bluuebunny/crossref_metadata_2025 huggingface dataset:
MkcDBGAS: a reference-free approach to identify comprehensive alternative splicing events in a transcriptome
Authors: Zhang Quanbao , Cao Lei , Song Hongtao , Lin Kui , Pang Erli
Published: October 2023

Alternative splicing (AS) is an essential post-transcriptional mechanism that regulates many biological processes. However, identifying comprehensive types of AS events without guidance from a reference genome is still a challenge. Here, we proposed a novel method, MkcDBGAS, to identify all seven types of AS events using transcriptome alone, without a reference genome. MkcDBGAS, modeled by full-length transcripts of human and Arabidopsis thaliana, consists of three modules. In the first module, MkcDBGAS, for the first time, uses a colored de Bruijn graph with dynamic- and mixed- kmers to identify bubbles generated by AS with precision higher than 98.17% and detect AS types overlooked by other tools. In the second module, to further classify types of AS, MkcDBGAS added the motifs of exons to construct the feature matrix followed by the XGBoost-based classifier with the accuracy of classification greater than 93.40%, which outperformed other widely used machine learning models and the state-of-the-art methods. Highly scalable, MkcDBGAS performed well when applied to Iso-Seq data of Amborella and transcriptome of mouse. In the third module, MkcDBGAS provides the analysis of differential splicing across multiple biological conditions when RNA-sequencing data is available. MkcDBGAS is the first accurate and scalable method for detecting all seven types of AS events using the transcriptome alone, which will greatly empower the studies of AS in a wider field.
Lineage diversification of the Sky Island treefrog Scinax curicica (Anura, Hylidae) in the Espinhaço Mountain Range
Authors: Santana Diego J , Ragalzi Eric , Koroiva Ricardo , Mângia Sarah , Ceron Karoline , Leite Felipe S F , Shepard Donald B
Published: October 2023

Sky Islands present unique landscapes for organismal evolution because they comprise high mountain peaks separated by low valleys with vastly different environmental conditions. The Espinhaço Mountain Range in eastern Brazil is formed of groups of Sky Islands in the states of Minas Gerais and Bahia. Several phylogeographic studies have discovered strong genetic structure among populations of organisms occupying the campo rupestre (rupestrian fields) in the mountains of the Espinhaço. In this study, we aimed to test the hypothesis of spatio-temporal structuring of populations of Scinax curicica in the campo rupestre of the Espinhaço. We recovered three lineages of S. curicica: one lineage occurs in the north portion of the Espinhaço (North Lineage) in an area called Chapada Diamantina, and other two occur in the south portion of the Espinhaço (South 1 and South 2 Lineages) in Minas Gerais. All three lineages showed stable population sizes through time, probably due to the climatic stability of mountaintop areas, which was supported by ecological niche modelling.
A picture is worth a thousand dollars: a photographic approach to studying colour in anoles
Authors: Jacobs Jake A , Salazar Jhan C , Winchell Kristin M
Published: October 2023

Colours relay information to conspecifics and predators unique to an environment and are shaped by natural selection favouring colours that enable higher fitness. For decades, ecologists have grappled with various methods of quantifying colour. Spectrophotometers offer precise and accurate data, but their high price limits accessibility. Here we test the validity of an accessible method of quantifying colour. We analysed photographs from four species of Anolis lizards from urban and forest habitats. We compared dewlap colour in order to determine if photographic analysis can detect inter- and intraspecific differences with the same power as a spectrophotometer. We hypothesized that photographs would capture colour data comparable to a spectrophotometer within the visible light range, and that habitat divergence would be associated with intraspecific differences in dewlap. We demonstrate, as hypothesized, that photographic colour data are consistent with spectrophotometer data and capable of differentiating dewlap variation within the visible light spectrum. Differences in colour between urban and forest populations were significant for some but not all species, and the part of the colour spectrum that shifted was not consistent across species. Our results support photographic analysis as an alternative for quantifying colour to study both inter- and intraspecific variation in visible colour.
Rise and fall of a continental mesic radiation in Australia: spine evolution, biogeography, and diversification of Cryptandra (Rhamnaceae: Pomaderreae)
Authors: Nge Francis J , Kellermann Jürgen , Biffin Ed , Thiele Kevin R , Waycott Michelle
Published: October 2023

The Australian continent has experienced progressive aridification since the Miocene, spurring recent radiations of arid-adapted lineages and the likely decline of mesic biotic groups. While examples of the former have been relatively well-documented, post-Miocene declines of non-arid sclerophyllous floras are less well understood. Here, we present a well-sampled time-calibrated nuclear phylogeny (140 accessions representing 60/65 species) of an Australian plant genus (Cryptandra Sm.: Rhamnaceae) and using ancestral range reconstructions and diversification analyses, elucidate its evolutionary history through space and time. We used high-throughput sequencing to recover 30 orthologous nuclear loci and BioGeoBEARS to infer ancestral areas. We show that the present-day distribution of Cryptandra can be explained by multiple vicariance events followed by in situ diversification with little exchange between regions. All diversification models show a speciation rate decline in Cryptandra after its radiation in the Miocene (c. 23 Mya). This coincides with aridification episodes across Australia and indicates that diversification of this genus has been negatively affected by the expansion of aridity. We also show that there were no significant differences in diversification rates between spinescent and non-spinescent Cryptandra lineages, suggesting that spinescent lineages may be the legacies of selection from extinct megaherbivores.
Seed morphology of the Eriostemon–Phebalium clade (Rutaceae–Zanthoxyloideae) and implications for systematics
Authors: Choi Bokyung , Duretto Marco F , Hong Suk-Pyo
Published: October 2023

