huanglongbing. In commercial citrus, ACP control currently relies on the application of insecticides, which may not be sustainable long-term, nor practical in urban areas. The sterile insect technique (SIT) is an alternative strategy in which large numbers of pests are reared, sterilized using radiation, and then released into the field to compete with wild individuals for matings, suppressing population growth. As a fundamental step toward the development of SIT for ACP, this study sought to identify the optimum radiation dose required to sterilize ACP without affecting their survival and mating capacity. Virgin adult ACP of both sexes were subjected to doses of X-ray irradiation ranging from 40 to 480 Gy, then paired with a nonirradiated mate and allowed to produce offspring. Fecundity was estimated as the number of eggs laid, and fertility as the proportion of those eggs that hatched. Females were more radio-sensitive than males, exhibiting a major drop in fecundity at even the lowest dose and 100% sterility at 80 Gy. In contrast, a fivefold higher dose (400 Gy) did not achieve complete sterility in males, with around 5% offspring survival. However, F1 progeny of males exposed to 320 Gy or higher were subsequently found to be 100% sterile. This confirmation of inherited sterility suggests that balancing the sterilizing effects of radiation against its mortality-inducing effects may warrant further evaluation.
The Nature, Content and Realisation of the Right to a Clean, Healthy and Sustainable Environment
Authors: Preston Brian J
Published: May 2024

The right to a clean, healthy and sustainable environment is being increasingly adopted internationally and nationally. Nevertheless, there remains ambiguity regarding what the right and the correlative duty to protect the right entail. This article examines the nature, content and realisation of the right. The nature of the right is suggested to be a cluster of rights, including civil and political rights, economic, social and cultural rights and other rights. The content of the right has at least three components: substantive, procedural and intertemporal. Realisation of the right depends on the correlative duty to respect, protect and fulfil the right. The content of the duty includes specific obligations to achieve the inviolable element of the right, the minimum core obligations and the progressive realisation of that right using maximum available resources. In this way, the article suggests a conceptual framework that can guide states in better realising the right.
Acoustic logging array signal denoising using U-net and a case study in a TangGu oil field
Authors: Fu Xin , Gou Yang , Wei Fuqiang
Published: May 2024

This study developed a noise-reduction method for acoustic logging array signals using a deep neural network algorithm in the time-frequency domain. Initially, we derived analytical solutions for the received waveforms when the acoustic logging tool was positioned either at the centre or eccentrically within the borehole. To simulate the received waveforms across various formations, we developed a real-axis integration algorithm. Subsequently, we devised a noise-reduction algorithm workflow based on a convolutional neural network and configured the structure and parameters of the U-net using TensorFlow. To address the scarcity of open datasets, we established both signal and noise datasets. The signal dataset was generated using theoretical simulation encompassing various model parameters, while the noise dataset was collected during tool testing and downhole operations. The trained model demonstrated substantial noise-reduction capabilities during validation. To validate the effectiveness of the algorithm, we applied noise reduction to actual data collected during downhole operations in a TangGu oil field, yielding impressive results across different types of noisy data. Therefore, the U-net-based time-domain noise-reduction algorithm proposed in this paper holds the potential to significantly improve the quality of acoustic logging array signals.
Aggressive interactions among white-tailed deer (Artiodactyla: Cervidae) at 4-poster devices for host-targeted tick control
Authors: Bai Ningzhu , Pesapane Risa , Machtinger Erika T , Li Andrew Y
Published: May 2024

