bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and characterization of CsSRP43, a major gene controlling leaf yellowing in cucumber
Authors: Zhang Tingting , Dong Xiangyu , Yuan Xin , Hong Yuanyuan , Zhang Lingling , Zhang Xuan , Chen Shuxia
Published: December 2022

Mutants are crucial to extending our understanding of genes and their functions in higher plants. In this study a spontaneous cucumber mutant, yf, showed yellow color leaves, had significant decreases in related physiological indexes of photosynthesis characteristics, and had more abnormal chloroplasts and thylakoids. Inheritance analysis indicated that the yellow color of the leaf was controlled by a recessive nuclear locus, yf. A candidate gene, CsSRP43, encoding a chloroplast signal recognition particle 43 protein, was identified through map-based cloning and whole-genome sequence analysis. Alignment of the CsSRP43 gene homologs between both parental lines revealed a 7-kb deletion mutation including the promoter region and the coding sequence in the yf mutant. In order to determine if the CsSRP43 gene was involved in the formation of leaf color, the CRISPR/Cas9-mediate system was used to modify CsSRP43 in the 9930 background; two independent transgenic lines, srp43-1 and srp43-2, were generated, and they showed yellow leaves with abnormal chloroplasts and thylakoids. Transcriptomic analysis revealed that differentially expressed genes associated with the photosynthesis-related pathway were highly enriched between srp43-1 and wild type, most of which were significantly downregulated in line srp43-1. Furthermore, yeast two-hybrid and biomolecular fluorescence complementation assays were used to confirm that CsSRP43 directly interacted with LHCP and cpSRP54 proteins. A model was established to explain the molecular mechanisms by which CsSRP43 participates in the leaf color and photosynthesis pathway, and it provides a valuable basis for understanding the molecular and genetic mechanisms of leaf color in cucumber.
Novel insights into reproductive ageing and menopause from genomics
Authors: Das Arunika , Destouni Aspasia
Published: December 2022

The post-reproductive phase or menopause in females is triggered by a physiological timer that depends on a threshold of follicle number in the ovary. Curiously, reproductive senescence appears to be decoupled from chronological age and is instead thought to be a function of physiological ageing. Ovarian ageing is associated with a decrease in oocyte developmental competence, attributed to a concomitant increase in meiotic errors. Although many biological hallmarks of general ageing are well characterized, the precise mechanisms underlying the programmed ageing of the female reproductive system remain elusive. In particular, the molecular pathways linking the external menopause trigger to the internal oocyte chromosome segregation machinery that controls fertility outcomes is unclear. However, recent large scale genomics studies have begun to provide insights into this process. Next-generation sequencing integrated with systems biology offers the advantage of sampling large datasets to uncover molecular pathways associated with a phenotype such as ageing. In this mini-review, we discuss findings from these studies that are crucial for advancing female reproductive senescence research. Targets identified in these studies can inform future animal models for menopause. We present three potential hypotheses for how external pathways governing ovarian ageing can influence meiotic chromosome segregation, with evidence from both animal models and molecular targets revealed from genomics studies. Although still in incipient stages, we discuss the potential of genomics studies combined with epigenetic age acceleration models for providing a predictive toolkit of biomarkers controlling menopause onset in women. We also speculate on future research directions to investigate extending female reproductive lifespan, such as comparative genomics in model systems that lack menopause. Novel genomics insights from such organisms are predicted to provide clues to preserving female fertility.
Effectiveness and Duration of Protection of a Fourth Dose of Coronavirus Disease 2019 Messenger RNA Vaccine Among Long-term Care Residents in Ontario, Canada
Authors: Grewal Ramandip , Nguyen Lena , Buchan Sarah A , Wilson Sarah E , Costa Andrew P , Kwong Jeffrey C
Published: December 2022

We estimated the effectiveness of a fourth dose of messenger RNA coronavirus disease 2019 vaccine against Omicron infections and severe outcomes over time among long-term care residents in Ontario, Canada. Fourth doses provide additional protection against Omicron-related outcomes, but the protection wanes over time, with more waning seen against infection than severe outcomes.
Proteomic Analysis of Hepatic Fibrosis in Human Immunodeficiency Virus–Associated Nonalcoholic Fatty Liver Disease Demonstrates Up-regulation of Immune Response and Tissue Repair Pathways
Authors: Fourman Lindsay T , Stanley Takara L , Ockene Mollie W , McClure Colin M , Toribio Mabel , Corey Kathleen E , Chung Raymond T , Torriani Martin , Kleiner David E , Hadigan Colleen M , Grinspoon Steven K
Published: December 2022

Background

Human immunodeficiency virus (HIV)–associated nonalcoholic fatty liver disease (NAFLD) is characterized by a high prevalence of hepatic fibrosis as a strong clinical predictor of all-cause and liver-specific mortality risk.

Methods

We leveraged data from an earlier clinical trial to define the circulating proteomic signature of hepatic fibrosis in HIV-associated NAFLD. A total of 183 plasma proteins within 2 high-multiplex panels were quantified at baseline and at 12 months (Olink Cardiovascular III; Immuno-Oncology).

Results

Twenty proteins were up-regulated at baseline among participants with fibrosis stages 2–3 versus 0–1. Proteins most differentially expressed included matrix metalloproteinase 2 (P < .001), insulin-like growth factor–binding protein 7 (P = .001), and collagen α1(I) chain (P = .001). Proteins were enriched within pathways including response to tumor necrosis factor and aminopeptidase activity. Key proteins correlated directly with visceral adiposity and glucose intolerance and inversely with CD4+ T-cell count. Within the placebo-treated arm, 11 proteins differentially increased among individuals with hepatic fibrosis progression over a 12-month period (P < .05).