The Eriostemon–Phebalium clade (Rutaceae) includes c. 200 species across 16 genera, and is distributed in Australia (including Tasmania), New Caledonia, New Hebrides, New Zealand, and New Guinea. Phylogenetic analyses based on DNA sequences have consistently shown that the Eriostemon–Phebalium group is robustly monophyletic. However, despite this, taxonomy within the group is still uncertain: relationships between the genera are not well understood, and the genus Philotheca is polyphyletic. Seed morphological characters can be useful in taxonomy in angiosperms, and in this study, 21 seed morphological characters for 29 taxa of all the 16 genera circumscribed in the Eriostemon–Phebalium clade were examined using stereo and scanning electron microscopy. Seed morphological traits such as testa type and hilum were informative for some of the robustly supported clades in molecular phylogenetic studies, and a combination of seed characters could be useful for species identification. This study highlights the potential of seed morphological traits for the systematics.
Dermatoscopic shiny white structures in benign cutaneous tumours
Authors: Lallas Aimilios , Toloza Claudio , Morales Juan Pablo , Santos-Ortiz María Fernanda , Lallas Konstantinos , Nikolaidou Christina , Sakellaropoulou Stella , Papageorgiou Chryssoula , Vakirlis Efstratios , Sotiriou Elena , Apalla Zoe
Published: October 2023

The dermatoscopic characteristics of shiny white structures (SWS) in malignant skin tumours are well described, but data on benign skin neoplasms are scarce. To evaluate the dermatoscopic features of SWS in common benign tumours, we reviewed our database for histopathologically confirmed cases. Dermatoscopic images were evaluated for the presence of any type of SWS. Images with SWS were further analysed for their quantity, distribution and shape. Of 2420 evaluated benign tumours, 357 (14.8%) displayed SWS. The highest frequencies were observed in pyogenic granuloma (n = 62/100; 62%), angioma (n = 63/113; 55.8%) and adnexal tumours (n = 42/84; 50%). The lowest frequency was found in common naevi (n = 16/1032; 1.6%) and solar lentigo (n = 0). The presence of SWS was not associated with sex or anatomical location. SWS were usually diffuse and multiple. SWS may be present in a broad spectrum of benign tumours and therefore they should not be considered as de facto indicators of malignancy.
Polarity and Strategic Competition: A Structural Explanation of Renewed Great Power Rivalry
Authors: Zhang Baohui
Published: October 2023

Strategic competition, or great power competition, has become a new buzz-word in international politics. Yet, few studies have undertaken any systematic examination of what caused its return to the centre stage of international relations. This study hence formulates a parsimonious structural explanation of renewed great power rivalry. Relying on the insights of neorealism and its two structural variants—defensive realism and offensive realism—the study first suggests that current definitions of strategic competition are, due to their emphasis on power competition, overly imbued with offensive realist nuances. However, security competition, which originates in the security dilemma, also underlies strategic competition. Employing neorealism’s polarity perspective, this study then posits that the end of US-led unipolarity and ongoing power deconcentration in the international system are major causes of renewed great power rivalry. While unipolarity harnesses the anarchic effect and compels second-tier major powers to exercise strategic restraint, multipolarity resurrects insecurity and removes disincentives for the aggressive pursuit of power, influence, and status. Ever intensifying security competition and power competition have thus shifted international politics into a new paradigm defined by great power conflict.
Three epochs on estimating the parameter values of thermodynamic Sharpe-Schoolfield-Ikemoto (SSI) model describing the relation of temperature and insect development rate
Authors: Ikemoto Takaya , Kurahashi Issei
Published: October 2023

The SSI model describes the relationship between temperature and development rate of insect based on the laws of thermodynamics. The greatest feature of the SSI model curve is that it defines the “Intrinsic optimum temperature for the development of ectotherms”. However, this model has 8 parameters, it was extremely difficult to estimate the values of these parameters from experimental data. This is because the curve fitting of experimental data yields multiple curves depending on the initial conditions. In the first epoch of estimating parameter values, the difficulties were overcome by clarifying the model and applying all the knowledge gained about the model, but it took several days to determine the model. In the second epoch, the OptimSSI-program, which incorporates a basic optimization function, was developed, making it possible to obtain parameter values instantaneously after inputting experimental data. Although this program mostly runs automatically on a PC, a manual calculation remains to be carried outs so that the obtained model curves do not deviate from Arrhenius’ law. Afterward, a new program was suggested. This new program called DEoptim.sqrt not only incorporates an optimization function available on the internet but also was completely different from OptimSSI-P in terms of the design concept. Users had hoped that this new program would be start of the third epoch; however, when we examined the output values, there were serious problems, and we were back in the state before the first epoch. After all, OptimSSI-P of the second epoch was decided to be more reliable.
Prevalence, risk factors, and optimal way to determine overweight, obesity, and morbid obesity in the first Dutch cohort of 2338 long-term survivors of childhood cancer: a DCCSS-LATER study
Authors: Pluimakers Vincent G , van Atteveld Jenneke E , de Winter Demi T C , Bolier Melissa , Fiocco Marta , Nievelstein Rutger Jan A J , Janssens Geert O R , Bresters Dorine , van der Heiden-van der Loo Margriet , de Vries Andrica C H , Louwerens Marloes , van der Pal Heleen J , Pluijm Saskia M F , Ronckers Cecile M , Versluijs Andrica B , Kremer Leontien C M , Loonen Jacqueline J , van Dulmen-den Broeder Eline , Tissing Wim J E , van Santen Hanneke M , van den Heuvel-Eibrink Marry M , Neggers Sebastian J C M M
Published: October 2023