White-tailed deer, Odocoileus virginianus Zimmermann (Artiodactyla: Cervidae), are the primary wildlife host for adult stages of blacklegged ticks (Acari: Ixodidae: Ixodes scapularis Say) and an important host for lone star ticks (Acari: Ixodidae: Amblyomma americanum Linnaeus), both of which are vectors of numerous tick-borne pathogens. The 4-poster passive deer treatment device is a topical, host-targeted method to control free-living tick populations and has been proven to successfully reduce tick abundance in several states. Aggressive behavior of white-tailed deer at concentrated feeding stations is hypothesized to interfere with the effective use of 4-poster devices and deer contact with acaricide applicators. We analyzed images collected by camera traps at 4-poster feeding stations deployed at 3 sites in Maryland and found a negative relationship between some aggressive interactions and contact with applicators. Our results emphasize the need for further investigation into whether deer social dynamics can impact 4-poster efficacy for tick control. This study serves as a reminder that intraspecific interactions are important to consider when using host-targeted acaricide approaches.
Multi-scalar and diasporic integration: Kurdish populations in Europe between state, diaspora and geopolitics
Authors: Adamson Fiona B , Dag Veysi , Craven Catherine R
Published: May 2024

This article challenges both methodological nationalist and decolonial approaches to ‘integration’ by drawing attention to how transnational factors—including trans-state diaspora networks and geopolitical relations between European states and Kurdish ‘homelands’—have direct impacts on the integration trajectories of newly arrived Kurdish displaced populations in Europe. Based on over 200 interviews with Kurdish immigrants, including refugees and asylum seekers across seventeen sites in rural and urban regions in six European countries, our research suggests the need to move beyond local and national-level understandings of integration to one which is also transnational, diasporic, and multi-scalar, taking account of the enduring effects of homeland politics on integration determinants. Such a model of integration does not throw out the concept, but recognizes both the protective and empowering role that local and national policies can play in enabling refugee and diaspora populations to function autonomously in a broader transnational and global context.
The black hole masses of high-redshift QSOs
Authors: King Andrew
Published: May 2024

Observations of high-redshift quasars frequently promote suggestions of large black hole masses, whose presence so early in cosmic time is not easily explicable. I consider the parallel with ultraluminous X-ray sources (ULXs) – now known to be stellar-mass black hole (and neutron star) binaries apparently radiating far above their Eddington luminosities LEdd. The true luminosity in ULXs is actually only of order LEdd, for stellar-mass accretors, but has a very anisotropic (‘beamed’) component, plus a near-isotropic component of similar luminosity but much lower specific intensity. Observers viewing ULXs from within the beam but assuming spherical symmetry deduce a luminosity ≫LEdd. These features appear because the accretors are fed mass at highly super-Eddington rates, most of it expelled in high-speed (v > 0.2c) outflows from the accretion disc. I show that in similarly beamed AGN, emission-line properties would be essentially the same as in unbeamed sources, but standard virial mass indicators unusable because velocity widths are dominated by the outflows, not bound motions about the black holes. In an ensemble of this kind the apparently most luminous systems are always the most distant, but have the lowest black hole masses. Interpreting observations of this ensemble without knowing that they are beamed leads instead to very high black hole mass estimates. The analogy with ULXs therefore suggests that high-redshift quasars might actually have central black hole masses which could have grown from stellar values within the lookback time. I consider how one might test these ideas observationally.
EPOCHS Paper V. The dependence of galaxy formation on galaxy structure at z < 7 from JWST observations
Authors: Conselice Christopher J , Basham Justin T F , Bettaney Daniel O , Ferreira Leonardo , Adams Nathan , Harvey Thomas , Ormerod Katherine , Caruana Joseph , Bluck Asa F L , Li Qiong , Roper William J , Trussler James , Irodotou Dimitrios , Austin Duncan
Published: May 2024