Conclusions

Among individuals with HIV-associated NAFLD, hepatic fibrosis was associated with a distinct proteomic signature involving up-regulation of tissue repair and immune response pathways. These findings enhance our understanding of potential mechanisms and biomarkers of hepatic fibrosis in HIV.
Frissons in Dance
Authors: Nanay Bence
Published: December 2022

Musical frissons (or chills) have been at the forefront of both philosophical and psychological research on audience responses to music. The aim of this article is to argue that frissons also play an important role in the experience of dance performances. Following Jerrold Levinson’s distinction between sound-quality frissons and sound-structure frissons, the article zooms in on the concept of conflict-induced frissons, which feature prominently in a variety of art forms besides music, from film to literature, and it is of crucial importance for understanding the audience reaction to some dance performances. A case study of Pina Bausch’s choreographies is given to illustrate this point.
Mental Imagery and Poetry
Authors: Liu Michelle
Published: December 2022

Poetry evokes mental imagery in its readers. But how is mental imagery precisely related to poetry? This article provides a systematic treatment. It clarifies two roles of mental imagery in relation to poetry—as an effect generated by poetry and as an efficient means for understanding and appreciating poetry. The article also relates mental imagery to the discussion on the ‘heresy of paraphrase’. It argues against the orthodox view that the imagistic effects of poetry cannot be captured by prosaic paraphrase, but points to features of poetry that can shape aspects of mental imagery that are liable to be lost in paraphrase.
Characterizing variability of electronic health record-driven phenotype definitions
Authors: Brandt Pascal S , Kho Abel , Luo Yuan , Pacheco Jennifer A , Walunas Theresa L , Hakonarson Hakon , Hripcsak George , Liu Cong , Shang Ning , Weng Chunhua , Walton Nephi , Carrell David S , Crane Paul K , Larson Eric B , Chute Christopher G , Kullo Iftikhar J , Carroll Robert , Denny Josh , Ramirez Andrea , Wei Wei-Qi , Pathak Jyoti , Wiley Laura K , Richesson Rachel , Starren Justin B , Rasmussen Luke V
Published: December 2022

Objective

The aim of this study was to analyze a publicly available sample of rule-based phenotype definitions to characterize and evaluate the variability of logical constructs used.

Materials and Methods

A sample of 33 preexisting phenotype definitions used in research that are represented using Fast Healthcare Interoperability Resources and Clinical Quality Language (CQL) was analyzed using automated analysis of the computable representation of the CQL libraries.

Results

Most of the phenotype definitions include narrative descriptions and flowcharts, while few provide pseudocode or executable artifacts. Most use 4 or fewer medical terminologies. The number of codes used ranges from 5 to 6865, and value sets from 1 to 19. We found that the most common expressions used were literal, data, and logical expressions. Aggregate and arithmetic expressions are the least common. Expression depth ranges from 4 to 27.

Discussion

Despite the range of conditions, we found that all of the phenotype definitions consisted of logical criteria, representing both clinical and operational logic, and tabular data, consisting of codes from standard terminologies and keywords for natural language processing. The total number and variety of expressions are low, which may be to simplify implementation, or authors may limit complexity due to data availability constraints.

Conclusions

The phenotype definitions analyzed show significant variation in specific logical, arithmetic, and other operators but are all composed of the same high-level components, namely tabular data and logical expressions. A standard representation for phenotype definitions should support these formats and be modular to support localization and shared logic.
Phosphorylation of PBX2, a novel downstream target of mTORC1, is determined by GSK3 and PP1
Authors: Wada Reona , Fujinuma Shun , Nakatsumi Hirokazu , Matsumoto Masaki , Nakayama Keiichi I
Published: December 2022

Mechanistic target of rapamycin complex 1 (mTORC1) is a serine–threonine kinase that is activated by extracellular signals, such as nutrients and growth factors. It plays a key role in the control of various biological processes, such as protein synthesis and energy metabolism by mediating or regulating the phosphorylation of multiple target molecules, some of which remain to be identified. We have here reanalysed a large-scale phosphoproteomics data set for mTORC1 target molecules and identified pre–B cell leukemia transcription factor 2 (PBX2) as such a novel target that is dephosphorylated downstream of mTORC1. We confirmed that PBX2, but not other members of the PBX family, is dephosphorylated in an mTORC1 activity–dependent manner. Furthermore, pharmacological and gene knockdown experiments revealed that glycogen synthase kinase 3 (GSK3) and protein phosphatase 1 (PP1) are responsible for the phosphorylation and dephosphorylation of PBX2, respectively. Our results thus suggest that the balance between the antagonistic actions of GSK3 and PP1 determines the phosphorylation status of PBX2 and its regulation by mTORC1.
Optimization of workpiece processing based on the orthogonal double-chain differential evolution algorithm
Authors: Huang Xin , Lv Danju , Chen Xu , Xi Rui , Zi Jiali , Gao Mingyuan , Zhang Yan
Published: December 2022