Background

Overweight and obesity are common challenges among childhood cancer survivors. Overweight may be disguised, as survivors can have normal weight but high fat percentage (fat%) on dual-energy X-ray absorptiometry (DXA). We aimed to assess prevalence, identify determinants and biomarkers, and assess which method captures overweight best, in a nationwide cohort.

Methods

The prevalence of overweight and obesity, primarily defined by body mass index (BMI), was assessed in the DCCSS-LATER cohort of adult survivors treated from 1963-2002, with the LifeLines cohort as reference. The associations between risk factors and overweight metrics were investigated using logistic regression. Additional overweight metrics included DXA fat%, waist circumference (WC), waist/hip ratio (WHR), waist/height ratio (WHtR), and high-molecular-weight (HMW) adiponectin.

Results

A total of 2338 (mean age 35.5 years, follow-up 28.3 years) survivors participated. The overweight prevalence was 46.3% in men and 44.3% in women (obesity 11.2% and 15.9%, morbid obesity 2.4% and 5.4%), with highest rates among brain tumor survivors. Compared to controls, there was no overall increased overweight rate, but this was higher in women > 50 years, morbid obesity in men > 50 years. Overweight at cancer diagnosis (adjusted odds ratio [aOR] = 3.83, 95% CI 2.19-6.69), cranial radiotherapy (aOR = 3.21, 95% CI 1.99-5.18), and growth hormone deficiency (separate model, aOR = 1.61, 95% CI 1.00-2.59) were associated with overweight. Using BMI, WC, WHR, and WHtR, overweight prevalence was similar. Low HMW adiponectin, present in only 4.5% of survivors, was an insensitive overweight marker. Dual-energy X-ray absorptiometry–based classification identified overweight in an additional 30%, particularly after abdominal radiotherapy, total body irradiation, anthracyclines, and platinum.

Conclusions

Overweight occurs in almost half of long-term survivors. There was no overall increased incidence of overweight compared to controls. We identified factors associated with overweight, as well as subgroups of survivors in whom DXA can more reliably assess overweight.
Genotype-phenotype correlations in pseudohypoparathyroidism type 1a patients: a systemic review
Authors: Jiang Siqi , Yang Yi , Song An , Jiang Yue , Jiang Yan , Li Mei , Xia Weibo , Nie Min , Wang Ou , Xing Xiaoping
Published: October 2023

Background

Pseudohypoparathyroidism type 1a (PHP1a) is a rare endocrine disease caused by partial defects of the α subunit of the stimulatory Guanosin triphosphate (GTP) binding protein (Gsα) resulting from maternal GNAS gene variation. The clinical manifestations are related to PTH resistance (hypocalcemia, hyperphosphatemia, and elevated serum intact PTH) in the presence or absence of multihormone resistance, and Albright's hereditary osteodystrophy (AHO).

Objectives

To summarize the molecular genetics results and clinical characteristics as well as to explore the correlations between them.

Methods

Articles pertaining to PHP1a until May, 31, 2021 were reviewed and 527 patients with genetic diagnosis were included in the data analysis. The clinical characteristics and molecular genetics results of these patients were analyzed and compared to explore the correlations between them.

Results

A total of 258 GNAS rare variants (RVs) were identified in 527 patients. The RVs were most commonly found in exons 1 and 7 (17.6% each), with frameshift (36.8%), and missense (31.3%) being the main types of RVs. The median age of onset was 5.0 years old. The most common clinical manifestations were elevation of PTH (86.7%) and AHO (87.5%). Thyroid stimulating hormone resistance was the most common hormone resistance (75.5%) other than PTH resistance. Patients with missense and in-frame RVs had lower incidence rates of the round face (P = .001) and subcutaneous ossifications (P < .001) than those with loss-of-function (non-sense, frameshift, splicing site variants, and large deletions) variants.

Conclusions

This study revealed the correlation between loss-of-function RVs with round faces and subcutaneous ossifications in PHP 1a patients. Further exploration of genotype-phenotype correlations through more standardized and prospective studies with long-term follow-up is necessary.
Hormonal control during infancy and testicular adrenal rest tumor development in males with congenital adrenal hyperplasia: a retrospective multicenter cohort study
Authors: Schröder Mariska A M , Neacşu Mihaela , Adriaansen Bas P H , Sweep Fred C G J , Ahmed S Faisal , Ali Salma R , Bachega Tânia A S S , Baronio Federico , Birkebæk Niels Holtum , de Bruin Christiaan , Bonfig Walter , Bryce Jillian , Clemente Maria , Cools Martine , Elsedfy Heba , Globa Evgenia , Guran Tulay , Güven Ayla , Amr Nermine Hussein , Janus Dominika , Taube Nina Lenherr , Markosyan Renata , Miranda Mirela , Poyrazoğlu Şükran , Rees Aled , Salerno Mariacarolina , Stancampiano Marianna Rita , Vieites Ana , de Vries Liat , Yavas Abali Zehra , Span Paul N , Claahsen-van der Grinten Hedi L
Published: October 2023

Importance

Testicular adrenal rest tumors (TARTs), often found in male patients with congenital adrenal hyperplasia (CAH), are benign lesions causing testicular damage and infertility. We hypothesize that chronically elevated adrenocorticotropic hormone exposure during early life may promote TART development.