We measure the broad impact of galaxy structure on galaxy formation by examining the ongoing star formation and integrated star formation history as revealed through the stellar masses of galaxies at z < 7 based on JWST CEERS data from the Extended Groth Strip (EGS). Using the morphological catalog of 3965 visually classified JWST galaxies from Ferreira et al. (2023), we investigate the evolution of stars, and when they form, as a function of morphological type as well as galaxies classified as passive and starburst through spectral energy distributions. Although disc galaxies dominate the structures of galaxies at z < 7, we find that these discs are in general either ‘passive’, or on the main sequence of star formation, and do not contain a large population of starburst galaxies. We also find no significant correlation between morphological type and the star formation rate or colours of galaxies at z < 7. In fact, we find that the morphologically classified ‘spheroids’ tend to be blue and are not found to be predominately passive systems at z > 1.5. We also find that the stellar mass function for disc galaxies does not evolve significantly during this time, whereas other galaxy types, such as the peculiar population, evolve dramatically, declining at lower redshifts. This indicates that massive peculiars are more common at higher redshifts. We further find that up to z ∼ 7, the specific star formation rate (sSFR) does not vary with visual morphology, but strongly depends on stellar mass and internal galaxy mass density. This demonstrates that at early epochs galaxy assembly is a mass-driven, rather than a morphologically driven process. Quenching of star formation is therefore a mass-dominated process throughout the universe’s history, likely due to the presence of supermassive black holes.
MARTIANS (MARs2020, TIANwen and So on) would see more potentially hazardous asteroids than Earthlings
Authors: Zhou Yufan Fane , Li Hailiang , Li Zhiyuan , Zhou Liyong
Published: May 2024

Potentially Hazardous Asteroids (PHAs) are a special subset of Near-Earth Objects (NEOs) that can come close to the Earth and are large enough to cause significant damage in the event of an impact. Observations and researches of Earth-PHAs have been underway for decades. Here, we extend the concept of PHAs to Mars and study the feasibility of detecting Mars-PHAs in the near future. We focus on PHAs that truly undergo close approaches with a planet (dubbed CAPHAs) and aim to compare the actual quantities of Earth-CAPHAs and Mars-CAPHAs by conducting numerical simulations incorporating the Yarkovsky effect, based on observed data of the main asteroid belt. The estimated number of Earth-CAPHAs and Mars-CAPHAs are 4675 and 16910, respectively. The occurrence frequency of Mars-CAPHAs is about 52 per year, which is 2.6 times that of Earth-CAPHAs, indicating significant potential for future Mars-based observations. Furthermore, a few Mars-CAPHAs are predicted to be observable even from Earth around the time of next Mars opposition in 2025.
Molecular phylogenetics of the trochid subfamily Umboniinae (Gastropoda: Trochoidea): working towards a new systematic framework
Authors: Williams Suzanne T , Dyal Patricia , Herbert David G
Published: May 2024

We present here the most taxon-rich phylogeny for the trochid subfamily Umboniinae published to date, with representatives from 14 of the 19 known genera, and as a result show that Umboniinae needs comprehensive taxonomic and systematic revision. We identified one clade corresponding to a new genus with four species collected from deeper water than is typical of most umboniine taxa and one new species likely belonging to a second, undescribed genus (all to be described elsewhere). Only four genera, as currently interpreted were recovered, as monophyletic: Umbonium, Lirularia, Monilea and Rossiteria. Zethalia (monotypic for extant taxa), Pseudominolia, Isanda and Parminolia were all represented by a single species (the latter by Gibbula vanwalleghemi; Poppe, Tagaro & Dekker, 2006). Conotalopia, Ethalia, Ethaliella, Ethminolia, Sericominolia and Vanitrochus were all polyphyletic. We formally recognize the following new combinations: Sericominolia glaphyrella (Melvill & Standen, 1895), Sericominolia vitiliginea (Menke, 1843), Vanitrochus ornatus (Sowerby III, 1903) and Parminolia vanwalleghemi (Poppe, Tagaro & Dekker, 2006), although further molecular studies are desirable to confirm these decisions. The first three generic reassignments make Sericominolia and Vanitrochus monophyletic in our tree. We also suggest that Ethaliella cf. rhodomphala (Souverbie, 1875) should be transferred to one of several clades with species previously assigned to Ethminolia, for which an appropriate genus name has not yet been resolved. This decision makes Ethaliella monophyletic. We also identified several cryptic species complexes, including Rossiteria nucleus (Philippi, 1850), the type species of Rossiteria. The phylogeny presented is a first step towards a more resolved systematic framework for Umboniinae and will allow future studies of key morphological innovations.
Factors contributing to the improvement in Japanese Health Assessment Questionnaire after 3 years of treatment with abatacept in biologic-naïve rheumatoid arthritis patients: Interim results of a long-term, observational, multicentre study in Japan (ORIGAMI)
Authors: Misaki Kenta , Tanaka Eiichi , Inoue Eisuke , Tamura Naoto , Hirano Fuminori , Taniguchi Yoshinori , Sato Hiroshi , Naniwa Taio , Oshikawa Hideto , Yoshitama Tamami , Takakubo Yuya , Suzuki Yoko , Himeno Shinkichi , Tsuritani Katsuki , Matsumoto Shigeru , Yamanaka Hisashi , Harigai Masayoshi
Published: May 2024