An orthogonal double-chain differential evolution (ODCDE) algorithm is proposed to optimize the problem’s parameters for workpiece processing. ODCDE improves the differential evolution structure by changing the parcels into the orthogonal chains in the adaptive search range of the solution, which can avoid falling into local optimum, improve the solution precision, and speed up the convergence speed. The superiority of the proposed algorithm was proved by the function performance test on three sets of bench functions, which reached the first place in the set of 23 functions with other 11 optimal algorithms, ranked the second in the CEC2017 functions with other more recent 5 algorithms, and ranked the seventh in the CEC2011 functions with other 11 algorithms including AMO, SFS, and GSK algorithms. Finally, two kinds of optimal workpiece processing, the tubular column design and the multipass milling, are studied, and the results show that our algorithm performs better than other methods.
The efficacy of a machine learning algorithm for assessing tumour components as a prognostic marker of surgically resected stage IA lung adenocarcinoma
Authors: Terada Yukihiro , Isaka Mitsuhiro , Kawata Takuya , Mizuno Kiyomichi , Muramatsu Koji , Katsumata Shinya , Konno Hayato , Nagata Toshiyuki , Mizuno Tetsuya , Serizawa Masakuni , Ono Akira , Sugino Takashi , Shimizu Kimihiro , Ohde Yasuhisa
Published: December 2022

Background

The importance of the stromal components in tumour progression has been discussed widely, but their prognostic role in small size tumours with lepidic components is not fully understood. Applying digital tissue image analysis to whole-slide imaging may enhance the accuracy and reproducibility of pathological assessment. This study aimed to evaluate the prognostic value of tumour components of lung adenocarcinoma by measuring the dimensions of the tumour consisting elements separately, using a machine learning algorithm.

Methods

Between September 2002 and December 2016, 317 patients with surgically resected, pathological stage IA adenocarcinoma with lepidic components were analysed. We assessed the whole tumour area, including the lepidic components, and measured the epithelium, collagen, elastin areas and alveolar air space. We analysed the prognostic impact of each tumour component.

Results

The dimensions of the epithelium and collagen areas were independent significant risk factors for recurrence-free survival (hazard ratio, 8.38; 95% confidence interval, 1.14–61.88; P = 0.037, and hazard ratio, 2.58; 95% confidence interval, 1.14–5.83; P = 0.022, respectively). According to the subgroup analysis when combining the epithelium and collagen areas as risk factors, patients with tumours consisting of both large epithelium and collagen areas showed significantly poor prognoses (P = 0.002).

Conclusions

We assessed tumour components using a machine learning algorithm to stratify the post-operative prognosis of surgically resected stage IA adenocarcinomas. This method might guide the selection of patients with a high risk of recurrence.
Role of perioperative chemotherapy and radiotherapy for localized high-grade malignant peripheral nerve sheath tumor at the extremities and trunk wall: a population-based cohort study
Authors: Kobayashi Hiroshi , Zhang Liuzhe , Okajima Koichi , Hirai Toshihide , Tsuda Yusuke , Ikegami Masachika , Kawai Akira , Tanaka Sakae
Published: December 2022

Background

Primary tumor resection is the mainstay of treatment for malignant peripheral nerve sheath tumors. However, the efficacy of perioperative chemotherapy and radiotherapy for malignant peripheral nerve sheath tumors has not been elucidated.

Methods

This retrospective analysis based on a Japanese registry included patients with localized malignant peripheral nerve sheath tumors arising at the extremities and trunk wall. Disease-specific overall survival and local recurrence-free survival were estimated using the Kaplan–Meier method. A Cox regression model was used to identify prognostic factors. Characteristics of groups with or without chemotherapy were adjusted using propensity score matching.

Results

In total, 291 patients were included. The 5-year disease-specific overall survival rate was 70.6%. Multivariate analysis of disease-specific overall survival revealed that deep-seated tumors were a poor prognostic factor, but perioperative chemotherapy was not associated with disease-specific overall survival (hazard ratio, 0.81; 95% confidence interval, 0.45–1.43, P = 0.46). Local recurrence was observed in 55 patients (19.0%), and surgical margins (R1 and R2) were significant risk factors. Overall, perioperative chemotherapy did not prolong disease-specific overall survival (5-year disease-specific overall survival: 74.1% vs. 69.3%, P = 0.75) and had limited efficacy in the group with tumor size ≥ 5 cm, although the difference was not statistically significant (5-year disease-specific overall survival: 77.2% vs. 68.6%, respectively, P = 0.13). After adjustment by propensity score matching, perioperative chemotherapy significantly prolonged disease-specific overall survival (5-year disease-specific overall survival: 74.9% vs. 57.1%, P = 0.03), but this effect was not observed in local recurrence-free survival. In all patients, perioperative radiotherapy did not correlate with local recurrence-free survival (hazard ratio, 1.43; 95% confidence interval 0.78–2.62, P = 0.25).

Conclusions

Perioperative chemotherapy had limited efficacy for disease-specific overall survival in patients with localized malignant peripheral nerve sheath tumors.
Phlebotominae Fauna (Diptera: Psychodidae) and the Spatial Distribution of Species in Sergipe, Brazil
Authors: Andrade David Campos , Lima Antônio Fernando Viana de Assis , Jeraldo Verónica de Lourdes Sierpe , de Melo Cláudia Moura , Pinto Mara Cristina , Madi Rubens Riscala
Published: December 2022