Objective

This study aimed to examine the association between commencing adequate glucocorticoid treatment early after birth and TART development.

Design and participants

This retrospective multicenter (n = 22) open cohort study collected longitudinal clinical and biochemical data of the first 4 years of life using the I-CAH registry and included 188 male patients (median age 13 years; interquartile range: 10-17) with 21-hydroxylase deficiency (n = 181) or 11-hydroxylase deficiency (n = 7). All patients underwent at least 1 testicular ultrasound.

Results

TART was detected in 72 (38%) of the patients. Prevalence varied between centers. When adjusted for CAH phenotype, a delayed CAH diagnosis of >1 year, compared with a diagnosis within 1 month of life, was associated with a 2.6 times higher risk of TART diagnosis. TART onset was not predicted by biochemical disease control or bone age advancement in the first 4 years of life, but increased height standard deviation scores at the end of the 4-year study period were associated with a 27% higher risk of TART diagnosis.

Conclusions and relevance

A delayed CAH diagnosis of >1 year vs CAH diagnosis within 1 month after birth was associated with a higher risk of TART development, which may be attributed to poor disease control in early life.
Shared and Distinct Associations of Manual Dexterity and Gross Motor Function With Brain Atrophy
Authors: Dougherty Ryan J , Wang Hang , Gross Alden L , Schrack Jennifer A , Agrawal Yuri , Davatzikos Christos , Cai Yurun , Simonsick Eleanor M , Ferrucci Luigi , Resnick Susan M , Tian Qu
Published: October 2023

Background

Poor motor function is associated with brain atrophy and cognitive impairment. Less is known about the relationship between motor domains and brain atrophy and whether associations are affected by cerebrovascular burden and/or physical activity.

Methods

We analyzed data from 726 Baltimore Longitudinal Study of Aging participants (mean age 70.6 ± 10.1 years, 56% women, 27% Black), 525 of whom had repeat MRI scans over an average of 5.0 ± 2.1 years. Two motor domains, manual dexterity and gross motor, were operationalized as latent variables. Associations between the latent variables and cortical and subcortical brain volumes of interest were examined using latent growth curve modeling, adjusted for demographics, white matter hyperintensities, and physical activity.

Results

Both higher manual dexterity and gross motor function were cross-sectionally associated with smaller ventricular volume and greater white matter volumes in the frontal, parietal, and temporal lobes (all p < .05). Manual dexterity was also cross-sectionally associated with parietal gray matter (B = 0.14; 95% CI: 0.05, 0.23), hippocampus (B = 0.10; 95% CI: 0.01, 0.20), postcentral gyrus (B = 0.11; 95% CI: 0.01, 0.20), and occipital white matter (B = 0.10; 95% CI: 0.01, 0.21) volumes, and gross motor function with temporal gray matter volume (B = 0.16; 95% CI: 0.05, 0.26). Longitudinally, both higher manual dexterity and gross motor function were associated with less temporal white matter and occipital gray matter atrophy (all p < .05). Manual dexterity was also associated with a slower rate of ventricular enlargement (B = −0.17; 95% CI: −0.29, −0.05) and less atrophy of occipital white matter (B = 0.39; 95% CI: 0.04, 0.71).

Conclusions

Among cognitively normal middle- and older-aged adults, manual dexterity and gross motor function exhibited shared as well as distinct associations with brain atrophy over time.
AI language models in human reproduction research: exploring ChatGPT’s potential to assist academic writing
Authors: Semrl N , Feigl S , Taumberger N , Bracic T , Fluhr H , Blockeel C , Kollmann M
Published: October 2023

Artificial intelligence (AI)-driven language models have the potential to serve as an educational tool, facilitate clinical decision-making, and support research and academic writing. The benefits of their use are yet to be evaluated and concerns have been raised regarding the accuracy, transparency, and ethical implications of using this AI technology in academic publishing. At the moment, Chat Generative Pre-trained Transformer (ChatGPT) is one of the most powerful and widely debated AI language models. Here, we discuss its feasibility to answer scientific questions, identify relevant literature, and assist writing in the field of human reproduction. With consideration of the scarcity of data on this topic, we assessed the feasibility of ChatGPT in academic writing, using data from six meta-analyses published in a leading journal of human reproduction. The text generated by ChatGPT was evaluated and compared to the original text by blinded reviewers. While ChatGPT can produce high-quality text and summarize information efficiently, its current ability to interpret data and answer scientific questions is limited, and it cannot be relied upon for a literature search or accurate source citation due to the potential spread of incomplete or false information. We advocate for open discussions within the reproductive medicine research community to explore the advantages and disadvantages of implementing this AI technology. Researchers and reviewers should be informed about AI language models, and we encourage authors to transparently disclose their use.
Review of brine droplets impacting heated surfaces
Authors: Liu Jiawei , Yang Xiaowei , Mu Jiaqi , Mu Lin , Liu Xiaohua
Published: October 2023