Objectives

We investigated the long-term effectiveness, safety, and factors affecting Japanese Health Assessment Questionnaire (J-HAQ) improvement during abatacept treatment in Japanese rheumatoid arthritis (RA) patients.

Methods

The Orencia® Registry in Geographically Assembled Multicenter Investigation (ORIGAMI) study is an ongoing observational study of biologic-naïve RA patients with moderate disease activity treated with subcutaneous abatacept (125 mg, once weekly). Patients treated with conventional synthetic disease-modifying antirheumatic drugs (csDMARDs) were extracted from the Institute of Rheumatology, Rheumatoid Arthritis (IORRA) registry as a historical, weighted control group. The primary end point for this interim analysis was the proportion of patients with J-HAQ remission (score ≤0.5) at 3 years.

Results

Among 279 abatacept-treated and 220 csDMARD-treated patients, J-HAQ remission was achieved at 3 years in 40.5% [95% confidence interval (CI) 34.7–46.2%] and 28.9% (95% CI 9.9–47.8%), respectively. Age, RA duration <1 year, baseline J-HAQ score, and Simplified Disease Activity Index remission at 6 months were associated with 3-year J-HAQ remission in the abatacept group. Overall, 24/298 patients (8.1%; safety analysis set) experienced serious adverse drug reactions with an incidence of 5.3 per 100 person-years.

Conclusions

This study confirmed the 3-year effectiveness and safety and revealed potential factors associated with J-HAQ remission in biologic-naïve RA patients treated with abatacept in real-world clinical practice.
The impacts of dietary antioxidants on cardiovascular events in hemodialysis patients: An update on the cellular and molecular mechanisms
Authors: Zununi Vahed Sepideh , Hejazian Seyyedeh Mina , Ardalan Mohammadreza , Anagnostou Fani , Pavon-Djavid Graciela , Barzegari Abolfazl
Published: May 2024

Cardiovascular-related complications (CVCs) are the primary cause of death in patients undergoing hemodialysis (HD), accounting for greater than half of all deaths. Beyond traditional risk factors, chronic inflammation, extreme oxidative stress (OS), and endothelial dysfunction emerge as major contributors to accelerated CVCs in HD patients. Ample evidence shows that HD patients are constantly exposed to excessive OS, due to uremic toxins and pro-oxidant molecules that overwhelm the defense antioxidant mechanisms. The present study highlights the efficiency of natural antioxidant supplementation in managing HD-induced inflammation, OS, and consequently CVCs. Moreover, it discusses the underlying molecular mechanisms by which these antioxidants can decrease mitochondrial and endothelial dysfunction and ameliorate CVCs in HD patients. Given the complex nature of OS and its molecular pathways, the utilization of specific antioxidants as a polypharmacotherapy may be necessary for targeting each dysregulated signaling pathway and reducing the burden of CVCs.
Conjugated linoleic acid metabolite impact in colorectal cancer: a potential microbiome-based precision nutrition approach
Authors: González Adriana , Fullaondo Asier , Rodríguez Javier , Tirnauca Cristina , Odriozola Iñaki , Odriozola Adrian
Published: May 2024