Some sand fly species are the vectors responsible for the transmission of Leishmania spp. (Kinetoplastida: Trypanosomatidae), the etiological agent of leishmaniasis, and in the state of Sergipe, the two main forms of the disease (visceral and cutaneous) are recorded. Few works show information about the species that form the Phlebotominae fauna in Sergipe. This study aimed to update and determine how they are distributed throughout the state. The study used data from surveys about phlebotomines in Sergipe, from the Program of Surveillance and Control of Visceral Leishmaniasis, carried out by the Central Public Health Laboratory of Sergipe, from 2008 to 2018, along with review and original data from 2022. The commentary on this information was developed with focus on the species that can be vectors for the disease. Sergipe has, up to now, 27 registered species of phlebotomines from 12 genera, 15 of them are of sanitary relevance. Twenty two of these species are in the mesoregion East, 19 in the Agreste, and 11 in the Sertão of Sergipe. The species with the greatest distribution was Evandromyia lenti (Mangabeira, 1938), present in 74.6% of the municipalities of Sergipe, followed by Lutzomyia longipalpis (Lutz & Neiva, 1912), the main vector of the etiological agent of visceral leishmaniasis in Brazil, present in 68% of the municipalities studied. This study expands the number and distribution of species recorded in the state. This information can contribute to disease containment plans and support health education actions aimed at the control of leishmaniasis in Sergipe.
Racial survival disparities in head and neck cancer clinical trials
Authors: Liu Jeffrey C , Egleston Brian L , Blackman Elizabeth , Ragin Camille
Published: December 2022

Background

Survival disparities between Black and White head and neck cancer patients are well documented, with access to care and socioeconomic status as major contributors. We set out to assess the role of self-reported race in head and neck cancer by evaluating treatment outcomes of patients enrolled in clinical trials, where access to care and socioeconomic status confounders are minimized.

Methods

Clinical trial data from the Radiation Therapy Oncology Group studies were obtained. Studies were included if they were therapeutic trials that employed survival as an endpoint. Studies that did not report survival as an endpoint were excluded; 7 Radiation Therapy Oncology Group Studies were included for study. For each Black patient enrolled in a clinical trial, a study arm–matched White patient was used as a control.

Results

A total of 468 Black participants were identified and matched with 468 White study arm–specific controls. White participants had better outcomes than Black participants in 60% of matched pairs (P < .001). Black participants were consistently more likely to have worse outcomes. When outcomes were measured by progression-free survival or disease-free survival, the failure rate was statistically significantly higher in Black participants (hazard ratio [HR] = 1.50, P < .001). Failure was largely due to locoregional failure, and Black participants were at higher risk (subdistribution HR =1.51, P = .002). The development of distant metastasis within the paired cohorts was not statistically significantly different.

Conclusion

In this study of clinical trial participants using self-reported race, Black participants consistently had worse outcomes in comparison to study arm–specific White controls. Further study is needed to confirm these findings and to explore causes underlying this disparity.
Impact of Penicillin Allergy Labels on Children Treated for Outpatient Respiratory Infections
Authors: Joerger Torsten , Taylor Margaret G , Li Yun , Palazzi Debra L , Gerber Jeffrey S
Published: December 2022

Background

Penicillin allergy is the most common antibiotic allergy, yet most children labeled as allergic tolerate penicillin. The impact of inaccurate penicillin allergy labels (PALs) on pediatric outpatients is unknown. The objective of this study was to compare outcomes between children with and without a PAL after treatment for outpatient respiratory tract infections (RTI).

Methods

A retrospective, longitudinal birth cohort study was performed in children who received care in 90 pediatric primary care practices in Philadelphia and Houston metropolitan areas. Prescribing and clinical outcomes of children with a PAL at the time of an RTI were compared to non-allergic children, adjusting for potential confounders.

Results

Antibiotics were prescribed for 663,473 non-recurrent RTIs among 200,977 children. Children with a PAL (5% of cohort) were more likely than non-allergic children to receive broad-spectrum antibiotics (adjusted relative risk (aRR) 3.24, 95% CI 3.22-3.26) and second-line antibiotics (aRR 4.87, 95% CI 4.83, 4.89). Compared to non-allergic children receiving first-line antibiotics, children with a PAL were more likely to return with adverse drug events (aRR 1.28, 95% CI 1.18–1.39). There was no difference in treatment failure between groups (aRR 0.95, 95% CI 0.90–1.00).

Conclusions

PALs lead to higher rates of broad-spectrum and second-line antibiotic prescribing in children treated for RTIs in primary care and contribute to unnecessary healthcare utilization through increased adverse events. Given the frequency of PALs, efforts to prevent inappropriate penicillin allergy labeling and promote de-labeling of existing inaccurate allergy labels may improve care of children treated for common bacterial infections.
Complementary water and nutrient utilization of perianth structural units help maintain long floral lifespan inDendrobium
Authors: Li Jia-Wei , Zhou Yi , Zhang Zi-Bin , Cui Xue-Qiang , Li Hong-Yan , Ou Mei-Jing , Cao Kun-Fang , Zhang Shi-Bao
Published: December 2022

Most orchids have high ornamental value with long-lived flowers. However, the mechanisms by which orchids maintain floral longevity are poorly understood. Here, we hypothesized that floral longevity in Dendrobium is maintained by high resource investment and complementary water and nutrient utilization in different structural units of the perianth. To test this hypothesis, we determined which water- and nutrient-related traits are correlated with flower longevity in 23 Dendrobium species or cultivars, and examined variations of the related traits during flower development of one long-lived cultivar. We found that floral longevity was correlated with dry mass per unit area of perianths and total flower biomass, which indicates that maintaining floral longevity requires increased resource investment. During development of long-lived flowers, labella showed a high capacity for water storage and nutrient reutilization, which could partly remedy high water demand and biomass investment. Sepals and petals, in contrast, had stronger desiccation avoidance and higher metabolic activity with lower biomass investment. These findings indicate that Dendrobium flowers maintain longevity by complementary water and nutrient utilization strategies in the sepals, petals and labella, with labella consuming more water and nutrients to extend flower display, and sepals and petals using a more conservative strategy.
Characterization of lodging variation of weedy rice
Authors: Wang Haoquan , Lu Huan , Yang Zixuan , Zhang Zixu , Li Mengshuo , Zhang Zheng , Dai Weimin , Song Xiaoling , Olsen Kenneth M , Qiang Sheng
Published: December 2022