So far, brine droplet impact has received less attention compared with water droplets, but the impact of brine droplets on heated surfaces frequently occurs in the industry, agriculture, biomedicine and other fields. The kinematics and evaporation of brine droplet impact on heated surfaces deserve paying much more attention due to their wide industry applications. This review provides a comprehensive summary of existing research on the dynamics, evaporation and crystallization characteristics of brine droplets impacting heated surfaces. The effect of salt in droplets on the evaporation rate, component transportation and crystal deposition are discussed. In addition, this review also summarized inadequacies of existing research and recommended concerning future research directions.
Metabolic advantages of regulatory T cells dictated by cancer cells
Authors: Kondo Masaki , Kumagai Shogo , Nishikawa Hiroyoshi
Published: October 2023

Cancer cells employ glycolysis for their survival and growth (the “Warburg effect”). Consequently, surrounding cells including immune cells in the tumor microenvironment (TME) are exposed to hypoglycemic, hypoxic, and low pH circumstances. Since effector T cells depend on the glycolysis for their survival and functions, the metabolically harsh TME established by cancer cells is unfavorable, resulting in the impairment of effective antitumor immune responses. By contrast, immunosuppressive cells such as regulatory T (Treg) cells can infiltrate, proliferate, survive, and exert immunosuppressive functions in the metabolically harsh TME, indicating the different metabolic dependance between effector T cells and Treg cells. Indeed, some metabolites that are harmful for effector T cells can be utilized by Treg cells; lactic acid, a harmful metabolite for effector T cells, is available for Treg cell proliferation and functions. Deficiency of amino acids such as tryptophan and glutamine in the TME impairs effector T cell activation but increases Treg cell populations. Furthermore, hypoxia upregulates fatty acid oxidation via hypoxia-inducible factor 1α (HIF-1α) and promotes Treg cell migration. Adenosine is induced by the ectonucleotidases CD39 and CD73, which are strongly induced by HIF-1α, and reportedly accelerates Treg cell development by upregulating Foxp3 expression in T cells via A2AR-mediated signals. Therefore, this review focuses on the current views of the unique metabolism of Treg cells dictated by cancer cells. In addition, potential cancer combination therapies with immunotherapy and metabolic molecularly targeted reagents that modulate Treg cells in the TME are discussed to develop “immune metabolism-based precision medicine”.
Exposure of Escherichia coli to antibiotic-efflux pump inhibitor combinations in a pharmacokinetic model: impact on bacterial clearance and drug resistance
Authors: MacGowan Alasdair P , Attwood M L G , Noel Alan R , Barber R , Aron Zachary , Opperman Timothy J , Grimsey Elizabeth , Stone Jack , Ricci Vito , Piddock L J V
Published: October 2023

Background

Efflux pump inhibitors (EPIs) offer an attractive therapeutic option when combined with existing classes. However, their optimal dosing strategies are unknown.

Methods

MICs of ciprofloxacin (CIP)+/−chlorpromazine, phenylalanine-arginine β naphthylamide (PAβN) and a developmental molecule MBX-4191 were determined and the pharmacodynamics (PD) was studied in an in vitro model employing Escherichia coli MG1655 and its isogenic MarR mutant (I1147). Exposure ranging experiments were performed initially then fractionation. Changes in bacterial load and population profiles were assessed. Strains recovered after EPI simulations were studied by WGS.

Results

The CIPMICs for E. coli MG1655 and I1147 were 0.08 and 0.03 mg/L. Chlorpromazine at a concentration of 60 mg/L, PAβN concentrations of 30 mg/L and MBX-4191 concentrations of 0.5–1.0 mg/L reduced CIP MICs for I1147 and enhanced bacterial killing. Using CIP at an AUC of 1.2 mg·h/L, chlorpromazine AUC was best related to reduction in bacterial load at 24 h, however, when the time drug concentration was greater than 25 mg/L (T > 25 mg/L) chlorpromazine was also strongly related to the effect. For PaβN with CIP AUC, 0.6 mg·h/L PaβN AUC was best related to a reduction in bacterial load. MBX-4191T > 0.5–0.75 mg·h/L was best related to reduction in bacterial load. Changes in population profiles were not seen in experiments of ciprofloxacin + EPIs. WGS of recovered strains from simulations with all three EPIs showed mutations in gyrA, gyrB or marR.

Conclusions

AUC was the pharmacodynamic driver for chlorpromazine and PAβN while T > threshold was the driver for MBX-4191 and important in the activity of chlorpromazine and PAβN. Changes in population profiles did not occur with combinations of ciprofloxacin + EPIs, however, mutations in gyrA, gyrB and marR were detected.
Dietary glycine supplementation enhances postweaning growth and meat quality of pigs with intrauterine growth restriction
Authors: He Wenliang , Posey Erin A , Steele Chandler C , Savell Jeffrey W , Bazer Fuller W , Wu Guoyao
Published: October 2023