Colorectal cancer (CRC) is the second most deadly and the third most diagnosed cancer in both sexes worldwide. CRC pathogenesis is associated with risk factors such as genetics, alcohol, smoking, sedentariness, obesity, unbalanced diets, and gut microbiota dysbiosis. The gut microbiota is the microbial community living in symbiosis in the intestine, in a dynamic balance vital for health. Increasing evidence underscores the influence of specific gut microbiota bacterial species on CRC incidence and pathogenesis. In this regard, conjugated linoleic acid (CLA) metabolites produced by certain gut microbiota have demonstrated an anticarcinogenic effect in CRC, influencing pathways for inflammation, proliferation, and apoptosis. CLA production occurs naturally in the rumen, and human bioavailability is through the consumption of food derived from ruminants. In recent years, biotechnological attempts to increase CLA bioavailability in humans have been unfruitful. Therefore, the conversion of essential dietary linoleic acid to CLA metabolite by specific intestinal bacteria has become a promising process. This article reviews the evidence regarding CLA and CLA-producing bacteria as therapeutic agents against CRC and investigates the best strategy for increasing the yield and bioavailability of CLA. Given the potential and limitations of the present strategies, a new microbiome-based precision nutrition approach based on endogenous CLA production by human gut bacteria is proposed. A literature search in the PubMed and PubMed Central databases identified 794 papers on human gut bacteria associated with CLA production. Of these, 51 studies exploring association consistency were selected. After excluding 19 papers, due to health concerns or discrepancies between studies, 32 papers were selected for analysis, encompassing data for 38 CLA-producing bacteria, such as Bifidobacterium and Lactobacillus species. The information was analyzed by a bioinformatics food recommendation system patented by our research group, Phymofood (EP22382095). This paper presents a new microbiome-based precision nutrition approach targeting CLA-producing gut bacterial species to maximize the anticarcinogenic effect of CLA in CRC.
Acute Coxiella burnetii Infection: A 10-Year Clinical Experience at a Tertiary Care Center in the United States
Authors: El Zein Said , Challener Doug W , Ranganath Nischal , Khodadadi Ryan B , Theel Elitza S , Abu Saleh Omar M
Published: May 2024

Background

Identifying and treating patients with acute Q fever who are at an increased risk of progressing to persistent disease is crucial for preventing future complications. In this study, we share our decade-long clinical experience with acute Q fever, highlighting the challenges that clinicians encounter from making an initial diagnosis and performing risk stratification to determining the appropriate prophylaxis regimen and duration.

Methods

We retrieved records of adult Mayo Clinic patients (≥18 years) with positive Coxiella burnetii serology results between 1 January 2012 and 31 March 2022. Patients with Q fever anti–phase II immunoglobulin G ≥1:256 by indirect immunofluorescence were further analyzed.

Results

Thirty-one patients were included. Their median age was 58 years (IQR, 50–64), and the majority were men (84%). Acute hepatitis (29%), flu-like illness (25.8%), and pneumonia (16%) were the most common presentations. Thirteen patients (42%) received antibiotic prophylaxis to prevent disease progression, with significant variation in the indications and duration across physicians. The combination of doxycycline and hydroxychloroquine was the preferred regimen. Prophylaxis was administered for a median 333 days (IQR, 168–414). Four patients (13%) progressed to Q fever native valve infective endocarditis, with elevated anticardiolipin immunoglobulin G levels being the sole risk factor in 2 cases. The small sample size precluded drawing conclusions on the impact of prophylaxis in preventing disease progression.