Weedy rice (Oryza spp.), one of the most notorious weeds of cultivated rice, evades eradication through stem lodging and seed shattering. Many studies have focused on seed shattering, whereas variations in lodging have received less attention and the underlying mechanisms that cause the differences in lodging between weedy and cultivated rice have not been studied in detail. Here, we compared lodging variation among diverse Chinese weedy rice strains and between weedy rice and co-occurring cultivated rice. The chemical composition of basal stems was determined, and transcriptome and methylome sequencing were used to assess the variation in expression of lodging-related genes. The results showed that the degree of lodging varied between indica-derived weed strains with high lodging levels, which occurred predominantly in southern China, and japonica-derived strains with lower lodging levels, which were found primarily in the north. The more lodging-prone indica weedy rice had a smaller bending stress and lower lignin content than non-lodging accessions. In comparison to co-occurring cultivated rice, there was a lower ratio of cellulose to lignin content in the lodging-prone weedy rice. Variation in DNA methylation of lignin synthesis-related OsSWN1, OsMYBX9, OsPAL1, and Os4CL3 mediated the differences in their expression levels and affected the ratio of cellulose to lignin content. Taken together, our results show that DNA methylation in lignin-related genes regulates variations in stem strength and lodging in weedy rice, and between weed strains and co-occurring cultivated rice.
Rfd1, a restorer to theAegilops juvenaliscytoplasm, functions in fertility restoration of wheat cytoplasmic male sterility
Authors: Niu Fuqiang , Bu Yaning , Yang Xuetong , Wu Yongfeng , He Mengting , Zhang Lingli , Song Xiyue
Published: December 2022

Cytoplasmic male sterility (CMS) is a crucial means for the utilization of heterosis, which is of great significance for improving the yield and quality of hybrids. Currently, fertility restoration has been extensively investigated in crops, but fertility restoration of CMS wheat with Aegilops juvenalis cytoplasm is poorly understood. Here, a backcross population BC1F1 derived from a cross between the male-sterile line Ju706A, its maintainer line 706B, and restorer line LK783 was used to map the Rfd1 locus by bulked segregant analysis and wheat 660K single nucleotide polymorphism genotyping. Ju706A displayed complete male sterility, and its fertility can be restored by LK783 with a pair of dominant genes Rfd1Rfd1. The locus was located to a 2.4 Mb region on chromosome 1BS by markers AX-174254104 and AX-111201011. Combined with transcriptomic analysis and quantitative real-time PCR assay, TraesCS1B02G197400LC, the most likely candidate gene for Rfd1, was found to encode a pectinesterase that was localized in the cell wall, and was highly expressed in fertile anthers. The silencing of Rfd1 resulted in decreased fertility, and heterogeneous expression of Rfd1 promoted pollen germination and affected vegetative growth. This implies that Rfd1 is required for anther or pollen development and male fertility in CMS wheat with Ae. juvenalis cytoplasm. Furthermore, a 7 bp deletion in Ju706A was employed to develop a specific marker, Xnwafu1, for molecular marker-assisted selection of restorers. This study provides a new understanding for exploring the fertility restoration mechanism of CMS.
Perforating Calcinosis Cutis as a Complication of Intraosseous Fluid Infusion in the Setting of a Near-Drowning Event
Authors: Marinelli Lisa M , Arballo Olivia M , Guerrero Giselle , Wohltmann Wendi E
Published: December 2022

Iatrogenic calcinosis cutis represents a subset of calcinosis cutis resulting secondary to treatments or procedures. We present the first report of calcinosis cutis resulting from the intraosseous infusion and one of a few cases with associated transepidermal elimination. A previously healthy 2-year-old female presented with a new-onset unilateral shin rash 1 week following hospitalization for a near-drowning event. A dermatologic exam revealed multiple small, tender, firm, chalky-white papules with surrounding erythema, in addition to two erythematous macules superior and medial to the papular lesions, corresponding to prior intraosseous access sites. The rash persisted despite trials of topical mupirocin and acyclovir cream, prompting a referral to a dermatologist. An excisional biopsy was performed, revealing circumscribed dermal deposits of acellular basophilic material connected to the overlying epidermis through an invaginated keratin plug. A von Kossa silver stain highlighted the deposits, confirming the diagnosis of perforating calcinosis cutis. The lesions did not recur following the excisional biopsy. Iatrogenic calcinosis cutis may be seen as a complication of the infusion of calcium-containing fluids via intraosseous access, in addition to the more commonly observed peripheral intravenous access. Awareness of this disorder is important in order to distinguish it from an infectious mimic and guide the selection of therapy.
FIRE-3: updated stellar evolution models, yields, and microphysics and fitting functions for applications in galaxy simulations
Authors: Hopkins Philip F , Wetzel Andrew , Wheeler Coral , Sanderson Robyn , Grudić Michael Y , Sameie Omid , Boylan-Kolchin Michael , Orr Matthew , Ma Xiangcheng , Faucher-Giguère Claude-André , Kereš Dušan , Quataert Eliot , Su Kung-Yi , Moreno Jorge , Feldmann Robert , Bullock James S , Loebman Sarah R , Anglés-Alcázar Daniel , Stern Jonathan , Necib Lina , Choban Caleb R , Hayward Christopher C
Published: December 2022