Pigs with intrauterine growth restriction (IUGR) have suboptimum growth performance and impaired synthesis of glycine (the most abundant amino acid in the body). Conventional corn- and soybean meal-based diets for postweaning pigs contain relatively low amounts of glycine and may not provide sufficient glycine to meet requirements for IUGR pigs. This hypothesis was tested using 52 IUGR pigs and 52 litter mates with normal birth weights (NBW). At weaning (21 d of age), IUGR or NBW pigs were assigned randomly to one of two nutritional groups: supplementation of a corn–soybean meal-based diet with either 1% glycine plus 0.19% cornstarch or 1.19% L-alanine (isonitrogenous control). Feed consumption and body weight (BW) of pigs were recorded daily and every 2 or 4 wks, respectively. All pigs had free access to their respective diets and clean drinking water. Within 1 wk after the feeding trial ended at 188 d of age, blood and other tissue samples were obtained from pigs to determine concentrations of amino acids and meat quality. Neither IUGR nor glycine supplementation affected (P > 0.05) feed intakes of pigs per kg BW. The final BW, gain:feed ratio, carcass dressing percentages, and four-lean-cuts percentages of IUGR pigs were 13.4 kg, 4.4%, 2%, and 15% lower (P < 0.05) for IUGR pigs than NBW pigs, respectively. Compared with pigs in the alanine group, dietary glycine supplementation increased (P < 0.05) final BW, gain:feed ratio, and meat a* value (a redness score) by 3.8 kg, 11%, and 10%, respectively, while reducing (P < 0.05) backfat thickness by 18%. IUGR pigs had lower (P < 0.05) concentrations of glycine in plasma (−45%), liver (−25%), jejunum (−19%), longissimus dorsi muscle (−23%), gastrocnemius muscle (−26%), kidney (−15%), and pancreas (−6%), as compared to NBW pigs. In addition, dietary glycine supplementation increased (P < 0.05) concentrations of glycine in plasma and all analyzed tissues. Thus, supplementing 1% of glycine to corn–soybean meal-based diets improves the growth performance, feed efficiency, and meat quality of IUGR pigs.
Derivation of indirect predictions using genomic recursions across generations in a broiler population
Authors: Hidalgo Jorge , Lourenco Daniela , Tsuruta Shogo , Bermann Matias , Breen Vivian , Misztal Ignacy
Published: October 2023

Genomic estimated breeding values (GEBV) of animals without phenotypes can be indirectly predicted using recursions on GEBV of a subset. To maximize predictive ability of indirect predictions (IP), the subset must represent the independent chromosome segments segregating in the population. We aimed to 1) determine the number of animals needed in recursions to maximize predictive ability, 2) evaluate equivalency IP—GEBV, and 3) investigate trends in predictive ability of IP derived from recent vs. distant generations or accumulating phenotypes from recent to past generations. Data comprised pedigree of 825K birds hatched over 12 overlapping generations, phenotypes for body weight (BW; 820K), residual feed intake (RF; 200K) and weight gain during a trial period (WG; 200K), and breast meat percent (BP; 43K). A total of 154K birds (last six generations) had genotypes. The number of animals that maximize predictive ability was assessed based on the number of largest eigenvalues explaining 99% of variation in the genomic relationship matrix (1Me = 7,131), twice (2Me), or a fraction of this number (i.e., 0.75, 0.50, or 0.25Me). Equivalency between IP and GEBV was measured by correlating these two sets of predictions. GEBV were obtained as if generation 12 (validation animals) was part of the evaluation. IP were derived from GEBV of animals from generations 8 to 11 or generations 11, 10, 9, or 8. IP predictive ability was defined as the correlation between IP and adjusted phenotypes. The IP predictive ability increased from 0.25Me to 1Me (11%, on average); the change from 1Me to 2Me was negligible (0.6%). The correlation IP—GEBV was the same when IP were derived from a subset of 1Me animals chosen randomly across generations (8 to 11) or from generation 11 (0.98 for BW, 0.99 for RF, WG, and BP). A marginal decline in the correlation was observed when IP were based on GEBV of animals from generation 8 (0.95 for BW, 0.98 for RF, WG, and BP). Predictive ability had a similar trend; from generation 11 to 8, it changed from 0.32 to 0.31 for BW, from 0.39 to 0.38 for BP, and was constant at 0.33(0.22) for RF(WG). Predictive ability had a slight to moderate increase accumulating up to four generations of phenotypes. 1Me animals provide accurate IP, equivalent to GEBV. A minimum decay in predictive ability is observed when IP are derived from GEBV of animals from four generations back, possibly because of strong selection or the model not being completely additive.
Nuclear energy in Brazil: regulation, corruption, and prospects for energy generation
Authors: Cordeiro Mikael Jhordan Lacerda , Oliveira Maurício Felipe Bemfica de , de Abreu PereiraUhr Daniel , Uhr Júlia Gallego Ziero
Published: October 2023

This article provides an overview of the historical development of the Brazilian nuclear regulatory environment and its implications for corruption in the nuclear energy sector. It explores Brazil's transition of nuclear energy policies from a military-centric approach to civilian perspectives following the country’s re-democratization in the 1980s. The article highlights the importance of nuclear energy diversification for stabilization and low-carbon energy generation in Brazil. It discusses the challenges and vulnerabilities of the Brazilian nuclear industry, focusing on the corruption scandal of 2015, revealing improper payments, mismanagement, bribery, and money laundering in constructing the Angra 3 nuclear power plant. The study proposes improvements in the corporate governance of the Brazilian sector to minimize potential corruption cases in future contracts. It analyses the conflict of interest among regulatory institutions, industry agents, and the corporate environment. This article also compares the Brazilian nuclear regulatory framework with international regulations and discusses strategies for combating corruption in nuclear power generation. The concluding remarks emphasize the need for institutional reforms to safeguard and develop the Brazilian nuclear industry.
Cliff collapse on Comet 67P/Churyumov–Gerasimenko – I. Aswan
Authors: Davidsson Björn J R
Published: October 2023