Conclusions

Management of acute Q fever is complicated by the lack of comprehensive clinical guidelines leading to varied clinical practices. There is a critical need for randomized trials to establish robust evidence-based protocols for management.
The Complex Latent Structure of Attenuated Psychotic Symptoms: Hierarchical and Bifactor Models of SIPS Symptoms Replicated in Two Large Samples at Clinical High Risk for Psychosis
Authors: Cowan Henry R , Williams Trevor F , Mittal Vijay A , Addington Jean , Bearden Carrie E , Cadenhead Kristin S , Cannon Tyrone D , Cornblatt Barbara A , Keshevan Matcheri , Perkins Diana O , Mathalon Daniel H , Stone William , Woods Scott W , Walker Elaine F
Published: May 2024

Background and Hypothesis

The Structured Interview for Psychosis-Risk Syndromes (SIPS) and other assessments of psychosis risk define clinical high risk for psychosis (CHR) by the presence of attenuated psychotic symptoms. Despite extensive research on attenuated psychotic symptoms, substantial questions remain about their internal psychometric structure and relationships to comorbid non-psychotic symptoms.

Study Design

Hierarchical and bifactor models were developed for the SIPS in a large CHR sample (NAPLS-3, N = 787) and confirmed through preregistered replication in an independent sample (NAPLS-2, N = 1043). Criterion validity was tested through relationships with CHR status, comorbid symptoms/diagnoses, functional impairment, demographics, neurocognition, and conversion to psychotic disorders.

Study Results

Most variance in SIPS items (75%–77%) was attributable to a general factor. Hierarchical and bifactor models included a general factor and five specific/lower-order factors (positive symptoms, eccentricity, avolition, lack of emotion, and deteriorated thought process). CHR participants were elevated on the general factor and the positive symptoms factor. The general factor was associated with depressive symptoms; functional impairment; and mood, anxiety, and schizotypal personality diagnoses. The general factor was the best predictor of psychotic disorders (d ≥ 0.50). Positive symptoms and eccentricity had specific effects on conversion outcomes. The deteriorated thought process was least meaningful/replicable.

Conclusions

Attenuated psychotic symptoms, measured by the SIPS, have a complex hierarchical structure with a strong general factor. The general factor relates to internalizing symptoms and functional impairment, emphasizing the roles of general psychopathological distress/impairment in psychosis risk. Shared symptom variance complicates the interpretation of raw symptom scores. Broad transdiagnostic assessment is warranted to model psychosis risk accurately.
A Developmental Perspective on Early and Current Motor Abnormalities and Psychotic-Like Symptoms
Authors: Fattal Jessica , Giljen Maksim , Vargas Teresa , Damme Katherine S F , Calkins Monica E , Pinkham Amy E , Mittal Vijay A
Published: May 2024

Background and hypothesis

Psychotic-like experiences (PLEs) are prevalent in the general population and, because they represent a lower end of the psychosis vulnerability spectrum, may be useful in informing mechanistic understanding. Although it is well-understood that motor signs characterize formal psychotic disorders, the developmental trajectory of these features and their relationships with PLEs are less well-understood.

Study Design

Data from 7559 adolescents and young adults (age 11–21) in the Philadelphia Neurodevelopmental Cohort were used to investigate whether early-life milestone-attainment delays relate to current adolescent sensorimotor functioning and positive and negative PLEs. Current sensorimotor functioning was assessed using the Computerized Finger Tapping task (assessing motor slowing) and Mouse Practice task (assessing sensorimotor planning).

Study Results

Early developmental abnormalities were related to current adolescent-aged motor slowing (t(7415.3) = −7.74, corrected-P < .001) and impaired sensorimotor planning (t(7502.5) = 5.57, corrected-P < .001). There was a significant interaction between developmental delays and current sensorimotor functioning on positive and negative PLEs (t = 1.67–4.51), such that individuals with early developmental delays had a stronger positive relationship between sensorimotor dysfunction and PLEs. Importantly, interaction models were significantly better at explaining current PLEs than those treating early and current sensorimotor dysfunction independently (χ2 = 4.89–20.34).

Conclusions

These findings suggest a relationship between early developmental delays and current sensorimotor functioning in psychosis proneness and inform an understanding of heterotypic continuity as well as a neurodevelopmental perspective of motor circuits. Furthermore, results indicate that motor signs are a clear factor in the psychosis continuum, suggesting that they may represent a core feature of psychosis vulnerability.