Increasingly, uncertainties in predictions from galaxy formation simulations (at sub-Milky Way masses) are dominated by uncertainties in stellar evolution inputs. In this paper, we present the full set of updates from the Feedback In Realistic Environment (FIRE)-2 version of the FIRE project code, to the next version, FIRE-3. While the transition from FIRE-1 to FIRE-2 focused on improving numerical methods, here we update the stellar evolution tracks used to determine stellar feedback inputs, e.g. stellar mass-loss (O/B and AGB), spectra (luminosities and ionization rates), and supernova rates (core-collapse and Ia), as well as detailed mass-dependent yields. We also update the low-temperature cooling and chemistry, to enable improved accuracy at $T \lesssim 10^{4}\,$K and densities $n\gg 1\, {\rm cm^{-3}}$, and the meta-galactic ionizing background. All of these synthesize newer empirical constraints on these quantities and updated stellar evolution and yield models from a number of groups, addressing different aspects of stellar evolution. To make the updated models as accessible as possible, we provide fitting functions for all of the relevant updated tracks, yields, etc, in a form specifically designed so they can be directly ‘plugged in’ to existing galaxy formation simulations. We also summarize the default FIRE-3 implementations of ‘optional’ physics, including spectrally resolved cosmic rays and supermassive black hole growth and feedback.
The cosmic shallows – I. Interaction of CMB photons in extended galaxy haloes
Authors: Luparello Heliana E , Boero Ezequiel F , Lares Marcelo , Sánchez Ariel G , Lambas Diego Garcia
Published: December 2022

We report and analyse a serendipitous finding of foregrounds in the cosmic microwave background (CMB) radiation associated with extended galactic haloes. Using the cross-correlation of Planck and Wilkinson Microwave Anisotropy Probe maps and the 2MRS galaxy catalogue, we find that the mean temperature radial profiles around nearby galaxies at $cz\le 4500~\rm {km~s^{-1}}$ show a statistically significant systematic decrease of $\sim 15~\mu \rm {K}$ extending up to several galaxy radii. This deficit in the temperature strongly depends on the galaxy morphological type at scales within several tens of times the galaxy size, becoming nearly independent of galaxy morphology at larger scales. The effect is significantly stronger for the more extended galaxies, with galaxy clustering having a large impact on the results. Our findings indicate the presence of statistically relevant foregrounds in the CMB maps that should be considered in detailed cosmological studies. Besides, we argue that these can be used to explore the intergalactic medium surrounding bright late-type galaxies and allow for diverse astrophysical analyses.
Flares in the changing look AGN Mrk 590 – I. The UV response to X-ray outbursts suggests a more complex reprocessing geometry than a standard disc
Authors: Lawther D , Vestergaard M , Raimundo S , Koay J Y , Peterson B M , Fan X , Grupe D , Mathur S
Published: December 2022

Mrk 590 is a known changing-look active galactic nuclei (AGNs) which almost turned off in 2012, and then in 2017 partially re-ignited into a repeat flaring state, unusual for an AGN. Our Swift observations since 2013 allow us to characterize the accretion-generated emission and its reprocessing in the central engine of a changing-look AGN. The X-ray and UV variability amplitudes are higher than those typically observed in ‘steady-state’ AGN at similar moderate accretion rates; instead, the variability is similar to that of highly accreting AGN. The unusually strong X-ray to UV correlation suggests that the UV-emitting region is directly illuminated by X-ray outbursts. We find evidence that the X-rays are reprocessed by two UV components, with the dominant one at ∼3 d and a faint additional reprocessor at near-zero lag. However, we exclude a significant contribution from diffuse broad line region continuum, known to contribute for bonafide AGN. A near-zero lag is expected for a standard ‘lamp-post’ disc reprocessing model with a driving continuum source near the black hole. That the overall UV response is dominated by the ∼3-d lagged component suggests a complicated reprocessing geometry, with most of the UV continuum not produced in a compact disc, as also found in recent studies of NGC 5548 and NGC 4151. None the less, the observed flares display characteristic time-scales of ∼100 rest-frame days, consistent with the expected thermal time-scale in an accretion disc.
What can Gaussian processes really tell us about supernova light curves? Consequences for Type II(b) morphologies and genealogies
Authors: Stevance H F , Lee A
Published: December 2022

Machine learning has become widely used in astronomy. Gaussian process (GP) regression in particular has been employed a number of times to fit or resample supernova (SN) light curves, however by their nature typical GP models are not suited to fit SN photometric data and they will be prone to overfitting. Recently GP resampling was used in the context of studying the morphologies of Type II and IIb SNe and they were found to be clearly distinct with respect to four parameters: the rise time (trise), the magnitude difference between 40 and 30 d post-explosion (Δm40–30), the earliest maximum (post-peak) of the first derivative (dm1), and minimum of the second derivative (dm2). Here we take a close look at GP regression and its limitations in the context of SN light curves in general, and we also discuss the uncertainties on these specific parameters, finding that dm1 and dm2 cannot give reliable astrophysical information. We do reproduce the clustering in trise–Δm40–30 space, although it is not as clear cut as previously presented. The best strategy to accurately populate the trise–Δm40–30 space will be to use an expanded sample of high-quality light curves [such as those in the Asteroid Terrestrial-impact Last Alert System (ATLAS) transient survey] and analytical fitting methods. Finally, using the bpass fiducial models, we predict that future photometric studies will reveal clear clustering of the Type IIb and II light curve morphologies with a distinct continuum of transitional events.
The circumgalactic medium of Milky Way-like galaxies in the TNG50 simulation – I: halo gas properties and the role of SMBH feedback
Authors: Ramesh Rahul , Nelson Dylan , Pillepich Annalisa
Published: December 2022