The Aswan cliff on Comet 67P/Churyumov–Gerasimenko collapsed on 2015 July 10. Thereby, relatively pristine comet material from a depth of $\sim 12\, \mathrm{m}$ was exposed at the surface. Observations of the collapse site by the microwave instrument Rosetta/Microwave Instrument for Rosetta Orbiter (MIRO) have been retrieved from 8 months prior to collapse, as well as from 5, 7, and 11 months post-collapse. The MIRO data are analysed with thermophysical and radiative transfer models. The pre-collapse observations are consistent with a 30 MKS thermal inertia dust mantle with a thickness of at least $3\, \mathrm{cm}$. The post-collapse data are consistent with (1) a dust/water–ice mass ratio of 0.9 ± 0.5 and a molar CO2 abundance of ∼30 per cent relative to water; (2) formation of a dust mantle after ∼7 months, having a thickness of a few millimetres or a fraction thereof; (3) a CO2 ice sublimation front at 0.4 cm that withdrew to 2.0 cm and later to $20\pm 6\, \mathrm{cm}$; (4) a thermal inertia ranging 10–45 MKS; (5) a gas diffusivity that decreased from $0.1$ to $0.001\, \mathrm{m^2\, s^{-1}}$; and (6) presence of a solid-state greenhouse effect parts of the time. The data and the analysis provide a first empirical glimpse of how ice-rich cometary material ages and evolves when exposed to solar heating.
Impact of modelling galaxy redshift uncertainties on the gravitational-wave dark standard siren measurement of the Hubble constant
Authors: Turski Cezary , Bilicki Maciej , Dálya Gergely , Gray Rachel , Ghosh Archisman
Published: October 2023

Gravitational wave science is a new and rapidly expanding field of observational astronomy. Multimessenger observations of the binary neutron star merger GW170817 have provided some iconic results including the first gravitational-wave standard siren measurement of the Hubble constant, opening up a new way to probe cosmology. The majority of the compact binary sources observed in gravitational waves are, however, without bright electromagnetic counterparts. In these cases, one can fall back on the ‘dark standard siren’ approach to include information statistically from potential host galaxies. For such a measurement, we need to be cautious about all possible sources of systematic errors. In this paper, we begin to study the possible errors coming from the galaxy catalogue sector, and in particular, look into the effect of galaxy redshift uncertainties for the cases where these are photometry-based. We recalculate the dark standard siren Hubble constant using the latest third Gravitational-Wave Transient Catalog (GWTC-3) events and associated galaxy catalogues, with different galaxy redshift uncertainty models, namely, the standard Gaussian, a modified Lorentzian, and no uncertainty at all. We find that not using redshift uncertainties at all can lead to a potential bias comparable with other potential systematic effects previously considered for the GWTC-3 H0 measurement (however still small compared to the overall statistical error in this measurement). The difference between different uncertainty models leads to small differences in the results for the current data; their impact is much smaller than the current statistical errors and other potential sources of systematic errors which have been considered in previous robustness studies.
The evolutionary route to form planetary nebulae with central neutron star–white dwarf binary systems
Authors: Ablimit Iminhaji , Soker Noam
Published: October 2023

We present a possible evolutionary pathway to form planetary nebulae (PNe) with close neutron star (NS)–white dwarf (WD) binary central stars. By employing the binary population synthesis technique, we find that the evolution involves two common envelope evolution (CEE) phases and a core collapse supernova explosion between them that forms the NS. Later the lower mass star engulfs the NS as it becomes a red giant, a process that leads to the second CEE phase and to the ejection of the envelope. This leaves a hot horizontal branch star that evolves to become a helium WD and an expanding nebula. Both the WD and the NS power the nebula. The NS in addition might power a pulsar wind nebula inside the expanding PN. From our simulations we find that the Galactic formation rate of NS–WD PNe is $1.8 \times 10^{-5}\, {\rm yr}^{-1}$ while the Galactic formation rate of all PNe is $0.42 \, {\rm yr}^{-1}$. There is a possibility that one of the observed Galactic PNe might be a NS–WD PN, and a few NS–WD PNe might exist in the Galaxy. The central binary systems might be sources for future gravitational wave detectors like LISA, and possibly of electromagnetic telescopes.
AT2023fhn (the Finch): a luminous fast blue optical transient at a large offset from its host galaxy
Authors: Chrimes A A , Jonker P G , Levan A J , Coppejans D L , Gaspari N , Gompertz B P , Groot P J , Malesani D B , Mummery A , Stanway E R , Wiersema K
Published: October 2023

Luminous fast blue optical transients (LFBOTs) – the prototypical example being AT 2018cow – are a rare class of events whose origins are poorly understood. They are characterized by rapid evolution, featureless blue spectra at early times, and luminous X-ray and radio emission. LFBOTs thus far have been found exclusively at small projected offsets from star-forming host galaxies. We present Hubble Space Telescope, Gemini, Chandra, and Very Large Array observations of a new LFBOT, AT 2023fhn. The Hubble Space Telescope data reveal a large offset (>3.5 half-light radii) from the two closest galaxies, both at redshift z ∼ 0.24. The location of AT 2023fhn is in stark contrast with previous events, and demonstrates that LFBOTs can occur in a range of galactic environments.
Oxygen bounty for Earth-like exoplanets: spectra of Earth through the Phanerozoic
Authors: Payne R C , Kaltenegger L
Published: October 2023