We analyse the physical properties of gas in the circumgalactic medium (CGM) of 132 Milky Way (MW)-like galaxies at z = 0 from the cosmological magneto-hydrodynamical simulation TNG50, part of the IllustrisTNG project. The properties and abundance of CGM gas across the sample are diverse, and the fractional budgets of different phases (cold, warm, and hot), as well as neutral H i mass and metal mass, vary considerably. Over our stellar mass range of $10^{10.5} < M_\star /{\rm M}_\odot < 10^{10.9}$, radial profiles of gas physical properties from $0.15 < R/R_{\rm 200c} < 1.0$ reveal great CGM structural complexity, with significant variations both at fixed distance around individual galaxies, and across different galaxies. CGM gas is multiphase: the distributions of density, temperature, and entropy are all multimodal, while metallicity and thermal pressure distributions are unimodal; all are broad. We present predictions for magnetic fields in MW-like haloes: a median field strength of $|B|\sim 1\,\mu{\rm G}$ in the inner halo decreases rapidly at larger distance, while magnetic pressure dominates over thermal pressure only within ${\sim}0.2 \times R_{\rm 200c}$. Virial temperature gas at ${\sim}10^6\,{\rm K}$ coexists with a subdominant cool, $\lt 10^5\,{\rm K}$, component in approximate pressure equilibrium. Finally, the physical properties of the CGM are tightly connected to the galactic star formation rate, in turn dependent on feedback from supermassive black holes (SMBHs). In TNG50, we find that energy from SMBH-driven kinetic winds generates high-velocity outflows (≳500–2000 km s−1), heats gas to supervirial temperatures (>106.5–7 K), and regulates the net balance of inflows versus outflows in otherwise quasi-static gaseous haloes.
Mineralogical analysis of 14 PHAs from ViNOS data
Authors: Morate D , Popescu M , Licandro J , Tinaut-Ruano F , Tatsumi E , de León J
Published: December 2022

Potentially hazardous asteroids (PHAs) are objects that can have close encounters with Earth and are significantly large to cause significant regional damage in the event of impact. The mitigation strategy requires to understand their physical properties. We aim to investigate the physical nature of PHAs, using data obtained within the framework of the Visible NEOs Observations Survey (ViNOS). We analysed and characterized a sample comprised of 14 of these objects. To conduct this study, we obtained visible spectra of 14 PHAs in the 0.5–0.9-μm region using the 2.5 m Nordic Optical Telescope, located at the El Roque De Los Muchachos Observatory in La Palma (Spain). The resulting spectra were combined with their corresponding near-infrared counterparts, available in the literature from the Small Main-Belt Asteroid Spectroscopic Survey (SMASS). We performed a taxonomical classification, computed several diagnostic spectral parameters (slopes, band centres, and band area ratios), and provide completely new mineralogical information for 10 of these objects. We also compared the data with laboratory spectra of meteorites from the RELAB data base. Among the studied sample of PHAs, approximately 90 per cent of the objects (13 out of 14) were classified as silicaceous (S-types and subclasses). Only one object, 489 486, was classified as carbonaceous. Five of the studied PHAs did not have previous taxonomic classifications. The comparisons of the silicaceous PHAs with meteoritic spectra yielded, in all cases, ordinary chondrites as the best match for meteoritic analogues. The computed mineralogy of all of our targets is also consistent with this results.
Imprint of f(R) gravity in the cosmic magnification
Authors: Duniya Didam G A , Abebe Amare , de la Cruz-Dombriz Álvaro , Dunsby Peter K S
Published: December 2022

f(R) gravity is one of the simplest viable modifications to General Relativity: it passes local astrophysical tests, predicts both the early-time cosmic inflation and the late-time cosmic acceleration, and describes dark matter. In this paper, we probe cosmic magnification on large scales in f(R) gravity, using the well-known Hu-Sawicki model as an example. Our results indicate that at redshifts $z \, {\lt }\, 3$, values of the model exponent $n \, {\gt }\, 1$ lead to inconsistent behaviour in the evolution of the scalar perturbations. Moreover, when relativistic effects are taken into account in the large-scale analysis, our results show that as z increases, large-scale changes in the cosmic magnification angular power spectrum owing to integral values of n tend to share a similar pattern, while those of decimal values tend to share another. This feature could be searched for in the experimental data, as a potential ‘smoking gun’ for the given class of gravity models. Furthermore, we found that at $z \, {=}\, 1$ and lower, relativistic effects lead to a suppression of the cosmic magnification on large scales in f(R) gravity, relative to the concordance model; whereas, at $z \, {\gt }\, 1$, relativistic effects lead to a relative boost of the cosmic magnification. In general, relativistic effects enhance the potential of the cosmic magnification as a cosmological probe.
Cosmological constraint precision of photometric and spectroscopic multi-probe surveys of China Space Station Telescope (CSST)
Authors: Miao Haitao , Gong Yan , Chen Xuelei , Huang Zhiqi , Li Xiao-Dong , Zhan Hu
Published: December 2022

As a Stage IV space-based telescope, the China Space Station Telescope (CSST) can perform photometric and spectroscopic surveys simultaneously to explore the Universe efficiently in extreme precision. In this work, we investigate several powerful CSST cosmological probes, including cosmic shear, galaxy–galaxy lensing, photometric and spectroscopic galaxy clustering, and number counts of galaxy clusters, and study the capability of these probes by forecasting the results of joint constraints on the cosmological parameters. By referring to real observational results, we generate mock data and estimate the measured errors based on CSST observational and instrumental designs. To study systematic effects on the results, we also consider a number of systematics in CSST photometric and spectroscopic surveys, such as the intrinsic alignment, shear calibration uncertainties, photometric redshift uncertainties, galaxy bias, non-linear effects, instrumental effects, etc. The Fisher matrix method is used to derive the constraint results on the cosmological and systematic parameters from individual or joint surveys. We find that the joint constraints achieved by including all these CSST cosmological probes can significantly improve the results from current observations by one order of magnitude at least, which gives Ωm and σ8 <1 per cent accuracy and w0 and wa <5 and 20 per cent accuracy, respectively. This indicates that CSST photometric and spectroscopic multi-probe surveys could provide powerful tools with which to explore the Universe and greatly improve the studies of relevant cosmological problems.
Gene nceA encodes a Ni/Co-sensing transcription factor to regulate metal efflux in Corynebacterium glutamicum
Authors: Choi Won-Woo , Jeong Haeri , Kim Younhee , Lee Heung-Shick
Published: December 2022

The function of Corynebacterium glutamicum open reading frame (ORF) NCgl2684 (named nceA in this study), which was annotated to encode a metalloregulator, was assessed using physiological, genetic, and biochemical approaches. Cells with deleted-nceA (ΔnceA) showed a resistant phenotype to NiSO4 and CoSO4 and showed faster growth in minimal medium containing 20 μM NiSO4 or 10 μM CoSO4 than both the wild-type and nceA-overexpressing (P180-nceA) cells. In the ΔnceA strain, the transcription of the downstream-located ORF NCgl2685 (nceB), annotated to encode efflux protein, was increased approximately 4-fold, whereas gene transcription decreased down to 30% level in the P180–nceA strain. The transcriptions of the nceA and nceB genes were stimulated, even when as little as 5 nM NiSO4 was added to the growth medium. Protein NceA was able to bind DNA comprising the promoter region (from −14 to + 18) of the nceA––nceB operon. The protein–DNA interaction was abolished in the presence of 20 μM NiSO4, 50 μM CoSO4, or 50 μM CdSO4. Although manganese induced the transcription of the nceA and nceB genes, it failed to interrupt protein–DNA interaction. Simultaneously, the P180–nceA cells showed increased sensitivity to oxidants such as menadione, hydrogen peroxide, and cumene hydroperoxide, but not diamide. Collectively, our data show that NceA is a nickel- and cobalt-sensing transcriptional regulator that controls the transcription of the probable efflux protein-encoding nceB. The genes are able to suppress intracellular levels of nickel to prevent reactions, which can cause oxidative damage to cellular components.
Calcium isotope ratio in kidney stones: preliminary exploration of mechanism from the geochemical perspective
Authors: Qu Rui , Han Guilin , Tian Yu , Zhao Ye
Published: December 2022

Stable calcium (Ca) isotope ratios are sensitive and radiation-free biomarkers in monitoring biological processes in human bodies. Recently, the Ca isotope ratios of bone, blood, and urine have been widely reported to study bone mineral balance. However, as a pure Ca crystallization product, there is no report on the Ca isotope ratios of kidney stones, even though the prevalence of kidney stones is currently on the rise. Here, we measured Ca isotope data of 21 kidney stone samples collected in Beijing, China. The δ44/42CaNIST 915a values ranged from 0.25‰ to 2.85‰ for calcium oxalate, and from 0.38‰ to 3.00‰ and 0.61‰ to 0.69‰ for carbonate apatite and uric acid, respectively. Kidney stones have heavier Ca isotope ratios than bone or blood, which is probably because complexed Ca contains more heavy Ca isotopes than free Ca2+. Ca isotope evidence suggests that magnesium (Mg) affects kidney stone formation, as the δ44/42CaNIST 915a value is inversely correlated with the Ca/Mg ratio. This study provides important preliminary reference values on the Ca isotopic composition of kidney stones and proposes a factor influencing Ca isotope fractionation in biological processes for future research.
Biological Magnetic Resonance Data Bank
Authors: Hoch Jeffrey C , Baskaran Kumaran , Burr Harrison , Chin John , Eghbalnia Hamid R , Fujiwara Toshimichi , Gryk Michael R , Iwata Takeshi , Kojima Chojiro , Kurisu Genji , Maziuk Dmitri , Miyanoiri Yohei , Wedell Jonathan R , Wilburn Colin , Yao Hongyang , Yokochi Masashi
Published: December 2022

The Biological Magnetic Resonance Data Bank (BMRB, https://bmrb.io) is the international open data repository for biomolecular nuclear magnetic resonance (NMR) data. Comprised of both empirical and derived data, BMRB has applications in the study of biomacromolecular structure and dynamics, biomolecular interactions, drug discovery, intrinsically disordered proteins, natural products, biomarkers, and metabolomics. Advances including GHz-class NMR instruments, national and trans-national NMR cyberinfrastructure, hybrid structural biology methods and machine learning are driving increases in the amount, type, and applications of NMR data in the biosciences. BMRB is a Core Archive and member of the World-wide Protein Data Bank (wwPDB).