In the search for life in the Universe, Earth provides a template of evolution for the one habitable planet we know. Earth’s atmospheric composition has changed significantly throughout its history. The last 500 Myr – the Phanerozoic Eon, which includes the origins of animals, dinosaurs, and land plants – saw oxygen rise from ≤10 per cent to 35 per cent. But the resulting transmission spectra are a crucial missing piece in our search for signs of life in exoplanet atmospheres. Here, we simulate the atmosphere and transmission spectra of the Phanerozoic, using estimates from established climate models, and present the first high-resolution transmission spectra for Phanerozoic Earth. We demonstrate that the spectral biosignature pairs O2 + CH4 and O3 + CH4 in the atmosphere of a transiting Earth-like planet would indicate a biosphere, with O2 and O3 features potentially stronger than for modern Earth. The full model and high-resolution transmission spectra, covering 0.4–20 µm, are available online and provides a tool to plan and optimize observations, train retrieval methods, and interpret upcoming observations with ground- and space-based telescopes.
Intermittent fasting in the management of diabetes: a review of glycemic control and safety
Authors: Santos Heitor O
Published: October 2023

Intermittent fasting (IF) regimens have emerged as a dietary tool to improve the glycemic profile, but a critical appraisal of clinical studies assessing the effects of IF regimens in patients with diabetes is needed. Thus, this review encompasses clinical studies examining the impact of different IF regimens on markers of glycemic control in patients with diabetes. Furthermore, clinical nuances relative to pharmacological treatment are also addressed, mainly insulin therapy, to discuss the risk of hypoglycemic events. Only a handful of clinical studies have investigated the effects of IF on patients with diabetes. Overall, IF regimens may elicit modest benefits on glycemic parameters in patients with diabetes, but their effects are not necessarily greater than those of control diets. Last, although IF regimens may be considered safe for patients receiving insulin therapy within interventional and observational research, markers of glycemic control must be constantly monitored in clinical practice to reduce the risk of hypoglycemia and its related complications.
Group VII ethylene response factors forming distinct regulatory loops mediate submergence responses
Authors: Hsiao Pao-Yuan , Zeng Cyong-Yu , Shih Ming-Che
Published: October 2023

Group VII ethylene response factors (ERFVIIs), whose stability is oxygen concentration-dependent, play key roles in regulating hypoxia response genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) during submergence. To understand the evolution of flooding tolerance in cereal crops, we evaluated whether Brachypodium distachyon ERFVII genes (BdERFVIIs) are related to submergence tolerance. We found that three BdERFVIIs, BdERF108, BdERF018, and BdERF961, form a feedback regulatory loop to mediate downstream responses. BdERF108 and BdERF018 activated the expression of BdERF961 and PHYTOGLOBIN 1 (PGB1), which promoted nitric oxide turnover and preserved ERFVII protein stability. The activation of PGB1 was subsequently counteracted by increased BdERF961 accumulation through negative feedback regulation. Interestingly, we found that OsERF67, the orthologue of BdERF961 in rice, activated PHYTOGLOBIN (OsHB2) expression and formed distinct regulatory loops during submergence. Overall, the divergent regulatory mechanisms exhibited by orthologs collectively offer perspectives for the development of submergence-tolerant crops.
Spinal cord stimulation for gait impairment in Parkinson Disease: scoping review and mechanistic considerations
Authors: Singh Omesh , Carvalho Diego Z , Espay Alberto J , Benarroch Eduardo E , Grewal Sanjeet S , Pagani-Estévez Gabriel L
Published: October 2023

Objective

Advanced Parkinson's Disease (PD) is associated with Parkinson’s Disease gait impairment (PDg), which increases the risk for falls and is often treatment-refractory. Subthalamic nucleus (STN) and globus pallidus pars interna (GPi) deep brain stimulation (DBS) often fails to improve axial symptoms like PDg. Spinal cord stimulation (SCS) has been suggested to improve PDg. SCS may benefit PDg by disrupting pathologic beta-oscillations and hypersynchrony in cortico-striatal-thalamic circuits to override excessive inhibition of brainstem locomotor regions. SCS may potentially improve locomotion by acting at any of these levels, either alone or in combination.

Methods

We conducted a comprehensive literature search and scoping review, identifying 106 patients in whom SCS was evaluated for PDg.

Results

Among the identified patients, 63% carried a pain diagnosis. Overall, the most common stimulation location was thoracic (78%), most commonly T9-T10. Burst (sub-perception) was the most common stimulation modality (59%). Prior treatment with DBS was used in 25%. Motor outcomes were assessed by the Unified Parkinson Disease Rating Scale (UPDRS) III-motor, UPDRS, the Timed Up and Go (TUG), and/or 10-/20-meter walking tests.

Among these patients, 95 (90%) had PDg amelioration and improved motor outcomes.

Conclusions

Despite small sample sizes, patient heterogeneity, and unblinded evaluations complicating interpretations of efficacy and safety, SCS may be beneficial for at least a subset of PDg. Further research is required to clarify the role of SCS for PDg and the patients most suitable to benefit from this intervention.